Index (cdk 2.9 API)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
All Classes All Packages

A

a - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
A - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
A - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
aaBondInfo() - Static method in class org.openscience.cdk.templates.AminoAcids: Creates matrix with info about the bonds in the amino acids.
Abbreviations - Class in org.openscience.cdk.depict: Utility class for abbreviating (sub)structures.
Abbreviations() - Constructor for class org.openscience.cdk.depict.Abbreviations
Abbreviations.Option - Enum in org.openscience.cdk.depict
ABINITFormat - Class in org.openscience.cdk.io.formats
ABINITFormat() - Constructor for class org.openscience.cdk.io.formats.ABINITFormat
abortOnErrors - Variable in class org.openscience.cdk.io.cml.CMLErrorHandler
absolute() - Static method in class org.openscience.cdk.smiles.SmilesGenerator: Create a absolute SMILES generator.
Absolute - Static variable in class org.openscience.cdk.smiles.SmiFlavor: Output canonical SMILES with stereochemistry, atomic masses.
AbstractAtomicDescriptor - Class in org.openscience.cdk.qsar: Abstract atomic descriptor class with helper functions for descriptors that require the whole molecule to calculate the descriptor values, which in turn need to be cached for all atoms, so that they can be retrieved one by one.
AbstractAtomicDescriptor() - Constructor for class org.openscience.cdk.qsar.AbstractAtomicDescriptor
AbstractAtomPairDescriptor - Class in org.openscience.cdk.qsar: A super class for atom pair descriptors allowing default implementations for interface methods.
AbstractAtomPairDescriptor() - Constructor for class org.openscience.cdk.qsar.AbstractAtomPairDescriptor
AbstractAWTDrawVisitor - Class in org.openscience.cdk.renderer.visitor: Partial implementation of the IDrawVisitor interface for the AWT widget toolkit, allowing molecules to be rendered with toolkits based on AWT, like the Java reference graphics platform Swing.
AbstractAWTDrawVisitor() - Constructor for class org.openscience.cdk.renderer.visitor.AbstractAWTDrawVisitor
AbstractBondDescriptor - Class in org.openscience.cdk.qsar: Abstract bond descriptor class with helper functions for descriptors that require the whole molecule to calculate the descriptor values, which in turn need to be cached for all bonds, so that they can be retrieved one by one.
AbstractBondDescriptor() - Constructor for class org.openscience.cdk.qsar.AbstractBondDescriptor
AbstractDifference - Class in org.openscience.cdk.tools.diff.tree: Difference between two IChemObjects.
AbstractDifference() - Constructor for class org.openscience.cdk.tools.diff.tree.AbstractDifference
AbstractDifferenceList - Class in org.openscience.cdk.tools.diff.tree: Diff between two IChemObjects.
AbstractDifferenceList() - Constructor for class org.openscience.cdk.tools.diff.tree.AbstractDifferenceList
AbstractFingerprinter - Class in org.openscience.cdk.fingerprint
AbstractFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.AbstractFingerprinter
AbstractFontManager - Class in org.openscience.cdk.renderer.font: Implements the common parts of the IFontManager interface.
AbstractFontManager() - Constructor for class org.openscience.cdk.renderer.font.AbstractFontManager: Call this in subclasses with the super() constructor.
AbstractGeneratorParameter<T> - Class in org.openscience.cdk.renderer.generators.parameter: Abstract class to provide the base functionality for IGeneratorParameter implementations.
AbstractGeneratorParameter() - Constructor for class org.openscience.cdk.renderer.generators.parameter.AbstractGeneratorParameter
AbstractMCS - Class in org.openscience.cdk.smsd.interfaces: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
AbstractMCS() - Constructor for class org.openscience.cdk.smsd.interfaces.AbstractMCS: Deprecated.
AbstractMCSAlgorithm - Class in org.openscience.cdk.smsd.interfaces: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
AbstractMCSAlgorithm() - Constructor for class org.openscience.cdk.smsd.interfaces.AbstractMCSAlgorithm: Deprecated.
AbstractMolecularDescriptor - Class in org.openscience.cdk.qsar: A super class for molecular descriptors allowing default implementations for interface methods.
AbstractMolecularDescriptor() - Constructor for class org.openscience.cdk.qsar.AbstractMolecularDescriptor
AbstractReactionLabeller - Class in org.openscience.cdk.smsd.labelling: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
AbstractReactionLabeller() - Constructor for class org.openscience.cdk.smsd.labelling.AbstractReactionLabeller: Deprecated.
AbstractRenderer<T extends IChemObject> - Class in org.openscience.cdk.renderer: The base class for all renderers, handling the core aspects of rendering such as the location of the model in 'model space' and the location on the screen to draw the model.
AbstractRenderer(RendererModel) - Constructor for class org.openscience.cdk.renderer.AbstractRenderer
AbstractResourceFormat - Class in org.openscience.cdk.io.formats: An abstract class providing AbstractResourceFormat.hashCode() and AbstractResourceFormat.equals(java.lang.Object) for IResourceFormats.
AbstractResourceFormat() - Constructor for class org.openscience.cdk.io.formats.AbstractResourceFormat
AbstractSelection - Class in org.openscience.cdk.renderer.selection: An abstract selection of IChemObjects.
AbstractSelection() - Constructor for class org.openscience.cdk.renderer.selection.AbstractSelection
AbstractSubGraph - Class in org.openscience.cdk.smsd.interfaces: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
AbstractSubGraph() - Constructor for class org.openscience.cdk.smsd.interfaces.AbstractSubGraph: Deprecated.
AbstractValidator - Class in org.openscience.cdk.validate: Abstract validator that does nothing but provide all the methods that the ValidatorInterface requires.
AbstractValidator() - Constructor for class org.openscience.cdk.validate.AbstractValidator
Ac - Static variable in interface org.openscience.cdk.interfaces.IElement
AC - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.ArrowElement: Converts this TextElement into widget specific objects.
accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.AtomSymbolElement: Converts this TextElement into widget specific objects.
accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.Bounds: Converts this TextElement into widget specific objects.
accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.ElementGroup: Converts this TextElement into widget specific objects.
accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.GeneralPath: Converts this TextElement into widget specific objects.
accept(IRenderingVisitor) - Method in interface org.openscience.cdk.renderer.elements.IRenderingElement: Converts this TextElement into widget specific objects.
accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.LineElement: Converts this TextElement into widget specific objects.
accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.MarkedElement: Converts this TextElement into widget specific objects.
accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.OvalElement: Converts this TextElement into widget specific objects.
accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.PathElement: Converts this TextElement into widget specific objects.
accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.RectangleElement: Converts this TextElement into widget specific objects.
accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.RingElement: Converts this TextElement into widget specific objects.
accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.TextElement: Converts this TextElement into widget specific objects.
accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.TextGroupElement: Converts this TextElement into widget specific objects.
accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.WedgeLineElement: Converts this TextElement into widget specific objects.
accepts(Class) - Method in class org.openscience.cdk.io.VASPReader
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.CDKSourceCodeWriter
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.CIFReader
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.CMLReader
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.CMLWriter
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.CrystClustReader
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.CrystClustWriter
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.CTXReader
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.GamessReader
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.Gaussian03Reader
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.Gaussian98Reader
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.GhemicalMMReader
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.HINReader
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.HINWriter
accepts(Class<? extends IChemObject>) - Method in interface org.openscience.cdk.io.IChemObjectIO: Returns whether the given IChemObject can be read or written.
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.INChIPlainTextReader
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.INChIReader
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.iterator.event.DefaultEventChemObjectReader
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MDLReader: Deprecated.
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MDLRXNReader: Deprecated.
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MDLRXNV2000Reader
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MDLRXNV3000Reader
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MDLRXNWriter
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MDLV2000Reader
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MDLV2000Writer
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MDLV3000Reader
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MDLV3000Writer: Returns whether the given IChemObject can be read or written.
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.Mol2Reader
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.Mol2Writer
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.Mopac7Reader
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MoSSOutputReader: Returns whether the given IChemObject can be read or written.
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.PCCompoundASNReader
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.PCCompoundXMLReader
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.PCSubstanceXMLReader
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.PDBReader
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.PDBWriter
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.PMPReader
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.program.GaussianInputWriter
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.program.Mopac7Writer
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.random.RandomAccessSDFReader
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.rdf.CDKOWLReader: Returns whether the given IChemObject can be read or written.
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.rdf.CDKOWLWriter: Returns whether the given IChemObject can be read or written.
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.RGroupQueryReader
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.RGroupQueryWriter: Returns true for accepted input types.
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.RssWriter
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.SDFWriter
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.ShelXReader
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.ShelXWriter
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.SMILESReader
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.SMILESWriter
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.XYZReader
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.XYZWriter
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.ZMatrixReader
accepts(IChemObject) - Method in class org.openscience.cdk.io.iterator.event.DefaultEventChemObjectReader
accepts(IChemObject) - Method in class org.openscience.cdk.io.MDLRXNReader: Deprecated.
accepts(IChemObject) - Method in class org.openscience.cdk.io.MDLRXNV2000Reader
accepts(IChemObject) - Method in class org.openscience.cdk.io.MDLRXNV3000Reader
accepts(IChemObject) - Method in class org.openscience.cdk.io.Mol2Reader
acceptStructure() - Method in class org.openscience.cdk.structgen.RandomGenerator: Tell the RandomGenerator to accept the last structure that had been proposed.
ACDLABS_LABEL - Static variable in class org.openscience.cdk.CDKConstants: Atom number/label that can be applied using the Manual Numbering Tool in ACD/ChemSketch.
Aces2Format - Class in org.openscience.cdk.io.formats
Aces2Format() - Constructor for class org.openscience.cdk.io.formats.Aces2Format
AcidicGroupCountDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Returns the number of acidic groups.
AcidicGroupCountDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor: Creates a new AcidicGroupCountDescriptor.
actArray(int[], Permutation) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Performing the permutation action on an int array.
Actinium - org.openscience.cdk.config.Elements
ACTINIUM - Static variable in enum org.openscience.cdk.config.Elements
ACTINIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
activity - Variable in class org.openscience.cdk.fingerprint.model.Bayesian
add(double) - Method in class org.openscience.cdk.qsar.result.DoubleArrayResult
add(double, double) - Method in class org.openscience.cdk.renderer.elements.Bounds: Ensure the point x,y is included in the bounding box.
add(int) - Method in class org.openscience.cdk.qsar.result.IntegerArrayResult
add(int, IAtomContainer) - Method in class org.openscience.cdk.ConformerContainer
add(String) - Method in class org.openscience.cdk.depict.Abbreviations: Convenience method to add an abbreviation from a SMILES string.
add(Map<Integer, Integer>) - Method in class org.openscience.cdk.smsd.helper.FinalMappings: Deprecated.

Adds mapping to the mapping list
add(Map<Integer, Integer>) - Method in interface org.openscience.cdk.smsd.interfaces.IFinalMapping: Deprecated.

Adds mapping to the mapping list
add(GIMatrix) - Method in class org.openscience.cdk.graph.invariant.GIMatrix: Addition from two matrices.
add(IAtomContainer) - Method in class org.openscience.cdk.AtomContainer: Adds all atoms and electronContainers of a given atomcontainer to this container.
add(IAtomContainer) - Method in class org.openscience.cdk.ConformerContainer: Add a conformer to the end of the list.
add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Adds all atoms and electronContainers of a given atomcontainer to this container.
add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Adds all atoms and electronContainers of a given atomcontainer to this container.
add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Adds all atoms and electronContainers of a given atomcontainer to this container.
add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugCrystal: Adds all atoms and electronContainers of a given atomcontainer to this container.
add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugMonomer: Adds all atoms and electronContainers of a given atomcontainer to this container.
add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugPolymer: Adds all atoms and electronContainers of a given atomcontainer to this container.
add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugRing: Adds all atoms and electronContainers of a given atomcontainer to this container.
add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugStrand: Adds all atoms and electronContainers of a given atomcontainer to this container.
add(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Adds all atoms and electronContainers of a given atomcontainer to this container.
add(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.ICrystal: Adds the atoms in the AtomContainer as cell content.
add(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Adds all atoms and electronContainers of a given atomcontainer to this container.
add(IAtomContainer) - Method in class org.openscience.cdk.silent.AtomContainer: Adds all atoms and electronContainers of a given atomcontainer to this container.
add(IAtomContainer, String) - Method in class org.openscience.cdk.depict.Abbreviations: Add an abbreviation to the factory.
add(IAtomContainerSet) - Method in class org.openscience.cdk.AtomContainerSet: Adds all atomContainers in the AtomContainerSet to this container.
add(IAtomContainerSet) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Adds all atomContainers in the AtomContainerSet to this container.
add(IAtomContainerSet) - Method in class org.openscience.cdk.debug.DebugSubstance: Adds all atomContainers in the AtomContainerSet to this container.
add(IAtomContainerSet) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet: Adds all atomContainers in the AtomContainerSet to this container.
add(IAtomContainerSet) - Method in class org.openscience.cdk.silent.AtomContainerSet: Adds all atomContainers in the AtomContainerSet to this container.
add(IChemObject) - Method in class org.openscience.cdk.io.random.RandomAccessReader
add(IIsotope) - Method in class org.openscience.cdk.config.IsotopeFactory: Protected methods only to be used by classes extending this class to add an IIsotope.
add(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugMolecularFormula: Adds an molecularFormula to this MolecularFormula.
add(IMolecularFormula) - Method in class org.openscience.cdk.formula.MolecularFormula: Adds an molecularFormula to this MolecularFormula.
add(IMolecularFormula) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula: Adds an molecularFormula to this MolecularFormula.
add(IMolecularFormula) - Method in class org.openscience.cdk.silent.MolecularFormula: Adds an molecularFormula to this MolecularFormula.
add(IMolecularFormulaSet) - Method in class org.openscience.cdk.debug.DebugAdductFormula: Adds all molecularFormulas in the AdductFormula to this chemObject.
add(IMolecularFormulaSet) - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet: Adds all molecularFormulas in the MolecularFormulaSet to this chemObject.
add(IMolecularFormulaSet) - Method in class org.openscience.cdk.formula.AdductFormula: Adds all molecularFormulas in the AdductFormula to this chemObject.
add(IMolecularFormulaSet) - Method in class org.openscience.cdk.formula.MolecularFormulaSet: Adds all molecularFormulas in the MolecularFormulaSet to this chemObject.
add(IMolecularFormulaSet) - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet: Adds all molecularFormulas in the MolecularFormulaSet to this chemObject.
add(IMolecularFormulaSet) - Method in class org.openscience.cdk.silent.AdductFormula: Adds all molecularFormulas in the AdductFormula to this chemObject.
add(IMolecularFormulaSet) - Method in class org.openscience.cdk.silent.MolecularFormulaSet: Adds all molecularFormulas in the MolecularFormulaSet to this chemObject.
add(IReactionScheme) - Method in class org.openscience.cdk.debug.DebugReactionScheme: Add a Scheme of Reactions.
add(IReactionScheme) - Method in interface org.openscience.cdk.interfaces.IReactionScheme: Add a scheme of reactions.
add(IReactionScheme) - Method in class org.openscience.cdk.ReactionScheme: Add a Scheme of Reactions.
add(IReactionScheme) - Method in class org.openscience.cdk.silent.ReactionScheme: Add a Scheme of Reactions.
add(IRingSet) - Method in class org.openscience.cdk.debug.DebugRingSet: Adds all rings of another RingSet if they are not already part of this ring set.
add(IRingSet) - Method in interface org.openscience.cdk.interfaces.IRingSet: Adds all rings of another RingSet if they are not allready part of this ring set.
add(IRingSet) - Method in class org.openscience.cdk.RingSet: Adds all rings of another RingSet if they are not already part of this ring set.
add(IRingSet) - Method in class org.openscience.cdk.silent.RingSet: Adds all rings of another RingSet if they are not already part of this ring set.
add(Complex) - Method in class org.openscience.cdk.math.Complex: Add a complex value
add(IMatrix) - Method in class org.openscience.cdk.math.IMatrix: Addition from two matrices
add(IMatrix, IMatrix) - Method in class org.openscience.cdk.math.IMatrix: Addition from two matrices
add(IVector) - Method in class org.openscience.cdk.math.IVector: Addition from two vectors
add(IVector, IVector) - Method in class org.openscience.cdk.math.IVector: Addition from two vectors
add(Matrix) - Method in class org.openscience.cdk.math.Matrix: Adds two matrices.
add(Quaternion) - Method in class org.openscience.cdk.math.Quaternion
add(Vector) - Method in class org.openscience.cdk.math.Vector: Addition from two vectors
add(Bounds) - Method in class org.openscience.cdk.renderer.elements.Bounds: Add one bounds to another.
add(IRenderingElement) - Method in class org.openscience.cdk.renderer.elements.Bounds: Add the specified element bounds.
add(IRenderingElement) - Method in class org.openscience.cdk.renderer.elements.ElementGroup: Add a new element to the group.
add(T) - Method in class org.openscience.cdk.io.setting.SettingManager: Add a setting to the manager and return the instance to use.
add3DCoordinates1(IAtomContainer) - Static method in class org.openscience.cdk.geometry.AtomTools: Generate coordinates for all atoms which are singly bonded and have no coordinates.
add3DCoordinatesForSinglyBondedLigands(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D: Generate coordinates for all atoms which are singly bonded and have no coordinates.
addAcidicOxygen(IAminoAcid) - Static method in class org.openscience.cdk.tools.manipulator.AminoAcidManipulator: Adds the singly bonded oxygen from the acid group of the AminoAcid.
addAgent(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugReaction: Adds an agent to this reaction.
addAgent(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IReaction: Adds an agent to this reaction.
addAgent(IAtomContainer) - Method in class org.openscience.cdk.Reaction: Adds an agent to this reaction.
addAgent(IAtomContainer) - Method in class org.openscience.cdk.silent.Reaction: Adds an agent to this reaction.
addAll(int, Collection<? extends IAtomContainer>) - Method in class org.openscience.cdk.ConformerContainer
addAll(Collection<? extends IAtomContainer>) - Method in class org.openscience.cdk.ConformerContainer
addAminoAcidAtCTerminus(IBioPolymer, IAminoAcid, IStrand, IAminoAcid) - Static method in class org.openscience.cdk.tools.ProteinBuilderTool: Builds a protein by connecting a new amino acid at the C-terminus of the given strand.
addAminoAcidAtNTerminus(IBioPolymer, IAminoAcid, IStrand, IAminoAcid) - Static method in class org.openscience.cdk.tools.ProteinBuilderTool: Builds a protein by connecting a new amino acid at the N-terminus of the given strand.
addArrayElementsTo(List<String>, String) - Method in class org.openscience.cdk.io.cml.CMLCoreModule
addAtom(int) - Method in class org.openscience.cdk.signature.Orbit: Adds an atom index to the orbit.
addAtom(IAtom) - Method in class org.openscience.cdk.AtomContainer: Adds an atom to this container.
addAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Adds an atom to this container.
addAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Adds an atom to this container.
addAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Adds an atom to this container.
addAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal: Adds an atom to this container.
addAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer: Adds an atom to this container.
addAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer: Adds an atom to this container.
addAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugRing: Adds an atom to this container.
addAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand: Adds the atom oAtom without specifying a Monomer or a Strand.
addAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Adds an atom to this container.
addAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.IBioPolymer: Adds the atom oAtom without specifying a Monomer or a Strand.
addAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.ICrystal: Adds the atom to the crystal.
addAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.IPolymer: Adds the atom oAtom without specifying a Monomer.
addAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.IStrand: Adds the atom oAtom without specifying a Monomer or a Strand.
addAtom(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Adds an atom to this container.
addAtom(IAtom) - Method in class org.openscience.cdk.sgroup.Sgroup: Add an atom to this Sgroup.
addAtom(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer: Adds an atom to this container.
addAtom(IAtom) - Method in class org.openscience.cdk.silent.Strand: Adds the atom oAtom without specifying a Monomer or a Strand.
addAtom(IAtom) - Method in class org.openscience.cdk.Strand: Adds the atom oAtom without specifying a Monomer or a Strand.
addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Adds the atom oAtom to a specified Monomer.
addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.debug.DebugPolymer: Adds the atom oAtom to a specified Monomer.
addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.debug.DebugStrand: Adds the atom oAtom to a specific Monomer.
addAtom(IAtom, IMonomer) - Method in interface org.openscience.cdk.interfaces.IPolymer: Adds the atom oAtom to a specified Monomer.
addAtom(IAtom, IMonomer) - Method in interface org.openscience.cdk.interfaces.IStrand: Adds the atom oAtom to a specific Monomer.
addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.Polymer: Adds the atom oAtom to a specified Monomer.
addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.protein.data.PDBStrand: Adds the atom oAtom to a specified Monomer.
addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.silent.Polymer: Adds the atom oAtom to a specified Monomer.
addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.silent.Strand: Adds the atom oAtom to a specific Monomer.
addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.Strand: Adds the atom oAtom to a specific Monomer.
addAtom(IAtom, IMonomer, IStrand) - Method in class org.openscience.cdk.BioPolymer: Adds the atom to a specified Strand and a specified Monomer.
addAtom(IAtom, IMonomer, IStrand) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Adds the atom to a specified Strand and a specified Monomer.
addAtom(IAtom, IMonomer, IStrand) - Method in interface org.openscience.cdk.interfaces.IBioPolymer: Adds the atom to a specified Strand and a specified Monomer.
addAtom(IAtom, IMonomer, IStrand) - Method in class org.openscience.cdk.silent.BioPolymer: Adds the atom to a specified Strand and a specified Monomer.
addAtom(IAtom, IStrand) - Method in class org.openscience.cdk.BioPolymer: Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.
addAtom(IAtom, IStrand) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.
addAtom(IAtom, IStrand) - Method in interface org.openscience.cdk.interfaces.IBioPolymer: Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.
addAtom(IAtom, IStrand) - Method in class org.openscience.cdk.silent.BioPolymer: Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.
addAtom(IPDBAtom) - Method in interface org.openscience.cdk.interfaces.IPDBPolymer: Adds the atom oAtom without specifying a Monomer or a Strand.
addAtom(IPDBAtom) - Method in class org.openscience.cdk.protein.data.PDBPolymer: Adds the atom oAtom without specifying a IMonomer or a Strand.
addAtom(IPDBAtom) - Method in class org.openscience.cdk.silent.PDBPolymer: Adds the atom oAtom without specifying a IMonomer or a Strand.
addAtom(IPDBAtom, IMonomer) - Method in class org.openscience.cdk.protein.data.PDBPolymer: Adds the atom oAtom to a specified Monomer.
addAtom(IPDBAtom, IMonomer) - Method in class org.openscience.cdk.silent.PDBPolymer: Adds the atom oAtom to a specified Monomer.
addAtom(IPDBAtom, IMonomer, IStrand) - Method in interface org.openscience.cdk.interfaces.IPDBPolymer: Adds the atom to a specified Strand and a specified Monomer.
addAtom(IPDBAtom, IMonomer, IStrand) - Method in class org.openscience.cdk.protein.data.PDBPolymer: Adds the IPDBAtom oAtom to a specified Monomer of a specified Strand.
addAtom(IPDBAtom, IMonomer, IStrand) - Method in class org.openscience.cdk.silent.PDBPolymer: Adds the IPDBAtom oAtom to a specified Monomer of a specified Strand.
addAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.AtomContainerSet: Adds an atomContainer to this container.
addAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Adds an atomContainer to this container.
addAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugSubstance: Adds an atomContainer to this container.
addAtomContainer(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet: Adds an atomContainer to this container.
addAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.silent.AtomContainerSet: Adds an atomContainer to this container.
addAtomContainer(IAtomContainer, double) - Method in class org.openscience.cdk.AtomContainerSet: Adds an atomContainer to this container with the given multiplier.
addAtomContainer(IAtomContainer, double) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Adds an atomContainer to this container with the given multiplier.
addAtomContainer(IAtomContainer, double) - Method in class org.openscience.cdk.debug.DebugSubstance: Adds an atomContainer to this container with the given multiplier.
addAtomContainer(IAtomContainer, double) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet: Adds an atomContainer to this container with the given multiplier.
addAtomContainer(IAtomContainer, double) - Method in class org.openscience.cdk.silent.AtomContainerSet: Adds an atomContainer to this container with the given multiplier.
addAtomVector(double[]) - Method in class org.openscience.cdk.Vibration: Adds a atom vector to the vibration.
addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.AtomContainer: Adds a bond to this container.
addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Adds a bond to this container.
addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Adds a bond to this container.
addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Adds a bond to this container.
addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugCrystal: Adds a bond to this container.
addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugMonomer: Adds a bond to this container.
addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugPolymer: Adds a bond to this container.
addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugRing: Adds a bond to this container.
addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugStrand: Adds a bond to this container.
addBond(int, int, IBond.Order) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Adds a bond to this container.
addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Adds a bond to this container.
addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.silent.AtomContainer: Adds a bond to this container.
addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.AtomContainer: Adds a bond to this container.
addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Adds a bond to this container.
addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Adds a bond to this container.
addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Adds a bond to this container.
addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugCrystal: Adds a bond to this container.
addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugMonomer: Adds a bond to this container.
addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugPolymer: Adds a bond to this container.
addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugRing: Adds a bond to this container.
addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugStrand: Adds a bond to this container.
addBond(int, int, IBond.Order, IBond.Stereo) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Adds a bond to this container.
addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Adds a bond to this container.
addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.silent.AtomContainer: Adds a bond to this container.
addBond(IBond) - Method in class org.openscience.cdk.AtomContainer: Adds a Bond to this AtomContainer.
addBond(IBond) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Adds a Bond to this AtomContainer.
addBond(IBond) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Adds a Bond to this AtomContainer.
addBond(IBond) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Adds a Bond to this AtomContainer.
addBond(IBond) - Method in class org.openscience.cdk.debug.DebugCrystal: Adds a Bond to this AtomContainer.
addBond(IBond) - Method in class org.openscience.cdk.debug.DebugMonomer: Adds a Bond to this AtomContainer.
addBond(IBond) - Method in class org.openscience.cdk.debug.DebugPolymer: Adds a Bond to this AtomContainer.
addBond(IBond) - Method in class org.openscience.cdk.debug.DebugRing: Adds a Bond to this AtomContainer.
addBond(IBond) - Method in class org.openscience.cdk.debug.DebugStrand: Adds a Bond to this AtomContainer.
addBond(IBond) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Adds a Bond to this AtomContainer.
addBond(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Adds a Bond to this AtomContainer.
addBond(IBond) - Method in class org.openscience.cdk.sgroup.Sgroup: Add a bond to this Sgroup.
addBond(IBond) - Method in class org.openscience.cdk.silent.AtomContainer: Adds a Bond to this AtomContainer.
addBracket(SgroupBracket) - Method in class org.openscience.cdk.sgroup.Sgroup: Add a bracket for this Sgroup.
addCDKChangeListener(ICDKChangeListener) - Method in class org.openscience.cdk.renderer.RendererModel: Adds a change listener to the list of listeners.
addCDKError(ValidationTest) - Method in class org.openscience.cdk.validate.ValidationReport: Adds a CDK problem.
addCell(int...) - Method in class org.openscience.cdk.group.Partition: Adds a new cell to the end of the partition containing these elements.
addCell(Collection<Integer>) - Method in class org.openscience.cdk.group.Partition: Adds a new cell to the end of the partition.
addChargeGroup(ChargeGroup) - Method in class org.openscience.cdk.libio.md.MDMolecule: Add a ChargeGroup to the MDMolecule if not already present.
addChemModel(IChemModel) - Method in class org.openscience.cdk.ChemSequence: Adds an chemModel to this container.
addChemModel(IChemModel) - Method in class org.openscience.cdk.debug.DebugChemSequence: Adds an chemModel to this container.
addChemModel(IChemModel) - Method in interface org.openscience.cdk.interfaces.IChemSequence: Adds an chemModel to this container.
addChemModel(IChemModel) - Method in class org.openscience.cdk.silent.ChemSequence: Adds an chemModel to this container.
addChemObjectIOListener(IChemObjectIOListener) - Method in class org.openscience.cdk.io.ChemObjectIO: Adds a IChemObjectIOListener to this IChemObjectIO.
addChemObjectIOListener(IChemObjectIOListener) - Method in interface org.openscience.cdk.io.IChemObjectIO: Adds a IChemObjectIOListener to this IChemObjectIO.
addChemObjectIOListener(IChemObjectIOListener) - Method in class org.openscience.cdk.io.random.DefaultRandomAccessChemObjectReader
addChemObjectIOListener(IChemObjectIOListener) - Method in class org.openscience.cdk.io.random.RandomAccessReader
addChemSequence(IChemSequence) - Method in class org.openscience.cdk.ChemFile: Adds a ChemSequence to this container.
addChemSequence(IChemSequence) - Method in class org.openscience.cdk.debug.DebugChemFile: Adds a ChemSequence to this container.
addChemSequence(IChemSequence) - Method in interface org.openscience.cdk.interfaces.IChemFile: Adds an IChemSequence to this container.
addChemSequence(IChemSequence) - Method in class org.openscience.cdk.silent.ChemFile: Adds a ChemSequence to this container.
addChild(String, String, TextGroupElement.Position) - Method in class org.openscience.cdk.renderer.elements.TextGroupElement: Add a child text element with a subscript.
addChild(String, TextGroupElement.Position) - Method in class org.openscience.cdk.renderer.elements.TextGroupElement: Add a child text element.
addChild(IDifference) - Method in class org.openscience.cdk.tools.diff.tree.AbstractDifferenceList: Adds a new IDifference as child to this tree.
addChild(IDifference) - Method in interface org.openscience.cdk.tools.diff.tree.IDifferenceList: Adds a new IDifference as child to this tree.
addChildren(List<IDifference>) - Method in class org.openscience.cdk.tools.diff.tree.AbstractDifferenceList: Adds multiple IDifferences as child to this tree.
addChildren(List<IDifference>) - Method in interface org.openscience.cdk.tools.diff.tree.IDifferenceList: Adds multiple IDifferences as child to this tree.
addCTerminus(IAtom) - Method in class org.openscience.cdk.AminoAcid: Add an Atom and makes it the C-terminus atom.
addCTerminus(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Add an Atom and makes it the C-terminus atom.
addCTerminus(IAtom) - Method in interface org.openscience.cdk.interfaces.IAminoAcid: Add an Atom and makes it the C-terminus atom.
addCTerminus(IAtom) - Method in class org.openscience.cdk.silent.AminoAcid: Add an Atom and makes it the C-terminus atom.
addEdge(EdgeBuilder) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.NodeBuilder: Deprecated.

Adds edge to the edge list.
addEdge(EdgeBuilder) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.INode: Deprecated.

Adds edge to the edge list.
addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.AtomContainer: Adds a ElectronContainer to this AtomContainer.
addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Adds a ElectronContainer to this AtomContainer.
addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Adds a ElectronContainer to this AtomContainer.
addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Adds a ElectronContainer to this AtomContainer.
addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugCrystal: Adds a ElectronContainer to this AtomContainer.
addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugMonomer: Adds a ElectronContainer to this AtomContainer.
addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugPolymer: Adds a ElectronContainer to this AtomContainer.
addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugRing: Adds a ElectronContainer to this AtomContainer.
addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugStrand: Adds a ElectronContainer to this AtomContainer.
addElectronContainer(IElectronContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Adds a ElectronContainer to this AtomContainer.
addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Adds a ElectronContainer to this AtomContainer.
addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.silent.AtomContainer: Adds a ElectronContainer to this AtomContainer.
addError(ValidationTest) - Method in class org.openscience.cdk.validate.ValidationReport: Adds a validation test which gives serious errors.
addEscapes(String) - Static method in error org.openscience.cdk.iupac.parser.TokenMgrError: Replaces unprintable characters by their escaped (or unicode escaped) equivalents in the given string
addEscapes(String) - Static method in error org.openscience.cdk.smiles.smarts.parser.TokenMgrError: Replaces unprintable characters by their escaped (or unicode escaped) equivalents in the given string
addExampleReaction(String) - Method in class org.openscience.cdk.dict.EntryReact: add a example for this reaction.
addFormula(IMolecularFormula) - Method in class org.openscience.cdk.formula.IsotopeContainer: Add a formula to this isotope container.
addFunction(IFunction) - Method in class org.openscience.cdk.renderer.GraphRendererModel: Add a function to the set of functions
addFunction(IFunction, Color) - Method in class org.openscience.cdk.renderer.GraphRendererModel: Add a function to the set of functions
addHydrogens(int[][], int, int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: After generating matrices, adding the hydrogen with respect to the pre-hydrogen distribution.
addImplicitHydrogens(IAtomContainer) - Method in class org.openscience.cdk.tools.CDKHydrogenAdder: Sets implicit hydrogen counts for all atoms in the given IAtomContainer.
addImplicitHydrogens(IAtomContainer, IAtom) - Method in class org.openscience.cdk.tools.CDKHydrogenAdder: Sets the implicit hydrogen count for the indicated IAtom in the given IAtomContainer.
addIsotope(IsotopeContainer) - Method in class org.openscience.cdk.formula.IsotopePattern: Add an isotope object.
addIsotope(IIsotope) - Method in class org.openscience.cdk.debug.DebugMolecularFormula: Adds an Isotope to this MolecularFormula one time.
addIsotope(IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormula: Adds an Isotope to this MolecularFormula one time.
addIsotope(IIsotope) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula: Adds an Isotope to this MolecularFormula one time.
addIsotope(IIsotope) - Method in class org.openscience.cdk.silent.MolecularFormula: Adds an Isotope to this MolecularFormula one time.
addIsotope(IIsotope, int) - Method in class org.openscience.cdk.debug.DebugMolecularFormula: Adds an Isotope to this MolecularFormula in a number of occurrences.
addIsotope(IIsotope, int) - Method in class org.openscience.cdk.formula.MolecularFormula: Adds an Isotope to this MolecularFormula in a number of occurrences.
addIsotope(IIsotope, int) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula: Adds an Isotope to this MolecularFormula in a number of occurrences.
addIsotope(IIsotope, int) - Method in class org.openscience.cdk.silent.MolecularFormula: Adds an Isotope to this MolecularFormula in a number of occurrences.
addIsotope(IIsotope, int, int) - Method in class org.openscience.cdk.formula.MolecularFormulaRange: Adds an Isotope to this MolecularFormulaExpand in a number of maximum and minimum occurrences allowed.
addLabel(String) - Method in class org.openscience.cdk.smsd.helper.LabelContainer: Deprecated.

Add label if its not present
addLine(int, int, double) - Method in class org.openscience.cdk.graph.invariant.GIMatrix: Returns the resulting matrix of an elementary linear operation that consists of adding one line, multiplied by some constant factor, to another line.
addListener(IChemObjectListener) - Method in class org.openscience.cdk.ChemObject: Use this to add yourself to this IChemObject as a listener.
addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Use this to add yourself to this IChemObject as a listener.
addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAtom: Use this to add yourself to this IChemObject as a listener.
addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Use this to add yourself to this IChemObject as a listener.
addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Use this to add yourself to this IChemObject as a listener.
addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAtomType: Use this to add yourself to this IChemObject as a listener.
addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Use this to add yourself to this IChemObject as a listener.
addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugBond: Use this to add yourself to this IChemObject as a listener.
addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugChemFile: Use this to add yourself to this IChemObject as a listener.
addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugChemModel: Use this to add yourself to this IChemObject as a listener.
addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugChemObject: Use this to add yourself to this IChemObject as a listener.
addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugChemSequence: Use this to add yourself to this IChemObject as a listener.
addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugCrystal: Use this to add yourself to this IChemObject as a listener.
addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugElectronContainer: Use this to add yourself to this IChemObject as a listener.
addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugElement: Use this to add yourself to this IChemObject as a listener.
addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Use this to add yourself to this IChemObject as a listener.
addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugIsotope: Use this to add yourself to this IChemObject as a listener.
addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugLonePair: Use this to add yourself to this IChemObject as a listener.
addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugMapping: Use this to add yourself to this IChemObject as a listener.
addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugMonomer: Use this to add yourself to this IChemObject as a listener.
addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugPolymer: Use this to add yourself to this IChemObject as a listener.
addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Use this to add yourself to this IChemObject as a listener.
addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugReaction: Use this to add yourself to this IChemObject as a listener.
addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugReactionScheme: Use this to add yourself to this IChemObject as a listener.
addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugReactionSet: Use this to add yourself to this IChemObject as a listener.
addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugRing: Use this to add yourself to this IChemObject as a listener.
addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugSingleElectron: Use this to add yourself to this IChemObject as a listener.
addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugStrand: Use this to add yourself to this IChemObject as a listener.
addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugSubstance: Use this to add yourself to this IChemObject as a listener.
addListener(IChemObjectListener) - Method in interface org.openscience.cdk.interfaces.IChemObject: Use this to add yourself to this IChemObject as a listener.
addListener(IChemObjectListener) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject: Use this to add yourself to this IChemObject as a listener.
addListener(IChemObjectListener) - Method in class org.openscience.cdk.silent.ChemObject: Use this to add yourself to this IChemObject as a listener.
addLonePair(int) - Method in class org.openscience.cdk.AtomContainer: Adds a LonePair to this Atom.
addLonePair(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Adds a LonePair to this Atom.
addLonePair(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Adds a LonePair to this Atom.
addLonePair(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Adds a LonePair to this Atom.
addLonePair(int) - Method in class org.openscience.cdk.debug.DebugCrystal: Adds a LonePair to this Atom.
addLonePair(int) - Method in class org.openscience.cdk.debug.DebugMonomer: Adds a LonePair to this Atom.
addLonePair(int) - Method in class org.openscience.cdk.debug.DebugPolymer: Adds a LonePair to this Atom.
addLonePair(int) - Method in class org.openscience.cdk.debug.DebugRing: Adds a LonePair to this Atom.
addLonePair(int) - Method in class org.openscience.cdk.debug.DebugStrand: Adds a LonePair to this Atom.
addLonePair(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Adds a LonePair to this Atom.
addLonePair(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Adds a LonePair to this Atom.
addLonePair(int) - Method in class org.openscience.cdk.silent.AtomContainer: Adds a LonePair to this Atom.
addLonePair(ILonePair) - Method in class org.openscience.cdk.AtomContainer: Adds a lone pair to this AtomContainer.
addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Adds a lone pair to this AtomContainer.
addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Adds a lone pair to this AtomContainer.
addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Adds a lone pair to this AtomContainer.
addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugCrystal: Adds a lone pair to this AtomContainer.
addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugMonomer: Adds a lone pair to this AtomContainer.
addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugPolymer: Adds a lone pair to this AtomContainer.
addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugRing: Adds a lone pair to this AtomContainer.
addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugStrand: Adds a lone pair to this AtomContainer.
addLonePair(ILonePair) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Adds a lone pair to this AtomContainer.
addLonePair(ILonePair) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Adds a lone pair to this AtomContainer.
addLonePair(ILonePair) - Method in class org.openscience.cdk.silent.AtomContainer: Adds a lone pair to this AtomContainer.
addMapping(IMapping) - Method in interface org.openscience.cdk.interfaces.IReaction: Adds a mapping between the reactant and product side to this Reaction.
addMapping(IMapping) - Method in class org.openscience.cdk.Reaction: Adds a mapping between the reactant and product side to this Reaction.
addMapping(IMapping) - Method in class org.openscience.cdk.silent.Reaction: Adds a mapping between the reactant and product side to this Reaction.
addMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugAdductFormula: Adds an molecularFormula to this chemObject.
addMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet: Adds an molecularFormula to this chemObject.
addMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.formula.AdductFormula: Adds an molecularFormula to this chemObject.
addMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.formula.MolecularFormulaSet: Adds an molecularFormula to this chemObject.
addMolecularFormula(IMolecularFormula) - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet: Adds an IMolecularFormula to this chemObject.
addMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.silent.AdductFormula: Adds an molecularFormula to this chemObject.
addMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.silent.MolecularFormulaSet: Adds an molecularFormula to this chemObject.
addMolecule(IAtomContainer) - Method in class org.openscience.cdk.layout.TemplateHandler: Adds a Molecule to the list of templates use by this TemplateHandler.
addMolecule(IAtomContainer, boolean) - Method in class org.openscience.cdk.fingerprint.model.Bayesian: Appends a new row to the model source data, which consists of a molecule and whether or not it is considered active.
addNeighbor(NodeBuilder) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.NodeBuilder: Deprecated.

Adds neighbor to the Neighbors List.
addNeighbor(NodeBuilder) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.INode: Deprecated.

Adds neighbor to the Neighbors List.
addNode(RNode) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Adds a new node to the RGraph.
addNode(VFAtomMatcher, IAtom) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder: Deprecated.

Add and return a node for a query atom
addNode(CDKRNode) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph: Deprecated.

Adds a new node to the CDKRGraph.
addNTerminus(IAtom) - Method in class org.openscience.cdk.AminoAcid: Add an Atom and makes it the N-terminus atom.
addNTerminus(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Add an Atom and makes it the N-terminus atom.
addNTerminus(IAtom) - Method in interface org.openscience.cdk.interfaces.IAminoAcid: Add an Atom and makes it the N-terminus atom.
addNTerminus(IAtom) - Method in class org.openscience.cdk.silent.AminoAcid: Add an Atom and makes it the N-terminus atom.
addOK(ValidationTest) - Method in class org.openscience.cdk.validate.ValidationReport: Adds a validation test which did not find a problem.
addOnes(int[], int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Add number of 1s into an ArrayList
addParameter(List<String>) - Method in class org.openscience.cdk.dict.EntryReact: Add a IParameterReact's of the reaction.
addParent(Sgroup) - Method in class org.openscience.cdk.sgroup.Sgroup: Add a parent Sgroup.
addPartition(int, int[], int[][], int[][]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Updating canonical partition list.
addProduct(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugReaction: Adds a product to this reaction.
addProduct(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IReaction: Adds a product to this reaction.
addProduct(IAtomContainer) - Method in class org.openscience.cdk.Reaction: Adds a product to this reaction.
addProduct(IAtomContainer) - Method in class org.openscience.cdk.silent.Reaction: Adds a product to this reaction.
addProduct(IAtomContainer, Double) - Method in class org.openscience.cdk.debug.DebugReaction: Adds a product to this reaction.
addProduct(IAtomContainer, Double) - Method in interface org.openscience.cdk.interfaces.IReaction: Adds a product to this reaction.
addProduct(IAtomContainer, Double) - Method in class org.openscience.cdk.Reaction: Adds a product to this reaction.
addProduct(IAtomContainer, Double) - Method in class org.openscience.cdk.silent.Reaction: Adds a product to this reaction.
addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.ChemObject: Sets the properties of this object.
addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Sets the properties of this object.
addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugAtom: Sets the properties of this object.
addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Sets the properties of this object.
addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Sets the properties of this object.
addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugAtomType: Sets the properties of this object.
addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Sets the properties of this object.
addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugBond: Sets the properties of this object.
addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugChemFile: Sets the properties of this object.
addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugChemModel: Sets the properties of this object.
addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugChemObject: Sets the properties of this object.
addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugChemSequence: Sets the properties of this object.
addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugCrystal: Sets the properties of this object.
addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugElectronContainer: Sets the properties of this object.
addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugElement: Sets the properties of this object.
addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Sets the properties of this object.
addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugIsotope: Sets the properties of this object.
addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugLonePair: Sets the properties of this object.
addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugMapping: Sets the properties of this object.
addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugMonomer: Sets the properties of this object.
addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugPolymer: Sets the properties of this object.
addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Sets the properties of this object.
addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugReaction: Sets the properties of this object.
addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugReactionScheme: Sets the properties of this object.
addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugReactionSet: Sets the properties of this object.
addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugRing: Sets the properties of this object.
addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugSingleElectron: Sets the properties of this object.
addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugStrand: Sets the properties of this object.
addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugSubstance: Sets the properties of this object.
addProperties(Map<Object, Object>) - Method in interface org.openscience.cdk.interfaces.IChemObject: Add properties to this object, duplicate keys will replace any existing value.
addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject: Sets the properties of this object.
addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.silent.ChemObject: Sets the properties of this object.
addReactant(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugReaction: Adds a reactant to this reaction.
addReactant(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IReaction: Adds a reactant to this reaction.
addReactant(IAtomContainer) - Method in class org.openscience.cdk.Reaction: Adds a reactant to this reaction.
addReactant(IAtomContainer) - Method in class org.openscience.cdk.silent.Reaction: Adds a reactant to this reaction.
addReactant(IAtomContainer, Double) - Method in class org.openscience.cdk.debug.DebugReaction: Adds a reactant to this reaction with a stoichiometry coefficient.
addReactant(IAtomContainer, Double) - Method in interface org.openscience.cdk.interfaces.IReaction: Adds a reactant to this reaction with a stoichiometry coefficient.
addReactant(IAtomContainer, Double) - Method in class org.openscience.cdk.Reaction: Adds a reactant to this reaction with a stoichiometry coefficient.
addReactant(IAtomContainer, Double) - Method in class org.openscience.cdk.silent.Reaction: Adds a reactant to this reaction with a stoichiometry coefficient.
addReaction(IReaction) - Method in class org.openscience.cdk.debug.DebugReactionSet: Adds an reaction to this container.
addReaction(IReaction) - Method in interface org.openscience.cdk.interfaces.IReactionSet: Adds an reaction to this container.
addReaction(IReaction) - Method in class org.openscience.cdk.ReactionSet: Adds an reaction to this container.
addReaction(IReaction) - Method in class org.openscience.cdk.silent.ReactionSet: Adds an reaction to this container.
addReaction(IReaction, int) - Method in class org.openscience.cdk.reaction.ReactionChain: Added a IReaction for this chain in position.
addReport(ValidationReport) - Method in class org.openscience.cdk.validate.ValidationReport: Merges the tests with the tests in this ValidationReport.
addResidue(Residue) - Method in class org.openscience.cdk.libio.md.MDMolecule: Add a Residue to the MDMolecule if not already present.
addSetting(IOSetting) - Method in class org.openscience.cdk.io.ChemObjectIO: Add an IOSetting to the reader/writer.
addSetting(IOSetting) - Method in interface org.openscience.cdk.io.IChemObjectIO: Add an IOSetting to the reader/writer.
addSettings(Collection<IOSetting>) - Method in class org.openscience.cdk.io.ChemObjectIO: Adds a collection of IOSettings to the reader/writer.
addSettings(Collection<IOSetting>) - Method in interface org.openscience.cdk.io.IChemObjectIO: Adds a collection of IOSettings to the reader/writer.
addSingleElectron(int) - Method in class org.openscience.cdk.AtomContainer: Adds a SingleElectron to this Atom.
addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Adds a SingleElectron to this Atom.
addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Adds a SingleElectron to this Atom.
addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Adds a SingleElectron to this Atom.
addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugCrystal: Adds a SingleElectron to this Atom.
addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugMonomer: Adds a SingleElectron to this Atom.
addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugPolymer: Adds a SingleElectron to this Atom.
addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugRing: Adds a SingleElectron to this Atom.
addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugStrand: Adds a SingleElectron to this Atom.
addSingleElectron(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Adds a SingleElectron to this Atom.
addSingleElectron(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Adds a LonePair to this Atom.
addSingleElectron(int) - Method in class org.openscience.cdk.silent.AtomContainer: Adds a SingleElectron to this Atom.
addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.AtomContainer: Adds a single electron to this AtomContainer.
addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Adds a single electron to this AtomContainer.
addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Adds a single electron to this AtomContainer.
addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Adds a single electron to this AtomContainer.
addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugCrystal: Adds a single electron to this AtomContainer.
addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugMonomer: Adds a single electron to this AtomContainer.
addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugPolymer: Adds a single electron to this AtomContainer.
addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugRing: Adds a single electron to this AtomContainer.
addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugStrand: Adds a single electron to this AtomContainer.
addSingleElectron(ISingleElectron) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Adds a single electron to this AtomContainer.
addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Adds a single electron to this AtomContainer.
addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.silent.AtomContainer: Adds a single electron to this AtomContainer.
addSingletonCell(int) - Method in class org.openscience.cdk.group.Partition: Add a new singleton cell to the end of the partition containing only this element.
addStereoElement(IStereoElement) - Method in class org.openscience.cdk.AtomContainer: Adds a stereo element to this container.
addStereoElement(IStereoElement) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Adds a stereo element to this container.
addStereoElement(IStereoElement) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Adds a stereo element to this container.
addStereoElement(IStereoElement) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Adds a stereo element to this container.
addStereoElement(IStereoElement) - Method in class org.openscience.cdk.debug.DebugCrystal: Adds a stereo element to this container.
addStereoElement(IStereoElement) - Method in class org.openscience.cdk.debug.DebugMonomer: Adds a stereo element to this container.
addStereoElement(IStereoElement) - Method in class org.openscience.cdk.debug.DebugPolymer: Adds a stereo element to this container.
addStereoElement(IStereoElement) - Method in class org.openscience.cdk.debug.DebugRing: Adds a stereo element to this container.
addStereoElement(IStereoElement) - Method in class org.openscience.cdk.debug.DebugStrand: Adds a stereo element to this container.
addStereoElement(IStereoElement) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Adds a stereo element to this container.
addStereoElement(IStereoElement) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Adds a stereo element to this container.
addStereoElement(IStereoElement) - Method in class org.openscience.cdk.silent.AtomContainer: Adds a stereo element to this container.
addStructure(IPDBStructure) - Method in class org.openscience.cdk.debug.DebugPDBPolymer: Adds the PDBStructure structure a this PDBPolymer.
addStructure(IPDBStructure) - Method in interface org.openscience.cdk.interfaces.IPDBPolymer: Adds the PDBStructure structure a this PDBPolymer.
addStructure(IPDBStructure) - Method in class org.openscience.cdk.protein.data.PDBPolymer
addStructure(IPDBStructure) - Method in class org.openscience.cdk.silent.PDBPolymer
addSymbol(String) - Method in class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom: Deprecated.

Add a symbol to this QueryAtom
addSymbol(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom: Deprecated.

Add a symbol to this QueryAtom
addToAtomContainer(IAtomContainer, IChemObject) - Method in class org.openscience.cdk.renderer.selection.AbstractSelection: Utility method to add an IChemObject to an IAtomContainer.
addToCell(int, int) - Method in class org.openscience.cdk.group.Partition: Add an element to a particular cell.
addTuple(Bspt.Tuple) - Method in class org.openscience.cdk.graph.rebond.Bspt
AdductFormula - Class in org.openscience.cdk.formula: Class defining an adduct object in a MolecularFormula.
AdductFormula - Class in org.openscience.cdk.silent: Class defining an adduct object in a MolecularFormula.
AdductFormula() - Constructor for class org.openscience.cdk.formula.AdductFormula: Constructs an empty AdductFormula.
AdductFormula() - Constructor for class org.openscience.cdk.silent.AdductFormula: Constructs an empty AdductFormula.
AdductFormula(IMolecularFormula) - Constructor for class org.openscience.cdk.formula.AdductFormula: Constructs an AdductFormula with a copy AdductFormula of another AdductFormula (A shallow copy, i.e., with the same objects as in the original AdductFormula).
AdductFormula(IMolecularFormula) - Constructor for class org.openscience.cdk.silent.AdductFormula: Constructs an AdductFormula with a copy AdductFormula of another AdductFormula (A shallow copy, i.e., with the same objects as in the original AdductFormula).
AdductionLPMechanism - Class in org.openscience.cdk.reaction.mechanism: This mechanism adduct together two fragments.
AdductionLPMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.AdductionLPMechanism
AdductionPBMechanism - Class in org.openscience.cdk.reaction.mechanism: This mechanism adduct together two fragments due to a double bond.
AdductionPBMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.AdductionPBMechanism
AdductionProtonLPReaction - Class in org.openscience.cdk.reaction.type: IReactionProcess which produces a protonation.
AdductionProtonLPReaction() - Constructor for class org.openscience.cdk.reaction.type.AdductionProtonLPReaction: Constructor of the AdductionProtonLPReaction object.
AdductionProtonPBReaction - Class in org.openscience.cdk.reaction.type: IReactionProcess which produces a protonation to double bond.
AdductionProtonPBReaction() - Constructor for class org.openscience.cdk.reaction.type.AdductionProtonPBReaction: Constructor of the AdductionProtonPBReaction object.
AdductionSodiumLPReaction - Class in org.openscience.cdk.reaction.type: IReactionProcess which produces an adduction of the Sodium.
AdductionSodiumLPReaction() - Constructor for class org.openscience.cdk.reaction.type.AdductionSodiumLPReaction: Constructor of the AdductionSodiumLPReaction object.
addValidator(IValidator) - Method in class org.openscience.cdk.validate.ValidatorEngine
addWarning(ValidationTest) - Method in class org.openscience.cdk.validate.ValidationReport: Adds a validation test which indicate a possible problem.
ADFFormat - Class in org.openscience.cdk.io.formats
ADFFormat() - Constructor for class org.openscience.cdk.io.formats.ADFFormat
AdjacencyMatrix - Class in org.openscience.cdk.graph.matrix: Calculator for a adjacency matrix representation of this AtomContainer.
AdjacencyMatrix() - Constructor for class org.openscience.cdk.graph.matrix.AdjacencyMatrix
adjustBeginLineColumn(int, int) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream: Method to adjust line and column numbers for the start of a token.
adjustBeginLineColumn(int, int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Method to adjust line and column numbers for the start of a token.
adjustProtonation(IMolecularFormula, int) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Adjust the protonation of a molecular formula.
Ag - Static variable in interface org.openscience.cdk.interfaces.IElement
AG - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Agent - org.openscience.cdk.ReactionRole
agents - Variable in class org.openscience.cdk.Reaction: These are the used solvent, catalysts etc that normally appear above the reaction arrow
agents - Variable in class org.openscience.cdk.silent.Reaction: These are the used solvent, catalysts etc that normally appear above the reaction arrow
Al - Static variable in interface org.openscience.cdk.interfaces.IElement
AL - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: ExtendedTetrahedral a.k.a.
AL - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
AL - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
AlchemyFormat - Class in org.openscience.cdk.io.formats
AlchemyFormat() - Constructor for class org.openscience.cdk.io.formats.AlchemyFormat
Algorithm - Enum in org.openscience.cdk.smsd.interfaces: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
align() - Method in class org.openscience.cdk.geometry.alignment.KabschAlignment: Perform an alignment.
alignment - Variable in class org.openscience.cdk.renderer.elements.AtomSymbolElement: The hydrogen alignment.
Aliphatic() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
ALIPHATIC_ELEMENT - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if the atomic number (IElement.getAtomicNumber() ()}) of an atom equals the specified 'value' and IAtom.isAromatic() is false.
ALIPHATIC_HETERO_SUBSTITUENT_COUNT - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if the number hetero atoms (see Expr.Type.IS_ALIPHATIC_HETERO) this atom is next to is equal to the specified value.
ALIPHATIC_ORDER - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if the bond order IBond.getOrder() equals the specified value and the bond is not marked as aromatic (IAtom.isAromatic()).
AliphaticAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
AliphaticAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AliphaticAtom: Deprecated.

Creates a new instance
AliphaticSymbolAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
AliphaticSymbolAtom(String, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AliphaticSymbolAtom: Deprecated.

Creates a new instance.
all() - Static method in class org.openscience.cdk.graph.Cycles: Create a cycle finder which will compute all simple cycles in a molecule.
all() - Method in class org.openscience.cdk.group.PermutationGroup: Generate the whole group from the compact list of permutations.
all() - Static method in class org.openscience.cdk.renderer.SymbolVisibility: All atom symbols are visible.
all(int) - Static method in class org.openscience.cdk.graph.Cycles: All cycles of smaller than or equal to the specified length.
all(IAtomContainer) - Static method in class org.openscience.cdk.graph.Cycles: Find all simple cycles in a molecule.
all(IAtomContainer, int) - Static method in class org.openscience.cdk.graph.Cycles: All cycles of smaller than or equal to the specified length.
all(SymbolVisibility) - Static method in class org.openscience.cdk.renderer.generators.standard.SelectionVisibility: Display the atom symbol if is selected, otherwise use the provided visibility.
ALL_RINGS - Static variable in class org.openscience.cdk.CDKConstants: A set of all rings computed for this molecule.
allBaseNumbers() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

The usual numbers .
allCoplanar(Vector3d, Point3d, Point3d...) - Static method in class org.openscience.cdk.stereo.StereoTool: Check that all the points in the list are coplanar (in the same plane) as the plane defined by the planeNormal and the pointInPlane.
AllCycles - Class in org.openscience.cdk.graph: Compute all simple cycles (rings) in a graph.
AllCycles(int[][], int, int) - Constructor for class org.openscience.cdk.graph.AllCycles: Compute all simple cycles up to given maxCycleSize in the provided graph.
Allenal - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: ExtendedTetrahedral (e.g.
allHeavyAtomsPlaced(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D: True is all the atoms in the given AtomContainer have been placed.
allIs0(int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Checks whether all the entries are equal to 0 or not.
allOrVertexShort() - Static method in class org.openscience.cdk.graph.Cycles: Deprecated.
use Cycles.or(org.openscience.cdk.graph.CycleFinder, org.openscience.cdk.graph.CycleFinder) to define a custom fall-back
ALLOW_SINGLETON - org.openscience.cdk.depict.Abbreviations.Option: Allow a structured to be collapsed to a single label.
AllPairsShortestPaths - Class in org.openscience.cdk.graph: Utility to determine the shortest paths between all pairs of atoms in a molecule.
AllPairsShortestPaths(IAtomContainer) - Constructor for class org.openscience.cdk.graph.AllPairsShortestPaths: Create a new all shortest paths utility for an IAtomContainer.
allPlaced(IAtomContainer) - Static method in class org.openscience.cdk.layout.AtomPlacer: True is all the atoms in the given AtomContainer have been placed
allPlaced(IRingSet) - Method in class org.openscience.cdk.layout.RingPlacer: True if coordinates have been assigned to all atoms in all rings.
AllRingsFinder - Class in org.openscience.cdk.ringsearch: Compute the set of all rings in a molecule.
AllRingsFinder() - Constructor for class org.openscience.cdk.ringsearch.AllRingsFinder: Default constructor using a threshold of AllRingsFinder.Threshold.PubChem_99.
AllRingsFinder(boolean) - Constructor for class org.openscience.cdk.ringsearch.AllRingsFinder: Deprecated.
turn logging off by setting the level in the logger implementation
AllRingsFinder.Threshold - Enum in org.openscience.cdk.ringsearch: The threshold values provide a limit at which the computation stops.
allSaturated(IAtomContainer) - Method in class org.openscience.cdk.tools.LonePairElectronChecker: Determines of all atoms on the AtomContainer have the right number the lone pair electrons.
allSaturated(IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker
allSaturated(IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
ALOGPDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: This class calculates ALOGP (Ghose-Crippen LogKow) and the Ghose-Crippen molar refractivity [Ghose, A.K. and Crippen, G.M. . Journal of Computational Chemistry. 1986. 7, Ghose, A.K. and Crippen, G.M. . Journal of Chemical Information and Computer Science. 1987. 27].
ALOGPDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
alogpfrag - Variable in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
Aluminium - org.openscience.cdk.config.Elements
ALUMINIUM - Static variable in enum org.openscience.cdk.config.Elements
ALUMINIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
ALUMINO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Am - Static variable in interface org.openscience.cdk.interfaces.IElement
AM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
AMERCIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Americium - org.openscience.cdk.config.Elements
AMERICIUM - Static variable in enum org.openscience.cdk.config.Elements
AMIDE - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
AMINE - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
AMINO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
AminoAcid - Class in org.openscience.cdk: A AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.
AminoAcid - Class in org.openscience.cdk.silent: A AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.
AminoAcid() - Constructor for class org.openscience.cdk.AminoAcid: Constructs a new AminoAcid.
AminoAcid() - Constructor for class org.openscience.cdk.silent.AminoAcid: Constructs a new AminoAcid.
AminoAcidCountDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Class that returns the number of each amino acid in an atom container.
AminoAcidCountDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor: Constructor for the AromaticAtomsCountDescriptor object.
AminoAcidManipulator - Class in org.openscience.cdk.tools.manipulator: Class with convenience methods that provide methods to manipulate AminoAcid's.
AminoAcidManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.AminoAcidManipulator
AminoAcids - Class in org.openscience.cdk.templates: Tool that provides templates for the (natural) amino acids.
AminoAcids() - Constructor for class org.openscience.cdk.templates.AminoAcids
AN - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
and(IBitFingerprint) - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
and(IBitFingerprint) - Method in interface org.openscience.cdk.fingerprint.IBitFingerprint: Performs a logical AND of the bits in this target bit set with the bits in the argument fingerprint.
and(IBitFingerprint) - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
and(IntArrayFingerprint) - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
and(Expr) - Method in class org.openscience.cdk.isomorphism.matchers.Expr: Utility, combine this expression with another, using conjunction.
and(IQueryAtom, IQueryAtom) - Static method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom: Deprecated.

Conjunction the provided expressions.
AND - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if both the subexpressions are true.
ANGSTROM_UNIT - Static variable in class org.openscience.cdk.io.GamessReader: Boolean constant used to specify that the coordinates are given in Ångstrom units.
AngularMomentum - Class in org.openscience.cdk.math.qm: This class is used to calculate angular momentum states.
AngularMomentum(double) - Constructor for class org.openscience.cdk.math.qm.AngularMomentum
ANNOTATION_LABEL - Static variable in class org.openscience.cdk.renderer.generators.standard.StandardGenerator: Defines the annotation label(s) of a chem object in a depiction.
AnnotationColor() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.AnnotationColor
AnnotationDistance() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.AnnotationDistance
AnnotationFontScale() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.AnnotationFontScale
ANNOTATIONS - Static variable in class org.openscience.cdk.CDKConstants: A List of annotation remarks.
anonymise(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Anonymise the provided container to single-bonded carbon atoms.
ANTI_CLOCKWISE - org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo
Antimony - org.openscience.cdk.config.Elements
ANTIMONY - Static variable in enum org.openscience.cdk.config.Elements
ANTIMONY - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
ANY - org.openscience.cdk.isomorphism.matchers.CTFileQueryBond.Type: Deprecated.
ANY_BOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
AnyAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
AnyAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AnyAtom: Deprecated.

Creates a new instance
AnyAtom() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
AnyOrderQueryBond - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
AnyOrderQueryBond(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AnyOrderQueryBond: Deprecated.
AnyOrderQueryBond(IQueryAtom, IQueryAtom, IBond.Order, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AnyOrderQueryBond: Deprecated.

Creates a new instance.
APolDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Sum of the atomic polarizabilities (including implicit hydrogens).
APolDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor: Constructor for the APolDescriptor object.
apply(int[]) - Method in class org.openscience.cdk.isomorphism.SmartsStereoMatch: Deprecated.

Backwards compatible method from when we used GUAVA predicates.
apply(PermutationGroup.Backtracker) - Method in class org.openscience.cdk.group.PermutationGroup: Apply the backtracker to all permutations in the larger group.
apply(IAtomContainer) - Method in class org.openscience.cdk.aromaticity.Aromaticity: Apply this aromaticity model to a molecule.
apply(IAtomContainer) - Method in class org.openscience.cdk.depict.Abbreviations: Generates and assigns abbreviations to a molecule.
apply(IAtomContainer, Map<IAtom, Integer>) - Method in class org.openscience.cdk.depict.Abbreviations: Generates and assigns abbreviations to a molecule.
applyTo(Permutation) - Method in interface org.openscience.cdk.group.PermutationGroup.Backtracker: Do something to the permutation
Ar - Static variable in interface org.openscience.cdk.interfaces.IElement
AR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
AR_BOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
areIntersected(IBond, IBond) - Method in class org.openscience.cdk.layout.OverlapResolver: Deprecated.

Checks if two bonds cross each other.
areRootAtomsDefined() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery: Checks validity of RGroupQuery.
areRootAtomsDefined() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
areSubstituentsDefined() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery: Checks validity of the RGroupQuery.
areSubstituentsDefined() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
Argon - org.openscience.cdk.config.Elements
ARGON - Static variable in enum org.openscience.cdk.config.Elements
aromatic() - Method in class org.openscience.cdk.smiles.SmilesGenerator: Deprecated.
configure with SmiFlavor
Aromatic() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
AROMATIC - org.openscience.cdk.isomorphism.matchers.CTFileQueryBond.Type: Deprecated.
AROMATIC_ELEMENT - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if the atomic number (IElement.getAtomicNumber() ()}) of an atom equals the specified 'value' and IAtom.isAromatic() is true.
AromaticAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
AromaticAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AromaticAtom: Deprecated.

Creates a new instance
AromaticAtomsCountDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Class that returns the number of aromatic atoms in an atom container.
AromaticAtomsCountDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor: Constructor for the AromaticAtomsCountDescriptor object.
AromaticBondsCountDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: This Class contains a method that returns the number of aromatic atoms in an AtomContainer.
AromaticBondsCountDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor: Constructor for the AromaticBondsCountDescriptor object.
Aromaticity - Class in org.openscience.cdk.aromaticity: A configurable model to perceive aromatic systems.
Aromaticity(ElectronDonation, CycleFinder) - Constructor for class org.openscience.cdk.aromaticity.Aromaticity: Create an aromaticity model using the specified electron donation model which is tested on the cycles.
AromaticityCalculator - Class in org.openscience.cdk.aromaticity: Deprecated.
use Aromaticity
AromaticityCalculator() - Constructor for class org.openscience.cdk.aromaticity.AromaticityCalculator: Deprecated.
AromaticOrSingleQueryBond - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
AromaticOrSingleQueryBond(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AromaticOrSingleQueryBond: Deprecated.

Creates a new instance.
AromaticOrSingleQueryBond(IQueryAtom, IQueryAtom, IBond.Order, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AromaticOrSingleQueryBond: Deprecated.

Creates a new instance
AromaticQueryBond - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
AromaticQueryBond(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AromaticQueryBond: Deprecated.

Creates a new instance.
AromaticQueryBond(IQueryAtom, IQueryAtom, IBond.Order, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AromaticQueryBond: Deprecated.

Creates a new instance
AromaticSymbolAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
AromaticSymbolAtom(String, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AromaticSymbolAtom: Deprecated.
aromatizeMolecule(IAtomContainer) - Static method in class org.openscience.cdk.normalize.SMSDNormalizer: Deprecated.

This function finds rings and uses aromaticity detection code to aromatize the molecule.
aromatizeMolecule(IAtomContainer) - Static method in class org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator: Deprecated.

This function finds rings and uses aromaticity detection code to aromatize the molecule.
ArrowBeg - org.openscience.cdk.interfaces.IBond.Display: Display as an arrow (e.g.
ArrowElement - Class in org.openscience.cdk.renderer.elements: IRenderingElement for linear arrows.
ArrowElement(double, double, double, double, double, boolean, Color) - Constructor for class org.openscience.cdk.renderer.elements.ArrowElement: Constructor for an arrow element, based on starting point, end point, width, direction, and color.
ArrowEnd - org.openscience.cdk.interfaces.IBond.Display: Display as an arrow (e.g.
ArrowHeadWidth() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ArrowHeadWidth
ArrowHeadWidth() - Constructor for class org.openscience.cdk.renderer.generators.ReactionSceneGenerator.ArrowHeadWidth
Arsenic - org.openscience.cdk.config.Elements
ARSENIC - Static variable in enum org.openscience.cdk.config.Elements
ARSENIC - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
as - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
As - Static variable in interface org.openscience.cdk.interfaces.IElement
AS - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
asBitSet() - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
asBitSet() - Method in interface org.openscience.cdk.fingerprint.IBitFingerprint: Returns a BitSet representation of the fingerprint.
asBitSet() - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
assignAtomTypePropertiesToAtom(IAtomContainer) - Method in class org.openscience.cdk.tools.AtomTypeTools
assignAtomTypePropertiesToAtom(IAtomContainer, boolean) - Method in class org.openscience.cdk.tools.AtomTypeTools: Method assigns certain properties to an atom.
assignAtomTypes(IAtomContainer) - Method in class org.openscience.cdk.forcefield.mmff.Mmff: Assign MMFF Symbolic atom types.
assignAtomTyps(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator: Method assigns atom types to atoms (calculates sssr and aromaticity)
assignGasteigerMarsiliSigmaPartialCharges(IAtomContainer, boolean) - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges: Main method which assigns Gasteiger Marisili partial sigma charges.
assignGasteigerPiPartialCharges(IAtomContainer, boolean) - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges: Main method which assigns Gasteiger partial pi charges.
assignGasteigerSigmaMarsiliFactors(IAtomContainer) - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges: Method which stores and assigns the factors a,b,c and CHI+.
assignInductivePartialCharges(IAtomContainer) - Method in class org.openscience.cdk.charges.InductivePartialCharges: Main method, set charge as atom properties.
assignMMFF94PartialCharges(IAtomContainer) - Method in class org.openscience.cdk.charges.MMFF94PartialCharges: Main method which assigns MMFF94 partial charges
assignProteinToGrid() - Method in class org.openscience.cdk.protein.ProteinPocketFinder: Method assigns the atoms of a biopolymer to the grid.
assignrPiMarsilliFactors(IAtomContainerSet) - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges: Method which stores and assigns the factors a,b,c and CHI+.
assignVdWRadiiToProtein() - Method in class org.openscience.cdk.protein.ProteinPocketFinder: Method which assigns van der Waals radii to the biopolymer default org/openscience/cdk/config/data/pdb_atomtypes.xml stored in the variable String vanDerWaalsFile.
Association - Class in org.openscience.cdk: Base class for storing interactions like hydrogen bonds and ionic interactions.
Association() - Constructor for class org.openscience.cdk.Association: Constructs an empty association.
Association(IAtom, IAtom) - Constructor for class org.openscience.cdk.Association: Constructs an association between two Atom's.
Astatine - org.openscience.cdk.config.Elements
ASTATINE - Static variable in enum org.openscience.cdk.config.Elements
At - Static variable in interface org.openscience.cdk.interfaces.IElement
AT - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Atropisomeric (e.g.
AT - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
atLeast(int) - Method in class org.openscience.cdk.isomorphism.Mappings: Efficiently determine if there are at least 'n' matches
atLowerBoundary() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager: Test the virtual font pointer to see if it is at the lower boundary of the font size range (0).
atMax() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager: Check if the font pointer is as the maximum value.
atMin() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager: Check if the font pointer is as the minimum value.
atof(String) - Static method in class org.openscience.cdk.math.FortranFormat: Converts a string of digits to an double.
atom - Variable in class org.openscience.cdk.LonePair: The atom with which this lone pair is associated.
atom - Variable in class org.openscience.cdk.silent.LonePair: The atom with which this lone pair is associated.
atom - Variable in class org.openscience.cdk.silent.SingleElectron: The atom with which this single electron is associated.
atom - Variable in class org.openscience.cdk.SingleElectron: The atom with which this single electron is associated.
Atom - Class in org.openscience.cdk: Represents the idea of an chemical atom.
Atom - Class in org.openscience.cdk.silent: Represents the idea of an chemical atom.
Atom() - Constructor for class org.openscience.cdk.Atom: Constructs an completely unset Atom.
Atom() - Constructor for class org.openscience.cdk.silent.Atom: Constructs an completely unset Atom.
Atom(int) - Constructor for class org.openscience.cdk.Atom: Create a new atom with of the specified element.
Atom(int) - Constructor for class org.openscience.cdk.silent.Atom: Create a new atom with of the specified element.
Atom(int, int) - Constructor for class org.openscience.cdk.Atom: Create a new atom with of the specified element and hydrogen count.
Atom(int, int) - Constructor for class org.openscience.cdk.silent.Atom: Create a new atom with of the specified element and hydrogen count.
Atom(int, int, int) - Constructor for class org.openscience.cdk.Atom: Create a new atom with of the specified element, hydrogen count, and formal charge.
Atom(int, int, int) - Constructor for class org.openscience.cdk.silent.Atom: Create a new atom with of the specified element, hydrogen count, and formal charge.
Atom(String) - Constructor for class org.openscience.cdk.Atom: Constructs an Atom from a string containing an element symbol and optionally the atomic mass, hydrogen count, and formal charge.
Atom(String) - Constructor for class org.openscience.cdk.silent.Atom: Constructs an Atom from a string containing an element symbol and optionally the atomic mass, hydrogen count, and formal charge.
Atom(String, Point2d) - Constructor for class org.openscience.cdk.Atom: Constructs an Atom from an Element and a Point2d.
Atom(String, Point2d) - Constructor for class org.openscience.cdk.silent.Atom: Constructs an Atom from an Element and a Point2d.
Atom(String, Point3d) - Constructor for class org.openscience.cdk.Atom: Constructs an Atom from an Element and a Point3d.
Atom(String, Point3d) - Constructor for class org.openscience.cdk.silent.Atom: Constructs an Atom from an Element and a Point3d.
Atom(IElement) - Constructor for class org.openscience.cdk.Atom: Constructs an isotope by copying the symbol, atomic number, flags, identifier, exact mass, natural abundance, mass number, maximum bond order, bond order sum, van der Waals and covalent radii, formal charge, hybridization, electron valency, formal neighbour count and atom type name from the given IAtomType.
Atom(IElement) - Constructor for class org.openscience.cdk.silent.Atom: Constructs an isotope by copying the symbol, atomic number, flags, identifier, exact mass, natural abundance, mass number, maximum bond order, bond order sum, van der Waals and covalent radii, formal charge, hybridization, electron valency, formal neighbour count and atom type name from the given IAtomType.
ATOM - Static variable in class org.openscience.cdk.libio.jena.CDK
ATOM_ATOM_MAPPING - Static variable in class org.openscience.cdk.CDKConstants
ATOM_EXPRESSION - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: Lexical state.
ATOM_NAME_FORMAT - Variable in class org.openscience.cdk.io.PDBWriter
atomAromaticities - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
AtomAtomMap - Static variable in class org.openscience.cdk.smiles.SmiFlavor: Output atom-atom mapping for reactions and atom classes for molecules.
AtomAtomMappingLineColor() - Constructor for class org.openscience.cdk.renderer.generators.MappingGenerator.AtomAtomMappingLineColor
AtomAtomMapRenumber - Static variable in class org.openscience.cdk.smiles.SmiFlavor: Renumber AtomAtomMaps during canonical generation
AtomColor() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.AtomColor
AtomColor() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.AtomColor
AtomColorer() - Constructor for class org.openscience.cdk.renderer.generators.AtomNumberGenerator.AtomColorer
AtomColorer() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.AtomColorer
atomContainer - Variable in class org.openscience.cdk.graph.AtomContainerPermutor: The atom container that is permuted at each step.
atomContainer - Variable in class org.openscience.cdk.inchi.InChIGenerator: AtomContainer instance refers to.
atomContainer - Variable in class org.openscience.cdk.tools.HOSECodeGenerator: The molecular structure on which we work
AtomContainer - Class in org.openscience.cdk: Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.
AtomContainer - Class in org.openscience.cdk.silent: Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.
AtomContainer() - Constructor for class org.openscience.cdk.AtomContainer: Constructs an empty AtomContainer.
AtomContainer() - Constructor for class org.openscience.cdk.silent.AtomContainer: Constructs an empty AtomContainer.
AtomContainer(int, int, int, int) - Constructor for class org.openscience.cdk.AtomContainer: Constructs an empty AtomContainer that will contain a certain number of atoms and electronContainers.
AtomContainer(int, int, int, int) - Constructor for class org.openscience.cdk.silent.AtomContainer: Constructs an empty AtomContainer that will contain a certain number of atoms and electronContainers.
AtomContainer(IAtomContainer) - Constructor for class org.openscience.cdk.AtomContainer: Constructs an AtomContainer with a copy of the atoms and electronContainers of another AtomContainer (A shallow copy, i.e., with the same objects as in the original AtomContainer).
AtomContainer(IAtomContainer) - Constructor for class org.openscience.cdk.silent.AtomContainer: Constructs an AtomContainer with a copy of the atoms and electronContainers of another AtomContainer (A shallow copy, i.e., with the same objects as in the original AtomContainer).
AtomContainerAtomPermutor - Class in org.openscience.cdk.graph: An atom container atom permutor that uses ranking and unranking to calculate the next permutation in the series.
AtomContainerAtomPermutor - Class in org.openscience.cdk.smsd.labelling: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
AtomContainerAtomPermutor(IAtomContainer) - Constructor for class org.openscience.cdk.graph.AtomContainerAtomPermutor: A permutor wraps the original atom container, and produces cloned (and permuted!) copies on demand.
AtomContainerAtomPermutor(IAtomContainer) - Constructor for class org.openscience.cdk.smsd.labelling.AtomContainerAtomPermutor: Deprecated.
AtomContainerBondPermutor - Class in org.openscience.cdk.graph: This class allows the user to iterate through the set of all possible permutations of the bond order in a given atom container.
AtomContainerBondPermutor(IAtomContainer) - Constructor for class org.openscience.cdk.graph.AtomContainerBondPermutor: A permutor wraps the original atom container, and produces cloned (and permuted!) copies on demand.
AtomContainerBoundsGenerator - Class in org.openscience.cdk.renderer.generators: IGenerator that draws a rectangular around the IAtomContainer.
AtomContainerBoundsGenerator() - Constructor for class org.openscience.cdk.renderer.generators.AtomContainerBoundsGenerator
AtomContainerComparator - Class in org.openscience.cdk.tools.manipulator: Compares two IAtomContainers for order with the following criteria with decreasing priority:
AtomContainerComparator() - Constructor for class org.openscience.cdk.tools.manipulator.AtomContainerComparator: Creates a new instance of AtomContainerComparator
AtomContainerComparatorBy2DCenter - Class in org.openscience.cdk.tools.manipulator: Compares two IAtomContainers based on their 2D position.
AtomContainerComparatorBy2DCenter() - Constructor for class org.openscience.cdk.tools.manipulator.AtomContainerComparatorBy2DCenter
atomContainerCount - Variable in class org.openscience.cdk.AtomContainerSet: Number of AtomContainers contained by this container.
atomContainerCount - Variable in class org.openscience.cdk.silent.AtomContainerSet: Number of AtomContainers contained by this container.
AtomContainerDiff - Class in org.openscience.cdk.tools.diff: Compares two IAtomContainer classes.
AtomContainerDiscretePartitionRefiner - Interface in org.openscience.cdk.group: A tool for determining the automorphism group of the atoms in a molecule, or for checking for a canonical form of a molecule.
AtomContainerManipulator - Class in org.openscience.cdk.tools.manipulator: Class with convenience methods that provide methods to manipulate AtomContainer's.
AtomContainerManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
AtomContainerPermutor - Class in org.openscience.cdk.graph: The base class for permutors of atom containers, with a single abstract method containerFromPermutation that should be implemented in concrete derived classes.
AtomContainerPermutor(int, IAtomContainer) - Constructor for class org.openscience.cdk.graph.AtomContainerPermutor: Start the permutor off with an initial atom container, and the size of the permutation.
AtomContainerPrinter - Class in org.openscience.cdk.smsd.labelling: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
AtomContainerPrinter() - Constructor for class org.openscience.cdk.smsd.labelling.AtomContainerPrinter: Deprecated.
AtomContainerRenderer - Class in org.openscience.cdk.renderer: A general renderer for IAtomContainers.
AtomContainerRenderer(List<IGenerator<IAtomContainer>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.AtomContainerRenderer: A renderer that generates diagrams using the specified generators and manages fonts with the supplied font manager.
AtomContainerRenderer(RendererModel, List<IGenerator<IAtomContainer>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.AtomContainerRenderer
atomContainers - Variable in class org.openscience.cdk.AtomContainerSet: Array of AtomContainers.
atomContainers - Variable in class org.openscience.cdk.silent.AtomContainerSet: Array of AtomContainers.
atomContainers() - Method in class org.openscience.cdk.AtomContainerSet: Get an iterator for this AtomContainerSet.
atomContainers() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Get an iterator for this AtomContainerSet.
atomContainers() - Method in class org.openscience.cdk.debug.DebugSubstance: Get an iterator for this AtomContainerSet.
atomContainers() - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet: Get an Iterable for this AtomContainerSet.
atomContainers() - Method in class org.openscience.cdk.silent.AtomContainerSet: Get an iterator for this AtomContainerSet.
AtomContainerSet - Class in org.openscience.cdk: A set of AtomContainers.
AtomContainerSet - Class in org.openscience.cdk.silent: A set of AtomContainers.
AtomContainerSet() - Constructor for class org.openscience.cdk.AtomContainerSet: Constructs an empty AtomContainerSet.
AtomContainerSet() - Constructor for class org.openscience.cdk.silent.AtomContainerSet: Constructs an empty AtomContainerSet.
AtomContainerSetManipulator - Class in org.openscience.cdk.tools.manipulator
AtomContainerSetManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
atomCount - Variable in class org.openscience.cdk.Association
atomCount - Variable in class org.openscience.cdk.AtomContainer: Number of atoms contained by this object.
atomCount - Variable in class org.openscience.cdk.Bond: Number of atoms contained by this object.
atomCount - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Number of atoms contained by this object.
atomCount - Variable in class org.openscience.cdk.isomorphism.matchers.QueryBond: Number of atoms contained by this object.
atomCount - Variable in class org.openscience.cdk.silent.AtomContainer: Number of atoms contained by this object.
atomCount - Variable in class org.openscience.cdk.silent.Bond: Number of atoms contained by this object.
AtomCountDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: IDescriptor based on the number of atoms of a certain element type.
AtomCountDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor: Constructor for the AtomCountDescriptor object.
atomCounter - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
atomCustomProperty - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
AtomDegreeDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic: This class returns the number of not-Hs substituents of an atom, also defined as "atom degree".
AtomDegreeDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor
atomDictRefs - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
AtomDiff - Class in org.openscience.cdk.tools.diff: Compares two IAtom classes.
AtomEncoder - Interface in org.openscience.cdk.hash: An encoder for invariant atom properties.
atomEnumeration - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
AtomExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
AtomHashGenerator - Interface in org.openscience.cdk.hash: A hash function which generates 64-bit hash codes for the atoms of a molecule.
AtomHybridizationDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic: This class returns the hybridization of an atom.
AtomHybridizationDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor
AtomHybridizationVSEPRDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic: This class returns the hybridization of an atom.
AtomHybridizationVSEPRDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor: Constructor for the AtomHybridizationVSEPRDescriptor object
atomic() - Method in class org.openscience.cdk.hash.HashGeneratorMaker: Given the current configuration create an AtomHashGenerator.
ATOMIC_NUMBER - org.openscience.cdk.hash.BasicAtomEncoder: Encode the atomic number of an atom.
AtomicMass - Static variable in class org.openscience.cdk.graph.invariant.CanonOpts: Distinguish atoms based on atomic mass.
AtomicMass - Static variable in class org.openscience.cdk.smiles.SmiFlavor: Output atomic mass on atoms.
AtomicMass() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
AtomicMassStrict - Static variable in class org.openscience.cdk.smiles.SmiFlavor: Deprecated.
no longer needed, default CDK behaviour is now to pass through mass numbers if non-null
atomicNumber - Variable in class org.openscience.cdk.Element: The atomic number for this element giving their position in the periodic table.
atomicNumber - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom: The atomic number for this element giving their position in the periodic table.
atomicNumber - Variable in class org.openscience.cdk.silent.Element: The atomic number for this element giving their position in the periodic table.
AtomicNumber() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
AtomicNumberAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
AtomicNumberAtom(int, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AtomicNumberAtom: Deprecated.

Creates a new instance.
AtomicNumberDifferenceDescriptor - Class in org.openscience.cdk.qsar.descriptors.bond: Describes the imbalance in atomic number of the IBond.
AtomicNumberDifferenceDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptor
atomicNumbers - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
AtomicProperties - Class in org.openscience.cdk.tools: Provides atomic property values for descriptor calculations.
AtomMappingTools - Class in org.openscience.cdk.isomorphism
AtomMappingTools() - Constructor for class org.openscience.cdk.isomorphism.AtomMappingTools
AtomMassGenerator - Class in org.openscience.cdk.renderer.generators: IGenerator that can render mass number information of atoms.
AtomMassGenerator() - Constructor for class org.openscience.cdk.renderer.generators.AtomMassGenerator
atomMassNumber - Variable in class org.openscience.cdk.renderer.elements.AtomMassSymbolElement: The IAtoms mass number.
AtomMassSymbolElement - Class in org.openscience.cdk.renderer.elements: Rendering element that shows the IAtom mass number information.
AtomMassSymbolElement(double, double, String, Integer, Integer, int, Integer, Color) - Constructor for class org.openscience.cdk.renderer.elements.AtomMassSymbolElement: Constructs a new TextElement displaying the atom's mass number information.
AtomMatcher - Class in org.openscience.cdk.isomorphism: Defines compatibility checking of atoms for (subgraph)-isomorphism mapping.
AtomMatcher - Interface in org.openscience.cdk.smsd.algorithm.matchers: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
AtomMatcher() - Constructor for class org.openscience.cdk.isomorphism.AtomMatcher
AtomNumberGenerator - Class in org.openscience.cdk.renderer.generators: IGenerator for IAtomContainers that will draw atom numbers for the atoms.
AtomNumberGenerator() - Constructor for class org.openscience.cdk.renderer.generators.AtomNumberGenerator
AtomNumberGenerator.AtomColorer - Class in org.openscience.cdk.renderer.generators: The color scheme by which to color the atom numbers, if the AtomNumberGenerator.ColorByType boolean is true.
AtomNumberGenerator.AtomNumberTextColor - Class in org.openscience.cdk.renderer.generators: Color to draw the atom numbers with.
AtomNumberGenerator.ColorByType - Class in org.openscience.cdk.renderer.generators: Boolean to indicate of the AtomNumberGenerator.AtomColorer scheme will be used.
AtomNumberGenerator.Offset - Class in org.openscience.cdk.renderer.generators: Offset vector in screen space coordinates where the atom number label will be placed.
AtomNumberGenerator.WillDrawAtomNumbers - Class in org.openscience.cdk.renderer.generators: Boolean parameter indicating if atom numbers should be drawn, allowing this feature to be disabled temporarily.
AtomNumberTextColor() - Constructor for class org.openscience.cdk.renderer.generators.AtomNumberGenerator.AtomNumberTextColor
atomOccurrence(String[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Getting the number of atoms' occurrences.
AtomPairs2DFingerprinter - Class in org.openscience.cdk.fingerprint: Generates an atom pair 2D fingerprint as implemented in PaDEL given an IAtomContainer, that extends the Fingerprinter.
AtomPairs2DFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.AtomPairs2DFingerprinter
atomParities - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
AtomPlacer - Class in org.openscience.cdk.layout: Methods for generating coordinates for atoms in various situations.
AtomPlacer() - Constructor for class org.openscience.cdk.layout.AtomPlacer: Constructor for the AtomPlacer object
AtomPlacer3D - Class in org.openscience.cdk.modeling.builder3d: Place aliphatic chains with Z matrix method.
AtomRadius() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.AtomRadius
AtomRef - Class in org.openscience.cdk: An atom ref, references a CDK IAtom indirectly.
AtomRef(IAtom) - Constructor for class org.openscience.cdk.AtomRef: Create a pointer for the provided atom.
AtomRefinerBuilder() - Constructor for class org.openscience.cdk.group.PartitionRefinement.AtomRefinerBuilder
atoms - Variable in class org.openscience.cdk.Association: The atoms which take part in the association.
atoms - Variable in class org.openscience.cdk.AtomContainer: Internal array of atoms.
atoms - Variable in class org.openscience.cdk.Bond: A list of atoms participating in this bond.
atoms - Variable in class org.openscience.cdk.fingerprint.CircularFingerprinter.FP
atoms - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Internal array of atoms.
atoms - Variable in class org.openscience.cdk.isomorphism.matchers.QueryBond: A list of atoms participating in this query bond.
atoms - Variable in class org.openscience.cdk.silent.AtomContainer: Internal array of atoms.
atoms - Variable in class org.openscience.cdk.silent.Bond: A list of atoms participating in this bond.
atoms() - Method in class org.openscience.cdk.AtomContainer: Returns an Iterable for looping over all atoms in this container.
atoms() - Method in class org.openscience.cdk.Bond: Returns the Iterator to atoms making up this bond.
atoms() - Method in class org.openscience.cdk.BondRef: Returns the Iterable to atoms making up this bond.
atoms() - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns an Iterable for looping over all atoms in this container.
atoms() - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns an Iterable for looping over all atoms in this container.
atoms() - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns an Iterable for looping over all atoms in this container.
atoms() - Method in class org.openscience.cdk.debug.DebugBond: Returns the Iterator to atoms making up this bond.
atoms() - Method in class org.openscience.cdk.debug.DebugCrystal: Returns an Iterable for looping over all atoms in this container.
atoms() - Method in class org.openscience.cdk.debug.DebugMonomer: Returns an Iterable for looping over all atoms in this container.
atoms() - Method in class org.openscience.cdk.debug.DebugPolymer: Returns an Iterable for looping over all atoms in this container.
atoms() - Method in class org.openscience.cdk.debug.DebugRing: Returns an Iterable for looping over all atoms in this container.
atoms() - Method in class org.openscience.cdk.debug.DebugStrand: Returns an Iterable for looping over all atoms in this container.
atoms() - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Returns an Iterable for looping over all atoms in this container.
atoms() - Method in interface org.openscience.cdk.interfaces.IBond: Returns the Iterable to atoms making up this bond.
atoms() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns an Iterable for looping over all atoms in this container.
atoms() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Returns the Iterator to atoms making up this query bond.
atoms() - Method in class org.openscience.cdk.silent.AtomContainer: Returns an Iterable for looping over all atoms in this container.
atoms() - Method in class org.openscience.cdk.silent.Bond: Returns the Iterator to atoms making up this bond.
AtomSignature - Class in org.openscience.cdk.signature: The signature [Faulon, J. L., Visco, D. P., and Pophale, R. S.. Journal of Chemical Information and Computer Sciences. 2003. 43, Faulon, J. L., Collins, M. J., and Carr, R. D.. Journal of Chemical Information and Computer Sciences. 2004. 44] for a molecule rooted at a particular atom.
AtomSignature(int, int, IAtomContainer) - Constructor for class org.openscience.cdk.signature.AtomSignature: Create an atom signature starting at atomIndex and with a maximum height of height.
AtomSignature(int, int, AbstractVertexSignature.InvariantType, IAtomContainer) - Constructor for class org.openscience.cdk.signature.AtomSignature: Create an atom signature starting at atomIndex, with maximum height of height, and using a particular invariant type.
AtomSignature(int, IAtomContainer) - Constructor for class org.openscience.cdk.signature.AtomSignature: Create an atom signature starting at atomIndex.
AtomSignature(IAtom, int, IAtomContainer) - Constructor for class org.openscience.cdk.signature.AtomSignature: Create an atom signature for the atom atom and with a maximum height of height.
AtomSignature(IAtom, int, AbstractVertexSignature.InvariantType, IAtomContainer) - Constructor for class org.openscience.cdk.signature.AtomSignature: Create an atom signature for the atom atom, with maximum height of height, and using a particular invariant type.
AtomSignature(IAtom, IAtomContainer) - Constructor for class org.openscience.cdk.signature.AtomSignature: Create an atom signature for the atom atom.
atomsTo(int) - Method in class org.openscience.cdk.graph.ShortestPaths: Reconstruct a shortest path to the provided end vertex.
atomsTo(IAtom) - Method in class org.openscience.cdk.graph.ShortestPaths: Reconstruct a shortest path to the provided end atom.
AtomSymbolElement - Class in org.openscience.cdk.renderer.elements: A text element with added information.
AtomSymbolElement(double, double, String, Integer, Integer, int, Color) - Constructor for class org.openscience.cdk.renderer.elements.AtomSymbolElement
AtomTetrahedralLigandPlacer3D - Class in org.openscience.cdk.modeling.builder3d: A set of static utility classes for geometric calculations on Atoms.
AtomTools - Class in org.openscience.cdk.geometry: A set of static utility classes for geometric calculations on Atoms.
AtomTools() - Constructor for class org.openscience.cdk.geometry.AtomTools
AtomType - Class in org.openscience.cdk: The base class for atom types.
AtomType - Class in org.openscience.cdk.silent: The base class for atom types.
AtomType(String) - Constructor for class org.openscience.cdk.AtomType: Constructor for the AtomType object.
AtomType(String) - Constructor for class org.openscience.cdk.silent.AtomType: Constructor for the AtomType object.
AtomType(String, String) - Constructor for class org.openscience.cdk.AtomType: Constructor for the AtomType object.
AtomType(String, String) - Constructor for class org.openscience.cdk.silent.AtomType: Constructor for the AtomType object.
AtomType(IElement) - Constructor for class org.openscience.cdk.AtomType: Constructs an isotope by copying the symbol, atomic number, flags, identifier, exact mass, natural abundance and mass number from the given IIsotope.
AtomType(IElement) - Constructor for class org.openscience.cdk.silent.AtomType: Constructs an isotope by copying the symbol, atomic number, flags, identifier, exact mass, natural abundance and mass number from the given IIsotope.
ATOMTYPE - Static variable in class org.openscience.cdk.libio.jena.CDK
ATOMTYPE_ID_JMOL - Static variable in class org.openscience.cdk.config.AtomTypeFactory: Used as an ID to describe the atom type.
ATOMTYPE_ID_MODELING - Static variable in class org.openscience.cdk.config.AtomTypeFactory: Used as an ID to describe the atom type.
ATOMTYPE_ID_STRUCTGEN - Static variable in class org.openscience.cdk.config.AtomTypeFactory: Used as an ID to describe the atom type.
AtomTypeAwareSaturationChecker - Class in org.openscience.cdk.tools: This class tries to figure out the bond order of the bonds that has the flag SINGLE_OR_DOUBLE raised (i.e.
AtomTypeAwareSaturationChecker() - Constructor for class org.openscience.cdk.tools.AtomTypeAwareSaturationChecker: Constructs an AtomTypeAwareSaturationChecker checker.
AtomTypeCharges - Class in org.openscience.cdk.charges: Assigns charges to atom types.
AtomTypeDiff - Class in org.openscience.cdk.tools.diff: Compares two IAtomType classes.
AtomTypeFactory - Class in org.openscience.cdk.config: General class for defining AtomTypes.
AtomTypeHandler - Class in org.openscience.cdk.config.atomtypes: SAX Handler for the AtomTypeReader.
AtomTypeHandler(IChemObjectBuilder) - Constructor for class org.openscience.cdk.config.atomtypes.AtomTypeHandler: Constructs a new AtomTypeHandler and will create IAtomType implementations using the given IChemObjectBuilder.
AtomTypeHybridizationDifference - Class in org.openscience.cdk.tools.diff.tree: IDifference between two IAtomType.Hybridizations.
AtomTypeManipulator - Class in org.openscience.cdk.tools.manipulator: Class with utilities for the IAtomType class.
AtomTypeManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.AtomTypeManipulator
AtomTypeMapper - Class in org.openscience.cdk.atomtype.mapper: An AtomTypeMapper allows the mapping of atom types between atom type schemes.
AtomTypeReader - Class in org.openscience.cdk.config.atomtypes: XML Reader for the CDKBasedAtomTypeConfigurator.
AtomTypeReader(Reader) - Constructor for class org.openscience.cdk.config.atomtypes.AtomTypeReader: Instantiates the XML based AtomTypeReader.
AtomTypeTools - Class in org.openscience.cdk.tools: AtomTypeTools is a helper class for assigning atom types to an atom.
AtomTypeTools() - Constructor for class org.openscience.cdk.tools.AtomTypeTools: Constructor for the MMFF94AtomTypeMatcher object.
AtomValenceDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic: This class returns the valence of an atom.
AtomValenceDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor: Constructor for the AtomValenceDescriptor object
AtomValenceTool - Class in org.openscience.cdk.qsar: This class returns the valence of an atom.
AtomValenceTool() - Constructor for class org.openscience.cdk.qsar.AtomValenceTool
Atropisomeric - Class in org.openscience.cdk.stereo: Restricted axial rotation around Aryl-Aryl bonds.
Atropisomeric - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Atropisomeric (e.g.
Atropisomeric(IBond, IAtom[], int) - Constructor for class org.openscience.cdk.stereo.Atropisomeric: Define a new atropisomer using the focus bond and the carrier atoms.
AttachedGroup - Class in org.openscience.cdk.iupac.parser: Holds data on a specific functional group or substituent.
AttachedGroup() - Constructor for class org.openscience.cdk.iupac.parser.AttachedGroup: Creates a new instance of FunctionalGroup
AttachedGroup(List<Token>, int) - Constructor for class org.openscience.cdk.iupac.parser.AttachedGroup: Creates a new instance of AttachedGroup with an int denoting the length of the substituent chain
AttachedGroup(List<Token>, String) - Constructor for class org.openscience.cdk.iupac.parser.AttachedGroup: Creates a new instance of AttachedGroup with a Sting denoting the functional group
attachLocationSpecified() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

An attach position has been specified using a comma seperated list followed by a dash
atUpperBoundary() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager: Test the virtual font pointer to see if it is at the upper boundary of the font size range (|fonts| - 1).
Au - Static variable in interface org.openscience.cdk.interfaces.IElement
AU - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
AUTO_CONTRACT_HETERO - org.openscience.cdk.depict.Abbreviations.Option: Automatically contract on hetero atoms, e.g.
AUTO_CONTRACT_LINKERS - org.openscience.cdk.depict.Abbreviations.Option: On auto-contract to linker, e.g.
AUTO_CONTRACT_TERMINAL - org.openscience.cdk.depict.Abbreviations.Option: Automatically contract on terminal atoms, e.g.
AutocorrelationDescriptorCharge - Class in org.openscience.cdk.qsar.descriptors.molecular: This class calculates ATS autocorrelation descriptor, where the weight equal to the charges.
AutocorrelationDescriptorCharge() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
AutocorrelationDescriptorMass - Class in org.openscience.cdk.qsar.descriptors.molecular: This class calculates ATS autocorrelation descriptor, where the weight equal to the scaled atomic mass [Moreau G. and Broto P.. Nouveau Journal de Chimie. 1980. null].
AutocorrelationDescriptorMass() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
AutocorrelationDescriptorPolarizability - Class in org.openscience.cdk.qsar.descriptors.molecular: This class calculates ATS autocorrelation descriptor, where the weight equal to the charges.
AutocorrelationDescriptorPolarizability() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
AUTOMATIC - Static variable in class org.openscience.cdk.depict.DepictionGenerator: Magic value for indicating automatic parameters.
AUTONOMNAME - Static variable in class org.openscience.cdk.CDKConstants: The IUPAC compatible name generated with AutoNom.
AuxNone - net.sf.jniinchi.INCHI_OPTION
AverageBondLengthCalculator - Class in org.openscience.cdk.renderer: Utility class for calculating the average bond length for various IChemObject subtypes : IReaction, IAtomContainerSet, IChemModel, and IReactionSet.
AverageBondLengthCalculator() - Constructor for class org.openscience.cdk.renderer.AverageBondLengthCalculator
AWTDrawVisitor - Class in org.openscience.cdk.renderer.visitor: Implementation of the IDrawVisitor interface for the AWT widget toolkit, allowing molecules to be rendered with toolkits based on AWT, like the Java reference graphics platform Swing.
AWTDrawVisitor(Graphics2D) - Constructor for class org.openscience.cdk.renderer.visitor.AWTDrawVisitor: Constructs a new IDrawVisitor using the AWT widget toolkit, taking a Graphics2D object to which the chemical content is drawn.
AWTFontManager - Class in org.openscience.cdk.renderer.font: AWT-specific font manager.
AWTFontManager() - Constructor for class org.openscience.cdk.renderer.font.AWTFontManager: Make a manager for fonts in AWT, with a minimum font size of 9.
axisScanX(int, int, int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder: Method performs a scan; works only for cubic grids!
axisScanY(int, int, int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder: Method performs a scan; works only for cubic grids!
axisScanZ(int, int, int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder: Method performs a scan; works only for cubic grids!

B

b - Variable in class org.openscience.cdk.io.random.RandomAccessReader
B - Static variable in interface org.openscience.cdk.interfaces.IElement
B - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Ba - Static variable in interface org.openscience.cdk.interfaces.IElement
BA - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
BackgroundColor() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.BackgroundColor
backTrack() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IState: Deprecated.

Returns this IState's atom map to its original condition.
backTrack() - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFState: Deprecated.

Returns this IState's atom map to its original condition.
backup(int) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream: Backup a number of characters.
backup(int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Backup a number of characters.
backward(int[][], int[], int[], int[], boolean[], int[], int[][][], int[][][], int[][][], boolean[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Backward step in the algorithm.
BACKWARD - org.openscience.cdk.interfaces.IReaction.Direction: Reaction equilibrium which is (almost) fully on the reactant side.
backwardCriteria(int, int, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: The criteria to decide which function is needed: forward or backward.
BAD_SMILES_INPUT - Static variable in class org.openscience.cdk.io.iterator.IteratingSMILESReader: Store the problem input as a property.
BadMatrixFormatException - Exception in org.openscience.cdk.graph.invariant.exception
BadMatrixFormatException() - Constructor for exception org.openscience.cdk.graph.invariant.exception.BadMatrixFormatException
Barium - org.openscience.cdk.config.Elements
BARIUM - Static variable in enum org.openscience.cdk.config.Elements
BARIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
BasicAtomEncoder - Enum in org.openscience.cdk.hash: Enumeration of atom encoders for seeding atomic hash codes.
BasicAtomGenerator - Class in org.openscience.cdk.renderer.generators: Generates basic IRenderingElements for atoms in an atom container.
BasicAtomGenerator() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator: An empty constructor necessary for reflection.
BasicAtomGenerator.AtomColor - Class in org.openscience.cdk.renderer.generators: Class to hold the color by which atom labels are drawn.
BasicAtomGenerator.AtomColorer - Class in org.openscience.cdk.renderer.generators: IAtomColorer used to draw elements.
BasicAtomGenerator.AtomRadius - Class in org.openscience.cdk.renderer.generators: Magic number with unknown units that defines the radius around an atom, e.g.
BasicAtomGenerator.ColorByType - Class in org.openscience.cdk.renderer.generators: Boolean property that triggers atoms to be colored by type when set to true.
BasicAtomGenerator.CompactAtom - Class in org.openscience.cdk.renderer.generators: Boolean parameters that will cause atoms to be drawn as filled shapes when set to true.
BasicAtomGenerator.CompactShape - Class in org.openscience.cdk.renderer.generators: Shape to be used when drawing atoms in compact mode, as defined by the BasicAtomGenerator.CompactAtom parameter.
BasicAtomGenerator.KekuleStructure - Class in org.openscience.cdk.renderer.generators: Determines whether structures should be drawn as Kekule structures, thus giving each carbon element explicitly, instead of not displaying the element symbol.
BasicAtomGenerator.Shape - Enum in org.openscience.cdk.renderer.generators: When atoms are selected or in compact mode, they will be covered by a shape determined by this enumeration.
BasicAtomGenerator.ShowEndCarbons - Class in org.openscience.cdk.renderer.generators: Boolean parameters that will show carbons with only one (non-hydrogen) neighbor to be drawn with an element symbol.
BasicAtomGenerator.ShowExplicitHydrogens - Class in org.openscience.cdk.renderer.generators: Boolean property that triggers explicit hydrogens to be drawn if set to true.
BasicBondGenerator - Class in org.openscience.cdk.renderer.generators: Generator for elements from bonds.
BasicBondGenerator() - Constructor for class org.openscience.cdk.renderer.generators.BasicBondGenerator: An empty constructor necessary for reflection.
BasicBondGenerator.BondDistance - Class in org.openscience.cdk.renderer.generators: The gap between double and triple bond lines on the screen.
BasicBondGenerator.BondWidth - Class in org.openscience.cdk.renderer.generators: The width on screen of a bond.
BasicBondGenerator.DefaultBondColor - Class in org.openscience.cdk.renderer.generators: The color to draw bonds if not other color is given.
BasicBondGenerator.TowardsRingCenterProportion - Class in org.openscience.cdk.renderer.generators: The proportion to move in towards the ring center.
BasicBondGenerator.WedgeWidth - Class in org.openscience.cdk.renderer.generators: The width on screen of the fat end of a wedge bond.
BasicCreator(Class<T>) - Constructor for class org.openscience.cdk.DynamicFactory.BasicCreator: Create a basic constructor with a given declaring class.
BasicGenerator - Class in org.openscience.cdk.renderer.generators: Combination generator for basic drawing of molecules.
BasicGenerator() - Constructor for class org.openscience.cdk.renderer.generators.BasicGenerator: Make a basic generator that creates elements for atoms and bonds.
BasicGroupCountDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Returns the number of basic groups.
BasicGroupCountDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor: Creates a new BasicGroupCountDescriptor.
basicInvariants(IAtomContainer, int[][]) - Static method in class org.openscience.cdk.graph.invariant.Canon: See Canon.basicInvariants(IAtomContainer, int[][], int).
basicInvariants(IAtomContainer, int[][], int) - Static method in class org.openscience.cdk.graph.invariant.Canon: Generate the initial invariants for each atom in the container.
BasicSceneGenerator - Class in org.openscience.cdk.renderer.generators: This generator does not create any elements, but acts as a holding place for various generator parameters used by most drawings, such as the zoom, background color, margin, etc.
BasicSceneGenerator() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator: An empty constructor necessary for reflection.
BasicSceneGenerator.ArrowHeadWidth - Class in org.openscience.cdk.renderer.generators: The width of the head of arrows.
BasicSceneGenerator.BackgroundColor - Class in org.openscience.cdk.renderer.generators: The background color of the drawn image.
BasicSceneGenerator.BondLength - Class in org.openscience.cdk.renderer.generators: The length on the screen of a typical bond.
BasicSceneGenerator.FitToScreen - Class in org.openscience.cdk.renderer.generators: If true, the scale is set such that the diagram fills the whole screen.
BasicSceneGenerator.FontName - Class in org.openscience.cdk.renderer.generators: Font to use for text.
BasicSceneGenerator.ForegroundColor - Class in org.openscience.cdk.renderer.generators: The foreground color, with which objects are drawn.
BasicSceneGenerator.Margin - Class in org.openscience.cdk.renderer.generators: Area on each of the four margins to keep empty.
BasicSceneGenerator.Scale - Class in org.openscience.cdk.renderer.generators: The scale is the factor to multiply model coordinates by to convert the coordinates to screen space coordinate, such that the entire structure fits the visible screen dimension.
BasicSceneGenerator.ShowMoleculeTitle - Class in org.openscience.cdk.renderer.generators: Determines if the molecule's title is depicted.
BasicSceneGenerator.ShowReactionTitle - Class in org.openscience.cdk.renderer.generators: Determines if the reaction's title is depicted.
BasicSceneGenerator.ShowTooltip - Class in org.openscience.cdk.renderer.generators: Determines if tooltips are to be shown.
BasicSceneGenerator.UseAntiAliasing - Class in org.openscience.cdk.renderer.generators: If set to true, uses anti-aliasing for drawing.
BasicSceneGenerator.UsedFontStyle - Class in org.openscience.cdk.renderer.generators: The font style to use for text.
BasicSceneGenerator.ZoomFactor - Class in org.openscience.cdk.renderer.generators: The zoom factor which is a user oriented parameter allowing the user to zoom in on parts of the molecule.
BasicValidator - Class in org.openscience.cdk.validate: Validator which tests a number of basic chemical semantics.
BasicValidator() - Constructor for class org.openscience.cdk.validate.BasicValidator
Bayesian - Class in org.openscience.cdk.fingerprint.model: Bayesian models using fingerprints: provides model creation, analysis, prediction and serialisation. Uses a variation of the classic Bayesian model, using a Laplacian correction, which sums log values of ratios rather than multiplying them together.
Bayesian(int) - Constructor for class org.openscience.cdk.fingerprint.model.Bayesian: Instantiate a Bayesian model with no data.
Bayesian(int, int) - Constructor for class org.openscience.cdk.fingerprint.model.Bayesian: Instantiate a Bayesian model with no data.
BCUTDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Eigenvalue based descriptor noted for its utility in chemical diversity.
BCUTDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor
Be - Static variable in interface org.openscience.cdk.interfaces.IElement
BE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
beginColumn - Variable in class org.openscience.cdk.iupac.parser.Token: The column number of the first character of this Token.
beginColumn - Variable in class org.openscience.cdk.smiles.smarts.parser.Token: The column number of the first character of this Token.
beginLine - Variable in class org.openscience.cdk.iupac.parser.Token: The line number of the first character of this Token.
beginLine - Variable in class org.openscience.cdk.smiles.smarts.parser.Token: The line number of the first character of this Token.
BeginToken() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream: Start.
BeginToken() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Start.
BEILSTEINRN - Static variable in class org.openscience.cdk.CDKConstants: The Beilstein Registry Number.
BELOWAREA - Static variable in class org.openscience.cdk.renderer.GraphRendererModel: Paints the area below the function
BENZENE_RING - Static variable in class org.openscience.cdk.tools.AtomTypeTools
Berkelium - org.openscience.cdk.config.Elements
BERKELIUM - Static variable in enum org.openscience.cdk.config.Elements
BERKELIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Beryllium - org.openscience.cdk.config.Elements
BERYLLIUM - Static variable in enum org.openscience.cdk.config.Elements
BERYLLIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
BFSShortestPath - Class in org.openscience.cdk.graph: Deprecated.
Use ShortestPaths
BGFFormat - Class in org.openscience.cdk.io.formats
BGFFormat() - Constructor for class org.openscience.cdk.io.formats.BGFFormat
Bh - Static variable in interface org.openscience.cdk.interfaces.IElement
Bi - Static variable in interface org.openscience.cdk.interfaces.IElement
BI - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
biconnectedSets() - Method in class org.openscience.cdk.graph.BiconnectivityInspector: Deprecated.

Returns a list of Sets, where each set contains all edge that are in the same biconnected component.
BiconnectivityInspector - Class in org.openscience.cdk.graph: Deprecated.
Use RingSearch or Cycles.markRingAtomsAndBonds(IAtomContainer)
BiconnectivityInspector(UndirectedGraph) - Constructor for class org.openscience.cdk.graph.BiconnectivityInspector: Deprecated.

Creates a biconnectivity inspector for the specified undirected graph.
Bicoordinate - org.openscience.cdk.stereo.Stereocenters.Type: An atom within a cumulated system.
BIDIRECTIONAL - org.openscience.cdk.interfaces.IReaction.Direction: Reaction equilibrium state.
biggerCheck(int, int[], int[], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Checks two arrays in descending order.
BinaryTree - Class in org.openscience.cdk.smsd.helper: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
BinaryTree(int) - Constructor for class org.openscience.cdk.smsd.helper.BinaryTree: Deprecated.

Creates a new instance of BinaryTree.
BINDSATOM - Static variable in class org.openscience.cdk.libio.jena.CDK
bindsHydrogen(IBond) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator: Check to see if any of the atoms in this bond are hydrogen atoms.
BioPolymer - Class in org.openscience.cdk: A BioPolymer is a subclass of a Polymer which is supposed to store additional informations about the Polymer which are connected to BioPolymers.
BioPolymer - Class in org.openscience.cdk.silent: A BioPolymer is a subclass of a Polymer which is supposed to store additional informations about the Polymer which are connected to BioPolymers.
BioPolymer() - Constructor for class org.openscience.cdk.BioPolymer: Constructs a new Polymer to store the Strands.
BioPolymer() - Constructor for class org.openscience.cdk.silent.BioPolymer: Constructs a new Polymer to store the Strands.
Bismuth - org.openscience.cdk.config.Elements
BISMUTH - Static variable in enum org.openscience.cdk.config.Elements
BISMUTH - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
BitSetFingerprint - Class in org.openscience.cdk.fingerprint
BitSetFingerprint() - Constructor for class org.openscience.cdk.fingerprint.BitSetFingerprint
BitSetFingerprint(int) - Constructor for class org.openscience.cdk.fingerprint.BitSetFingerprint
BitSetFingerprint(BitSet) - Constructor for class org.openscience.cdk.fingerprint.BitSetFingerprint
BitSetFingerprint(IBitFingerprint) - Constructor for class org.openscience.cdk.fingerprint.BitSetFingerprint
bitSetToRMap(BitSet) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Converts a RGraph bitset (set of RNode) to a list of RMap that represents the mapping between to substructures in G1 and G2 (the projection of the RGraph bitset on G1 and G2).
bitSetToRMap(BitSet) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph: Deprecated.

Converts a CDKRGraph bitset (set of CDKRNode) to a list of CDKRMap that represents the mapping between to substructures in G1 and G2 (the projection of the CDKRGraph bitset on G1 and G2).
Bk - Static variable in interface org.openscience.cdk.interfaces.IElement
BK - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
BKKCKCF - Class in org.openscience.cdk.smsd.algorithm.mcsplus: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
BKKCKCF(List<Integer>, List<Integer>, List<Integer>) - Constructor for class org.openscience.cdk.smsd.algorithm.mcsplus.BKKCKCF: Deprecated.

Creates index new instance of Bron Kerbosch Cazals Karande Koch Clique Finder This class implements Bron-Kerbosch clique detection algorithm as it is described in [F.
BOHR_TO_ANGSTROM - Static variable in class org.openscience.cdk.io.GamessReader: Double constant that contains the conversion factor from Bohr unit to Ångstrom unit.
BOHR_TO_ANGSTROM - Static variable in class org.openscience.cdk.PhysicalConstants: Factor for the conversion of Bohr's to Angstrom's.
BOHR_UNIT - Static variable in class org.openscience.cdk.io.GamessReader: Boolean constant used to specify that the coordinates are given in Bohr units.
Bohrium - org.openscience.cdk.config.Elements
BOHRIUM - Static variable in enum org.openscience.cdk.config.Elements
BOHRIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Bold - org.openscience.cdk.interfaces.IBond.Display: A bold line.
BOLD - org.openscience.cdk.renderer.font.IFontManager.FontStyle: Bold font style.
Bond - Class in org.openscience.cdk: Implements the concept of a covalent bond between two or more atoms.
Bond - Class in org.openscience.cdk.silent: Implements the concept of a covalent bond between two or more atoms.
Bond() - Constructor for class org.openscience.cdk.Bond: Constructs an empty bond.
Bond() - Constructor for class org.openscience.cdk.silent.Bond: Constructs an empty bond.
Bond(IAtom[]) - Constructor for class org.openscience.cdk.Bond: Constructs a multi-center bond, with undefined order and no stereo information.
Bond(IAtom[]) - Constructor for class org.openscience.cdk.silent.Bond: Constructs a multi-center bond, with undefined order and no stereo information.
Bond(IAtom[], IBond.Order) - Constructor for class org.openscience.cdk.Bond: Constructs a multi-center bond, with a specified order and no stereo information.
Bond(IAtom[], IBond.Order) - Constructor for class org.openscience.cdk.silent.Bond: Constructs a multi-center bond, with a specified order and no stereo information.
Bond(IAtom, IAtom) - Constructor for class org.openscience.cdk.Bond: Constructs a bond with a single bond order..
Bond(IAtom, IAtom) - Constructor for class org.openscience.cdk.silent.Bond: Constructs a bond with a single bond order..
Bond(IAtom, IAtom, IBond.Order) - Constructor for class org.openscience.cdk.Bond: Constructs a bond with a given order.
Bond(IAtom, IAtom, IBond.Order) - Constructor for class org.openscience.cdk.silent.Bond: Constructs a bond with a given order.
Bond(IAtom, IAtom, IBond.Order, IBond.Stereo) - Constructor for class org.openscience.cdk.Bond: Constructs a bond with a given order and stereo orientation from an array of atoms.
Bond(IAtom, IAtom, IBond.Order, IBond.Stereo) - Constructor for class org.openscience.cdk.silent.Bond: Constructs a bond with a given order and stereo orientation from an array of atoms.
BOND - Static variable in class org.openscience.cdk.libio.jena.CDK
BOND_ORDER_SUM - org.openscience.cdk.hash.BasicAtomEncoder: Encode the explicit bond order sum of an atom.
bondARef1 - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
bondARef2 - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
bondAromaticity - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
bondCount - Variable in class org.openscience.cdk.AtomContainer: Number of bonds contained by this object.
bondCount - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Number of bonds contained by this object.
bondCount - Variable in class org.openscience.cdk.silent.AtomContainer: Number of bonds contained by this object.
BondCountDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: IDescriptor based on the number of bonds of a certain bond order.
BondCountDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor: Constructor for the BondCountDescriptor object
bondCounter - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
bondCustomProperty - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
bondDictRefs - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
BondDiff - Class in org.openscience.cdk.tools.diff: Compares two IBond classes.
BondDistance() - Constructor for class org.openscience.cdk.renderer.generators.BasicBondGenerator.BondDistance
bondElid - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
BondEnergies - Class in org.openscience.cdk.smsd.tools: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
BondEnergies() - Constructor for class org.openscience.cdk.smsd.tools.BondEnergies: Deprecated.
BondEnergy - Class in org.openscience.cdk.smsd.helper: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
BondEnergy(String, String, IBond.Order, int) - Constructor for class org.openscience.cdk.smsd.helper.BondEnergy: Deprecated.

Creates a new bond energy for the given elements and bond order.
bondid - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
BondLength() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.BondLength
BondManipulator - Class in org.openscience.cdk.tools.manipulator: Class with convenience methods that provide methods to manipulate AtomContainer's.
BondManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.BondManipulator
bondMap - Variable in class org.openscience.cdk.stereo.StereoElementFactory: A bond map for fast access to bond labels between two atom indices.
BondMatcher - Class in org.openscience.cdk.isomorphism: Defines compatibility checking of bonds for (subgraph)-isomorphism mapping.
BondMatcher - Interface in org.openscience.cdk.smsd.algorithm.matchers: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
BondMatcher() - Constructor for class org.openscience.cdk.isomorphism.BondMatcher
BONDORDER_DOUBLE - Static variable in class org.openscience.cdk.CDKConstants: Deprecated.
Use IBond.Order DOUBLE directly.
BONDORDER_QUADRUPLE - Static variable in class org.openscience.cdk.CDKConstants: Deprecated.
Use IBond.Order QUADRUPLE directly.
BONDORDER_SINGLE - Static variable in class org.openscience.cdk.CDKConstants: Deprecated.
Use IBond.Order SINGLE directly.
BONDORDER_TRIPLE - Static variable in class org.openscience.cdk.CDKConstants: Deprecated.
Use IBond.Order TRIPLE directly.
bondOrderCanBeIncreased(IBond, IAtomContainer) - Method in class org.openscience.cdk.tools.AtomTypeAwareSaturationChecker: Check if the bond order can be increased.
BondOrderDifference - Class in org.openscience.cdk.tools.diff.tree: IDifference between two IBond.Orders.
BondPartialPiChargeDescriptor - Class in org.openscience.cdk.qsar.descriptors.bond: The calculation of bond-pi Partial charge is calculated determining the difference the Partial Pi Charge on atoms A and B of a bond.
BondPartialPiChargeDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor: Constructor for the BondPartialPiChargeDescriptor object.
BondPartialSigmaChargeDescriptor - Class in org.openscience.cdk.qsar.descriptors.bond: The calculation of bond-sigma Partial charge is calculated determining the difference the Partial Sigma Charge on atoms A and B of a bond.
BondPartialSigmaChargeDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor: Constructor for the BondPartialSigmaChargeDescriptor object.
BondPartialTChargeDescriptor - Class in org.openscience.cdk.qsar.descriptors.bond: The calculation of bond total Partial charge is calculated determining the difference the Partial Total Charge on atoms A and B of a bond.
BondPartialTChargeDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor: Constructor for the BondPartialTChargeDescriptor object.
BondRef - Class in org.openscience.cdk: A bond ref, references a CDK IBond indirectly.
BondRef(IBond) - Constructor for class org.openscience.cdk.BondRef: Create a pointer for the provided bond.
BondRefinerBuilder() - Constructor for class org.openscience.cdk.group.PartitionRefinement.BondRefinerBuilder
bonds - Variable in class org.openscience.cdk.AtomContainer: Internal array of bonds.
bonds - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Internal array of bonds.
bonds - Variable in class org.openscience.cdk.silent.AtomContainer: Internal array of bonds.
bonds() - Method in class org.openscience.cdk.Atom: Returns the bonds connected to this atom.
bonds() - Method in class org.openscience.cdk.AtomContainer: Returns an Iterable for looping over all bonds in this container.
bonds() - Method in class org.openscience.cdk.AtomRef
bonds() - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns an Iterable for looping over all bonds in this container.
bonds() - Method in class org.openscience.cdk.debug.DebugAtom: Returns the bonds connected to this atom.
bonds() - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns an Iterable for looping over all bonds in this container.
bonds() - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns an Iterable for looping over all bonds in this container.
bonds() - Method in class org.openscience.cdk.debug.DebugCrystal: Returns an Iterable for looping over all bonds in this container.
bonds() - Method in class org.openscience.cdk.debug.DebugMonomer: Returns an Iterable for looping over all bonds in this container.
bonds() - Method in class org.openscience.cdk.debug.DebugPolymer: Returns an Iterable for looping over all bonds in this container.
bonds() - Method in class org.openscience.cdk.debug.DebugRing: Returns an Iterable for looping over all bonds in this container.
bonds() - Method in class org.openscience.cdk.debug.DebugStrand: Returns an Iterable for looping over all bonds in this container.
bonds() - Method in interface org.openscience.cdk.interfaces.IAtom: Returns the bonds connected to this atom.
bonds() - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Returns an Iterable for looping over all bonds in this container.
bonds() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Returns the bonds connected to this atom.
bonds() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns an Iterable for looping over all bonds in this container.
bonds() - Method in class org.openscience.cdk.silent.Atom: Returns the bonds connected to this atom.
bonds() - Method in class org.openscience.cdk.silent.AtomContainer: Returns an Iterable for looping over all bonds in this container.
BondSeparation() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.BondSeparation
BondSigmaElectronegativityDescriptor - Class in org.openscience.cdk.qsar.descriptors.bond: The calculation of bond-Polarizability is calculated determining the difference the Sigma electronegativity on atoms A and B of a bond.
BondSigmaElectronegativityDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor: Constructor for the BondSigmaElectronegativityDescriptor object.
bondsInTree - Variable in class org.openscience.cdk.graph.SpanningTree
bondStereo - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
BondsToAtomDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic: This class returns the number of bonds on the shortest path between two atoms.
BondsToAtomDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor: Constructor for the BondsToAtomDescriptor object
bondSymbols - Variable in class org.openscience.cdk.tools.HOSECodeGenerator: The bond symbols used for bond orders "single", "double", "triple" and "aromatic"
BondTools - Class in org.openscience.cdk.geometry: A set of static utility classes for geometric calculations on IBonds.
BondTools() - Constructor for class org.openscience.cdk.geometry.BondTools
bondType() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Tokens which affect the bond order of the first bond.
BondWidth() - Constructor for class org.openscience.cdk.renderer.generators.BasicBondGenerator.BondWidth
BooleanArrayDifference - Class in org.openscience.cdk.tools.diff.tree: Difference between two boolean[]'s.
BooleanDifference - Class in org.openscience.cdk.tools.diff.tree: IDifference between two Booleans.
BooleanIOSetting - Class in org.openscience.cdk.io.setting: An class for a reader setting which must be of type String.
BooleanIOSetting(String, IOSetting.Importance, String, String) - Constructor for class org.openscience.cdk.io.setting.BooleanIOSetting
BooleanResult - Class in org.openscience.cdk.qsar.result: Object that provides access to the calculated descriptor value.
BooleanResult(boolean) - Constructor for class org.openscience.cdk.qsar.result.BooleanResult
BooleanResultType - Class in org.openscience.cdk.qsar.result: IDescriptorResult type for boolean.
BooleanResultType() - Constructor for class org.openscience.cdk.qsar.result.BooleanResultType
booleanValue() - Method in class org.openscience.cdk.qsar.result.BooleanResult
Boron - org.openscience.cdk.config.Elements
BORON - Static variable in enum org.openscience.cdk.config.Elements
Bounds - Class in org.openscience.cdk.renderer.elements: Defines a bounding box element which the renderer can use to determine the true drawing limits.
Bounds() - Constructor for class org.openscience.cdk.renderer.elements.Bounds: An empty bounding box.
Bounds(double, double, double, double) - Constructor for class org.openscience.cdk.renderer.elements.Bounds: Specify the min/max coordinates of the bounding box.
Bounds(IRenderingElement) - Constructor for class org.openscience.cdk.renderer.elements.Bounds: An bounding box around the specified element.
BoundsCalculator - Class in org.openscience.cdk.renderer: Utility class for calculating the 2D bounding rectangles (bounds) of various IChemObject subtypes - IChemModel, IReactionSet, IReaction, IAtomContainerSet, and IAtomContainer.
BoundsCalculator() - Constructor for class org.openscience.cdk.renderer.BoundsCalculator
BoundsColor() - Constructor for class org.openscience.cdk.renderer.generators.BoundsGenerator.BoundsColor
BoundsGenerator - Class in org.openscience.cdk.renderer.generators: Produce a bounding rectangle for various chem objects.
BoundsGenerator() - Constructor for class org.openscience.cdk.renderer.generators.BoundsGenerator
BoundsGenerator.BoundsColor - Class in org.openscience.cdk.renderer.generators: The color of the box drawn at the bounds of a molecule, molecule set, or reaction.
boundTo(IAtom, String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor.JPlogPCalculator
BPolDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Sum of the absolute value of the difference between atomic polarizabilities of all bonded atoms in the molecule (including implicit hydrogens) with polarizabilities taken from http://www.sunysccc.edu/academic/mst/ptable/p-table2.htm This descriptor assumes 2-centered bonds.
BPolDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor: Constructor for the APolDescriptor object
Br - Static variable in interface org.openscience.cdk.interfaces.IElement
BR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
breadthFirstSearch(IAtomContainer, List<IAtom>, IAtomContainer) - Static method in class org.openscience.cdk.graph.PathTools: Performs a breadthFirstSearch in an AtomContainer starting with a particular sphere, which usually consists of one start atom.
breadthFirstSearch(IAtomContainer, List<IAtom>, IAtomContainer[]) - Static method in class org.openscience.cdk.layout.AtomPlacer: Performs a breadthFirstSearch in an AtomContainer starting with a particular sphere, which usually consists of one start atom, and searches for the longest aliphatic chain which is yet unplaced.
breadthFirstSearch(IAtomContainer, List<IAtom>, IAtomContainer, int) - Static method in class org.openscience.cdk.graph.PathTools: Performs a breadthFirstSearch in an AtomContainer starting with a particular sphere, which usually consists of one start atom.
breadthFirstTargetSearch(IAtomContainer, List<IAtom>, IAtom, int, int) - Static method in class org.openscience.cdk.graph.PathTools: Performs a breadthFirstTargetSearch in an AtomContainer starting with a particular sphere, which usually consists of one start atom.
BremserOneSphereHOSECodePredictor - Class in org.openscience.cdk.tools
BremserOneSphereHOSECodePredictor() - Constructor for class org.openscience.cdk.tools.BremserOneSphereHOSECodePredictor
Bromine - org.openscience.cdk.config.Elements
BROMINE - Static variable in enum org.openscience.cdk.config.Elements
BROMO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
BSFormat - Class in org.openscience.cdk.io.formats: See here.
BSFormat() - Constructor for class org.openscience.cdk.io.formats.BSFormat
Bspt - Class in org.openscience.cdk.graph.rebond: BSP-Tree stands for Binary Space Partitioning Tree.
Bspt(int) - Constructor for class org.openscience.cdk.graph.rebond.Bspt
Bspt.Tuple - Interface in org.openscience.cdk.graph.rebond
bufcolumn - Variable in class org.openscience.cdk.iupac.parser.SimpleCharStream
bufcolumn - Variable in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
buffer - Variable in class org.openscience.cdk.iupac.parser.SimpleCharStream
buffer - Variable in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
bufline - Variable in class org.openscience.cdk.iupac.parser.SimpleCharStream
bufline - Variable in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
bufpos - Variable in class org.openscience.cdk.iupac.parser.SimpleCharStream: Position in buffer.
bufpos - Variable in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Position in buffer.
build() - Method in class org.openscience.cdk.fingerprint.model.Bayesian: Performs that Bayesian model generation, using the {molecule:activity} pairs that have been submitted up to this point.
buildArray(int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Building the copy of the partition array
buildAtomContainerFromMatrix(int[][], IAtomContainer) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Building an atom container for an adjacency matrix.
buildBondMatrix() - Method in class org.openscience.cdk.graph.invariant.EquivalentClassPartitioner: Build bond matrix.
buildContainer4SDF(int[][]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Building an atom container for an adjacency matrix.
buildContainer4SDF(String[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Building an atom container for SDF output from its symbols
buildContainer4SDF(IAtomContainer, int[][]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Building an atom container for an adjacency matrix.
builder - Variable in class org.openscience.cdk.io.random.RandomAccessReader
buildMolecule(int, List<AttachedGroup>, List<AttachedGroup>, boolean, String) - Method in class org.openscience.cdk.iupac.parser.MoleculeBuilder: Start of the process of building a molecule from the parsed data.
buildNodeMatrix(double[]) - Method in class org.openscience.cdk.graph.invariant.EquivalentClassPartitioner: Build node Matrix.
buildRGraph(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: Builds the RGraph ( resolution graph ), from two atomContainer (description of the two molecules to compare) This is the interface point between the CDK model and the generic MCSS algorithm based on the RGRaph.
buildRGraph(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS: Deprecated.

Builds the CDKRGraph ( resolution graph ), from two atomContainer (description of the two molecules to compare) This is the interface point between the CDK model and the generic MCSS algorithm based on the RGRaph.
buildSymbolArray() - Method in class org.openscience.cdk.structgen.maygen.Maygen
buildTrialNodeMatrix(double[]) - Method in class org.openscience.cdk.graph.invariant.EquivalentClassPartitioner: Build trial node Matrix.
buildWeightMatrix(double[][], double[][]) - Method in class org.openscience.cdk.graph.invariant.EquivalentClassPartitioner: Build weight array for the given node matrix and bond matrix.
BUILTIN - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
BUSY - net.sf.jniinchi.INCHI_RET
BUT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.

C

c - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
C - Static variable in interface org.openscience.cdk.interfaces.IElement: Carbon atomic number
C - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
C_TERMINAL_AMINO_ACID - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor
Ca - Static variable in interface org.openscience.cdk.interfaces.IElement
CA - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
CacaoCartesianFormat - Class in org.openscience.cdk.io.formats: See here.
CacaoCartesianFormat() - Constructor for class org.openscience.cdk.io.formats.CacaoCartesianFormat
CacaoInternalFormat - Class in org.openscience.cdk.io.formats: See here.
CacaoInternalFormat() - Constructor for class org.openscience.cdk.io.formats.CacaoInternalFormat
cachedDiagram - Variable in class org.openscience.cdk.renderer.AbstractRenderer: Used when repainting an unchanged model.
cacheDescriptorValue(IAtom, IAtomContainer, IDescriptorResult) - Method in class org.openscience.cdk.qsar.AbstractAtomicDescriptor: Caches a DescriptorValue for a given IAtom.
cacheDescriptorValue(IBond, IAtomContainer, IDescriptorResult) - Method in class org.openscience.cdk.qsar.AbstractBondDescriptor: Caches a DescriptorValue for a given IBond.
CACheFormat - Class in org.openscience.cdk.io.formats
CACheFormat() - Constructor for class org.openscience.cdk.io.formats.CACheFormat
Cadmium - org.openscience.cdk.config.Elements
CADMIUM - Static variable in enum org.openscience.cdk.config.Elements
CADMIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Caesium - org.openscience.cdk.config.Elements
CAESIUM - Static variable in enum org.openscience.cdk.config.Elements
calcD(double, double, double, double, Vector, Vector) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
calcFitting(Dimensions, Dimensions, double) - Method in class org.openscience.cdk.depict.Depiction
calcG(int, double, double, double, double, double, double) - Method in class org.openscience.cdk.math.qm.GaussiansBasis: Transfer equation for the calculation of core potentials
calcG(int, int, double, double, double, double, double, double, double, double, double) - Method in class org.openscience.cdk.math.qm.GaussiansBasis: Transfer equation for a four center integral.
calcI(int, int, int, int) - Method in class org.openscience.cdk.math.qm.FourierGridBasis
calcI(int, int, int, int) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
calcI(int, int, int, int) - Method in interface org.openscience.cdk.math.qm.IBasis: Calculates a two eletron fout center integral I = <chi_i chi_j | 1/r12 | chi_k chi_l >.
calcI(int, int, int, int, double, double, double, double, double, double, double, double, double) - Method in class org.openscience.cdk.math.qm.GaussiansBasis: Transfer equation for a four center integral.
calcInvertedAxes(Vector3d, Vector3d, Vector3d) - Static method in class org.openscience.cdk.geometry.CrystalGeometryTools: Inverts three cell axes.
Calcium - org.openscience.cdk.config.Elements
CALCIUM - Static variable in enum org.openscience.cdk.config.Elements
CALCIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
calcJ(int, int) - Method in class org.openscience.cdk.math.qm.FourierGridBasis
calcJ(int, int) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
calcJ(int, int) - Method in interface org.openscience.cdk.math.qm.IBasis: Calculates the impulse J = -<d/dr chi_i | d/dr chi_j>.
calcJ(int, int, double, double, double, double) - Method in class org.openscience.cdk.math.qm.GaussiansBasis: Transfer equation the the calculation of the impulse
calcLogP(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor.JPlogPCalculator: Given a structure in the correct configuration (explicit H and aromatised) it will return the logP as a Double or if it is out of domain (encounters an unknown atomtype) it will return Double.NaN
calcS(int, int) - Method in class org.openscience.cdk.math.qm.FourierGridBasis
calcS(int, int) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
calcS(int, int) - Method in interface org.openscience.cdk.math.qm.IBasis: Calculate the overlap integral S = <phi_i|phi_j>.
calculate() - Method in class org.openscience.cdk.math.qm.ClosedShellJob
calculate() - Method in class org.openscience.cdk.math.qm.OneElectronJob
calculate(double[], double[]) - Static method in class org.openscience.cdk.similarity.Tanimoto: Evaluates the continuous Tanimoto coefficient for two real valued vectors.
calculate(BitSet, BitSet) - Static method in class org.openscience.cdk.similarity.Tanimoto: Evaluates Tanimoto coefficient for two bit sets.
calculate(Map<String, Integer>, Map<String, Integer>) - Static method in class org.openscience.cdk.similarity.LingoSimilarity: Evaluate the LINGO similarity between two key,value sty;e fingerprints.
calculate(Map<String, Integer>, Map<String, Integer>) - Static method in class org.openscience.cdk.similarity.Tanimoto: Evaluate continuous Tanimoto coefficient for two feature, count fingerprint representations.
calculate(IBitFingerprint, IBitFingerprint) - Static method in class org.openscience.cdk.similarity.Tanimoto: Evaluates Tanimoto coefficient for two IBitFingerprint.
calculate(ICountFingerprint, ICountFingerprint) - Static method in class org.openscience.cdk.similarity.Tanimoto: Evaluate continuous Tanimoto coefficient for two feature, count fingerprint representations.
calculate(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter: Calculates the fingerprints for the given IAtomContainer, and stores them for subsequent retrieval.
calculate(IAtomContainer) - Static method in class org.openscience.cdk.geometry.volume.VABCVolume: Calculates the volume for the given IAtomContainer.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor: Calculates the descriptor value for the given IAtomContainer.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor: The AlogP descriptor.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor: Determine the number of amino acids groups the supplied IAtomContainer.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor: Calculate the sum of atomic polarizabilities in an IAtomContainer.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor: Calculate the count of aromatic atoms in the supplied IAtomContainer.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor: Calculate the count of aromatic atoms in the supplied IAtomContainer.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor: This method calculate the number of atoms of a given type in an IAtomContainer.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass: This method calculate the ATS Autocorrelation descriptor.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability: This method calculate the ATS Autocorrelation descriptor.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor: Calculates the descriptor value for the given IAtomContainer.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor: Calculates the three classes of BCUT descriptors.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor: This method calculate the number of bonds of a given type in an atomContainer
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor: This method calculate the sum of the absolute value of the difference between atomic polarizabilities of all bonded atoms in the molecule
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor: Calculates the 9 carbon types descriptors
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor: Evaluates the 29 CPSA descriptors using Gasteiger-Marsilli charges.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor: Calculates the eccentric connectivity
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor: Calculates the FMF descriptor value for the given IAtomContainer.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalCSP3Descriptor: Calculates the Fsp³ descriptor value for the given IAtomContainer.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor: Calculates the topological polar surface area and expresses it as a ratio to molecule size.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor: Calculate the complexity in the supplied IAtomContainer.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor: Calculates the 9 gravitational indices.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor: Calculates the number of H bond acceptors.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor: Calculates the number of H bond donors.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor: Calculate sp3/sp2 hybridization ratio in the supplied IAtomContainer.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor: Deprecated.

It calculates the first ionization energy of a molecule.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor: calculates the kier shape indices for an atom container
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor: This method calculates occurrences of the Kier & Hall E-state fragments.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor: Calculate the count of atoms of the largest chain in the supplied IAtomContainer.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor: Calculate the count of atoms of the largest pi system in the supplied IAtomContainer.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor: Evaluate the descriptor for the molecule.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor: Calculate the count of atoms of the longest aliphatic chain in the supplied IAtomContainer.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor: Calculates the Mannhold LogP for an atom container.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor: Calculate the weight of specified element type in the supplied IAtomContainer.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor: Calculates the 3 MI's, 3 ration and the R_gyr value.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor: Evaluate the descriptor for the molecule.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor: Calculates the two Petitjean shape indices.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor: The method calculates the number of rotatable bonds of an atom container.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor: the method take a boolean checkAromaticity: if the boolean is true, it means that aromaticity has to be checked.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor: Performs the calculation: the graph will be analyzed and ring information will be determined and wrapped up into descriptors.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.SpiroAtomCountDescriptor: Calculates the descriptor value for the given IAtomContainer.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor: Calculates the TPSA for an atom container.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor: Calculates the descriptor value using the VABCVolume class.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor: calculates the VAdjMa descriptor for an atom container
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor: Calculate the natural weight of specified elements type in the supplied IAtomContainer.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor: Calculates the weighted path descriptors.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor: Calculates 11 directional and 6 non-directional WHIM descriptors for.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor: Calculate the Wiener numbers.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor: Calculates the xlogP for an atom container.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor: Evaluate the Zagreb Index for a molecule.
calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor: Calculates the 147 TAE descriptors for amino acids.
calculate(IAtomContainer) - Method in interface org.openscience.cdk.qsar.IMolecularDescriptor: Calculates the descriptor value for the given IAtomContainer.
calculate(IAtomContainer, IAtom) - Method in class org.openscience.cdk.geometry.RDFCalculator: Calculates a RDF for Atom atom in the environment of the atoms in the AtomContainer.
calculate(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.similarity.DistanceMoment: Evaluate the 3D similarity between two molecules.
calculate(IAtom, IAtom) - Method in interface org.openscience.cdk.geometry.IRDFWeightFunction: Calculates the weight for the interaction between the two atoms.
calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor: This method calculates the number of not-H substituents of an atom.
calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor: This method calculates the hybridization of an atom.
calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor: This method calculates the hybridization of an atom.
calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor: This method calculates the valence of an atom.
calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor: This method calculate the number of bonds on the shortest path between two atoms.
calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor: This method calculates the Covalent radius of an atom.
calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor: This method calculate the 3D distance between two atoms.
calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor: The method calculates the Effective Atom Polarizability of a given atom It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor: It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder, and 3D coordinates.
calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor: It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder, and 3D coordinates.
calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor: This method calculates the ionization potential of an atom.
calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor: Deprecated.

This method calculates the ionization potential of an atom.
calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor: The method is a proton descriptor that evaluate if a proton is bonded to an aromatic system or if there is distance of 2 bonds.
calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInConjugatedPiSystemDescriptor: The method is a proton descriptor that evaluates if a proton is joined to a conjugated system.
calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor: The method returns apha partial charges assigned to an heavy atom through Gasteiger Marsili It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor: The method returns apha partial charges assigned to an heavy atom through Gasteiger Marsili It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor: The method returns partial charges assigned to an heavy atom through MMFF94 method.
calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor: The method returns partial total charges assigned to an heavy atom through PEOE method.
calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor: This method calculates the period of an atom.
calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor: The method calculates the pi electronegativity of a given atom It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor: This method calculates the protonation affinity of an atom.
calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor: The method returns partial charges assigned to an heavy atom and its protons through Gasteiger Marsili It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R
calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR
calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol
calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR
calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR
calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor: The method calculates the sigma electronegativity of a given atom It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor: The method calculates the stabilization of charge of a given atom It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor: This method calculate the Van der Waals radius of an atom.
calculate(IAtom, IAtomContainer) - Method in interface org.openscience.cdk.qsar.IAtomicDescriptor: Calculates the descriptor value for the given IAtom.
calculate(IAtom, IAtomContainer, IRingSet) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R
calculate(IAtom, IAtomContainer, IRingSet) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR
calculate(IAtom, IAtomContainer, IRingSet) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol
calculate(IAtom, IAtomContainer, IRingSet) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR
calculate(IAtom, IAtomContainer, IRingSet) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR
calculate(IAtom, IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor: The method returns if two atoms have pi-contact.
calculate(IAtom, IAtom, IAtomContainer) - Method in interface org.openscience.cdk.qsar.IAtomPairDescriptor: Calculates the descriptor value for the given IAtom.
calculate(IBond, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptor
calculate(IBond, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor: The method calculates the bond-pi Partial charge of a given bond It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
calculate(IBond, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor: The method calculates the bond-sigma Partial charge of a given bond It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
calculate(IBond, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor: The method calculates the bond total Partial charge of a given bond It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
calculate(IBond, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor: The method calculates the sigma electronegativity of a given bond It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
calculate(IBond, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor: Deprecated.

This method calculates the ionization potential of a bond.
calculate(IBond, IAtomContainer) - Method in interface org.openscience.cdk.qsar.IBondDescriptor: Calculates the descriptor value for the given IBond.
calculate(ISubstance) - Method in interface org.openscience.cdk.qsar.descriptors.substance.ISubstanceDescriptor: Calculates the descriptor value for the given ISubstance.
calculate(ISubstance) - Method in class org.openscience.cdk.qsar.descriptors.substance.OxygenAtomCountDescriptor: Calculates the descriptor value for the given ISubstance.
calculate3DCoordinates0(Point3d, int, double) - Static method in class org.openscience.cdk.geometry.AtomTools: Calculates substituent points.
calculate3DCoordinates0(Point3d, int, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D: Calculates substituent points.
calculate3DCoordinates1(Point3d, Point3d, Point3d, int, double, double) - Static method in class org.openscience.cdk.geometry.AtomTools: Calculate new point(s) X in a B-A system to form B-A-X.
calculate3DCoordinates1(Point3d, Point3d, Point3d, int, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D: Calculate new point(s) X in a B-A system to form B-A-X.
calculate3DCoordinates2(Point3d, Point3d, Point3d, int, double, double) - Static method in class org.openscience.cdk.geometry.AtomTools: Calculate new point(s) X in a B-A-C system.
calculate3DCoordinates2(Point3d, Point3d, Point3d, int, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D: Calculate new point(s) X in a B-A-C system, it forms a B-A(-C)-X system.
calculate3DCoordinates3(Point3d, Point3d, Point3d, Point3d, double) - Static method in class org.openscience.cdk.geometry.AtomTools: Calculate new point X in a B-A(-D)-C system.
calculate3DCoordinates3(Point3d, Point3d, Point3d, Point3d, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D: Calculate new point X in a B-A(-D)-C system.
calculate3DCoordinatesForLigands(IAtomContainer, IAtom, int, double, double) - Static method in class org.openscience.cdk.geometry.AtomTools: Adds 3D coordinates for singly-bonded ligands of a reference atom (A).
calculate3DCoordinatesSP2_1(Point3d, Point3d, Point3d, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D: Calculate new point in B-A-C system.
calculate3DCoordinatesSP2_2(Point3d, Point3d, Point3d, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D: Calculate two new points in B-A system.
calculateAverageBondLength(IAtomContainerSet) - Static method in class org.openscience.cdk.renderer.AverageBondLengthCalculator: Calculate the average bond length for the bonds in a molecule set.
calculateAverageBondLength(IChemModel) - Static method in class org.openscience.cdk.renderer.AverageBondLengthCalculator: Calculate the average bond length for the bonds in a chem model.
calculateAverageBondLength(IReaction) - Static method in class org.openscience.cdk.renderer.AverageBondLengthCalculator: Calculate the average bond length for the bonds in a reaction.
calculateAverageBondLength(IReactionSet) - Static method in class org.openscience.cdk.renderer.AverageBondLengthCalculator: Calculate the average bond length for the bonds in a reaction set.
calculateBondPolarizability(IAtomContainer, IBond) - Method in class org.openscience.cdk.charges.Polarizability: calculate bond polarizability.
calculateBounds(IAtomContainer) - Static method in class org.openscience.cdk.renderer.BoundsCalculator: Calculate the bounding rectangle for an atom container.
calculateBounds(IAtomContainerSet) - Static method in class org.openscience.cdk.renderer.BoundsCalculator: Calculate the bounding rectangle for a molecule set.
calculateBounds(IChemModel) - Static method in class org.openscience.cdk.renderer.BoundsCalculator: Calculate the bounding rectangle for a chem model.
calculateBounds(IReaction) - Static method in class org.openscience.cdk.renderer.BoundsCalculator: Calculate the bounding rectangle for a reaction.
calculateBounds(IReactionSet) - Static method in class org.openscience.cdk.renderer.BoundsCalculator: Calculate the bounding rectangle for a reaction set.
calculateCharges(IAtomContainer) - Method in class org.openscience.cdk.charges.AtomTypeCharges
calculateCharges(IAtomContainer) - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
calculateCharges(IAtomContainer) - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges
calculateCharges(IAtomContainer) - Method in interface org.openscience.cdk.charges.IElectronicPropertyCalculator
calculateCharges(IAtomContainer) - Method in class org.openscience.cdk.charges.InductivePartialCharges
calculateCharges(IAtomContainer) - Method in class org.openscience.cdk.charges.MMFF94PartialCharges
calculateDiagramBounds(IAtomContainer) - Method in class org.openscience.cdk.renderer.AtomContainerRenderer: Given a IChemObject, calculates the bounding rectangle in screen space.
calculateDiagramBounds(IAtomContainerSet) - Method in class org.openscience.cdk.renderer.MoleculeSetRenderer: Given a IChemObject, calculates the bounding rectangle in screen space.
calculateDiagramBounds(IChemModel) - Method in class org.openscience.cdk.renderer.ChemModelRenderer: Given a chem model, calculates the bounding rectangle in screen space.
calculateDiagramBounds(IReaction) - Method in class org.openscience.cdk.renderer.ReactionRenderer: Given a IChemObject, calculates the bounding rectangle in screen space.
calculateDiagramBounds(IReactionSet) - Method in class org.openscience.cdk.renderer.ReactionSetRenderer: Given a IChemObject, calculates the bounding rectangle in screen space.
calculateDiagramBounds(T) - Method in interface org.openscience.cdk.renderer.IRenderer: Given a IChemObject, calculates the bounding rectangle in screen space.
calculateGHEffectiveAtomPolarizability(IAtomContainer, IAtom, boolean, int[][]) - Method in class org.openscience.cdk.charges.Polarizability: calculate effective atom polarizability.
calculateGHEffectiveAtomPolarizability(IAtomContainer, IAtom, int, boolean) - Method in class org.openscience.cdk.charges.Polarizability: calculate effective atom polarizability.
calculateIsomorphs(IAtomContainer, IAtomContainer, boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler: Deprecated.

This function calculates only one solution (exact) because we are looking at the molecules which are exactly same in terms of the bonds and atoms determined by the Fingerprint
calculateKJMeanMolecularPolarizability(IAtomContainer) - Method in class org.openscience.cdk.charges.Polarizability: calculates the mean molecular polarizability as described in paper of Kang and Jhorn.
calculateMaxRank() - Method in class org.openscience.cdk.graph.Permutor: Calculate the max possible rank for permutations of N numbers.
calculateMaxRank() - Method in class org.openscience.cdk.smsd.labelling.Permutor: Deprecated.

Calculate the max possible rank for permutations of N numbers.
calculateNumberOfImplicitHydrogens(IAtom) - Method in class org.openscience.cdk.tools.SaturationChecker
calculateNumberOfImplicitHydrogens(IAtom, double, double, List<IBond>, boolean) - Method in class org.openscience.cdk.tools.SaturationChecker: Calculate the number of missing hydrogens by subtracting the number of bonds for the atom from the expected number of bonds.
calculateNumberOfImplicitHydrogens(IAtom, double, IBond.Order, int) - Method in class org.openscience.cdk.tools.SmilesValencyChecker: Calculates the number of hydrogens that can be added to the given atom to fullfil the atom's valency.
calculateNumberOfImplicitHydrogens(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker: Calculate the number of missing hydrogens by subtracting the number of bonds for the atom from the expected number of bonds.
calculateNumberOfImplicitHydrogens(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
calculateNumberOfImplicitHydrogens(IAtom, IAtomContainer, boolean) - Method in class org.openscience.cdk.tools.SaturationChecker
calculateOrbits() - Method in class org.openscience.cdk.signature.MoleculeSignature: Calculates the orbits of the atoms of the molecule.
calculateOverlapsAndReduce(IAtomContainer, IAtomContainer, boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler: Deprecated.

This function calculates all the possible combinations of MCS
calculateOverlapsAndReduceExactMatch(IAtomContainer, IAtomContainer, boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler: Deprecated.

This function calculates only one solution (exact) because we are looking at the molecules which are exactly same in terms of the bonds and atoms determined by the Fingerprint
calculatePerpendicularUnitVector(Point2d, Point2d) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Determines the normalized vector orthogonal on the vector p1->p2.
calculatePerpendicularUnitVector(Point2d, Point2d) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Determines the normalized vector orthogonal on the vector p1->p2.
calculatePiElectronegativity(IAtomContainer, IAtom) - Method in class org.openscience.cdk.charges.PiElectronegativity: calculate the electronegativity of orbitals pi.
calculatePiElectronegativity(IAtomContainer, IAtom, int, int) - Method in class org.openscience.cdk.charges.PiElectronegativity: calculate the electronegativity of orbitals pi.
calculatePlus(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor: Deprecated.

It calculates the 1,2,..
calculatePositive(IAtomContainer, IAtom) - Method in class org.openscience.cdk.charges.StabilizationCharges: calculate the stabilization of orbitals when they contain deficiency of charge.
calculateScaleForBondLength(double) - Method in class org.openscience.cdk.renderer.AbstractRenderer: Calculate the scale to convert the model bonds into bonds of the length supplied.
calculateScaleForBondLength(double) - Method in class org.openscience.cdk.renderer.AtomContainerRenderer: Given a bond length for a model, calculate the scale that will transform this length to the on screen bond length in RendererModel.
calculateScaleForBondLength(double) - Method in class org.openscience.cdk.renderer.ChemModelRenderer: Given a bond length for a model, calculate the scale that will transform this length to the on screen bond length in RendererModel.
calculateScaleForBondLength(double) - Method in class org.openscience.cdk.renderer.MoleculeSetRenderer: Given a bond length for a model, calculate the scale that will transform this length to the on screen bond length in RendererModel.
calculateScaleForBondLength(double) - Method in class org.openscience.cdk.renderer.ReactionRenderer: Given a bond length for a model, calculate the scale that will transform this length to the on screen bond length in RendererModel.
calculateScaleForBondLength(double) - Method in class org.openscience.cdk.renderer.ReactionSetRenderer: Given a bond length for a model, calculate the scale that will transform this length to the on screen bond length in RendererModel.
calculateScreenBounds(Rectangle2D) - Method in class org.openscience.cdk.renderer.AbstractRenderer: Converts a bounding rectangle in 'model space' into the equivalent bounds in 'screen space'.
calculateSigmaElectronegativity(IAtomContainer, IAtom) - Method in class org.openscience.cdk.charges.Electronegativity: calculate the electronegativity of orbitals sigma.
calculateSigmaElectronegativity(IAtomContainer, IAtom, int, int) - Method in class org.openscience.cdk.charges.Electronegativity: calculate the electronegativity of orbitals sigma.
calculateSubGraphs(IAtomContainer, IAtomContainer, boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler: Deprecated.

This function calculates only one solution (exact) because we are looking at the molecules which are exactly same in terms of the bonds and atoms determined by the Fingerprint
calculateSurface() - Method in class org.openscience.cdk.geometry.surface.NumericalSurface: Deprecated.
calcV(int, int) - Method in class org.openscience.cdk.math.qm.FourierGridBasis
calcV(int, int) - Method in class org.openscience.cdk.math.qm.GaussiansBasis: Calculates the core potential.
calcV(int, int) - Method in interface org.openscience.cdk.math.qm.IBasis: Calculates the potential V = <chi_i | 1/r | chi_j>.
calcV(int, int, Vector, double) - Method in class org.openscience.cdk.math.qm.GaussiansBasis: Calculates the core potential.
Californium - org.openscience.cdk.config.Elements
CALIFORNIUM - Static variable in enum org.openscience.cdk.config.Elements
CALIFORNIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
canBuildIsomer(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Checking whether a molecular formula can represent a graph or not.
canBuildIsomerSingle(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Checking whether a molecular formula can represent a graph or not.
cancel() - Method in class org.openscience.cdk.formula.MolecularFormulaGenerator: Cancel the current search.
candidatePermutations(int, List<Permutation>, List<ArrayList<Permutation>>) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Calculating all candidate permutations for row canonical test.
canDraw(IAtom, IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator: Checks an atom to see if it should be drawn.
Canon - Class in org.openscience.cdk.graph.invariant: An implementation based on the canon algorithm [Weininger, David et. al.. Journal of Chemical Information and Computer Sciences. 1989. 29].
Canonical - Static variable in class org.openscience.cdk.smiles.SmiFlavor: Output SMILES in a canonical order.
CANONICAL_LABEL - Static variable in class org.openscience.cdk.smiles.InvPair
canonicalizeAtoms(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.SimpleAtomCanonicalizer
CanonicalLabeler - Class in org.openscience.cdk.graph.invariant: Deprecated.
this labeller uses slow data structures and has been replaced - Canon
CanonicalLabeler() - Constructor for class org.openscience.cdk.graph.invariant.CanonicalLabeler: Deprecated.
CanonicalLabellingAdaptor - Class in org.openscience.cdk.smsd.labelling: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
CanonicalLabellingAdaptor() - Constructor for class org.openscience.cdk.smsd.labelling.CanonicalLabellingAdaptor: Deprecated.
canonicalPartition(int, int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: To get the canonical partition.
canonicalTest(int[][], int[], int[][], int[], List<ArrayList<Permutation>>, int[], int[], int[], int[], int[][], int[][], boolean[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen
canonLabel(IAtomContainer) - Method in class org.openscience.cdk.graph.invariant.CanonicalLabeler: Deprecated.

Canonically label the fragment.
CanonOpts - Class in org.openscience.cdk.graph.invariant: Basic flavor options to tweak canonical invariants, note these deliberately mirror some fields from the SmiFlavor settings.
CanonOpts() - Constructor for class org.openscience.cdk.graph.invariant.CanonOpts
Carbon - org.openscience.cdk.config.Elements
CARBON - Static variable in enum org.openscience.cdk.config.Elements
CarbonTypesDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Topological descriptor characterizing the carbon connectivity.
CarbonTypesDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor
carbonylConjugated(IAtom) - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor.JPlogPCalculator
CarbonylEliminationReaction - Class in org.openscience.cdk.reaction.type: IReactionProcess which participate mass spectrum process.
CarbonylEliminationReaction() - Constructor for class org.openscience.cdk.reaction.type.CarbonylEliminationReaction: Constructor of the CarbonylEliminationReaction object.
cardinality() - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
cardinality() - Method in interface org.openscience.cdk.fingerprint.IBitFingerprint: Returns the number of bits set to true in the fingerprint.
cardinality() - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
CARET - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
cartesianToFractional(Vector3d, Vector3d, Vector3d, Point3d) - Static method in class org.openscience.cdk.geometry.CrystalGeometryTools
cartesianToNotional(Vector3d, Vector3d, Vector3d) - Static method in class org.openscience.cdk.geometry.CrystalGeometryTools
case1(int, int, int, int, int, int, int) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks: Deprecated.
case2(int, int, int, int, int, int, int) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks: Deprecated.
case3(int, int, int, int, int, int, int) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks: Deprecated.
case4(int, int, int, int, int, int, int) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks: Deprecated.
cases(int, int, int, int, int, int, int, int) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks: Deprecated.
CASNumber - Class in org.openscience.cdk.index: Tools to work with CAS registry numbers.
CASNumber() - Constructor for class org.openscience.cdk.index.CASNumber
CASRN - Static variable in class org.openscience.cdk.CDKConstants: The CAS Registry Number.
Cd - Static variable in interface org.openscience.cdk.interfaces.IElement
CD - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
cdk() - Static method in class org.openscience.cdk.aromaticity.ElectronDonation: Use the preset CDK atom types to determine the electron contribution of atoms.
CDK - Class in org.openscience.cdk: Helper class to provide general information about this CDK library.
CDK - Class in org.openscience.cdk.libio.jena: Helper class to provide a Java API to the CDK OWL ontology, following the design of similar namespace classes in the Jena library, like RDF.
CDK() - Constructor for class org.openscience.cdk.CDK
CDK() - Constructor for class org.openscience.cdk.libio.jena.CDK
CDK2DAtomColors - Class in org.openscience.cdk.renderer.color: Gives a short table of atom colors for 2D display.
CDK2DAtomColors() - Constructor for class org.openscience.cdk.renderer.color.CDK2DAtomColors
cdkAllowingExocyclic() - Static method in class org.openscience.cdk.aromaticity.ElectronDonation: Use the preset CDK atom types to determine the electron contribution of atoms.
cdkAromaticSet() - Static method in class org.openscience.cdk.graph.Cycles: Create a cycle finder which will compute a set of cycles traditionally used by the CDK to test for aromaticity.
CDKAtomColors - Class in org.openscience.cdk.renderer.color: Deprecated.
JmolColors provides more comprehensive color pallet for 3D
CDKAtomColors() - Constructor for class org.openscience.cdk.renderer.color.CDKAtomColors: Deprecated.
cdkAtomContainerSetToCMLList(IAtomContainerSet) - Method in class org.openscience.cdk.libio.cml.Convertor
cdkAtomContainerToCMLMolecule(IAtomContainer) - Method in class org.openscience.cdk.libio.cml.Convertor
cdkAtomToCMLAtom(IAtom) - Method in class org.openscience.cdk.libio.cml.Convertor
cdkAtomToCMLAtom(IAtomContainer, IAtom) - Method in class org.openscience.cdk.libio.cml.Convertor
CDKAtomTypeMatcher - Class in org.openscience.cdk.atomtype: Atom Type matcher that perceives atom types as defined in the CDK atom type list org/openscience/cdk/dict/data/cdk-atom-types.owl.
CDKBasedAtomTypeConfigurator - Class in org.openscience.cdk.config: AtomType resource that reads the atom type configuration from an XML file.
CDKBasedAtomTypeConfigurator() - Constructor for class org.openscience.cdk.config.CDKBasedAtomTypeConfigurator
cdkBondToCMLBond(IBond) - Method in class org.openscience.cdk.libio.cml.Convertor
cdkChemFileToCMLList(IChemFile) - Method in class org.openscience.cdk.libio.cml.Convertor
cdkChemModelToCMLList(IChemModel) - Method in class org.openscience.cdk.libio.cml.Convertor
cdkChemSequenceToCMLList(IChemSequence) - Method in class org.openscience.cdk.libio.cml.Convertor
CDKConstants - Class in org.openscience.cdk: An interface providing predefined values for a number of constants used throughout the CDK.
CDKConstants() - Constructor for class org.openscience.cdk.CDKConstants
CDKConvention - Class in org.openscience.cdk.io.cml: This is an implementation for the CDK convention.
CDKConvention(IChemFile) - Constructor for class org.openscience.cdk.io.cml.CDKConvention
CDKConvention(ICMLModule) - Constructor for class org.openscience.cdk.io.cml.CDKConvention
cdkCrystalToCMLMolecule(ICrystal) - Method in class org.openscience.cdk.libio.cml.Convertor
CDKDictionaryReferences - Class in org.openscience.cdk.dict: This class transforms implicit references to dictionary of CDK objects into explicit references.
CDKDictionaryReferences() - Constructor for class org.openscience.cdk.dict.CDKDictionaryReferences
CDKException - Exception in org.openscience.cdk.exception: Exception that is thrown by CDK classes when some problem has occurred.
CDKException(String) - Constructor for exception org.openscience.cdk.exception.CDKException: Constructs a new CDKException with the given message.
CDKException(String, Throwable) - Constructor for exception org.openscience.cdk.exception.CDKException: Constructs a new CDKException with the given message and the Exception as cause.
CDKHueckelAromaticityDetector - Class in org.openscience.cdk.aromaticity: Deprecated.
use Aromaticity with the ElectronDonation.cdk() model
CDKHueckelAromaticityDetector() - Constructor for class org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector: Deprecated.
CDKHydrogenAdder - Class in org.openscience.cdk.tools: Adds implicit hydrogens based on atom type definitions.
cdkLegacy() - Static method in class org.openscience.cdk.aromaticity.Aromaticity: Access an aromaticity instance that replicates the previously utilised - CDKHueckelAromaticityDetector.
CDKMCS - Class in org.openscience.cdk.smsd.algorithm.rgraph: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
CDKMCS - org.openscience.cdk.smsd.interfaces.Algorithm: Deprecated.

CDK UIT MCS.
CDKMCS() - Constructor for class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS: Deprecated.
CDKMCSHandler - Class in org.openscience.cdk.smsd.algorithm.rgraph: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
CDKMCSHandler() - Constructor for class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler: Deprecated.
cdkMonomerToCMLMolecule(IMonomer) - Method in class org.openscience.cdk.libio.cml.Convertor
CDKOWLFormat - Class in org.openscience.cdk.io.formats: Serializes a CDK model into the Web Ontology Language using the N3 format.
CDKOWLFormat() - Constructor for class org.openscience.cdk.io.formats.CDKOWLFormat
CDKOWLReader - Class in org.openscience.cdk.io.rdf: Reads content from a CDK OWL serialization.
CDKOWLReader() - Constructor for class org.openscience.cdk.io.rdf.CDKOWLReader: Creates a new CDKOWLReader with an undefined input.
CDKOWLReader(Reader) - Constructor for class org.openscience.cdk.io.rdf.CDKOWLReader: Creates a new CDKOWLReader sending output to the given Writer.
CDKOWLWriter - Class in org.openscience.cdk.io.rdf: Serializes the data model into CDK OWL.
CDKOWLWriter() - Constructor for class org.openscience.cdk.io.rdf.CDKOWLWriter: Creates a new CDKOWLWriter with an undefined output.
CDKOWLWriter(Writer) - Constructor for class org.openscience.cdk.io.rdf.CDKOWLWriter: Creates a new CDKOWLWriter sending output to the given Writer.
cdkPDBPolymerToCMLMolecule(IPDBPolymer) - Method in class org.openscience.cdk.libio.cml.Convertor
cdkReactionSchemeToCMLReactionScheme(IReactionScheme) - Method in class org.openscience.cdk.libio.cml.Convertor
cdkReactionSchemeToCMLReactionSchemeAndMoleculeList(IReactionScheme) - Method in class org.openscience.cdk.libio.cml.Convertor
cdkReactionSetToCMLReactionList(IReactionSet) - Method in class org.openscience.cdk.libio.cml.Convertor
cdkReactionToCMLReaction(IReaction) - Method in class org.openscience.cdk.libio.cml.Convertor
cdkReactionToCMLReactionStep(IReaction) - Method in class org.openscience.cdk.libio.cml.Convertor
CDKRGraph - Class in org.openscience.cdk.smsd.algorithm.rgraph: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
CDKRGraph() - Constructor for class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph: Deprecated.

Constructor for the CDKRGraph object and creates an empty CDKRGraph.
CDKRMap - Class in org.openscience.cdk.smsd.algorithm.rgraph: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
CDKRMap(int, int) - Constructor for class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMap: Deprecated.

Constructor for the CDKRMap
CDKRMapHandler - Class in org.openscience.cdk.smsd.algorithm.rgraph: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
CDKRMapHandler() - Constructor for class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler: Deprecated.
CDKRNode - Class in org.openscience.cdk.smsd.algorithm.rgraph: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
CDKRNode(int, int) - Constructor for class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode: Deprecated.

Constructor for the RNode object
CDKSourceCodeFormat - Class in org.openscience.cdk.io.formats
CDKSourceCodeFormat() - Constructor for class org.openscience.cdk.io.formats.CDKSourceCodeFormat
CDKSourceCodeWriter - Class in org.openscience.cdk.io: Converts a Molecule into CDK source code that would build the same molecule.
CDKSourceCodeWriter() - Constructor for class org.openscience.cdk.io.CDKSourceCodeWriter
CDKSourceCodeWriter(OutputStream) - Constructor for class org.openscience.cdk.io.CDKSourceCodeWriter
CDKSourceCodeWriter(Writer) - Constructor for class org.openscience.cdk.io.CDKSourceCodeWriter: Constructs a new CDKSourceCodeWriter.
CDKStyleAromaticity() - Constructor for class org.openscience.cdk.renderer.generators.RingGenerator.CDKStyleAromaticity
CDKSubGraphHandler - Class in org.openscience.cdk.smsd.algorithm.rgraph: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
CDKSubGraphHandler() - Constructor for class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler: Deprecated.
CDKUtilities - Class in org.openscience.cdk.tools: Deprecated.
better accomplished with SMARTS patterns or simple REGEX
CDKUtilities() - Constructor for class org.openscience.cdk.tools.CDKUtilities: Deprecated.
CDKValencyChecker - Class in org.openscience.cdk.tools: Assumes CDK atom types to be detected and adds missing hydrogens based on the atom typing.
CDKValidator - Class in org.openscience.cdk.validate: This Validator tests the internal data structures, and tries to detect inconsistencies in it.
CDKValidator() - Constructor for class org.openscience.cdk.validate.CDKValidator
Ce - Static variable in interface org.openscience.cdk.interfaces.IElement
CE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
center(IAtomContainer, double[]) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Centers the molecule in the given area.
center(IAtomContainer, Dimension) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Centers the molecule in the given area.
centerCode - Variable in class org.openscience.cdk.tools.HOSECodeGenerator
Cerium - org.openscience.cdk.config.Elements
CERIUM - Static variable in enum org.openscience.cdk.config.Elements
CERIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
CESIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Cf - Static variable in interface org.openscience.cdk.interfaces.IElement
CF - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
CFG_MASK - Static variable in interface org.openscience.cdk.interfaces.IStereoElement
chainPrefix() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

A list of known tokens denoting a chain's length.
Chair - org.openscience.cdk.stereo.Projection: Projection of the low energy conformation (chair) of a cyclohexane.
changeBase(Permutation) - Method in class org.openscience.cdk.group.PermutationGroup: Change the base of the group to the new base newBase.
changeCharBonds(int, String, int, List<Integer>, List<String>) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks: Deprecated.
changeCharBonds(int, String, int, IAtomContainer, List<String>) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks: Deprecated.
characterData(CMLStack, char[], int, int) - Method in class org.openscience.cdk.io.cml.CDKConvention
characterData(CMLStack, char[], int, int) - Method in class org.openscience.cdk.io.cml.CMLCoreModule
characterData(CMLStack, char[], int, int) - Method in interface org.openscience.cdk.io.cml.ICMLModule
characterData(CMLStack, char[], int, int) - Method in class org.openscience.cdk.io.cml.JMOLANIMATIONConvention
characterData(CMLStack, char[], int, int) - Method in class org.openscience.cdk.io.cml.MDLMolConvention
characterData(CMLStack, char[], int, int) - Method in class org.openscience.cdk.io.cml.PDBConvention
characterData(CMLStack, char[], int, int) - Method in class org.openscience.cdk.io.cml.PMPConvention
characters(char[], int, int) - Method in class org.openscience.cdk.config.atomtypes.AtomTypeHandler
characters(char[], int, int) - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeHandler
characters(char[], int, int) - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingHandler
characters(char[], int, int) - Method in class org.openscience.cdk.config.isotopes.IsotopeHandler
characters(char[], int, int) - Method in class org.openscience.cdk.dict.DictionaryHandler
characters(char[], int, int) - Method in class org.openscience.cdk.io.cml.CMLHandler: Implementation of the characters() procedure overwriting the DefaultHandler interface.
characters(char[], int, int) - Method in class org.openscience.cdk.io.inchi.INChIHandler: Deprecated.

Implementation of the characters() procedure overwriting the DefaultHandler interface.
charge - Variable in class org.openscience.cdk.Atom: The partial charge of the atom.
charge - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom: The partial charge of the atom.
charge - Variable in class org.openscience.cdk.silent.Atom: The partial charge of the atom.
Charge() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
charged() - Method in class org.openscience.cdk.hash.HashGeneratorMaker: Discriminate protonation states.
ChargeGroup - Class in org.openscience.cdk.libio.md: A ChargeGroup (CG) is a numbered collection of atoms in an MDMolecule.
ChargeGroup() - Constructor for class org.openscience.cdk.libio.md.ChargeGroup: Empty constructor.
ChargeGroup(IAtomContainer, int, MDMolecule) - Constructor for class org.openscience.cdk.libio.md.ChargeGroup: Constructor to create a ChargeGroup based on an AC, a number, and a MDMolecule.
ChargeRule - Class in org.openscience.cdk.formula.rules: This class validate if the charge in the IMolecularFormula correspond with a specific value.
ChargeRule() - Constructor for class org.openscience.cdk.formula.rules.ChargeRule: Constructor for the ChargeRule object.
check - Variable in class org.openscience.cdk.stereo.StereoElementFactory: Verify if created stereochemistry are actually stereo-centres.
check(int, int, int[][], int[], List<ArrayList<Permutation>>) - Method in class org.openscience.cdk.structgen.maygen.Maygen
CHECK_RING_SYSTEM - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor
checkAlphaCarbonyl(IAtom, String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor.JPlogPCalculator: Should be called from the carbonyl oxygen
checkAndCleanMolecule(IAtomContainer) - Static method in class org.openscience.cdk.smsd.tools.MoleculeSanityCheck: Deprecated.

Modules for cleaning a molecule
checkAndMarkPlaced(IRingSet) - Method in class org.openscience.cdk.layout.RingPlacer: Walks throught the atoms of each ring in a ring set and marks a ring as PLACED if all of its atoms have been placed.
checkConsistency() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycle: Deprecated.
checkDiffNumber(double[]) - Method in class org.openscience.cdk.graph.invariant.EquivalentClassPartitioner: Get different number of the given number.
checkForceFieldType(String) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator: Sets the forceFieldType attribute of the ForceFieldConfigurator object
checkIfAllLigandsAreDifferent(ILigand[]) - Static method in class org.openscience.cdk.geometry.cip.CIPTool: Checks if each next ILigand is different from the previous one according to the CIPLigandRule.
checkInputParameters(IChemObjectBuilder, double, double, MolecularFormulaRange) - Method in class org.openscience.cdk.formula.MolecularFormulaGenerator: Checks if input parameters are valid and throws an IllegalArgumentException otherwise.
checkJustH(int[][][], int, int, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen
checkLengthTwoFormula(String[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: checking whether a molecular formula is length 2 or not.
checkOxygenSulfur(String[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen
checkSingleAtomCases(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: Checks for single atom cases before doing subgraph/isomorphism search.
checkSingleAtomCases(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS: Deprecated.

Checks for single atom cases before doing subgraph/isomorphism search
checkSymmetry(boolean) - Method in class org.openscience.cdk.stereo.StereoElementFactory
checkTimeout() - Method in class org.openscience.cdk.ringsearch.AllRingsFinder: Deprecated.
timeout not used
Chem3D_Cartesian_1Format - Class in org.openscience.cdk.io.formats
Chem3D_Cartesian_1Format() - Constructor for class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
Chem3D_Cartesian_2Format - Class in org.openscience.cdk.io.formats
Chem3D_Cartesian_2Format() - Constructor for class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
ChemDrawFormat - Class in org.openscience.cdk.io.formats
ChemDrawFormat() - Constructor for class org.openscience.cdk.io.formats.ChemDrawFormat
ChemFile - Class in org.openscience.cdk: A Object containing a number of ChemSequences.
ChemFile - Class in org.openscience.cdk.silent: A Object containing a number of ChemSequences.
ChemFile() - Constructor for class org.openscience.cdk.ChemFile: Constructs an empty ChemFile.
ChemFile() - Constructor for class org.openscience.cdk.silent.ChemFile: Constructs an empty ChemFile.
ChemFileManipulator - Class in org.openscience.cdk.tools.manipulator: Class with convenience methods that provide methods from methods from ChemObjects within the ChemFile.
ChemFileManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.ChemFileManipulator
ChemGraph - Class in org.openscience.cdk.structgen.stochastic.operator
ChemGraph(IAtomContainer) - Constructor for class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
CHEMICAL_GROUP_CONSTANT - Static variable in class org.openscience.cdk.CDKConstants: Used as property key for indicating the chemical group of a certain atom type.
ChemicalFilters - Class in org.openscience.cdk.smsd.filters: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
ChemicalFilters(List<Map<Integer, Integer>>, List<Map<IAtom, IAtom>>, Map<Integer, Integer>, Map<IAtom, IAtom>, IAtomContainer, IAtomContainer) - Constructor for class org.openscience.cdk.smsd.filters.ChemicalFilters: Deprecated.

This class has all the three chemical filters supported by the SMSD.
ChemModel - Class in org.openscience.cdk: An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.
ChemModel - Class in org.openscience.cdk.silent: An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.
ChemModel() - Constructor for class org.openscience.cdk.ChemModel: Constructs an new ChemModel with a null setOfMolecules.
ChemModel() - Constructor for class org.openscience.cdk.silent.ChemModel: Constructs an new ChemModel with a null setOfMolecules.
chemModelCount - Variable in class org.openscience.cdk.ChemSequence: Number of ChemModels contained by this container.
chemModelCount - Variable in class org.openscience.cdk.silent.ChemSequence: Number of ChemModels contained by this container.
ChemModelManipulator - Class in org.openscience.cdk.tools.manipulator: Class with convenience methods that provide methods from methods from ChemObjects within the ChemModel.
ChemModelManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.ChemModelManipulator
ChemModelRenderer - Class in org.openscience.cdk.renderer: A general renderer for IChemModels, IReactions, and IAtomContainers.
ChemModelRenderer(List<IGenerator<IAtomContainer>>, List<IGenerator<IReaction>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.ChemModelRenderer
ChemModelRenderer(List<IGenerator<IAtomContainer>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.ChemModelRenderer: A renderer that generates diagrams using the specified generators and manages fonts with the supplied font manager.
chemModels - Variable in class org.openscience.cdk.ChemSequence: Array of ChemModels.
chemModels - Variable in class org.openscience.cdk.silent.ChemSequence: Array of ChemModels.
chemModels() - Method in class org.openscience.cdk.ChemSequence: Returns an Iterable to ChemModels in this container.
chemModels() - Method in class org.openscience.cdk.debug.DebugChemSequence: Returns an Iterable to ChemModels in this container.
chemModels() - Method in interface org.openscience.cdk.interfaces.IChemSequence: Returns an Iterable to ChemModels in this container.
chemModels() - Method in class org.openscience.cdk.silent.ChemSequence: Returns an Iterable to ChemModels in this container.
ChemObject - Class in org.openscience.cdk: The base class for all chemical objects in this cdk.
ChemObject - Class in org.openscience.cdk.silent: The base class for all chemical objects in this cdk.
ChemObject() - Constructor for class org.openscience.cdk.ChemObject: Constructs a new IChemObject.
ChemObject() - Constructor for class org.openscience.cdk.silent.ChemObject: Constructs a new IChemObject.
ChemObject(IChemObject) - Constructor for class org.openscience.cdk.ChemObject: Constructs a new IChemObject by copying the flags, and the identifier.
ChemObject(IChemObject) - Constructor for class org.openscience.cdk.silent.ChemObject: Constructs a new IChemObject by copying the flags, and the identifier.
CHEMOBJECT - Static variable in class org.openscience.cdk.libio.jena.CDK
ChemObjectChangeEvent - Class in org.openscience.cdk.event: Event fired by cdk classes to their registered listeners in case something changes within them.
ChemObjectChangeEvent(Object) - Constructor for class org.openscience.cdk.event.ChemObjectChangeEvent: Constructs a ChemObjectChangeEvent with a reference to the object where it originated.
ChemObjectDiff - Class in org.openscience.cdk.tools.diff: Compares two IChemObject classes.
ChemObjectDifference - Class in org.openscience.cdk.tools.diff.tree: IDifference between two IChemObjects.
ChemObjectDifference(String) - Constructor for class org.openscience.cdk.tools.diff.tree.ChemObjectDifference
ChemObjectIO - Class in org.openscience.cdk.io: Provides some basic functionality for readers and writers.
ChemObjectIO() - Constructor for class org.openscience.cdk.io.ChemObjectIO
chemObjectReader - Variable in class org.openscience.cdk.io.random.RandomAccessReader
ChemSequence - Class in org.openscience.cdk: A sequence of ChemModels, which can, for example, be used to store the course of a reaction.
ChemSequence - Class in org.openscience.cdk.silent: A sequence of ChemModels, which can, for example, be used to store the course of a reaction.
ChemSequence() - Constructor for class org.openscience.cdk.ChemSequence: Constructs an empty ChemSequence.
ChemSequence() - Constructor for class org.openscience.cdk.silent.ChemSequence: Constructs an empty ChemSequence.
chemSequenceCount - Variable in class org.openscience.cdk.ChemFile: Number of ChemSequences contained by this container.
chemSequenceCount - Variable in class org.openscience.cdk.silent.ChemFile: Number of ChemSequences contained by this container.
ChemSequenceManipulator - Class in org.openscience.cdk.tools.manipulator: Class with convenience methods that provide methods from methods from ChemObjects within the ChemSequence.
ChemSequenceManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.ChemSequenceManipulator
chemSequences - Variable in class org.openscience.cdk.ChemFile: Array of ChemSquences.
chemSequences - Variable in class org.openscience.cdk.silent.ChemFile: Array of ChemSquences.
chemSequences() - Method in class org.openscience.cdk.ChemFile: Returns the Iterable to ChemSequences of this container.
chemSequences() - Method in class org.openscience.cdk.debug.DebugChemFile: Returns the Iterable to ChemSequences of this container.
chemSequences() - Method in interface org.openscience.cdk.interfaces.IChemFile: Returns the Iterable to ChemSequences of this container.
chemSequences() - Method in class org.openscience.cdk.silent.ChemFile: Returns the Iterable to ChemSequences of this container.
ChemtoolFormat - Class in org.openscience.cdk.io.formats: See here.
ChemtoolFormat() - Constructor for class org.openscience.cdk.io.formats.ChemtoolFormat
ChiChainDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Evaluates chi chain descriptors.
ChiChainDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
ChiClusterDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Evaluates chi cluster descriptors.
ChiClusterDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
Child(String, String, TextGroupElement.Position) - Constructor for class org.openscience.cdk.renderer.elements.TextGroupElement.Child: Make a child element with the specified text, subscript, and position.
Child(String, TextGroupElement.Position) - Constructor for class org.openscience.cdk.renderer.elements.TextGroupElement.Child: Make a child element with the specified text and position.
childCount() - Method in class org.openscience.cdk.tools.diff.tree.AbstractDifferenceList: Returns the number of children of this IDifference.
childCount() - Method in interface org.openscience.cdk.tools.diff.tree.IDifferenceList: Returns the number of children of this IDifference.
children - Variable in class org.openscience.cdk.renderer.elements.TextGroupElement: The child text elements.
ChiPathClusterDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Evaluates chi path cluster descriptors.
ChiPathClusterDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
ChiPathDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Evaluates chi path descriptors.
ChiPathDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
chiral() - Method in class org.openscience.cdk.hash.HashGeneratorMaker: Generate different hash codes for stereoisomers.
ChiralFlagOFF - net.sf.jniinchi.INCHI_OPTION
ChiralFlagON - net.sf.jniinchi.INCHI_OPTION
Chirality() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
ChiralityAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
ChiralityAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom: Deprecated.

Creates a new instance
chiralityMatches(IAtom, int, int) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom: Deprecated.

Check if the atom-based chirality of the target matches.
chiralityMatches(IAtom, int, int) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom: Deprecated.

Check if the atom-based chirality of the target matches.
Chlorine - org.openscience.cdk.config.Elements
CHLORINE - Static variable in enum org.openscience.cdk.config.Elements
CHLORO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Chromium - org.openscience.cdk.config.Elements
CHROMIUM - Static variable in enum org.openscience.cdk.config.Elements
CHROMIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
CIFFormat - Class in org.openscience.cdk.io.formats
CIFFormat() - Constructor for class org.openscience.cdk.io.formats.CIFFormat
CIFReader - Class in org.openscience.cdk.io: This is not a reader for the CIF and mmCIF crystallographic formats.
CIFReader() - Constructor for class org.openscience.cdk.io.CIFReader
CIFReader(InputStream) - Constructor for class org.openscience.cdk.io.CIFReader
CIFReader(Reader) - Constructor for class org.openscience.cdk.io.CIFReader: Create an CIF like file reader.
cInverse(int, int, int[][], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Calculating the sum of the entries in the jth column until the ith row.
CIP_DESCRIPTOR - Static variable in class org.openscience.cdk.CDKConstants: Property key to store the CIP descriptor label for an atom / bond.
CIPLigandRule - Class in org.openscience.cdk.geometry.cip.rules: Compares to ILigands based on CIP sequences sub rules.
CIPLigandRule() - Constructor for class org.openscience.cdk.geometry.cip.rules.CIPLigandRule
CIPTool - Class in org.openscience.cdk.geometry.cip: Tool to help determine the R,S and stereochemistry definitions of a subset of the CIP rules [Cahn, R.S. et. al.. Angew. Chem. Int. Ed.. 1966. 5].
CIPTool() - Constructor for class org.openscience.cdk.geometry.cip.CIPTool
CIPTool.CIP_CHIRALITY - Enum in org.openscience.cdk.geometry.cip: Enumeration with the two tetrahedral chiralities defined by the CIP schema.
CircularFingerprinter - Class in org.openscience.cdk.fingerprint: Circular fingerprints: for generating fingerprints that are functionally equivalent to ECFP-2/4/6 and FCFP-2/4/6 fingerprints, which are partially described by Rogers et al.
CircularFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.CircularFingerprinter: Default constructor: uses the ECFP6 type.
CircularFingerprinter(int) - Constructor for class org.openscience.cdk.fingerprint.CircularFingerprinter: Specific constructor: initializes with descriptor class type, one of ECFP_{p} or FCFP_{p}, where ECFP is for the extended-connectivity fingerprints, FCFP is for the functional class version, and {p} is the path diameter, and may be 0, 2, 4 or 6.
CircularFingerprinter(int, int) - Constructor for class org.openscience.cdk.fingerprint.CircularFingerprinter: Specific constructor: initializes with descriptor class type, one of ECFP_{p} or FCFP_{p}, where ECFP is for the extended-connectivity fingerprints, FCFP is for the functional class version, and {p} is the path diameter, and may be 0, 2, 4 or 6.
CircularFingerprinter.FP - Class in org.openscience.cdk.fingerprint
CisTrans - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Geometric CisTrans (e.g.
Cl - Static variable in interface org.openscience.cdk.interfaces.IElement
CL - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
CLASS_ECFP0 - Static variable in class org.openscience.cdk.fingerprint.CircularFingerprinter
CLASS_ECFP2 - Static variable in class org.openscience.cdk.fingerprint.CircularFingerprinter
CLASS_ECFP4 - Static variable in class org.openscience.cdk.fingerprint.CircularFingerprinter
CLASS_ECFP6 - Static variable in class org.openscience.cdk.fingerprint.CircularFingerprinter
CLASS_FCFP0 - Static variable in class org.openscience.cdk.fingerprint.CircularFingerprinter
CLASS_FCFP2 - Static variable in class org.openscience.cdk.fingerprint.CircularFingerprinter
CLASS_FCFP4 - Static variable in class org.openscience.cdk.fingerprint.CircularFingerprinter
CLASS_FCFP6 - Static variable in class org.openscience.cdk.fingerprint.CircularFingerprinter
CLASS_KEY - Static variable in class org.openscience.cdk.renderer.elements.MarkedElement
cleanDataSet(String) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor
clear() - Method in class org.openscience.cdk.ConformerContainer: Get rid of all the conformers but keeps atom and bond information.
clear() - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Reinitialisation of the TGraph.
clear() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph: Deprecated.
clear() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph: Deprecated.

Reinitialisation of the TGraph.
clear() - Method in class org.openscience.cdk.smsd.helper.FinalMappings: Deprecated.

clear the mapping
clear() - Method in interface org.openscience.cdk.smsd.interfaces.IFinalMapping: Deprecated.

clear the mapping
clearAtomConfigurations(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: This method will reset all atom configuration to UNSET.
clearAtomConfigurations(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator: This method will reset all atom properties related to atom configuration to the value CDKConstants.UNSET.
clearCEgdes() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph: Deprecated.
clearCompGraphNodes() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph: Deprecated.
clearCompGraphNodesCZero() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph: Deprecated.
clearDEgdes() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph: Deprecated.
clearFormers(boolean, int, int[][], List<ArrayList<Permutation>>) - Method in class org.openscience.cdk.structgen.maygen.Maygen: When an adjacency matrix is non-canonical, cleaning the formerPermutations and partitionList from the first row of the tested block.
clearGlobals() - Method in class org.openscience.cdk.structgen.maygen.Maygen: For several calls of the run function, setting the global variables.
clearMajorIsotopes(IAtomContainer) - Static method in class org.openscience.cdk.config.Isotopes: Clear the isotope information from atoms that are major isotopes (e.g.
clearMajorIsotopes(IMolecularFormula) - Static method in class org.openscience.cdk.config.Isotopes: Clear the isotope information from istopes that are major (e.g.
clearNodeScope(Node) - Method in class org.openscience.cdk.smiles.smarts.parser.JJTSMARTSParserState
clearProps(IAtomContainer) - Method in class org.openscience.cdk.forcefield.mmff.Mmff: Clear all transient properties assigned by this class.
clearTraining() - Method in class org.openscience.cdk.fingerprint.model.Bayesian: Clears out the training set, to free up memory.
CLOCKWISE - org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo
clone() - Method in class org.openscience.cdk.AminoAcid: Clones this AminoAcid object.
clone() - Method in class org.openscience.cdk.Atom: Clones this atom object and its content.
clone() - Method in class org.openscience.cdk.AtomContainer: Clones this IChemObject.
clone() - Method in class org.openscience.cdk.AtomContainerSet: Clones this AtomContainerSet and its content.
clone() - Method in class org.openscience.cdk.AtomRef: Returns a deep clone of this IChemObject.
clone() - Method in class org.openscience.cdk.AtomType
clone() - Method in class org.openscience.cdk.BioPolymer
clone() - Method in class org.openscience.cdk.Bond: Clones this bond object, including clones of the atoms between which the bond is defined.
clone() - Method in class org.openscience.cdk.BondRef: Returns a deep clone of this IChemObject.
clone() - Method in class org.openscience.cdk.ChemFile: Allows for getting an clone of this object.
clone() - Method in class org.openscience.cdk.ChemModel: Clones this ChemModel and its content.
clone() - Method in class org.openscience.cdk.ChemObject: Clones this IChemObject.
clone() - Method in class org.openscience.cdk.ChemSequence
clone() - Method in class org.openscience.cdk.Crystal: Makes a clone of this crystal.
clone() - Method in class org.openscience.cdk.debug.DebugAminoAcid: Clones this AminoAcid object.
clone() - Method in class org.openscience.cdk.debug.DebugAtom: Clones this atom object and its content.
clone() - Method in class org.openscience.cdk.debug.DebugAtomContainer: Clones this IChemObject.
clone() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Clones this AtomContainerSet and its content.
clone() - Method in class org.openscience.cdk.debug.DebugAtomType: Clones this IChemObject.
clone() - Method in class org.openscience.cdk.debug.DebugBioPolymer: Clones this IChemObject.
clone() - Method in class org.openscience.cdk.debug.DebugBond: Clones this bond object, including clones of the atoms between which the bond is defined.
clone() - Method in class org.openscience.cdk.debug.DebugChemFile: Allows for getting an clone of this object.
clone() - Method in class org.openscience.cdk.debug.DebugChemModel: Clones this ChemModel and its content.
clone() - Method in class org.openscience.cdk.debug.DebugChemObject: Clones this IChemObject.
clone() - Method in class org.openscience.cdk.debug.DebugChemSequence: Clones this IChemObject.
clone() - Method in class org.openscience.cdk.debug.DebugCrystal: Makes a clone of this crystal.
clone() - Method in class org.openscience.cdk.debug.DebugElectronContainer: Clones this IChemObject.
clone() - Method in class org.openscience.cdk.debug.DebugElement: Clones this IChemObject.
clone() - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Clones this atom object and its content.
clone() - Method in class org.openscience.cdk.debug.DebugIsotope: Clones this IChemObject.
clone() - Method in class org.openscience.cdk.debug.DebugLonePair: Clones this LonePair object, including a clone of the atom for which the lone pair is defined.
clone() - Method in class org.openscience.cdk.debug.DebugMapping: Clones this Mapping and the mapped IChemObjects.
clone() - Method in class org.openscience.cdk.debug.DebugMonomer: Clones this IChemObject.
clone() - Method in class org.openscience.cdk.debug.DebugPolymer: Clones this IChemObject.
clone() - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Clones this atom object and its content.
clone() - Method in class org.openscience.cdk.debug.DebugReaction: Clones this Reaction and its content.
clone() - Method in class org.openscience.cdk.debug.DebugReactionScheme: Clones this ReactionScheme object and its content.
clone() - Method in class org.openscience.cdk.debug.DebugReactionSet: Clones this ReactionSet and the contained Reactions too.
clone() - Method in class org.openscience.cdk.debug.DebugRing: Clones this IChemObject.
clone() - Method in class org.openscience.cdk.debug.DebugSingleElectron: Clones this SingleElectron object, including a clone of the atom for which the SingleElectron is defined.
clone() - Method in class org.openscience.cdk.debug.DebugStrand: Clones this IChemObject.
clone() - Method in class org.openscience.cdk.debug.DebugSubstance: Clones this AtomContainerSet and its content.
clone() - Method in class org.openscience.cdk.ElectronContainer
clone() - Method in class org.openscience.cdk.Element
clone() - Method in class org.openscience.cdk.formula.AdductFormula: Clones this AdductFormula object and its content.
clone() - Method in class org.openscience.cdk.formula.IsotopeContainer: Clones this IsotopeContainer object and its content.
clone() - Method in class org.openscience.cdk.formula.IsotopePattern: Clones this IsotopePattern object and its content.
clone() - Method in class org.openscience.cdk.formula.MolecularFormula: Clones this MolecularFormula object and its content.
clone() - Method in class org.openscience.cdk.formula.MolecularFormulaRange: Clones this MolecularFormulaExpand object and its content.
clone() - Method in class org.openscience.cdk.formula.MolecularFormulaSet: Clones this MolecularFormulaSet object and its content.
clone() - Method in class org.openscience.cdk.FragmentAtom
clone() - Method in interface org.openscience.cdk.interfaces.IAdductFormula: Clones this IAdductFormula object and its content.
clone() - Method in interface org.openscience.cdk.interfaces.IAminoAcid: Returns a deep clone of this IChemObject.
clone() - Method in interface org.openscience.cdk.interfaces.IAtom: Returns a deep clone of this IChemObject.
clone() - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Returns a deep clone of this IChemObject.
clone() - Method in interface org.openscience.cdk.interfaces.IBioPolymer: Returns a deep clone of this IChemObject.
clone() - Method in interface org.openscience.cdk.interfaces.IBond: Returns a deep clone of this IChemObject.
clone() - Method in interface org.openscience.cdk.interfaces.IChemObject: Returns a deep clone of this IChemObject.
clone() - Method in interface org.openscience.cdk.interfaces.ICrystal: Returns a deep clone of this IChemObject.
clone() - Method in interface org.openscience.cdk.interfaces.IMolecularFormula: Clones this MolecularFormula object and its content.
clone() - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet: Clones this IMolecularFormulaSet object and its content.
clone() - Method in interface org.openscience.cdk.interfaces.IMonomer: Returns a deep clone of this IChemObject.
clone() - Method in interface org.openscience.cdk.interfaces.IPDBMonomer: Returns a deep clone of this IChemObject.
clone() - Method in interface org.openscience.cdk.interfaces.IPDBPolymer: Returns a deep clone of this IChemObject.
clone() - Method in interface org.openscience.cdk.interfaces.IPolymer: Returns a deep clone of this IChemObject.
clone() - Method in interface org.openscience.cdk.interfaces.IPseudoAtom: Returns a deep clone of this IChemObject.
clone() - Method in interface org.openscience.cdk.interfaces.IReactionScheme: Clones this IReactionScheme object and its content.
clone() - Method in interface org.openscience.cdk.interfaces.IRing: Returns a deep clone of this IChemObject.
clone() - Method in interface org.openscience.cdk.interfaces.IStrand: Returns a deep clone of this IChemObject.
clone() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
clone() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Clones this AtomContainer object and its content.
clone() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Clones this query bond object, including clones of the atoms between which the query bond is defined.
clone() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
clone() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolAndChargeQueryAtom: Deprecated.
clone() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolChargeIDQueryAtom
clone() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom: Deprecated.
clone() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom: Deprecated.
clone() - Method in class org.openscience.cdk.Isotope
clone() - Method in class org.openscience.cdk.LonePair: Clones this LonePair object, including a clone of the atom for which the lone pair is defined.
clone() - Method in class org.openscience.cdk.Mapping: Clones this Mapping and the mapped IChemObjects.
clone() - Method in class org.openscience.cdk.Monomer: Clones this IChemObject.
clone() - Method in class org.openscience.cdk.Polymer
clone() - Method in class org.openscience.cdk.protein.data.PDBMonomer: Clones this IChemObject.
clone() - Method in class org.openscience.cdk.protein.data.PDBPolymer: Clones this IChemObject.
clone() - Method in class org.openscience.cdk.PseudoAtom
clone() - Method in class org.openscience.cdk.Reaction: Clones this Reaction and its content.
clone() - Method in class org.openscience.cdk.ReactionScheme: Clones this ReactionScheme object and its content.
clone() - Method in class org.openscience.cdk.ReactionSet: Clones this ReactionSet and the contained Reactions too.
clone() - Method in class org.openscience.cdk.Ring: Clones this IChemObject.
clone() - Method in class org.openscience.cdk.RingSet: Clones this RingSet including the Rings.
clone() - Method in class org.openscience.cdk.signature.Orbit
clone() - Method in class org.openscience.cdk.silent.AdductFormula: Clones this AdductFormula object and its content.
clone() - Method in class org.openscience.cdk.silent.AminoAcid: Clones this AminoAcid object.
clone() - Method in class org.openscience.cdk.silent.Atom: Clones this atom object and its content.
clone() - Method in class org.openscience.cdk.silent.AtomContainer: Clones this IChemObject.
clone() - Method in class org.openscience.cdk.silent.AtomContainerSet: Clones this AtomContainerSet and its content.
clone() - Method in class org.openscience.cdk.silent.AtomType
clone() - Method in class org.openscience.cdk.silent.BioPolymer
clone() - Method in class org.openscience.cdk.silent.Bond: Clones this bond object, including clones of the atoms between which the bond is defined.
clone() - Method in class org.openscience.cdk.silent.ChemFile: Allows for getting an clone of this object.
clone() - Method in class org.openscience.cdk.silent.ChemModel: Clones this ChemModel and its content.
clone() - Method in class org.openscience.cdk.silent.ChemObject: Clones this IChemObject.
clone() - Method in class org.openscience.cdk.silent.ChemSequence
clone() - Method in class org.openscience.cdk.silent.Crystal: Makes a clone of this crystal.
clone() - Method in class org.openscience.cdk.silent.ElectronContainer
clone() - Method in class org.openscience.cdk.silent.Element
clone() - Method in class org.openscience.cdk.silent.FragmentAtom
clone() - Method in class org.openscience.cdk.silent.Isotope
clone() - Method in class org.openscience.cdk.silent.LonePair: Clones this LonePair object, including a clone of the atom for which the lone pair is defined.
clone() - Method in class org.openscience.cdk.silent.Mapping: Clones this Mapping and the mapped IChemObjects.
clone() - Method in class org.openscience.cdk.silent.MolecularFormula: Clones this MolecularFormula object and its content.
clone() - Method in class org.openscience.cdk.silent.MolecularFormulaSet: Clones this MolecularFormulaSet object and its content.
clone() - Method in class org.openscience.cdk.silent.Monomer: Clones this IChemObject.
clone() - Method in class org.openscience.cdk.silent.PDBMonomer: Clones this IChemObject.
clone() - Method in class org.openscience.cdk.silent.PDBPolymer: Clones this IChemObject.
clone() - Method in class org.openscience.cdk.silent.Polymer
clone() - Method in class org.openscience.cdk.silent.PseudoAtom
clone() - Method in class org.openscience.cdk.silent.Reaction: Clones this Reaction and its content.
clone() - Method in class org.openscience.cdk.silent.ReactionScheme: Clones this ReactionScheme object and its content.
clone() - Method in class org.openscience.cdk.silent.ReactionSet: Clones this ReactionSet and the contained Reactions too.
clone() - Method in class org.openscience.cdk.silent.Ring: Clones this IChemObject.
clone() - Method in class org.openscience.cdk.silent.RingSet: Clones this RingSet including the Rings.
clone() - Method in class org.openscience.cdk.silent.SingleElectron: Clones this SingleElectron object, including a clone of the atom for which the SingleElectron is defined.
clone() - Method in class org.openscience.cdk.silent.Strand
clone() - Method in class org.openscience.cdk.SingleElectron: Clones this SingleElectron object, including a clone of the atom for which the SingleElectron is defined.
clone() - Method in class org.openscience.cdk.Strand
clone(IAtomContainer) - Static method in class org.openscience.cdk.qsar.AbstractMolecularDescriptor
cloneArray(int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Cloning int array
close() - Method in class org.openscience.cdk.io.CDKSourceCodeWriter: Flushes the output and closes this object.
close() - Method in class org.openscience.cdk.io.CIFReader
close() - Method in class org.openscience.cdk.io.CMLReader
close() - Method in class org.openscience.cdk.io.CMLWriter: Flushes the output and closes this object.
close() - Method in class org.openscience.cdk.io.CrystClustReader
close() - Method in class org.openscience.cdk.io.CrystClustWriter: Flushes the output and closes this object.
close() - Method in class org.openscience.cdk.io.CTXReader
close() - Method in class org.openscience.cdk.io.GamessReader
close() - Method in class org.openscience.cdk.io.Gaussian03Reader
close() - Method in class org.openscience.cdk.io.Gaussian98Reader
close() - Method in class org.openscience.cdk.io.GhemicalMMReader
close() - Method in class org.openscience.cdk.io.HINReader
close() - Method in class org.openscience.cdk.io.HINWriter: Flushes the output and closes this object.
close() - Method in interface org.openscience.cdk.io.IChemObjectIO: Closes this IChemObjectIO's resources.
close() - Method in class org.openscience.cdk.io.INChIPlainTextReader
close() - Method in class org.openscience.cdk.io.INChIReader
close() - Method in class org.openscience.cdk.io.iterator.event.EventCMLReader
close() - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundASNReader
close() - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader
close() - Method in class org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader
close() - Method in class org.openscience.cdk.io.iterator.IteratingSDFReader
close() - Method in class org.openscience.cdk.io.iterator.IteratingSMILESReader: Close the reader.
close() - Method in class org.openscience.cdk.io.MDLReader: Deprecated.
close() - Method in class org.openscience.cdk.io.MDLRXNReader: Deprecated.
close() - Method in class org.openscience.cdk.io.MDLRXNV2000Reader
close() - Method in class org.openscience.cdk.io.MDLRXNV3000Reader
close() - Method in class org.openscience.cdk.io.MDLRXNWriter: Flushes the output and closes this object.
close() - Method in class org.openscience.cdk.io.MDLV2000Reader
close() - Method in class org.openscience.cdk.io.MDLV2000Writer: Flushes the output and closes this object.
close() - Method in class org.openscience.cdk.io.MDLV3000Reader
close() - Method in class org.openscience.cdk.io.MDLV3000Writer: Closes this IChemObjectIO's resources.
close() - Method in class org.openscience.cdk.io.Mol2Reader
close() - Method in class org.openscience.cdk.io.Mol2Writer: Flushes the output and closes this object.
close() - Method in class org.openscience.cdk.io.Mopac7Reader
close() - Method in class org.openscience.cdk.io.MoSSOutputReader: Closes this IChemObjectIO's resources.
close() - Method in class org.openscience.cdk.io.PCCompoundASNReader
close() - Method in class org.openscience.cdk.io.PCCompoundXMLReader
close() - Method in class org.openscience.cdk.io.PCSubstanceXMLReader
close() - Method in class org.openscience.cdk.io.PDBReader
close() - Method in class org.openscience.cdk.io.PDBWriter: Flushes the output and closes this object.
close() - Method in class org.openscience.cdk.io.PMPReader
close() - Method in class org.openscience.cdk.io.program.GaussianInputWriter
close() - Method in class org.openscience.cdk.io.program.Mopac7Writer
close() - Method in class org.openscience.cdk.io.random.RandomAccessReader
close() - Method in class org.openscience.cdk.io.rdf.CDKOWLReader: Closes this IChemObjectIO's resources.
close() - Method in class org.openscience.cdk.io.rdf.CDKOWLWriter: Closes this IChemObjectIO's resources.
close() - Method in class org.openscience.cdk.io.RGroupQueryReader
close() - Method in class org.openscience.cdk.io.RGroupQueryWriter: Flushes the output and closes this object.
close() - Method in class org.openscience.cdk.io.RssWriter: Flushes the output and closes this object.
close() - Method in class org.openscience.cdk.io.SDFWriter: Flushes the output and closes this object.
close() - Method in class org.openscience.cdk.io.ShelXReader
close() - Method in class org.openscience.cdk.io.ShelXWriter: Flushes the output and closes this object.
close() - Method in class org.openscience.cdk.io.SMILESReader
close() - Method in class org.openscience.cdk.io.SMILESWriter: Flushes the output and closes this object.
close() - Method in class org.openscience.cdk.io.VASPReader
close() - Method in class org.openscience.cdk.io.XYZReader
close() - Method in class org.openscience.cdk.io.XYZWriter: Flushes the output and closes this object.
close() - Method in class org.openscience.cdk.io.ZMatrixReader
close() - Method in class org.openscience.cdk.renderer.elements.path.PathBuilder: Close the path.
close() - Method in interface org.openscience.cdk.structgen.maygen.Maygen.Consumer
Close - Class in org.openscience.cdk.renderer.elements.path: Indicates the closing point of the path.
Close - org.openscience.cdk.renderer.elements.path.Type
Close() - Constructor for class org.openscience.cdk.renderer.elements.path.Close: Make a Close PathElement.
ClosedShellJob - Class in org.openscience.cdk.math.qm: Calculates the orbitals and orbital energies of electron systems with closed shells
ClosedShellJob(Orbitals) - Constructor for class org.openscience.cdk.math.qm.ClosedShellJob
closeEnoughToBond(IAtom, IAtom, double) - Static method in class org.openscience.cdk.geometry.BondTools: Returns true if the two atoms are within the distance fudge factor of each other.
closeFilesAndDisplayStatistic(long) - Method in class org.openscience.cdk.structgen.maygen.Maygen
closeNodeScope(Node, boolean) - Method in class org.openscience.cdk.smiles.smarts.parser.JJTSMARTSParserState
closeNodeScope(Node, int) - Method in class org.openscience.cdk.smiles.smarts.parser.JJTSMARTSParserState
CLS_MASK - Static variable in interface org.openscience.cdk.interfaces.IStereoElement
clusterPSPPocket(Point3d, List<Point3d>, int[]) - Method in class org.openscience.cdk.protein.ProteinPocketFinder: Method performs the clustering, is called by findPockets().
Cm - Static variable in interface org.openscience.cdk.interfaces.IElement
CM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
CMLCoreModule - Class in org.openscience.cdk.io.cml: Core CML 1.x and 2.x elements are parsed by this class (see [Willighagen, E.L.. Internet Journal of Chemistry. 2001. 4]).
CMLCoreModule(IChemFile) - Constructor for class org.openscience.cdk.io.cml.CMLCoreModule
CMLCoreModule(ICMLModule) - Constructor for class org.openscience.cdk.io.cml.CMLCoreModule
CMLErrorHandler - Class in org.openscience.cdk.io.cml: CDK's SAX2 ErrorHandler for giving feedback on XML errors in the CML document.
CMLErrorHandler() - Constructor for class org.openscience.cdk.io.cml.CMLErrorHandler: Constructor a SAX2 ErrorHandler that uses the cdk.tools.LoggingTool class to output errors and warnings to.
CMLFormat - Class in org.openscience.cdk.io.formats: See here.
CMLFormat() - Constructor for class org.openscience.cdk.io.formats.CMLFormat
CMLHandler - Class in org.openscience.cdk.io.cml: SAX2 implementation for CML XML fragment reading.
CMLHandler(IChemFile) - Constructor for class org.openscience.cdk.io.cml.CMLHandler: Constructor for the CMLHandler.
CMLModuleStack - Class in org.openscience.cdk.io.cml: Low weight alternative to Sun's Stack class.
CMLModuleStack() - Constructor for class org.openscience.cdk.io.cml.CMLModuleStack
CMLReactionModule - Class in org.openscience.cdk.io.cml
CMLReactionModule(IChemFile) - Constructor for class org.openscience.cdk.io.cml.CMLReactionModule
CMLReactionModule(ICMLModule) - Constructor for class org.openscience.cdk.io.cml.CMLReactionModule
CMLReader - Class in org.openscience.cdk.io: Reads a molecule in CML 1.x and 2.0 format.
CMLReader() - Constructor for class org.openscience.cdk.io.CMLReader
CMLReader(InputStream) - Constructor for class org.openscience.cdk.io.CMLReader: Reads CML from an java.io.InputStream, for example the FileInputStream.
CMLReader(String) - Constructor for class org.openscience.cdk.io.CMLReader: Define this CMLReader to take the input from a java.io.Reader class.
CMLResolver - Class in org.openscience.cdk.io.cml: This class resolves DOCTYPE declaration for Chemical Markup Language (CML) files and uses a local version for validation.
CMLResolver() - Constructor for class org.openscience.cdk.io.cml.CMLResolver
CMLRSSFormat - Class in org.openscience.cdk.io.formats
CMLRSSFormat() - Constructor for class org.openscience.cdk.io.formats.CMLRSSFormat
CMLWriter - Class in org.openscience.cdk.io: Serializes a IAtomContainerSet or a IAtomContainer object to CML 2 code.
CMLWriter() - Constructor for class org.openscience.cdk.io.CMLWriter
CMLWriter(OutputStream) - Constructor for class org.openscience.cdk.io.CMLWriter
CMLWriter(Writer) - Constructor for class org.openscience.cdk.io.CMLWriter: Constructs a new CMLWriter class.
Cn - Static variable in interface org.openscience.cdk.interfaces.IElement
Co - Static variable in interface org.openscience.cdk.interfaces.IElement
CO - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Cobalt - org.openscience.cdk.config.Elements
COBALT - Static variable in enum org.openscience.cdk.config.Elements
COBALT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
color - Variable in class org.openscience.cdk.renderer.elements.ArrowElement: Color of the arrow.
color - Variable in class org.openscience.cdk.renderer.elements.GeneralPath: The color of the path.
color - Variable in class org.openscience.cdk.renderer.elements.LineElement: The color of the line.
color - Variable in class org.openscience.cdk.renderer.elements.OvalElement: The color to draw the oval.
color - Variable in class org.openscience.cdk.renderer.elements.PathElement: The color of the path.
color - Variable in class org.openscience.cdk.renderer.elements.RectangleElement: The color of the rectangle.
color - Variable in class org.openscience.cdk.renderer.elements.TextElement: The color of the text.
color(int) - Method in interface org.openscience.cdk.renderer.generators.HighlightGenerator.Palette: Obtain the color in index, id.
color(Color) - Method in class org.openscience.cdk.renderer.elements.path.PathBuilder: Sets the color if this path.
ColorByType() - Constructor for class org.openscience.cdk.renderer.generators.AtomNumberGenerator.ColorByType
ColorByType() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.ColorByType
Colored - org.openscience.cdk.renderer.generators.standard.StandardGenerator.HighlightStyle: Displayed atom symbols and bonds are coloured.
ColorHash() - Constructor for class org.openscience.cdk.renderer.RendererModel.ColorHash
column - Variable in class org.openscience.cdk.iupac.parser.SimpleCharStream
column - Variable in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
columns - Variable in class org.openscience.cdk.math.IMatrix: the count of columns of the matrix
columns - Variable in class org.openscience.cdk.math.Matrix: the number of columns of this matrix
Combinations(Object[], int) - Constructor for class org.openscience.cdk.formula.rules.RDBERule.Combinations: Create a Combination to enumerate through all subsets of the supplied Object array, selecting m at a time.
COMMA - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
COMMENT - Static variable in class org.openscience.cdk.CDKConstants: A String comment.
commit() - Method in class org.openscience.cdk.smiles.InvPair
CompactAtom() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.CompactAtom
CompactShape() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.CompactShape
compare(int[], int[], int, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Comparing two arrays for specific range of entries, whether the first array is bigger than the second one or not.
compare(ILigand, ILigand) - Method in interface org.openscience.cdk.geometry.cip.rules.ISequenceSubRule: Compares two ligands according to the particular sequence sub rule.
compare(Object) - Method in class org.openscience.cdk.Atom: Compares a atom with this atom.
compare(Object) - Method in class org.openscience.cdk.AtomType: Compares a atom type with this atom type.
compare(Object) - Method in class org.openscience.cdk.Bond: Compares a bond with this bond.
compare(Object) - Method in class org.openscience.cdk.BondRef: Compares a bond with this bond.
compare(Object) - Method in class org.openscience.cdk.ChemObject: Compares a IChemObject with this IChemObject.
compare(Object) - Method in class org.openscience.cdk.debug.DebugBond: Compares a bond with this bond.
compare(Object) - Method in class org.openscience.cdk.Element: Compares an Element with this Element.
compare(Object) - Method in interface org.openscience.cdk.interfaces.IBond: Compares a bond with this bond.
compare(Object) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Compares a query bond with this query bond.
compare(Object) - Method in class org.openscience.cdk.Isotope: Compares a atom type with this atom type.
compare(Object) - Method in class org.openscience.cdk.silent.Atom: Compares a atom with this atom.
compare(Object) - Method in class org.openscience.cdk.silent.AtomType: Compares a atom type with this atom type.
compare(Object) - Method in class org.openscience.cdk.silent.Bond: Compares a bond with this bond.
compare(Object) - Method in class org.openscience.cdk.silent.ChemObject: Compares a IChemObject with this IChemObject.
compare(Object) - Method in class org.openscience.cdk.silent.Element: Compares an Element with this Element.
compare(Object) - Method in class org.openscience.cdk.silent.Isotope: Compares an isotope with this isotope.
compare(String, String) - Method in class org.openscience.cdk.tools.ElementComparator: Returns a negative if o1 comes before o2 in a molecular formula, returns zero if they are identical, and positive if o1 comes after o2 in the formula.
compare(IsotopePattern, IsotopePattern) - Method in class org.openscience.cdk.formula.IsotopePatternSimilarity: Compare the IMolecularFormula with a isotope abundance pattern.
compare(ILigand, ILigand) - Method in class org.openscience.cdk.geometry.cip.rules.CIPLigandRule: Compares two ligands according to the particular sequence sub rule.
compare(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.tools.manipulator.AtomContainerComparator
compare(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.tools.manipulator.AtomContainerComparatorBy2DCenter: Compare two AtomContainers based on their 2D position.
compare(IAtom, IAtom) - Method in class org.openscience.cdk.fingerprint.SimpleAtomComparator
compare(IMolecularFormula, IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Compare two IMolecularFormula looking at type and number of IIsotope and charge of the formula.
compare(IRing, IRing) - Method in class org.openscience.cdk.tools.manipulator.RingSizeComparator
compareIndexwise(int[], int[], int, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Comparing two int arrays are equal or not for given range of entries.
compareTo(DynamicFactory.ConstructorKey) - Method in class org.openscience.cdk.DynamicFactory.ConstructorKey: Orders constructor keys by the number of parameters and then this name.
compareTo(IChemFormatMatcher.MatchResult) - Method in class org.openscience.cdk.io.formats.IChemFormatMatcher.MatchResult: Compares the match result with another, results with lower position are ordered before those with higher position.
compatibilityGraph() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph: Deprecated.

Generate Compatibility Graph Nodes Bond Insensitive
compatibilityGraphCEdgeZero() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph: Deprecated.

compatibilityGraphCEdgeZero is used to build up of the edges of the compatibility graph BIS
compatibilityGraphNodes() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph: Deprecated.

Generate Compatibility Graph Nodes
compatibilityGraphNodesIfCEdgeIsZero() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph: Deprecated.

compGraphNodesCZero is used to build up of the edges of the compatibility graph
compile() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQueryCompiler: Deprecated.

Parse and build a query graph from the query moleucle.
compile() - Method in class org.openscience.cdk.smsd.algorithm.vflib.query.QueryCompiler: Deprecated.

Parse and build a query graph from the query moleucle.
completeChemicalName() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

The general form all chemical names must follow.
completed() - Method in class org.openscience.cdk.graph.AllCycles: Did the cycle perception complete - if not the molecule was considered impractical and computation was aborted.
Complex - Class in org.openscience.cdk.math: This class handles complex values.
Complex(double, double) - Constructor for class org.openscience.cdk.math.Complex: Creates a complex number
Complex(Complex) - Constructor for class org.openscience.cdk.math.Complex: Creates a copy of a complex object
components() - Method in class org.openscience.cdk.graph.ConnectedComponents: Access the components each vertex belongs to.
Compress - net.sf.jniinchi.INCHI_OPTION
computeFloydAPSP(double[][]) - Static method in class org.openscience.cdk.graph.PathTools: All-Pairs-Shortest-Path computation based on Floyd's algorithm [Floyd, R.W.. Commun. ACM. 1962. 5].
computeFloydAPSP(int[][]) - Static method in class org.openscience.cdk.graph.PathTools: All-Pairs-Shortest-Path computation based on Floyd's algorithm [Floyd, R.W.. Commun. ACM. 1962. 5].
configure(String) - Method in interface org.openscience.cdk.structgen.maygen.Maygen.Consumer
configure(IAtom) - Method in class org.openscience.cdk.config.AtomTypeFactory: Configures an atom.
configure(IAtom) - Method in class org.openscience.cdk.config.IsotopeFactory: Configures an atom.
configure(IAtomContainer) - Static method in class org.openscience.cdk.smsd.tools.MoleculeSanityCheck: Deprecated.

Fixes Aromaticity of the molecule i.e.
configure(IAtom, IAtomType) - Static method in class org.openscience.cdk.tools.manipulator.AtomTypeManipulator: Method that assign properties to an atom given a particular atomType.
configure(IAtom, IIsotope) - Method in class org.openscience.cdk.config.IsotopeFactory: Configures an atom to have all the data of the given isotope.
configureAtom(IAtom, String, boolean) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
configureAtoms(IAtomContainer) - Method in class org.openscience.cdk.config.IsotopeFactory: Configures atoms in an AtomContainer to carry all the correct data according to their element type.
configureMM2BasedAtom(IAtom, String, boolean) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator: Configures an atom to a mm2 based atom type
configureMMFF94BasedAtom(IAtom, String, boolean) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator: Configures an atom to a mmff94 based atom type
configureUnsetProperties(IAtom, IAtomType) - Static method in class org.openscience.cdk.tools.manipulator.AtomTypeManipulator: Method that assign properties to an atom given a particular atomType.
ConformerContainer - Class in org.openscience.cdk: A memory-efficient data structure to store conformers for a single molecule.
ConformerContainer() - Constructor for class org.openscience.cdk.ConformerContainer
ConformerContainer(IAtomContainer) - Constructor for class org.openscience.cdk.ConformerContainer: Create a ConformerContainer object from a single molecule object.
ConformerContainer(IAtomContainer[]) - Constructor for class org.openscience.cdk.ConformerContainer: Create a ConformerContainer from an array of molecules.
ConjugatedPiSystemsDetector - Class in org.openscience.cdk.graph.invariant
ConjugatedPiSystemsDetector() - Constructor for class org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector
connect(INode, INode, VFBondMatcher) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder: Deprecated.

Construct and return an edge for a given query and target node
ConnectedComponents - Class in org.openscience.cdk.graph: Compute the connected components of an adjacency list.
ConnectedComponents(int[][]) - Constructor for class org.openscience.cdk.graph.ConnectedComponents: Compute the connected components of an adjacency list, g.
connectingFunctionalGroupsConstruct() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

The layout of a functional group(s) which can connect anywhere.
connectingFunctionalGroupSuffix() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Functional groups suffixs for groups which can be connected anywhere along the main chain.
ConnectionMatrix - Class in org.openscience.cdk.graph.matrix: Calculator for a connection matrix representation of this AtomContainer.
ConnectionMatrix() - Constructor for class org.openscience.cdk.graph.matrix.ConnectionMatrix
ConnectivityChecker - Class in org.openscience.cdk.graph: Tool class for checking whether the (sub)structure in an AtomContainer is connected.
ConnectivityChecker() - Constructor for class org.openscience.cdk.graph.ConnectivityChecker
connectivityTest(int[][], int[], boolean[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Test whether an adjacency matrix is connected or disconnected.
CONSTANT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
construct(String, boolean[], boolean[]) - Static method in class org.openscience.cdk.tools.diff.tree.BooleanArrayDifference: Constructs a new IDifference object.
construct(String, Boolean, Boolean) - Static method in class org.openscience.cdk.tools.diff.tree.BooleanDifference: Constructs a new IDifference object.
construct(String, Double, Double) - Static method in class org.openscience.cdk.tools.diff.tree.DoubleDifference: Constructs a new IDifference object.
construct(String, Integer, Integer) - Static method in class org.openscience.cdk.tools.diff.tree.IntegerDifference: Constructs a new IDifference object.
construct(String, String, String) - Static method in class org.openscience.cdk.tools.diff.tree.StringDifference: Constructs a new IDifference object.
construct(String, Point2d, Point2d) - Static method in class org.openscience.cdk.tools.diff.tree.Point2dDifference: Constructs a new IDifference object.
construct(String, Point3d, Point3d) - Static method in class org.openscience.cdk.tools.diff.tree.Point3dDifference: Constructs a new IDifference object.
construct(String, IAtomType.Hybridization, IAtomType.Hybridization) - Static method in class org.openscience.cdk.tools.diff.tree.AtomTypeHybridizationDifference: Constructs a new IDifference object.
construct(String, IBond.Order, IBond.Order) - Static method in class org.openscience.cdk.tools.diff.tree.BondOrderDifference: Constructs a new IDifference object.
ConstructorKey() - Constructor for class org.openscience.cdk.DynamicFactory.ConstructorKey
consume(IAtomContainer) - Method in interface org.openscience.cdk.structgen.maygen.Maygen.Consumer
CONT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
contab - Variable in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
container - Variable in class org.openscience.cdk.stereo.StereoElementFactory: Native CDK structure representation.
containerFromPermutation(int[]) - Method in class org.openscience.cdk.graph.AtomContainerAtomPermutor: Generate the atom container with this permutation of the atoms.
containerFromPermutation(int[]) - Method in class org.openscience.cdk.graph.AtomContainerBondPermutor
containerFromPermutation(int[]) - Method in class org.openscience.cdk.graph.AtomContainerPermutor: Convert a permutation (expressed as a list of numbers) into a permuted atom container.
contains(int) - Method in class org.openscience.cdk.signature.Orbit: Checks to see if the orbit contains this atom index.
contains(Object) - Method in class org.openscience.cdk.ConformerContainer: Checks to see whether the specified conformer is currently stored.
contains(IAtom) - Method in class org.openscience.cdk.Association: Returns true if the given atom participates in this Association.
contains(IAtom) - Method in class org.openscience.cdk.AtomContainer: True, if the AtomContainer contains the given atom object.
contains(IAtom) - Method in class org.openscience.cdk.Bond: Returns true if the given atom participates in this bond.
contains(IAtom) - Method in class org.openscience.cdk.BondRef: Returns true if the given atom participates in this bond.
contains(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid: True, if the AtomContainer contains the given atom object.
contains(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer: True, if the AtomContainer contains the given atom object.
contains(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer: True, if the AtomContainer contains the given atom object.
contains(IAtom) - Method in class org.openscience.cdk.debug.DebugBond: Returns true if the given atom participates in this bond.
contains(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal: True, if the AtomContainer contains the given atom object.
contains(IAtom) - Method in class org.openscience.cdk.debug.DebugLonePair: Returns true if the given atom participates in this lone pair.
contains(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer: True, if the AtomContainer contains the given atom object.
contains(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer: True, if the AtomContainer contains the given atom object.
contains(IAtom) - Method in class org.openscience.cdk.debug.DebugRing: True, if the AtomContainer contains the given atom object.
contains(IAtom) - Method in class org.openscience.cdk.debug.DebugRingSet: True, if at least one of the rings in the ringset contains the given atom.
contains(IAtom) - Method in class org.openscience.cdk.debug.DebugSingleElectron: Returns true if the given atom participates in this SingleElectron.
contains(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand: True, if the AtomContainer contains the given atom object.
contains(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: True, if the AtomContainer contains the given atom object.
contains(IAtom) - Method in interface org.openscience.cdk.interfaces.IBond: Returns true if the given atom participates in this bond.
contains(IAtom) - Method in interface org.openscience.cdk.interfaces.ILonePair: Returns true if the given atom participates in this lone pair.
contains(IAtom) - Method in interface org.openscience.cdk.interfaces.IRingSet: True, if at least one of the rings in the ringset contains the given atom.
contains(IAtom) - Method in interface org.openscience.cdk.interfaces.ISingleElectron: Returns true if the given atom participates in this SingleElectron.
contains(IAtom) - Method in interface org.openscience.cdk.interfaces.IStereoElement: Does the stereo element contain the provided atom.
contains(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: True, if the AtomContainer contains the given atom object.
contains(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Returns true if the given atom participates in this query bond.
contains(IAtom) - Method in class org.openscience.cdk.LonePair: Returns true if the given atom participates in this lone pair.
contains(IAtom) - Method in class org.openscience.cdk.RingSet: True, if at least one of the rings in the ringset contains the given atom.
contains(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer: True, if the AtomContainer contains the given atom object.
contains(IAtom) - Method in class org.openscience.cdk.silent.Bond: Returns true if the given atom participates in this bond.
contains(IAtom) - Method in class org.openscience.cdk.silent.LonePair: Returns true if the given atom participates in this lone pair.
contains(IAtom) - Method in class org.openscience.cdk.silent.RingSet: True, if at least one of the rings in the ringset contains the given atom.
contains(IAtom) - Method in class org.openscience.cdk.silent.SingleElectron: Returns true if the given atom participates in this SingleElectron.
contains(IAtom) - Method in class org.openscience.cdk.SingleElectron: Returns true if the given atom participates in this SingleElectron.
contains(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IRingSet: True, if this set contains the IAtomContainer.
contains(IAtomContainer) - Method in class org.openscience.cdk.RingSet: Checks for presence of a ring in this RingSet.
contains(IAtomContainer) - Method in class org.openscience.cdk.silent.RingSet: Checks for presence of a ring in this RingSet.
contains(IBond) - Method in class org.openscience.cdk.AtomContainer: True, if the AtomContainer contains the given bond object.
contains(IBond) - Method in class org.openscience.cdk.debug.DebugAminoAcid: True, if the AtomContainer contains the given bond object.
contains(IBond) - Method in class org.openscience.cdk.debug.DebugAtomContainer: True, if the AtomContainer contains the given bond object.
contains(IBond) - Method in class org.openscience.cdk.debug.DebugBioPolymer: True, if the AtomContainer contains the given bond object.
contains(IBond) - Method in class org.openscience.cdk.debug.DebugCrystal: True, if the AtomContainer contains the given bond object.
contains(IBond) - Method in class org.openscience.cdk.debug.DebugMonomer: True, if the AtomContainer contains the given bond object.
contains(IBond) - Method in class org.openscience.cdk.debug.DebugPolymer: True, if the AtomContainer contains the given bond object.
contains(IBond) - Method in class org.openscience.cdk.debug.DebugRing: True, if the AtomContainer contains the given bond object.
contains(IBond) - Method in class org.openscience.cdk.debug.DebugStrand: True, if the AtomContainer contains the given bond object.
contains(IBond) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: True, if the AtomContainer contains the given bond object.
contains(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: True, if the AtomContainer contains the given bond object.
contains(IBond) - Method in class org.openscience.cdk.silent.AtomContainer: True, if the AtomContainer contains the given bond object.
contains(IChemObject) - Method in interface org.openscience.cdk.renderer.selection.IChemObjectSelection: Determines if the IChemObject is part of the current selection.
contains(IElectronContainer) - Method in class org.openscience.cdk.AtomContainer: True, if the AtomContainer contains the given ElectronContainer object.
contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugAminoAcid: True, if the AtomContainer contains the given ElectronContainer object.
contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainer: True, if the AtomContainer contains the given ElectronContainer object.
contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugBioPolymer: True, if the AtomContainer contains the given ElectronContainer object.
contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugCrystal: True, if the AtomContainer contains the given ElectronContainer object.
contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugMonomer: True, if the AtomContainer contains the given ElectronContainer object.
contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugPolymer: True, if the AtomContainer contains the given ElectronContainer object.
contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugRing: True, if the AtomContainer contains the given ElectronContainer object.
contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugStrand: True, if the AtomContainer contains the given ElectronContainer object.
contains(IElectronContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: True, if the AtomContainer contains the given ElectronContainer object.
contains(IElectronContainer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: True, if the AtomContainer contains the given ElectronContainer object.
contains(IElectronContainer) - Method in class org.openscience.cdk.silent.AtomContainer: True, if the AtomContainer contains the given ElectronContainer object.
contains(IIsotope) - Method in class org.openscience.cdk.debug.DebugAdductFormula: True, if the AdductFormula contains the given IIsotope object and not the instance.
contains(IIsotope) - Method in class org.openscience.cdk.debug.DebugMolecularFormula: True, if the MolecularFormula contains the given IIsotope object and not the instance.
contains(IIsotope) - Method in class org.openscience.cdk.formula.AdductFormula: True, if the AdductFormula contains the given IIsotope object and not the instance.
contains(IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormula: True, if the MolecularFormula contains the given IIsotope object and not the instance.
contains(IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormulaRange: True, if the MolecularFormulaExpand contains the given IIsotope.
contains(IIsotope) - Method in interface org.openscience.cdk.interfaces.IAdductFormula: True, if the AdductFormula contains the given IIsotope object.
contains(IIsotope) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula: True, if the MolecularFormula contains the given IIsotope object.
contains(IIsotope) - Method in class org.openscience.cdk.silent.AdductFormula: True, if the AdductFormula contains the given IIsotope object and not the instance.
contains(IIsotope) - Method in class org.openscience.cdk.silent.MolecularFormula: True, if the MolecularFormula contains the given IIsotope object and not the instance.
contains(ILonePair) - Method in class org.openscience.cdk.AtomContainer: True, if the AtomContainer contains the given LonePair object.
contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugAminoAcid: True, if the AtomContainer contains the given LonePair object.
contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugAtomContainer: True, if the AtomContainer contains the given LonePair object.
contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugBioPolymer: True, if the AtomContainer contains the given LonePair object.
contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugCrystal: True, if the AtomContainer contains the given LonePair object.
contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugMonomer: True, if the AtomContainer contains the given LonePair object.
contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugPolymer: True, if the AtomContainer contains the given LonePair object.
contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugRing: True, if the AtomContainer contains the given LonePair object.
contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugStrand: True, if the AtomContainer contains the given LonePair object.
contains(ILonePair) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: True, if the AtomContainer contains the given LonePair object.
contains(ILonePair) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: True, if the AtomContainer contains the given LonePair object.
contains(ILonePair) - Method in class org.openscience.cdk.silent.AtomContainer: True, if the AtomContainer contains the given LonePair object.
contains(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugAdductFormula: True, if the AdductFormula contains the given IMolecularFormula object.
contains(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet: True, if the MolecularFormulaSet contains the given IMolecularFormula object.
contains(IMolecularFormula) - Method in class org.openscience.cdk.formula.AdductFormula: True, if the AdductFormula contains the given IMolecularFormula object.
contains(IMolecularFormula) - Method in class org.openscience.cdk.formula.MolecularFormulaSet: True, if the MolecularFormulaSet contains the given IMolecularFormula object.
contains(IMolecularFormula) - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet: True, if the IMolecularFormulaSet contains the given IMolecularFormula object.
contains(IMolecularFormula) - Method in class org.openscience.cdk.silent.AdductFormula: True, if the AdductFormula contains the given IMolecularFormula object.
contains(IMolecularFormula) - Method in class org.openscience.cdk.silent.MolecularFormulaSet: True, if the MolecularFormulaSet contains the given IMolecularFormula object.
contains(IMolecularFormulaSet, IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaSetManipulator: True, if the IMolecularFormulaSet contains the given IMolecularFormula but not as object.
contains(ISingleElectron) - Method in class org.openscience.cdk.AtomContainer: True, if the AtomContainer contains the given SingleElectron object.
contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAminoAcid: True, if the AtomContainer contains the given SingleElectron object.
contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAtomContainer: True, if the AtomContainer contains the given SingleElectron object.
contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugBioPolymer: True, if the AtomContainer contains the given SingleElectron object.
contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugCrystal: True, if the AtomContainer contains the given SingleElectron object.
contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugMonomer: True, if the AtomContainer contains the given SingleElectron object.
contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugPolymer: True, if the AtomContainer contains the given SingleElectron object.
contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugRing: True, if the AtomContainer contains the given SingleElectron object.
contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugStrand: True, if the AtomContainer contains the given SingleElectron object.
contains(ISingleElectron) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: True, if the AtomContainer contains the given SingleElectron object.
contains(ISingleElectron) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: True, if the AtomContainer contains the given SingleElectron object.
contains(ISingleElectron) - Method in class org.openscience.cdk.silent.AtomContainer: True, if the AtomContainer contains the given SingleElectron object.
containsAll(Collection<?>) - Method in class org.openscience.cdk.ConformerContainer
containsByID(IAtomContainerSet, String) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator: Tells if an AtomContainerSet contains at least one AtomContainer with the same ID as atomContainer.
containsElement(IMolecularFormula, IElement) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: True, if the MolecularFormula contains the given element as IIsotope object.
contraction() - Method in class org.openscience.cdk.math.IMatrix: Calculates the contraction from a matrix
contraction() - Method in class org.openscience.cdk.math.Matrix
contribs - Variable in class org.openscience.cdk.fingerprint.model.Bayesian
convertBondOrder(IBond) - Static method in class org.openscience.cdk.smsd.filters.ChemicalFilters: Deprecated.

Get bond order value as int value.
convertBondStereo(IBond) - Static method in class org.openscience.cdk.smsd.filters.ChemicalFilters: Deprecated.

Get stereo value as integer
convertEdgeLabelToColor(String) - Method in class org.openscience.cdk.signature.AtomSignature
convertExplicitToImplicitHydrogens(IAtomContainer) - Static method in class org.openscience.cdk.normalize.SMSDNormalizer: Deprecated.

Returns IAtomContainer without Hydrogen.
convertExplicitToImplicitHydrogens(IAtomContainer) - Static method in class org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator: Deprecated.

Returns IAtomContainer without Hydrogen.
convertImplicitToExplicitHydrogens(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Adds explicit hydrogens (without coordinates) to the IAtomContainer, equaling the number of set implicit hydrogens.
convertOneLetterCodeToThreeLetterCode(String) - Static method in class org.openscience.cdk.templates.AminoAcids: Returns the three letter code of an amino acid given a one letter code.
Convertor - Class in org.openscience.cdk.libio.cml
Convertor - Class in org.openscience.cdk.libio.jena: Helper class that converts a CDK IChemObject into RDF using a Jena model and the CDK data model ontology.
Convertor() - Constructor for class org.openscience.cdk.libio.jena.Convertor
Convertor(boolean, String) - Constructor for class org.openscience.cdk.libio.cml.Convertor: Constructs a CML convertor.
convertOrder(double) - Static method in class org.openscience.cdk.smsd.filters.ChemicalFilters: Deprecated.

Get bond order value as IBond.Order.
convertStereo(int) - Static method in class org.openscience.cdk.smsd.filters.ChemicalFilters: Deprecated.

Get stereo value as Stereo enum
convertThreeLetterCodeToOneLetterCode(String) - Static method in class org.openscience.cdk.templates.AminoAcids: Returns the one letter code of an amino acid given a three letter code.
convertToAtomContainer(IRingSet) - Static method in class org.openscience.cdk.ringsearch.RingPartitioner: Converts a RingSet to an AtomContainer.
convertToDiagramBounds(Rectangle2D) - Method in class org.openscience.cdk.renderer.AbstractRenderer: Calculate the bounds of the diagram on screen, given the current scale, zoom, and margin.
coords - Variable in class org.openscience.cdk.renderer.elements.path.CubicTo: Coordinates of control point 1, control point 2 and end point.
coords - Variable in class org.openscience.cdk.renderer.elements.path.LineTo: The point to make a line to.
coords - Variable in class org.openscience.cdk.renderer.elements.path.MoveTo: The point to move to.
coords - Variable in class org.openscience.cdk.renderer.elements.path.QuadTo: Coordinates of control point and end point.
Copernicium - org.openscience.cdk.config.Elements
Copper - org.openscience.cdk.config.Elements
COPPER - Static variable in enum org.openscience.cdk.config.Elements
COPPER - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
copy(Collection<Sgroup>, Map<? extends IChemObject, ? extends IChemObject>) - Static method in class org.openscience.cdk.tools.manipulator.SgroupManipulator: Copy a collection of Sgroups, replacing any IAtom/IBond references with those present in the provided 'replace' map.
copy(IAtomContainer, IAtomContainer, Collection<IAtom>) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Copy atoms in the collection from a 'source' molecule to the provided destination.
copy(IAtomContainer, IAtomContainer, Predicate<IAtom>) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Copy selected atoms from a 'source' molecule to the provided destination.
copy(IAtomContainer, IAtomContainer, Predicate<IAtom>, Predicate<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Copy selected atoms/bonds from a 'source' molecule to the provided destination.
copyAndSuppressedHydrogens(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Copy the input container and suppress any explicit hydrogens.
copyBlock(int) - Method in class org.openscience.cdk.group.Partition: Creates and returns a copy of the cell at cell index.
COS - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
couldMatchAtomType(IAtomContainer, IAtom, IAtomType) - Method in class org.openscience.cdk.tools.SaturationChecker: Determines if the atom can be of type AtomType.
couldMatchAtomType(IAtomContainer, IAtom, IAtomType) - Method in class org.openscience.cdk.tools.SmilesValencyChecker: Determines if the atom can be of type AtomType.
couldMatchAtomType(IAtom, double, IBond.Order, IAtomType) - Method in class org.openscience.cdk.tools.SmilesValencyChecker: Determines if the atom can be of type AtomType.
count() - Method in class org.openscience.cdk.isomorphism.Mappings: Convenience method to count the number mappings.
count() - Method in enum org.openscience.cdk.renderer.elements.LineElement.LineType: Returns the count for this line type.
countArcsLeft(List<Integer>, int, int) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks: Deprecated.
countEdges() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder: Deprecated.

Returns edge count.
countEdges() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQuery: Deprecated.

Returns edge count.
countExplicitHydrogens(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Count explicit hydrogens.
countHydrogens(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
countMaps(IAtomContainer) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper: Deprecated.

Returns solution map count.
countMaps(IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper: Deprecated.

Returns solution map count.
countMaps(IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper: Deprecated.

Returns solution map count.
countMaps(TargetProperties) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper: Deprecated.

Returns solution map count.
countMaps(TargetProperties) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper: Deprecated.

Returns solution map count.
countMaps(TargetProperties) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper: Deprecated.

Returns solution map count.
countMatches() - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool: Deprecated.

Returns the number of times the pattern was found in the target molecule.
countNeighbors() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.NodeBuilder: Deprecated.

Returns Neighbors count.
countNeighbors() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.INode: Deprecated.

Returns Neighbors count.
countNeighbors(IAtom) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.TargetProperties: Deprecated.
countNodes() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder: Deprecated.

Returns node count.
countNodes() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQuery: Deprecated.

Returns node count.
countUnique() - Method in class org.openscience.cdk.isomorphism.Mappings: Convenience method to count the number of unique atom mappings.
covalentRadius() - Method in enum org.openscience.cdk.config.Elements: The covalent radius, r_cov, is a measure of the size of an atom that forms part of one covalent bond.
CovalentRadiusDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic: This class returns the covalent radius of a given atom.
CovalentRadiusDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor: Constructor for the CovalentRadiusDescriptor object.
CPKAtomColors - Class in org.openscience.cdk.renderer.color: Deprecated.
JmolColors provides more comprehensive CPK color pallet
CPKAtomColors() - Constructor for class org.openscience.cdk.renderer.color.CPKAtomColors: Deprecated.
CPSADescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Calculates 29 Charged Partial Surface Area (CPSA) descriptors.
CPSADescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor
Cr - Static variable in interface org.openscience.cdk.interfaces.IElement
CR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
create() - Method in class org.openscience.cdk.group.PartitionRefinement.AtomRefinerBuilder
create() - Method in class org.openscience.cdk.group.PartitionRefinement.BondRefinerBuilder
create(Class<?>) - Static method in class org.openscience.cdk.tools.SystemOutLoggingTool: Deprecated.

Creates a new SystemOutLoggingTool for the given class.
create(Object[]) - Method in interface org.openscience.cdk.DynamicFactory.Creator: Create a new instance with the provided object parameters.
create(String) - Static method in class org.openscience.cdk.smarts.SmartsPattern: Default SMARTS pattern constructor, passes in a null chem object builder.
create(String) - Static method in class org.openscience.cdk.smiles.smarts.SmartsPattern: Deprecated.

Default SMARTS pattern constructor, passes in a null chem object builder.
create(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.smarts.SmartsPattern: Create a Pattern that will match the given smarts query.
create(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.smiles.smarts.SmartsPattern: Deprecated.

Create a Pattern that will match the given smarts query.
create(IAtomContainer) - Method in class org.openscience.cdk.smiles.SmilesGenerator: Generate SMILES for the provided molecule.
create(IAtomContainer, int[]) - Method in class org.openscience.cdk.smiles.SmilesGenerator: Creates a SMILES string of the flavour specified in the constructor and write the output order to the provided array.
create(IAtomContainer, int[][]) - Method in class org.openscience.cdk.hash.stereo.DoubleBondElementEncoderFactory: Create a stereo-encoder for possible stereo-chemical configurations.
create(IAtomContainer, int[][]) - Method in class org.openscience.cdk.hash.stereo.GeometricCumulativeDoubleBondFactory: Create a stereo encoder for cumulative double bonds.
create(IAtomContainer, int[][]) - Method in class org.openscience.cdk.hash.stereo.GeometricDoubleBondEncoderFactory: Create a stereo encoder for all potential 2D and 3D double bond stereo configurations.
create(IAtomContainer, int[][]) - Method in class org.openscience.cdk.hash.stereo.GeometricTetrahedralEncoderFactory: Create a stereo encoder for all potential 2D and 3D tetrahedral elements.
create(IAtomContainer, int[][]) - Method in interface org.openscience.cdk.hash.stereo.StereoEncoderFactory: Create a stereo-encoder for possible stereo-chemical configurations.
create(IAtomContainer, int[][]) - Method in class org.openscience.cdk.hash.stereo.TetrahedralElementEncoderFactory: Create a stereo-encoder for possible stereo-chemical configurations.
create(IAtomContainer, int, int[]) - Static method in class org.openscience.cdk.smiles.SmilesGenerator: Creates a SMILES string of the flavour specified as a parameter and write the output order to the provided array.
create(IAtomContainer, IAtomContainer, Expr.Type...) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Populate a query from a molecule and a provided set of expressions.
create(IAtomContainer, Expr.Type...) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Create a query from a molecule and a provided set of expressions.
create(IAtom, List<IAtom>, int) - Method in class org.openscience.cdk.stereo.ExtendedTetrahedral
create(IAtom, List<IAtom>, int) - Method in class org.openscience.cdk.stereo.Octahedral
create(IAtom, List<IAtom>, int) - Method in class org.openscience.cdk.stereo.SquarePlanar
create(IAtom, List<IAtom>, int) - Method in class org.openscience.cdk.stereo.TetrahedralChirality
create(IAtom, List<IAtom>, int) - Method in class org.openscience.cdk.stereo.TrigonalBipyramidal
create(IBond, List<IAtom>, int) - Method in class org.openscience.cdk.stereo.Atropisomeric
create(IBond, List<IBond>, int) - Method in class org.openscience.cdk.stereo.DoubleBondStereochemistry
create(IBond, List<IBond>, int) - Method in class org.openscience.cdk.stereo.ExtendedCisTrans
create(IReaction) - Method in class org.openscience.cdk.smiles.SmilesGenerator: Create a SMILES for a reaction of the flavour specified in the constructor.
create(IReaction, int[]) - Method in class org.openscience.cdk.smiles.SmilesGenerator: Create a SMILES for a reaction of the flavour specified in the constructor and write the output order to the provided array.
createAAs() - Static method in class org.openscience.cdk.templates.AminoAcids: Creates amino acid AminoAcid objects.
createAll() - Method in class org.openscience.cdk.stereo.StereoElementFactory: Creates all stereo elements found by Stereocenters using the or 2D/3D coordinates to specify the configuration (clockwise/anticlockwise).
createAllCarbonAllSingleNonAromaticBondAtomContainer(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Deprecated.
not all attributes are removed producing unexpected results, use AtomContainerManipulator.anonymise(org.openscience.cdk.interfaces.IAtomContainer)
createAnyAtomAnyBondContainer(IAtomContainer, boolean) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator: Creates a QueryAtomContainer with the following settings:
createAnyAtomAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor
createAnyAtomContainer(IAtomContainer, boolean) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator: Creates a QueryAtomContainer with the following settings:
createAnyAtomForPseudoAtomQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator: Creates a QueryAtomContainer with the following settings:
createAutoGenPalette(boolean) - Static method in class org.openscience.cdk.renderer.generators.HighlightGenerator: Create an auto generating palette which will generate colors using the provided parameters.
createAutoGenPalette(float, float, boolean) - Static method in class org.openscience.cdk.renderer.generators.HighlightGenerator: Create an auto generating palette which will generate colors using the provided parameters.
createAutoPalette(float, float, int) - Static method in class org.openscience.cdk.renderer.generators.HighlightGenerator: Create an auto generating palette which will generate colors using the provided parameters.
createBasicQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator: Creates a QueryAtomContainer with the following settings:
createBondOrder(double) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator: Convenience method to convert a double into an IBond.Order.
createChemObjectReader() - Method in class org.openscience.cdk.io.random.RandomAccessReader
createChemObjectReader() - Method in class org.openscience.cdk.io.random.RandomAccessSDFReader
createComparator(IAtomContainer, int) - Static method in class org.openscience.cdk.smiles.SmilesGenerator
createCubicGrid() - Method in class org.openscience.cdk.protein.ProteinPocketFinder: Method creates a cubic grid with the grid generator class.
createFromSubstructure(Pattern, Iterable<IAtomContainer>) - Static method in class org.openscience.cdk.layout.TemplateHandler: Create a template from a substructure pattern.
createFromSubstructure(Pattern, IAtomContainer) - Static method in class org.openscience.cdk.layout.TemplateHandler: Create a template from a substructure pattern.
createIDs(IChemObject) - Static method in class org.openscience.cdk.tools.IDCreator: Labels the Atom's and Bond's in the AtomContainer using the a1, a2, b1, b2 scheme often used in CML.
createLoggingTool(Class<?>) - Static method in class org.openscience.cdk.tools.LoggingToolFactory: Dynamically create a ILoggingTool for the given sourceClass.
createNewMolecule(IChemModel) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator: Adds a new Molecule to the MoleculeSet inside a given ChemModel.
createPalette(Color[]) - Static method in class org.openscience.cdk.renderer.generators.HighlightGenerator: Create a palette which uses the provided colors.
createPalette(Color, Color...) - Static method in class org.openscience.cdk.renderer.generators.HighlightGenerator: Create a palette which uses the provided colors.
createPath() - Method in class org.openscience.cdk.renderer.elements.path.PathBuilder: Create and return the final path.
createProtein(String) - Static method in class org.openscience.cdk.tools.ProteinBuilderTool: Creates a BioPolymer from a sequence of amino acid as identified by a the sequence of their one letter codes.
createProtein(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.ProteinBuilderTool: Creates a BioPolymer from a sequence of amino acid as identified by a the sequence of their one letter codes.
createReactionScheme(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator: Create a IReactionScheme give a IReactionSet object.
createReactionSMILES(IReaction) - Method in class org.openscience.cdk.smiles.SmilesGenerator: Deprecated.
use SmilesGenerator.create(IAtomContainer)
createReader(InputStream) - Method in class org.openscience.cdk.io.ReaderFactory: Detects the format of the Reader input, and if known, it will return a CDK Reader to read the format, or null when the reader is not implemented.
createReader(Reader) - Method in class org.openscience.cdk.io.ReaderFactory: Detects the format of the Reader input, and if known, it will return a CDK Reader to read the format.
createReader(IChemFormat) - Method in class org.openscience.cdk.io.ReaderFactory: Creates a new IChemObjectReader based on the given IChemFormat.
createSingleton(IAtomContainer) - Static method in class org.openscience.cdk.layout.TemplateHandler: Singleton template instance, mainly useful for aligning molecules.
createSMILES(IAtomContainer) - Method in class org.openscience.cdk.smiles.SmilesGenerator: Deprecated.
use #create
createSMILES(IReaction) - Method in class org.openscience.cdk.smiles.SmilesGenerator: Deprecated.
use #createReactionSMILES
createSymbolAndBondOrderQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator: Creates a QueryAtomContainer with the following settings:
createSymbolAndChargeQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator: Creates a QueryAtomContainer with the following settings:
createSymbolChargeIDQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
createWriter(IChemFormat) - Method in class org.openscience.cdk.io.WriterFactory: Creates a new IChemObjectWriter based on the given IChemFormat.
CRK2DFormat - Class in org.openscience.cdk.io.formats: See here.
CRK2DFormat() - Constructor for class org.openscience.cdk.io.formats.CRK2DFormat
CRK3DFormat - Class in org.openscience.cdk.io.formats: See here.
CRK3DFormat() - Constructor for class org.openscience.cdk.io.formats.CRK3DFormat
cross(Vector) - Method in class org.openscience.cdk.math.Vector: Cross product, only well definited in R^3
CrossoverMachine - Class in org.openscience.cdk.structgen.stochastic.operator: Modified molecular structures by applying crossover operator on a pair of parent structures and generate a pair of offspring structures.
CrossoverMachine() - Constructor for class org.openscience.cdk.structgen.stochastic.operator.CrossoverMachine: Constructs a new CrossoverMachine operator.
crystal - Variable in class org.openscience.cdk.ChemModel: A Crystal.
crystal - Variable in class org.openscience.cdk.silent.ChemModel: A Crystal.
Crystal - Class in org.openscience.cdk: Class representing a molecular crystal.
Crystal - Class in org.openscience.cdk.silent: Class representing a molecular crystal.
Crystal() - Constructor for class org.openscience.cdk.Crystal: Constructs a new crystal with zero length cell axis.
Crystal() - Constructor for class org.openscience.cdk.silent.Crystal: Constructs a new crystal with zero length cell axis.
Crystal(IAtomContainer) - Constructor for class org.openscience.cdk.Crystal: Constructs a new crystal with zero length cell axis and adds the atoms in the AtomContainer as cell content.
Crystal(IAtomContainer) - Constructor for class org.openscience.cdk.silent.Crystal: Constructs a new crystal with zero length cell axis and adds the atoms in the AtomContainer as cell content.
CrystalGeometryTools - Class in org.openscience.cdk.geometry: A set of static methods for working with crystal coordinates.
CrystalGeometryTools() - Constructor for class org.openscience.cdk.geometry.CrystalGeometryTools
crystalScalar - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
CrystClustFormat - Class in org.openscience.cdk.io.formats
CrystClustFormat() - Constructor for class org.openscience.cdk.io.formats.CrystClustFormat
CrystClustReader - Class in org.openscience.cdk.io
CrystClustReader() - Constructor for class org.openscience.cdk.io.CrystClustReader
CrystClustReader(InputStream) - Constructor for class org.openscience.cdk.io.CrystClustReader
CrystClustReader(Reader) - Constructor for class org.openscience.cdk.io.CrystClustReader
CrystClustWriter - Class in org.openscience.cdk.io: Rather stupid file format used for storing crystal information.
CrystClustWriter() - Constructor for class org.openscience.cdk.io.CrystClustWriter
CrystClustWriter(OutputStream) - Constructor for class org.openscience.cdk.io.CrystClustWriter
CrystClustWriter(Writer) - Constructor for class org.openscience.cdk.io.CrystClustWriter: Constructs a new CrystClustWriter class.
Cs - Static variable in interface org.openscience.cdk.interfaces.IElement
CS - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
csum(int, int, int[][][]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Summing ith column entries starting from the jth row.
CT - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Geometric CisTrans (e.g.
CTAB_SGROUPS - Static variable in class org.openscience.cdk.CDKConstants: Key to store/fetch CTab Sgroups from Molfiles.
CtabAbbreviation - org.openscience.cdk.sgroup.SgroupType
CtabAbbreviationAttachPoint - org.openscience.cdk.sgroup.SgroupKey
CtabAbbreviationVector - org.openscience.cdk.sgroup.SgroupKey
CtabAnyPolymer - org.openscience.cdk.sgroup.SgroupType
CtabBracket - org.openscience.cdk.sgroup.SgroupKey
CtabBracketStyle - org.openscience.cdk.sgroup.SgroupKey
CtabClass - org.openscience.cdk.sgroup.SgroupKey
CtabComponent - org.openscience.cdk.sgroup.SgroupType
CtabComponentNumber - org.openscience.cdk.sgroup.SgroupKey
CtabConnectivity - org.openscience.cdk.sgroup.SgroupKey
CtabCopolymer - org.openscience.cdk.sgroup.SgroupType
CtabCorrespondence - org.openscience.cdk.sgroup.SgroupKey
CtabCrossLink - org.openscience.cdk.sgroup.SgroupType
CtabData - org.openscience.cdk.sgroup.SgroupType
CtabDisplayInfo - org.openscience.cdk.sgroup.SgroupKey
CtabExpansion - org.openscience.cdk.sgroup.SgroupKey
CtabFormulation - org.openscience.cdk.sgroup.SgroupType
CtabGeneric - org.openscience.cdk.sgroup.SgroupType
CtabGraft - org.openscience.cdk.sgroup.SgroupType
CtabLabel - org.openscience.cdk.sgroup.SgroupKey: Not to be confused with the subscript key this is Sgroup label not the bracket label (e.g.
CtabMer - org.openscience.cdk.sgroup.SgroupType
CtabMixture - org.openscience.cdk.sgroup.SgroupType
CtabModified - org.openscience.cdk.sgroup.SgroupType
CtabMonomer - org.openscience.cdk.sgroup.SgroupType
CtabMultipleGroup - org.openscience.cdk.sgroup.SgroupType
CtabParentAtomList - org.openscience.cdk.sgroup.SgroupKey
CtabStructureRepeatUnit - org.openscience.cdk.sgroup.SgroupType
CtabSubScript - org.openscience.cdk.sgroup.SgroupKey
CtabSubType - org.openscience.cdk.sgroup.SgroupKey
CtabType - org.openscience.cdk.sgroup.SgroupKey
CTFileQueryBond - Class in org.openscience.cdk.isomorphism.matchers: Deprecated.
Use Expr.Type.SINGLE_OR_AROMATIC etc.
CTFileQueryBond(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.CTFileQueryBond: Deprecated.
CTFileQueryBond.Type - Enum in org.openscience.cdk.isomorphism.matchers: Deprecated.
CTXFormat - Class in org.openscience.cdk.io.formats
CTXFormat() - Constructor for class org.openscience.cdk.io.formats.CTXFormat
CTXReader - Class in org.openscience.cdk.io: Reader that extracts information from the IDENT, NAME, ATOMS and BONDS blocks in CTX files.
CTXReader() - Constructor for class org.openscience.cdk.io.CTXReader
CTXReader(InputStream) - Constructor for class org.openscience.cdk.io.CTXReader
CTXReader(Reader) - Constructor for class org.openscience.cdk.io.CTXReader
Cu - Static variable in interface org.openscience.cdk.interfaces.IElement
CU - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: ExtendedCisTrans a.k.a.
CU - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
cubicTo(Point2d, Point2d, Point2d) - Method in class org.openscience.cdk.renderer.elements.path.PathBuilder: Make a cubic curve in the path, with two control points.
CubicTo - Class in org.openscience.cdk.renderer.elements.path: A cubic curve in the path.
CubicTo - org.openscience.cdk.renderer.elements.path.Type
CubicTo(double[]) - Constructor for class org.openscience.cdk.renderer.elements.path.CubicTo: Make a cubic curve path element.
CubicTo(double, double, double, double, double, double) - Constructor for class org.openscience.cdk.renderer.elements.path.CubicTo: Make a cubic curve path element.
CubicTo(Point2d, Point2d, Point2d) - Constructor for class org.openscience.cdk.renderer.elements.path.CubicTo: Make a cubic curve path element.
Cumulene - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Cumulene
curChar - Variable in class org.openscience.cdk.iupac.parser.NomParserTokenManager
curChar - Variable in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager
Curium - org.openscience.cdk.config.Elements
CURIUM - Static variable in enum org.openscience.cdk.config.Elements
CURIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
curRef - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
current() - Method in class org.openscience.cdk.io.cml.CMLModuleStack: Returns the last added entry.
currentAtom - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
currentBond - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
currentChars - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
currentChemFile - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
currentChemModel - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
currentChemSequence - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
CurrentElement - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
currentFontIndex - Variable in class org.openscience.cdk.renderer.font.AbstractFontManager
currentMolecule - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
currentMoleculeSet - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
currentMonomer - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
currentReaction - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
currentReactionSet - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
currentRecord - Variable in class org.openscience.cdk.io.random.RandomAccessReader
currentStrand - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
currentToken - Variable in exception org.openscience.cdk.iupac.parser.ParseException: This is the last token that has been consumed successfully.
currentToken - Variable in exception org.openscience.cdk.smiles.smarts.parser.ParseException: This is the last token that has been consumed successfully.
customize(IAtomContainer, Object) - Method in interface org.openscience.cdk.libio.cml.ICMLCustomizer: Customized the nodeToAdd for the given Molecule.
customize(IAtomContainer, Object) - Method in class org.openscience.cdk.libio.cml.MDMoleculeCustomizer: Customize Molecule.
customize(IAtomContainer, Object) - Method in class org.openscience.cdk.libio.cml.PDBAtomCustomizer
customize(IAtomContainer, Object) - Method in class org.openscience.cdk.libio.cml.QSARCustomizer
customize(IAtom, Object) - Method in interface org.openscience.cdk.libio.cml.ICMLCustomizer: Customized the nodeToAdd for the given Atom.
customize(IAtom, Object) - Method in class org.openscience.cdk.libio.cml.MDMoleculeCustomizer: Customize Atom.
customize(IAtom, Object) - Method in class org.openscience.cdk.libio.cml.PDBAtomCustomizer
customize(IAtom, Object) - Method in class org.openscience.cdk.libio.cml.QSARCustomizer
customize(IBond, Object) - Method in interface org.openscience.cdk.libio.cml.ICMLCustomizer: Customized the nodeToAdd for the given IBond.
customize(IBond, Object) - Method in class org.openscience.cdk.libio.cml.MDMoleculeCustomizer: No customization for bonds.
customize(IBond, Object) - Method in class org.openscience.cdk.libio.cml.PDBAtomCustomizer
customize(IBond, Object) - Method in class org.openscience.cdk.libio.cml.QSARCustomizer
customizeJob() - Method in class org.openscience.cdk.io.iterator.IteratingSDFReader
customizeJob() - Method in class org.openscience.cdk.io.MDLReader: Deprecated.
customizeJob() - Method in class org.openscience.cdk.io.MDLV2000Reader
customizeJob() - Method in class org.openscience.cdk.io.MDLV2000Writer
customizeJob() - Method in class org.openscience.cdk.io.MDLV3000Writer
customizeJob() - Method in class org.openscience.cdk.io.PDBReader
customizeJob() - Method in class org.openscience.cdk.io.SDFWriter
customizeJob() - Method in class org.openscience.cdk.io.SMILESWriter
CustomSerializer - Class in org.openscience.cdk.io.cml: Custom Serializer with the sole purpose and functionality to not output the XML declaration.
CustomSerializer(OutputStream) - Constructor for class org.openscience.cdk.io.cml.CustomSerializer: Instantiates a new CustomSerializer using the matching Serializer(OutputStream).
CustomSerializer(OutputStream, String) - Constructor for class org.openscience.cdk.io.cml.CustomSerializer: Instantiates a new CustomSerializer using the matching Serializer(OutputStream, String).
Cx2dCoordinates - Static variable in class org.openscience.cdk.smiles.SmiFlavor: Output 2D coordinates.
Cx3dCoordinates - Static variable in class org.openscience.cdk.smiles.SmiFlavor: Output 3D coordinates.
CxAtomLabel - Static variable in class org.openscience.cdk.smiles.SmiFlavor: Output atom labels, atom labels are specified by IPseudoAtom.getLabel().
CxAtomValue - Static variable in class org.openscience.cdk.smiles.SmiFlavor: Output atom values, atom values are specified by the property CDKConstants.COMMENT using IChemObject.setProperty(Object, Object)
CxCoordinates - Static variable in class org.openscience.cdk.smiles.SmiFlavor: Output either 2D/3D coordinates.
CxDataSgroups - Static variable in class org.openscience.cdk.smiles.SmiFlavor: Output data Sgroups.
CxEnhancedStereo - Static variable in class org.openscience.cdk.smiles.SmiFlavor: Output enhanced stereo.
CxFragmentGroup - Static variable in class org.openscience.cdk.smiles.SmiFlavor: Output fragment grouping for reactions.
CxLigandOrder - Static variable in class org.openscience.cdk.smiles.SmiFlavor: Output ligand order information.
CxMulticenter - Static variable in class org.openscience.cdk.smiles.SmiFlavor: Output multicenter bonds, positional variation is specified with Sgroups of the type SgroupType.ExtMulticenter.
CxPolymer - Static variable in class org.openscience.cdk.smiles.SmiFlavor: Output polymer repeat units is specified with Sgroups.
CxRadical - Static variable in class org.openscience.cdk.smiles.SmiFlavor: Output radicals, radicals are specified by IAtomContainer.getConnectedSingleElectronsCount(IAtom)
CxSmiles - Static variable in class org.openscience.cdk.smiles.SmiFlavor: Output CXSMILES layers.
CxSmilesGenerator - Class in org.openscience.cdk.smiles
CxSmilesGenerator() - Constructor for class org.openscience.cdk.smiles.CxSmilesGenerator
CxSmilesWithCoords - Static variable in class org.openscience.cdk.smiles.SmiFlavor: Output CXSMILES layers and coordinates.
cycle() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Deals with cyclic main chains.
cycle(int[][], int[]) - Static method in class org.openscience.cdk.graph.GraphUtil: Arrange the vertices in a simple cyclic path.
CycleBasis - Class in org.openscience.cdk.ringsearch.cyclebasis: Deprecated.
internal implemenation detail from SSSRFinder, do not use
CycleBasis(UndirectedGraph) - Constructor for class org.openscience.cdk.ringsearch.cyclebasis.CycleBasis: Deprecated.

Constructs a minimum cycle basis of a graph.
CycleFinder - Interface in org.openscience.cdk.graph: Defines a method to find the cycles of a molecule.
cycles() - Method in class org.openscience.cdk.ringsearch.cyclebasis.CycleBasis: Deprecated.

Returns the cycles that form the cycle basis.
cycles() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis: Deprecated.
Cycles - Class in org.openscience.cdk.graph: A utility class for storing and computing the cycles of a chemical graph.
cycleTranspositions(int, int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Getting the list of cycle transpositions for a given atom partition and the row index
cyclic() - Method in interface org.openscience.cdk.ringsearch.CyclicVertexSearch: The set of cyclic vertices.
cyclic() - Method in class org.openscience.cdk.ringsearch.RingSearch: Construct a set of vertices which belong to any cycle (ring).
cyclic(int) - Method in interface org.openscience.cdk.ringsearch.CyclicVertexSearch: Returns true if the vertex v is in a cycle.
cyclic(int) - Method in class org.openscience.cdk.ringsearch.RingSearch: Determine whether the vertex at index i is a cyclic vertex.
cyclic(int, int) - Method in interface org.openscience.cdk.ringsearch.CyclicVertexSearch: Is the edge between the two vertices u and v in a cycle?
cyclic(int, int) - Method in class org.openscience.cdk.ringsearch.RingSearch: Determine whether the edge between the vertices u and v is cyclic.
cyclic(IAtom) - Method in class org.openscience.cdk.ringsearch.RingSearch: Determine whether the provided atom belongs to a ring (is cyclic).
cyclic(IBond) - Method in class org.openscience.cdk.ringsearch.RingSearch: Determine whether the bond is cyclic.
CyclicVertexSearch - Interface in org.openscience.cdk.ringsearch: Describes a search to identify vertices which belong to elementary cycles and if those cycles are isolated or are part of a fused system.
CYCLO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.

D

D - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
D_BOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
DaltonFormat - Class in org.openscience.cdk.io.formats
DaltonFormat() - Constructor for class org.openscience.cdk.io.formats.DaltonFormat
Darmstadtium - org.openscience.cdk.config.Elements
DARMSTADTIUM - Static variable in enum org.openscience.cdk.config.Elements
Dash - org.openscience.cdk.interfaces.IBond.Display: A dashed line.
DASH - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
DASHED - org.openscience.cdk.renderer.elements.WedgeLineElement.TYPE
DashSection() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.DashSection
Data - org.openscience.cdk.sgroup.SgroupKey
DataDisplayInformation - org.openscience.cdk.sgroup.SgroupKey
DataFeatures - Class in org.openscience.cdk.tools: Class with constants for possible data features defined in the a Data Feature Ontology.
DataFeatures() - Constructor for class org.openscience.cdk.tools.DataFeatures
DataFeaturesTool - Class in org.openscience.cdk.tools: Utility that helps determine which data features are present.
DataFeaturesTool() - Constructor for class org.openscience.cdk.tools.DataFeaturesTool
DataFieldFormat - org.openscience.cdk.sgroup.SgroupKey
DataFieldName - org.openscience.cdk.sgroup.SgroupKey
DataFieldUnits - org.openscience.cdk.sgroup.SgroupKey
daylight() - Static method in class org.openscience.cdk.aromaticity.ElectronDonation: Electron donation model closely mirroring the Daylight model for use in generating SMILES.
Db - Static variable in interface org.openscience.cdk.interfaces.IElement
dBlockMetals() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.
DeAromatizationTool - Class in org.openscience.cdk.tools: Deprecated.
the newer Kekulization provides a faster, more generic and comprehensive algorithm.
DeAromatizationTool() - Constructor for class org.openscience.cdk.tools.DeAromatizationTool: Deprecated.
deAromatize(IRing) - Static method in class org.openscience.cdk.tools.DeAromatizationTool: Deprecated.

Methods that takes a ring of which all bonds are aromatic, and assigns single and double bonds.
Dearomatize(IAtomContainer) - Static method in class org.openscience.cdk.tools.DeAromatizationTool: Deprecated.
Dearomatize566Rings(IRingSet) - Static method in class org.openscience.cdk.tools.DeAromatizationTool: Deprecated.
Dearomatize56Rings(IRingSet) - Static method in class org.openscience.cdk.tools.DeAromatizationTool: Deprecated.
Dearomatize5Ring(IRingSet) - Static method in class org.openscience.cdk.tools.DeAromatizationTool: Deprecated.
Dearomatize666Rings(IRingSet) - Static method in class org.openscience.cdk.tools.DeAromatizationTool: Deprecated.
Dearomatize66Rings(IRingSet) - Static method in class org.openscience.cdk.tools.DeAromatizationTool: Deprecated.
Dearomatize6Ring(IRingSet) - Static method in class org.openscience.cdk.tools.DeAromatizationTool: Deprecated.
debug - Static variable in class org.openscience.cdk.layout.AtomPlacer
debug - Static variable in class org.openscience.cdk.ringsearch.RingPartitioner: Debugging on/off
debug - Static variable in class org.openscience.cdk.tools.SwissArmyKnife: Deprecated.
debug(Object) - Method in interface org.openscience.cdk.tools.ILoggingTool: Shows DEBUG output for the Object.
debug(Object) - Method in class org.openscience.cdk.tools.SystemOutLoggingTool: Deprecated.

Shows DEBUG output for the Object.
debug(Object, Object...) - Method in interface org.openscience.cdk.tools.ILoggingTool: Shows DEBUG output for the given Object's.
debug(Object, Object...) - Method in class org.openscience.cdk.tools.SystemOutLoggingTool: Deprecated.

Shows DEBUG output for the given Object's.
DEBUG - Static variable in class org.openscience.cdk.graph.PathTools: Boolean with which debugging can be turned on.
DEBUG - Static variable in interface org.openscience.cdk.tools.ILoggingTool: Debug, Info, Warn, Error, and Fatal messages will be emitted.
DebugAdductFormula - Class in org.openscience.cdk.debug: Debugging implementation of IAdductFormula.
DebugAdductFormula() - Constructor for class org.openscience.cdk.debug.DebugAdductFormula
DebugAdductFormula(IMolecularFormula) - Constructor for class org.openscience.cdk.debug.DebugAdductFormula
DebugAminoAcid - Class in org.openscience.cdk.debug: Debugging data class.
DebugAminoAcid() - Constructor for class org.openscience.cdk.debug.DebugAminoAcid
DebugAtom - Class in org.openscience.cdk.debug: Debugging data class.
DebugAtom() - Constructor for class org.openscience.cdk.debug.DebugAtom
DebugAtom(String) - Constructor for class org.openscience.cdk.debug.DebugAtom
DebugAtom(String, Point2d) - Constructor for class org.openscience.cdk.debug.DebugAtom
DebugAtom(String, Point3d) - Constructor for class org.openscience.cdk.debug.DebugAtom
DebugAtom(IElement) - Constructor for class org.openscience.cdk.debug.DebugAtom
DebugAtomContainer - Class in org.openscience.cdk.debug: Debugging data class.
DebugAtomContainer() - Constructor for class org.openscience.cdk.debug.DebugAtomContainer
DebugAtomContainer(int, int, int, int) - Constructor for class org.openscience.cdk.debug.DebugAtomContainer
DebugAtomContainer(IAtomContainer) - Constructor for class org.openscience.cdk.debug.DebugAtomContainer
DebugAtomContainerSet - Class in org.openscience.cdk.debug: Debugging data class.
DebugAtomContainerSet() - Constructor for class org.openscience.cdk.debug.DebugAtomContainerSet
DebugAtomType - Class in org.openscience.cdk.debug: Debugging data class.
DebugAtomType(String) - Constructor for class org.openscience.cdk.debug.DebugAtomType
DebugAtomType(String, String) - Constructor for class org.openscience.cdk.debug.DebugAtomType
DebugAtomType(IElement) - Constructor for class org.openscience.cdk.debug.DebugAtomType
DebugBioPolymer - Class in org.openscience.cdk.debug: Debugging data class.
DebugBioPolymer() - Constructor for class org.openscience.cdk.debug.DebugBioPolymer
DebugBond - Class in org.openscience.cdk.debug: Debugging data class.
DebugBond() - Constructor for class org.openscience.cdk.debug.DebugBond
DebugBond(IAtom[]) - Constructor for class org.openscience.cdk.debug.DebugBond
DebugBond(IAtom[], IBond.Order) - Constructor for class org.openscience.cdk.debug.DebugBond
DebugBond(IAtom, IAtom) - Constructor for class org.openscience.cdk.debug.DebugBond
DebugBond(IAtom, IAtom, IBond.Order) - Constructor for class org.openscience.cdk.debug.DebugBond
DebugBond(IAtom, IAtom, IBond.Order, IBond.Stereo) - Constructor for class org.openscience.cdk.debug.DebugBond
DebugChemFile - Class in org.openscience.cdk.debug: Debugging data class.
DebugChemFile() - Constructor for class org.openscience.cdk.debug.DebugChemFile
DebugChemModel - Class in org.openscience.cdk.debug: Debugging data class.
DebugChemModel() - Constructor for class org.openscience.cdk.debug.DebugChemModel
DebugChemObject - Class in org.openscience.cdk.debug: Debugging data class.
DebugChemObject() - Constructor for class org.openscience.cdk.debug.DebugChemObject
DebugChemObject(IChemObject) - Constructor for class org.openscience.cdk.debug.DebugChemObject
DebugChemObjectBuilder - Class in org.openscience.cdk.debug: A helper class to instantiate a IChemObject for the original CDK implementation.
DebugChemObjectBuilder() - Constructor for class org.openscience.cdk.debug.DebugChemObjectBuilder
DebugChemSequence - Class in org.openscience.cdk.debug: Debugging data class.
DebugChemSequence() - Constructor for class org.openscience.cdk.debug.DebugChemSequence
DebugCrystal - Class in org.openscience.cdk.debug: Debugging data class.
DebugCrystal() - Constructor for class org.openscience.cdk.debug.DebugCrystal
DebugCrystal(IAtomContainer) - Constructor for class org.openscience.cdk.debug.DebugCrystal
DebugElectronContainer - Class in org.openscience.cdk.debug: Debugging data class.
DebugElectronContainer() - Constructor for class org.openscience.cdk.debug.DebugElectronContainer
DebugElement - Class in org.openscience.cdk.debug: Debugging data class.
DebugElement() - Constructor for class org.openscience.cdk.debug.DebugElement
DebugElement(String) - Constructor for class org.openscience.cdk.debug.DebugElement
DebugElement(String, int) - Constructor for class org.openscience.cdk.debug.DebugElement
DebugElement(IElement) - Constructor for class org.openscience.cdk.debug.DebugElement
DebugFragmentAtom - Class in org.openscience.cdk.debug: Class to represent an IPseudoAtom which embeds an IAtomContainer.
DebugFragmentAtom() - Constructor for class org.openscience.cdk.debug.DebugFragmentAtom
debuggCheckPSPEvent() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
DebugIsotope - Class in org.openscience.cdk.debug: Debugging data class.
DebugIsotope(int, String, double, double) - Constructor for class org.openscience.cdk.debug.DebugIsotope
DebugIsotope(int, String, int, double, double) - Constructor for class org.openscience.cdk.debug.DebugIsotope
DebugIsotope(String) - Constructor for class org.openscience.cdk.debug.DebugIsotope
DebugIsotope(String, int) - Constructor for class org.openscience.cdk.debug.DebugIsotope
DebugIsotope(IElement) - Constructor for class org.openscience.cdk.debug.DebugIsotope
DebugLonePair - Class in org.openscience.cdk.debug: Debugging data class.
DebugLonePair() - Constructor for class org.openscience.cdk.debug.DebugLonePair
DebugLonePair(IAtom) - Constructor for class org.openscience.cdk.debug.DebugLonePair
DebugMapping - Class in org.openscience.cdk.debug: Debugging data class.
DebugMapping(IChemObject, IChemObject) - Constructor for class org.openscience.cdk.debug.DebugMapping
DebugMolecularFormula - Class in org.openscience.cdk.debug: Debugging implementation of IMolecularFormula.
DebugMolecularFormula() - Constructor for class org.openscience.cdk.debug.DebugMolecularFormula
DebugMolecularFormulaSet - Class in org.openscience.cdk.debug: Debugging implementation of IMolecularFormulaSet.
DebugMolecularFormulaSet() - Constructor for class org.openscience.cdk.debug.DebugMolecularFormulaSet
DebugMolecularFormulaSet(IMolecularFormula) - Constructor for class org.openscience.cdk.debug.DebugMolecularFormulaSet
DebugMonomer - Class in org.openscience.cdk.debug: Debugging data class.
DebugMonomer() - Constructor for class org.openscience.cdk.debug.DebugMonomer
DebugPDBAtom - Class in org.openscience.cdk.debug: Debugging data class.
DebugPDBAtom(String) - Constructor for class org.openscience.cdk.debug.DebugPDBAtom
DebugPDBAtom(String, Point3d) - Constructor for class org.openscience.cdk.debug.DebugPDBAtom
DebugPDBAtom(IElement) - Constructor for class org.openscience.cdk.debug.DebugPDBAtom
DebugPDBMonomer - Class in org.openscience.cdk.debug: Debugging data class.
DebugPDBMonomer() - Constructor for class org.openscience.cdk.debug.DebugPDBMonomer
DebugPDBPolymer - Class in org.openscience.cdk.debug: Debugging data class.
DebugPDBPolymer() - Constructor for class org.openscience.cdk.debug.DebugPDBPolymer
DebugPDBStructure - Class in org.openscience.cdk.debug: Debugging data class.
DebugPDBStructure() - Constructor for class org.openscience.cdk.debug.DebugPDBStructure
DebugPolymer - Class in org.openscience.cdk.debug: Debugging data class.
DebugPolymer() - Constructor for class org.openscience.cdk.debug.DebugPolymer
DebugPseudoAtom - Class in org.openscience.cdk.debug: Debugging data class.
DebugPseudoAtom() - Constructor for class org.openscience.cdk.debug.DebugPseudoAtom
DebugPseudoAtom(String) - Constructor for class org.openscience.cdk.debug.DebugPseudoAtom
DebugPseudoAtom(String, Point2d) - Constructor for class org.openscience.cdk.debug.DebugPseudoAtom
DebugPseudoAtom(String, Point3d) - Constructor for class org.openscience.cdk.debug.DebugPseudoAtom
DebugPseudoAtom(IElement) - Constructor for class org.openscience.cdk.debug.DebugPseudoAtom
DebugReaction - Class in org.openscience.cdk.debug: Debugging data class.
DebugReaction() - Constructor for class org.openscience.cdk.debug.DebugReaction
DebugReactionScheme - Class in org.openscience.cdk.debug: Debugging data class.
DebugReactionScheme() - Constructor for class org.openscience.cdk.debug.DebugReactionScheme
DebugReactionSet - Class in org.openscience.cdk.debug: Debugging data class.
DebugReactionSet() - Constructor for class org.openscience.cdk.debug.DebugReactionSet
DebugRing - Class in org.openscience.cdk.debug: Debugging data class.
DebugRing() - Constructor for class org.openscience.cdk.debug.DebugRing
DebugRing(int) - Constructor for class org.openscience.cdk.debug.DebugRing
DebugRing(int, String) - Constructor for class org.openscience.cdk.debug.DebugRing
DebugRing(IAtomContainer) - Constructor for class org.openscience.cdk.debug.DebugRing
DebugRingSet - Class in org.openscience.cdk.debug: Debugging data class.
DebugRingSet() - Constructor for class org.openscience.cdk.debug.DebugRingSet
DebugSingleElectron - Class in org.openscience.cdk.debug: Debugging data class.
DebugSingleElectron() - Constructor for class org.openscience.cdk.debug.DebugSingleElectron
DebugSingleElectron(IAtom) - Constructor for class org.openscience.cdk.debug.DebugSingleElectron
DebugStrand - Class in org.openscience.cdk.debug: Debugging data class.
DebugStrand() - Constructor for class org.openscience.cdk.debug.DebugStrand
debugStream - Variable in class org.openscience.cdk.iupac.parser.NomParserTokenManager: Debug output.
debugStream - Variable in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager: Debug output.
DebugSubstance - Class in org.openscience.cdk.debug: Debugging data class.
DebugSubstance() - Constructor for class org.openscience.cdk.debug.DebugSubstance
DEC - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
decideBondOrder(IAtomContainer) - Method in class org.openscience.cdk.tools.AtomTypeAwareSaturationChecker: This method decides the bond order on bonds that has the SINGLE_OR_DOUBLE-flag raised.
decideBondOrder(IAtomContainer, boolean) - Method in class org.openscience.cdk.tools.AtomTypeAwareSaturationChecker: This method decides the bond order on bonds that has the SINGLE_OR_DOUBLE-flag raised.
decode(String) - Static method in class org.openscience.cdk.fingerprint.PubchemFingerprinter: Returns a fingerprint from a Base64 encoded Pubchem fingerprint.
decreaseBondOrder(IBond) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator: Decrease the order of a bond.
decreaseBondOrder(IBond.Order) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator: Returns the IBond.Order one lower.
decreaseFontSize() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager: Move the font size pointer down.
DeduceBondSystemTool - Class in org.openscience.cdk.smiles: Deprecated.
Use the newer Kekulization
DeduceBondSystemTool() - Constructor for class org.openscience.cdk.smiles.DeduceBondSystemTool: Deprecated.

Constructor for the DeduceBondSystemTool object.
DeduceBondSystemTool(AllRingsFinder) - Constructor for class org.openscience.cdk.smiles.DeduceBondSystemTool: Deprecated.

Constructor for the DeduceBondSystemTool object accepting a custom AllRingsFinder.
Default - Static variable in class org.openscience.cdk.graph.invariant.CanonOpts: Default canon flavour options.
Default - Static variable in class org.openscience.cdk.smiles.SmiFlavor: Default SMILES output write Stereochemistry, Atomic Mass, and CXSMILES layers.
DEFAULT - org.openscience.cdk.smsd.interfaces.Algorithm: Deprecated.

Default SMSD algorithm.
DEFAULT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: Lexical state.
DEFAULT - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: Lexical state.
DEFAULT_BOND_LENGTH_H - Static variable in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
DEFAULT_LOGGING_TOOL_CLASS - Static variable in class org.openscience.cdk.tools.LoggingToolFactory: Default logging tool.
DEFAULT_MM_MARGIN - Static variable in class org.openscience.cdk.depict.DepictionGenerator: Default margin for vector graphics formats.
DEFAULT_OCCURRENCE - Static variable in class org.openscience.cdk.isomorphism.matchers.RGroupList: Default value for occurrence field.
DEFAULT_PADDING_FACTOR - Static variable in class org.openscience.cdk.depict.Depiction: When no fixed padding value is specified we use margin multiplied by this value.
DEFAULT_PX_MARGIN - Static variable in class org.openscience.cdk.depict.DepictionGenerator: Default margin for raster graphics formats.
DEFAULT_SCALE - Static variable in class org.openscience.cdk.renderer.AtomContainerRenderer: The default scale is used when the model is empty.
DEFAULT_SEARCH_DEPTH - Static variable in class org.openscience.cdk.fingerprint.Fingerprinter: The default search depth used to create the fingerprints.
DEFAULT_SIZE - Static variable in class org.openscience.cdk.fingerprint.Fingerprinter: The default length of created fingerprints.
DEFAULT_SIZE - Static variable in class org.openscience.cdk.fingerprint.ShortestPathFingerprinter: The default length of created fingerprints.
DEFAULT_STACK_LENGTH - Static variable in interface org.openscience.cdk.tools.ILoggingTool: Default number of StackTraceElements to be printed by debug(Exception).
defaultAngles - Static variable in class org.openscience.cdk.layout.RingPlacer: Default ring start angles.
DefaultBondColor() - Constructor for class org.openscience.cdk.renderer.generators.BasicBondGenerator.DefaultBondColor
DefaultBondMatcher - Class in org.openscience.cdk.smsd.algorithm.matchers: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
DefaultBondMatcher() - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultBondMatcher: Deprecated.

Constructor
DefaultBondMatcher(IAtomContainer, IBond, boolean) - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultBondMatcher: Deprecated.

Constructor
DefaultBondMatcher(IQueryBond) - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultBondMatcher: Deprecated.

Constructor
DefaultChemObjectBuilder - Class in org.openscience.cdk: A factory class to provide implementation independent ICDKObjects.
DefaultChemObjectBuilder() - Constructor for class org.openscience.cdk.DefaultChemObjectBuilder
DefaultChemObjectReader - Class in org.openscience.cdk.io: Abstract class that ChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners.
DefaultChemObjectReader() - Constructor for class org.openscience.cdk.io.DefaultChemObjectReader
DefaultChemObjectWriter - Class in org.openscience.cdk.io: Abstract class that ChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners.
DefaultChemObjectWriter() - Constructor for class org.openscience.cdk.io.DefaultChemObjectWriter
DefaultEventChemObjectReader - Class in org.openscience.cdk.io.iterator.event: Abstract class that IteratingChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners.
DefaultEventChemObjectReader() - Constructor for class org.openscience.cdk.io.iterator.event.DefaultEventChemObjectReader
DefaultInterfaceProvider() - Constructor for class org.openscience.cdk.DynamicFactory.DefaultInterfaceProvider
DefaultIteratingChemObjectReader<T extends IChemObject> - Class in org.openscience.cdk.io.iterator: Abstract class that IteratingChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners.
DefaultIteratingChemObjectReader() - Constructor for class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader
DefaultMatcher - Class in org.openscience.cdk.smsd.algorithm.matchers: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
DefaultMatcher() - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultMatcher: Deprecated.
DefaultMCSPlusAtomMatcher - Class in org.openscience.cdk.smsd.algorithm.matchers: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
DefaultMCSPlusAtomMatcher() - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultMCSPlusAtomMatcher: Deprecated.

Constructor
DefaultMCSPlusAtomMatcher(IAtomContainer, IAtom, boolean) - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultMCSPlusAtomMatcher: Deprecated.

Constructor
DefaultMCSPlusAtomMatcher(IAtomContainer, IAtom, int, boolean) - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultMCSPlusAtomMatcher: Deprecated.

Constructor
DefaultMCSPlusAtomMatcher(IQueryAtom, IQueryAtomContainer) - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultMCSPlusAtomMatcher: Deprecated.

Constructor
DefaultRandomAccessChemObjectReader - Class in org.openscience.cdk.io.random: Abstract class that IRandomAccessChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners.
DefaultRandomAccessChemObjectReader() - Constructor for class org.openscience.cdk.io.random.DefaultRandomAccessChemObjectReader
DefaultRGraphAtomMatcher - Class in org.openscience.cdk.smsd.algorithm.matchers: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
DefaultRGraphAtomMatcher() - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultRGraphAtomMatcher: Deprecated.

Constructor
DefaultRGraphAtomMatcher(IAtomContainer, IAtom, boolean) - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultRGraphAtomMatcher: Deprecated.

Constructor
DefaultRGraphAtomMatcher(IAtomContainer, IAtom, int, boolean) - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultRGraphAtomMatcher: Deprecated.

Constructor
DefaultVFAtomMatcher - Class in org.openscience.cdk.smsd.algorithm.matchers: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
DefaultVFAtomMatcher() - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFAtomMatcher: Deprecated.

Constructor
DefaultVFAtomMatcher(IAtomContainer, IAtom, boolean) - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFAtomMatcher: Deprecated.

Constructor
DefaultVFAtomMatcher(IAtomContainer, IAtom, int, boolean) - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFAtomMatcher: Deprecated.

Constructor
DefaultVFAtomMatcher(IQueryAtom, IQueryAtomContainer) - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFAtomMatcher: Deprecated.

Constructor
DefaultVFBondMatcher - Class in org.openscience.cdk.smsd.algorithm.matchers: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
DefaultVFBondMatcher() - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFBondMatcher: Deprecated.

Constructor
DefaultVFBondMatcher(IAtomContainer, IBond, boolean) - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFBondMatcher: Deprecated.

Constructor
DefaultVFBondMatcher(IQueryBond) - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFBondMatcher: Deprecated.

Constructor
defaultVisit(SimpleNode, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
defineLigancyFourChirality(IAtomContainer, int, int, int, int, int, ITetrahedralChirality.Stereo) - Static method in class org.openscience.cdk.geometry.cip.CIPTool: Creates a ligancy for chirality around a single chiral atom, where the involved atoms are identified by there index in the IAtomContainer.
defineLigand(IAtomContainer, VisitedAtoms, int, int) - Static method in class org.openscience.cdk.geometry.cip.CIPTool: Creates a ligand attached to a single chiral atom, where the involved atoms are identified by there index in the IAtomContainer.
DEGREE - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if the degree (IAtom.getBondCount()) of an atom equals the specified 'value'.
degree2graph() - Method in class org.openscience.cdk.structgen.maygen.Maygen: Building a degree 2 graph for a single element type.
DelocalisedDonutsBondDisplay() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.DelocalisedDonutsBondDisplay
depict(Iterable<IAtomContainer>) - Method in class org.openscience.cdk.depict.DepictionGenerator: Depict a set of molecules, they will be depicted in a grid.
depict(Iterable<IAtomContainer>, int, int) - Method in class org.openscience.cdk.depict.DepictionGenerator: Depict a set of molecules, they will be depicted in a grid with the specified number of rows and columns.
depict(IAtomContainer) - Method in class org.openscience.cdk.depict.DepictionGenerator: Depict a single molecule.
depict(IReaction) - Method in class org.openscience.cdk.depict.DepictionGenerator: Depict a reaction.
depict(IReactionSet) - Method in class org.openscience.cdk.depict.DepictionGenerator
Depiction - Class in org.openscience.cdk.depict: Base class of a pre-rendered depiction.
DepictionGenerator - Class in org.openscience.cdk.depict: A high-level API for depicting molecules and reactions.
DepictionGenerator() - Constructor for class org.openscience.cdk.depict.DepictionGenerator: Create a depiction generator using the standard sans-serif system font.
DepictionGenerator(Font) - Constructor for class org.openscience.cdk.depict.DepictionGenerator: Create a depiction generator that will render atom labels using the specified AWT font.
depth(int) - Method in class org.openscience.cdk.hash.HashGeneratorMaker: Specify the depth of the hash generator.
depthFirstTargetSearch(IAtomContainer, IAtom, IAtom, IAtomContainer) - Static method in class org.openscience.cdk.graph.PathTools: Recursively performs a depth first search in a molecular graphs contained in the AtomContainer molecule, starting at the root atom and returning when it hits the target atom.
deref() - Method in class org.openscience.cdk.AtomRef: Dereference the atom pointer once providing access to the base atom.
deref() - Method in class org.openscience.cdk.BondRef: Dereference the bond pointer once providing access to the base bond.
deref(IAtom) - Static method in class org.openscience.cdk.AtomRef: Utility method to dereference an atom.
deref(IBond) - Static method in class org.openscience.cdk.BondRef: Utility method to dereference an bond pointer.
descendingOrderCheck(int[], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Checks a int array is in descending order or not with respect to a given atom partition.
descendingOrderCheck(int[], int, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Checks subarray of specified range of entries, the array is descending order or not.
descendingOrderUpperMatrixCheck(int, int[], int[], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Checks the first row is bigger than the second row just in the upper matrix.
descendingSort(int[], int, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Sorting entries of a subarray specified by indices.
descendingSortWithPartition(int[], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Sorting entries of a int array for a given atom partition.
description() - Method in enum org.openscience.cdk.smsd.interfaces.Algorithm: Deprecated.

Returns short description of the algorithm.
DESCRIPTION - Static variable in class org.openscience.cdk.CDKConstants: A description for a IChemObject.
DescriptorEngine - Class in org.openscience.cdk.qsar: A class that provides access to automatic descriptor calculation and more.
DescriptorEngine(Class<? extends IDescriptor>, IChemObjectBuilder) - Constructor for class org.openscience.cdk.qsar.DescriptorEngine: Create a descriptor engine for all descriptor types.
DescriptorEngine(List<String>, IChemObjectBuilder) - Constructor for class org.openscience.cdk.qsar.DescriptorEngine: Instantiates the DescriptorEngine.
DescriptorException - Exception in org.openscience.cdk.qsar: Exception that is thrown by descriptor routines when a problem has occurred.
DescriptorException(String) - Constructor for exception org.openscience.cdk.qsar.DescriptorException: Constructs a new DescriptorException with the given message.
DescriptorException(String, String) - Constructor for exception org.openscience.cdk.qsar.DescriptorException: Constructs a new DescriptorException with from the supplied descriptor name and associated message.
DescriptorSpecification - Class in org.openscience.cdk.qsar: Class that is used to distribute descriptor specifications.
DescriptorSpecification(String, String, String) - Constructor for class org.openscience.cdk.qsar.DescriptorSpecification: Container for specifying the type of descriptor.
DescriptorSpecification(String, String, String, String) - Constructor for class org.openscience.cdk.qsar.DescriptorSpecification: Container for specifying the type of descriptor.
DescriptorValue - Class in org.openscience.cdk.qsar: Class that is used to store descriptor values as IChemObject properties.
DescriptorValue(DescriptorSpecification, String[], Object[], IDescriptorResult, String[]) - Constructor for class org.openscience.cdk.qsar.DescriptorValue: Construct a descriptor value object, representing the numeric values as well as parameters and provenance.
DescriptorValue(DescriptorSpecification, String[], Object[], IDescriptorResult, String[], Exception) - Constructor for class org.openscience.cdk.qsar.DescriptorValue: Construct a descriptor value object, representing the numeric values as well as parameters and provenance.
deserialise(BufferedReader) - Static method in class org.openscience.cdk.fingerprint.model.Bayesian: Reads the incoming stream and attempts to convert it into an instantiated model.
deserialise(String) - Static method in class org.openscience.cdk.fingerprint.model.Bayesian: Converts a given string into a Bayesian model instance, or throws an exception if it is not valid.
destroyBondOrder(IBond.Order) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator: Deprecated.
use IBond.Order.numeric().doubleValue() instead
detect(IAtomContainer) - Static method in class org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector: Detect all conjugated pi systems in an AtomContainer.
detectAromaticity(IAtomContainer) - Static method in class org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector: Deprecated.
detectAromaticity(IAtomContainer) - Static method in class org.openscience.cdk.aromaticity.DoubleBondAcceptingAromaticityDetector: Deprecated.
determinant() - Method in class org.openscience.cdk.graph.invariant.GIMatrix: Returns the determinant of this matrix.
DeuteriumSymbol() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.DeuteriumSymbol
DfPattern - Class in org.openscience.cdk.isomorphism: The depth-first (DF) backtracking sub-structure matching algorithm so named because it matches the molecule in a depth-first manner (bond by bond).
DI - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
diagonal() - Method in class org.openscience.cdk.graph.invariant.GIMatrix: Returns a matrix containing all of the diagonal elements of this matrix and zero (0) everywhere else.
diagonalAxisScanXYZ(int, int, int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder: Method performs a scan; works only for cubic grids!
diagonalAxisScanXZY(int, int, int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder: Method performs a scan; works only for cubic grids!
diagonalAxisScanYXZ(int, int, int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder: Method performs a scan; works only for cubic grids!
diagonalAxisScanYZX(int, int, int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder: Method performs a scan; works only for cubic grids!
diagonalize(int) - Method in class org.openscience.cdk.math.Matrix: Diagonalize this matrix with the Jacobi algorithm.
Dictionary - Class in org.openscience.cdk.dict: Dictionary with entries.
Dictionary() - Constructor for class org.openscience.cdk.dict.Dictionary
DictionaryDatabase - Class in org.openscience.cdk.dict: Database of dictionaries listing entries with compounds, fragments and entities.
DictionaryDatabase() - Constructor for class org.openscience.cdk.dict.DictionaryDatabase
DictionaryHandler - Class in org.openscience.cdk.dict: Class for unmarshalling a dictionary schema file.
DictionaryHandler() - Constructor for class org.openscience.cdk.dict.DictionaryHandler
DictionaryValidator - Class in org.openscience.cdk.validate: Validates the existence of references to dictionaries.
DictionaryValidator(DictionaryDatabase) - Constructor for class org.openscience.cdk.validate.DictionaryValidator
DictRef - Class in org.openscience.cdk.dict: Object that can be used as key in IChemObject.setProperty(key, value) to denote that this property is a dictionary reference for this IChemObject.
DictRef(String, String) - Constructor for class org.openscience.cdk.dict.DictRef
DICTREF - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
DICTREFPROPERTYNAME - Static variable in class org.openscience.cdk.dict.DictionaryDatabase
diff(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.AtomContainerDiff: Compare two IChemObject classes and return the difference as a String.
diff(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.AtomDiff: Compare two IChemObject classes and return the difference as a String.
diff(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.AtomTypeDiff: Compare two IChemObject classes and return the difference as a String.
diff(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.BondDiff: Compare two IChemObject classes and return the difference as a String.
diff(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.ChemObjectDiff: Compare two IChemObject classes and return the difference as a String.
diff(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.ElectronContainerDiff: Compare two IChemObject classes and return the difference as a String.
diff(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.ElementDiff: Compare two IChemObject classes and return the difference as a String.
diff(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.IsotopeDiff: Compare two IChemObject classes and return the difference as a String.
diff(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.LonePairDiff: Compare two IChemObject classes and return the difference as a String.
diff(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.SingleElectronDiff: Compare two IChemObject classes and return the difference as a String.
difference(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.AtomContainerDiff: Compare two IChemObject classes and return the difference as an IDifference.
difference(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.AtomDiff: Compare two IChemObject classes and return the difference as an IDifference.
difference(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.AtomTypeDiff: Compare two IChemObject classes and return the difference as an IDifference.
difference(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.BondDiff: Compare two IChemObject classes and return the difference as an IDifference.
difference(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.ChemObjectDiff: Compare two IChemObject classes and return the difference as an IDifference.
difference(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.ElectronContainerDiff: Compare two IChemObject classes and return the difference as an IDifference.
difference(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.ElementDiff: Compare two IChemObject classes and return the difference as an IDifference.
difference(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.IsotopeDiff: Compare two IChemObject classes and return the difference as an IDifference.
difference(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.LonePairDiff: Compare two IChemObject classes and return the difference as an IDifference.
difference(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.SingleElectronDiff: Compare two IChemObject classes and return the difference as an IDifference.
differences - Variable in class org.openscience.cdk.tools.diff.tree.AbstractDifferenceList
differences(BitSet, BitSet) - Static method in class org.openscience.cdk.fingerprint.FingerprinterTool: List all differences between the two bit vectors.
DIGIT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
DIGIT - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
dim - Variable in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
direction - Variable in class org.openscience.cdk.renderer.elements.ArrowElement: Boolean that is true if the arrow points from start to end, false if from end to start.
direction - Variable in class org.openscience.cdk.renderer.elements.WedgeLineElement: The direction indicates which way the wedge gets thicker.
direction(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.StereoBond: Deprecated.
disable_tracing() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Disable tracing.
disable_tracing() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser: Disable tracing.
disconnected(SymbolVisibility) - Static method in class org.openscience.cdk.renderer.generators.standard.SelectionVisibility: Display the atom symbol if is disconnected from any other selected atoms or bonds.
DiscretePartitionRefiner - Interface in org.openscience.cdk.group: A mechanism for refining partitions of graph-like objects.
DisjointSetForest - Class in org.openscience.cdk.group: Implementation of a union-find data structure, largely copied from code due to Derrick Stolee.
DisjointSetForest(int) - Constructor for class org.openscience.cdk.group.DisjointSetForest: Initialize a disjoint set forest with a number of elements.
displace(IAtomContainer, Vector, Vector) - Method in class org.openscience.cdk.layout.OverlapResolver: Deprecated.

Makes a small displacement to some atoms or rings in the given atomcontainer.
display - Variable in class org.openscience.cdk.Bond
display - Variable in class org.openscience.cdk.silent.Bond
displayErrorLocation() - Method in class org.openscience.cdk.smarts.SmartsResult: Displays where the error occurred on the input string.
displayStatistic(long, String) - Method in class org.openscience.cdk.structgen.maygen.Maygen
distanceCalculator(double[], double) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.
distanceCalculator(double[], double) - Static method in class org.openscience.cdk.geometry.GeometryUtil
distanceCalculator(int[], double) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Gets the coordinates of two points (that represent a bond) and calculates for each the coordinates of two new points that have the given distance vertical to the bond.
distanceCalculator(int[], double) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Gets the coordinates of two points (that represent a bond) and calculates for each the coordinates of two new points that have the given distance vertical to the bond.
DistanceMoment - Class in org.openscience.cdk.similarity: Fast similarity measure for 3D structures.
DistanceMoment() - Constructor for class org.openscience.cdk.similarity.DistanceMoment
distanceTo(int) - Method in class org.openscience.cdk.graph.ShortestPaths: Access the distance to the provided end vertex.
distanceTo(IAtom) - Method in class org.openscience.cdk.graph.ShortestPaths: Access the distance to the provided end atom.
DistanceToAtomDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic: This class returns the 3D distance between two atoms.
DistanceToAtomDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor: Constructor for the DistanceToAtomDescriptor object
distributeHydrogens() - Method in class org.openscience.cdk.structgen.maygen.Maygen: If there are hydrogens in the formula, calling the hydrogenDistributor.
distributePartners(IAtom, IAtomContainer, Point2d, IAtomContainer, double) - Method in class org.openscience.cdk.layout.AtomPlacer: Distribute the bonded atoms (neighbours) of an atom such that they fill the remaining space around an atom in a geometrically nice way.
distributeSulfurOxygen(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen
distributeSymbols(int, int, int, int, int, int, int, boolean) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Main function for the distribution of atom symbols: O and S for OnSm form formulae.
distributeSymbolsNextSizeAboveGraphSize(int, boolean) - Method in class org.openscience.cdk.structgen.maygen.Maygen
div(Complex) - Method in class org.openscience.cdk.math.Complex: Div this value by a complex value
div(Quaternion) - Method in class org.openscience.cdk.math.Quaternion
DivalentSinglet - org.openscience.cdk.io.MDLV2000Writer.SPIN_MULTIPLICITY
DivalentTriplet - org.openscience.cdk.io.MDLV2000Writer.SPIN_MULTIPLICITY
DMol3Format - Class in org.openscience.cdk.io.formats
DMol3Format() - Constructor for class org.openscience.cdk.io.formats.DMol3Format
DN_OR_UNSPECIFIED_S_BOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
DN_S_BOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
DNP - org.openscience.cdk.formula.rules.MMElementRule.Database: Dictionary of Natural Products Online mass spectral database.
DO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
DOCK5Format - Class in org.openscience.cdk.io.formats: See here.
DOCK5Format() - Constructor for class org.openscience.cdk.io.formats.DOCK5Format
doCrossover(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.structgen.stochastic.operator.CrossoverMachine: Performs the n point crossover of two IAtomContainer.
doctypeDecl(String, String, String) - Method in class org.openscience.cdk.dict.DictionaryHandler
doctypeDecl(String, String, String) - Method in class org.openscience.cdk.io.cml.CMLHandler
doctypeDecl(String, String, String) - Method in class org.openscience.cdk.io.inchi.INChIHandler: Deprecated.
DOLLAR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Done() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream: Reset buffer when finished.
Done() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Reset buffer when finished.
DoNotAddH - net.sf.jniinchi.INCHI_OPTION
doRun(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen
dot(IVector) - Method in class org.openscience.cdk.math.IVector: Multiplication from two vectors
dot(Vector) - Method in class org.openscience.cdk.math.Vector: Multiplikation from two vectors
Dot - org.openscience.cdk.interfaces.IBond.Display: A dotted line.
doTessellate() - Method in class org.openscience.cdk.geometry.surface.Tessellate
DOUBLE - org.openscience.cdk.interfaces.IBond.Order
DOUBLE - org.openscience.cdk.isomorphism.matchers.CTFileQueryBond.Type: Deprecated.
DOUBLE - org.openscience.cdk.renderer.elements.LineElement.LineType
DOUBLE_OR_AROMATIC - org.openscience.cdk.isomorphism.matchers.CTFileQueryBond.Type: Deprecated.
DOUBLE_OR_AROMATIC - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if the bond order (IBond.getOrder()) is double or the bond is marked as aromatic (IBond.isAromatic()).
DoubleArrayResult - Class in org.openscience.cdk.qsar.result
DoubleArrayResult() - Constructor for class org.openscience.cdk.qsar.result.DoubleArrayResult
DoubleArrayResult(int) - Constructor for class org.openscience.cdk.qsar.result.DoubleArrayResult
DoubleArrayResultType - Class in org.openscience.cdk.qsar.result: IDescriptorResult type for doubles.
DoubleArrayResultType(int) - Constructor for class org.openscience.cdk.qsar.result.DoubleArrayResultType
DOUBLEBOND - Static variable in class org.openscience.cdk.libio.jena.CDK
DoubleBondAcceptingAromaticityDetector - Class in org.openscience.cdk.aromaticity: Deprecated.
use Aromaticity with the ElectronDonation.cdkAllowingExocyclic() model
DoubleBondAcceptingAromaticityDetector() - Constructor for class org.openscience.cdk.aromaticity.DoubleBondAcceptingAromaticityDetector: Deprecated.
DoubleBondElementEncoderFactory - Class in org.openscience.cdk.hash.stereo: Defines a stereo encoder factory for the hash code.
DoubleBondElementEncoderFactory() - Constructor for class org.openscience.cdk.hash.stereo.DoubleBondElementEncoderFactory
doubleBondHetero(IAtom) - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor.JPlogPCalculator
DoubleBondStereochemistry - Class in org.openscience.cdk.stereo: Stereochemistry specification for double bonds.
DoubleBondStereochemistry(IBond, IBond[], int) - Constructor for class org.openscience.cdk.stereo.DoubleBondStereochemistry
DoubleBondStereochemistry(IBond, IBond[], IDoubleBondStereochemistry.Conformation) - Constructor for class org.openscience.cdk.stereo.DoubleBondStereochemistry: Creates a new double bond stereo chemistry.
DoubleDifference - Class in org.openscience.cdk.tools.diff.tree: IDifference between two Double.
DoubleResult - Class in org.openscience.cdk.qsar.result
DoubleResult(double) - Constructor for class org.openscience.cdk.qsar.result.DoubleResult
DoubleResultType - Class in org.openscience.cdk.qsar.result: IDescriptorResult type for double.
DoubleResultType() - Constructor for class org.openscience.cdk.qsar.result.DoubleResultType
doubleValue() - Method in class org.openscience.cdk.qsar.result.DoubleResult
DOWN - org.openscience.cdk.interfaces.IBond.Stereo: A bond pointing down of which the start atom is the stereocenter and the end atom is below the drawing plane.
DOWN - org.openscience.cdk.isomorphism.matchers.smarts.StereoBond.Direction: Deprecated.
DOWN_INVERTED - org.openscience.cdk.interfaces.IBond.Stereo: A bond pointing down of which the end atom is the stereocenter and the start atom is below the drawing plane.
downcast() - Method in class org.openscience.cdk.sgroup.Sgroup: Downcast this, maybe generic, Sgroup to a specific concrete implementation.
draw(IDrawVisitor, double, Bounds, Rectangle2D) - Method in class org.openscience.cdk.depict.Depiction: Low-level draw method used by other rendering methods.
drawCenter - Variable in class org.openscience.cdk.renderer.AbstractRenderer: The center of the desired position on screen to draw.
Ds - Static variable in interface org.openscience.cdk.interfaces.IElement
Dubnium - org.openscience.cdk.config.Elements
DUBNIUM - Static variable in enum org.openscience.cdk.config.Elements
DUBNIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
DUMMY - Static variable in enum org.openscience.cdk.config.Elements: These instances are for backards compatability.
DUMMY_POINTER - Static variable in class org.openscience.cdk.CDKConstants: Flag used for JUnit testing the pointer functionality.
dump() - Method in class org.openscience.cdk.graph.rebond.Bspt
dumpClasspath() - Method in interface org.openscience.cdk.tools.ILoggingTool: Outputs the system property for java.class.path.
dumpClasspath() - Method in class org.openscience.cdk.tools.SystemOutLoggingTool: Deprecated.

Outputs the system property for java.class.path.
dumpSystemProperties() - Method in interface org.openscience.cdk.tools.ILoggingTool: Outputs system properties for the operating system and the java version.
dumpSystemProperties() - Method in class org.openscience.cdk.tools.SystemOutLoggingTool: Deprecated.

Outputs system properties for the operating system and the java version.
duplicate() - Method in class org.openscience.cdk.math.IMatrix: Copy a matrix
duplicate() - Method in class org.openscience.cdk.math.IVector: Copy a vector
duplicate() - Method in class org.openscience.cdk.math.Matrix: Copies a matrix.
duplicate() - Method in class org.openscience.cdk.math.Vector: Copy a vector
duplicate(IMatrix) - Method in class org.openscience.cdk.math.IMatrix: Copy a matrix
duplicate(IVector) - Method in class org.openscience.cdk.math.IVector: Copy a vector
Dy - Static variable in interface org.openscience.cdk.interfaces.IElement
DY - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
DynamicFactory - Class in org.openscience.cdk: A factory class for constructing ICDKObject and IChemObject implementations.
DynamicFactory(int) - Constructor for class org.openscience.cdk.DynamicFactory: Create a new default factory with an expected number of registered classes and a default interface provider.
DynamicFactory(DynamicFactory.InterfaceProvider, int) - Constructor for class org.openscience.cdk.DynamicFactory: Create a new default factory with an expected number of registered classes and an interface provider.
DynamicFactory.BasicCreator<T> - Class in org.openscience.cdk: A simple creator that helps in creating an anonymous classes for a creator.
DynamicFactory.ConstructorKey - Class in org.openscience.cdk: A class which encapsulates the information about an interface (of this implementation) and the parameter types of the constructor.
DynamicFactory.CreationModifier<T> - Interface in org.openscience.cdk: An interface that allows posterior modification of an instance after it has been created.
DynamicFactory.Creator<T> - Interface in org.openscience.cdk: An interface that wraps object creation via the DynamicFactory.Creator.create(Object[]) method.
DynamicFactory.DefaultInterfaceProvider - Class in org.openscience.cdk: A default interface provider implementation that simply returns the classes from Class.getInterfaces().
DynamicFactory.InterfaceProvider - Interface in org.openscience.cdk: An interface that can provide which interfaces the given class implements.
Dysprosium - org.openscience.cdk.config.Elements
DYSPROSIUM - Static variable in enum org.openscience.cdk.config.Elements
DYSPROSIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.

E

E - org.openscience.cdk.geometry.cip.CIPTool.CIP_CHIRALITY
E - org.openscience.cdk.interfaces.IBond.Stereo: Indication that this double bond has a E configuration.
E - org.openscience.cdk.renderer.elements.TextGroupElement.Position
E - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
E_OR_Z - org.openscience.cdk.interfaces.IBond.Stereo: Indication that this double bond has a fixed, but unknown E/Z configuration.
E_Z_BY_COORDINATES - org.openscience.cdk.interfaces.IBond.Stereo: Indication that this double bond has a fixed configuration, defined by the 2D and/or 3D coordinates.
EccentricConnectivityIndexDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: A topological descriptor combining distance and adjacency information.
EccentricConnectivityIndexDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor
edgeAdded(GraphEdgeChangeEvent) - Method in class org.openscience.cdk.graph.BiconnectivityInspector: Deprecated.
EdgeBuilder - Class in org.openscience.cdk.smsd.algorithm.vflib.builder: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
EdgeBuilder(NodeBuilder, NodeBuilder, VFBondMatcher) - Constructor for class org.openscience.cdk.smsd.algorithm.vflib.builder.EdgeBuilder: Deprecated.
edgeRemoved(GraphEdgeChangeEvent) - Method in class org.openscience.cdk.graph.BiconnectivityInspector: Deprecated.
edges() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis: Deprecated.
edges() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder: Deprecated.

Returns edges of the query.
edges() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQuery: Deprecated.

Returns edges of the query.
edgeShort() - Static method in class org.openscience.cdk.graph.Cycles: Create a cycle finder which will compute the shortest cycles of each vertex in a molecule.
edgeShort(IAtomContainer) - Static method in class org.openscience.cdk.graph.Cycles: Find the edge short cycles of a molecule.
EffectiveAtomPolarizabilityDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic: Effective polarizability of a heavy atom Parameters for this descriptor: Name Default Description no parameters
EffectiveAtomPolarizabilityDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor: Constructor for the EffectiveAtomPolarizabilityDescriptor object
effectiveCharges(IAtomContainer) - Method in class org.openscience.cdk.forcefield.mmff.Mmff: Assign the effective formal charges used by MMFF in calculating the final partial charge values.
EICOS - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Einsteinium - org.openscience.cdk.config.Elements
EINSTEINIUM - Static variable in enum org.openscience.cdk.config.Elements
EINSTEINIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
EL_ATOM_CONFORMER - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_ATOM_CONFORMER_X - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_ATOM_CONFORMER_XE - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_ATOM_CONFORMER_Y - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_ATOM_CONFORMER_YE - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_ATOM_CONFORMER_Z - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_ATOM_CONFORMER_ZE - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_ATOMBLOCK - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_ATOMINT - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_ATOMINT_AID - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_ATOMINT_VALUE - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_ATOMSCHARGE - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_ATOMSELEMENT - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_BONDBLOCK - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_BONDID1 - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_BONDID2 - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_BONDORDER - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_COORDINATES_AID - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_COORDINATES_AIDE - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_COORDINATESBLOCK - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_ELEMENT - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_PCCOMPOUND - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_PCCOMPOUND_CID - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_PCCOMPOUND_ID - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_PCCOMPOUNDS - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_PCID_ID - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_PCSUBSTANCE - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_PCSUBSTANCE_SID - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_PROPS_BVAL - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_PROPS_FVAL - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_PROPS_INFODATA - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_PROPS_SVAL - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_PROPS_URNLABEL - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_PROPS_URNNAME - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
EL_PROPSBLOCK - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
ElectronContainer - Class in org.openscience.cdk: Base class for entities containing electrons, like bonds, orbitals, lone-pairs.
ElectronContainer - Class in org.openscience.cdk.silent: Base class for entities containing electrons, like bonds, orbitals, lone-pairs.
ElectronContainer() - Constructor for class org.openscience.cdk.ElectronContainer: Constructs an empty ElectronContainer.
ElectronContainer() - Constructor for class org.openscience.cdk.silent.ElectronContainer: Constructs an empty ElectronContainer.
ElectronContainerDiff - Class in org.openscience.cdk.tools.diff: Compares two IChemObject classes.
electronContainers() - Method in class org.openscience.cdk.AtomContainer: Returns an Iterable for looping over all electron containers in this container.
electronContainers() - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns an Iterable for looping over all electron containers in this container.
electronContainers() - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns an Iterable for looping over all electron containers in this container.
electronContainers() - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns an Iterable for looping over all electron containers in this container.
electronContainers() - Method in class org.openscience.cdk.debug.DebugCrystal: Returns an Iterable for looping over all electron containers in this container.
electronContainers() - Method in class org.openscience.cdk.debug.DebugMonomer: Returns an Iterable for looping over all electron containers in this container.
electronContainers() - Method in class org.openscience.cdk.debug.DebugPolymer: Returns an Iterable for looping over all electron containers in this container.
electronContainers() - Method in class org.openscience.cdk.debug.DebugRing: Returns an Iterable for looping over all electron containers in this container.
electronContainers() - Method in class org.openscience.cdk.debug.DebugStrand: Returns an Iterable for looping over all electron containers in this container.
electronContainers() - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Returns an Iterable for looping over all electron containers in this container.
electronContainers() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns an Iterable for looping over all electron containers in this container.
electronContainers() - Method in class org.openscience.cdk.silent.AtomContainer: Returns an Iterable for looping over all electron containers in this container.
electronCount - Variable in class org.openscience.cdk.Association: Number of electrons in the association.
electronCount - Variable in class org.openscience.cdk.ElectronContainer: Number of electrons in the ElectronContainer.
electronCount - Variable in class org.openscience.cdk.isomorphism.matchers.QueryBond: Number of electrons in the ElectronContainer.
electronCount - Variable in class org.openscience.cdk.LonePair: Number of electrons in the lone pair.
electronCount - Variable in class org.openscience.cdk.silent.ElectronContainer: Number of electrons in the ElectronContainer.
electronCount - Variable in class org.openscience.cdk.silent.LonePair: Number of electrons in the lone pair.
electronCount - Variable in class org.openscience.cdk.silent.SingleElectron: Number of electron for this class is defined as one.
electronCount - Variable in class org.openscience.cdk.SingleElectron: Number of electron for this class is defined as one.
ElectronDonation - Class in org.openscience.cdk.aromaticity: Defines an electron donation model for perceiving aromatic systems.
ElectronDonation() - Constructor for class org.openscience.cdk.aromaticity.ElectronDonation
electronegativity() - Method in enum org.openscience.cdk.config.Elements: Electronegativity, symbol χ, is a chemical property that describes the tendency of an atom or a functional group to attract electrons (or electron density) towards itself.
Electronegativity - Class in org.openscience.cdk.charges: Calculation of the electronegativity of orbitals of a molecule by the method Gasteiger based on electronegativity is given by X = a + bq + c(q*q).
Electronegativity() - Constructor for class org.openscience.cdk.charges.Electronegativity: Constructor for the PiElectronegativity object.
Electronegativity(int, int) - Constructor for class org.openscience.cdk.charges.Electronegativity: Constructor for the Electronegativity object.
ElectronImpactNBEReaction - Class in org.openscience.cdk.reaction.type: IReactionProcess which make an electron impact for for Non-Bonding Electron Lost.
ElectronImpactNBEReaction() - Constructor for class org.openscience.cdk.reaction.type.ElectronImpactNBEReaction: Constructor of the ElectronImpactNBEReaction object.
ElectronImpactPDBReaction - Class in org.openscience.cdk.reaction.type: IReactionProcess which make an electron impact for pi-Bond Dissociation.
ElectronImpactPDBReaction() - Constructor for class org.openscience.cdk.reaction.type.ElectronImpactPDBReaction: Constructor of the ElectronImpactPDBReaction object.
ElectronImpactSDBReaction - Class in org.openscience.cdk.reaction.type: IReactionProcess which make an electron impact for Sigma Bond Dissociation.
ElectronImpactSDBReaction() - Constructor for class org.openscience.cdk.reaction.type.ElectronImpactSDBReaction: Constructor of the ElectronImpactSDBReaction object.
electronValency - Variable in class org.openscience.cdk.AtomType: The electron Valency of this atom with CDKConstants.UNSET as default.
electronValency - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom: The electron Valency of this atom with CDKConstants.UNSET as default.
electronValency - Variable in class org.openscience.cdk.silent.AtomType: The electron Valency of this atom with CDKConstants.UNSET as default.
electronWithdrawing(IAtom) - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor.JPlogPCalculator
element() - Method in class org.openscience.cdk.renderer.elements.MarkedElement: Access the element of which the id and classes apply.
Element - Class in org.openscience.cdk: Implements the idea of an element in the periodic table.
Element - Class in org.openscience.cdk.silent: Implements the idea of an element in the periodic table.
Element() - Constructor for class org.openscience.cdk.Element: Constructs an empty Element.
Element() - Constructor for class org.openscience.cdk.silent.Element: Constructs an empty Element.
Element(String) - Constructor for class org.openscience.cdk.Element: Constructs an Element with a given element symbol.
Element(String) - Constructor for class org.openscience.cdk.silent.Element: Constructs an Element with a given element symbol.
Element(String, Integer) - Constructor for class org.openscience.cdk.Element: Constructs an Element with a given element symbol, atomic number and atomic mass.
Element(String, Integer) - Constructor for class org.openscience.cdk.silent.Element: Constructs an Element with a given element symbol, atomic number and atomic mass.
Element(IElement) - Constructor for class org.openscience.cdk.Element: Constructs an empty by copying the symbol, atomic number, flags, and identifier from the given IElement.
Element(IElement) - Constructor for class org.openscience.cdk.silent.Element: Constructs an empty by copying the symbol, atomic number, flags, and identifier from the given IElement.
ELEMENT - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if the atomic number (IElement.getAtomicNumber() ()}) of an atom equals the specified 'value'.
ELEMENT - Static variable in class org.openscience.cdk.libio.jena.CDK
elemental() - Method in class org.openscience.cdk.hash.HashGeneratorMaker: Discriminate elements.
ElementComparator - Class in org.openscience.cdk.tools: Compares elements based on the order commonly used in molecular formula.
ElementComparator() - Constructor for class org.openscience.cdk.tools.ElementComparator
ElementDiff - Class in org.openscience.cdk.tools.diff: Compares two IElement classes.
ElementGroup - Class in org.openscience.cdk.renderer.elements: A group of rendering elements, of any type.
ElementGroup() - Constructor for class org.openscience.cdk.renderer.elements.ElementGroup: Create an empty element group.
ElementRule - Class in org.openscience.cdk.formula.rules: This class validate if the occurrence of the IElements in the IMolecularFormula are into a limits.
ElementRule() - Constructor for class org.openscience.cdk.formula.rules.ElementRule: Constructor for the ElementRule object.
elements - Variable in class org.openscience.cdk.renderer.elements.GeneralPath: The elements in the path.
elements(Class<E>) - Method in interface org.openscience.cdk.renderer.selection.IChemObjectSelection: Returns a Collection of all selected IChemObjects of the given type.
elements(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Get a list of all Elements which are contained molecular.
Elements - Enum in org.openscience.cdk.config: Enumeration of chemical elements.
elementTitle - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
elementType(int) - Method in class org.openscience.cdk.stereo.Stereocenters: Obtain the type of stereo element support for atom at index v.
elid - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
elimination(Matrix, Vector) - Static method in class org.openscience.cdk.math.Matrix: Solves a linear equation system with Gauss elimination.
elsym - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
eltitles - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
embedText(Font, String, Color, double) - Static method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator: Make an embedded text label for display in a CDK renderer.
emit(IAtomContainer) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Emits a molecule to whomever is listening.
EMPTY - Static variable in interface org.openscience.cdk.hash.stereo.StereoEncoder: empty stereo encoder when no stereo can be perceived
EMPTY - Static variable in interface org.openscience.cdk.hash.stereo.StereoEncoderFactory: Empty factory for when stereo encoding is not required
EMPTY_FINGERPRINTS_PROVIDED - Static variable in class org.openscience.cdk.similarity.Tanimoto
EMPTY_ISOTOPE_ARRAY - Static variable in class org.openscience.cdk.config.IsotopeFactory
EMPTY_SELECTION - Static variable in class org.openscience.cdk.renderer.selection.AbstractSelection: Static implementation of an empty selection.
EN - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
enable_tracing() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Enable tracing.
enable_tracing() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser: Enable tracing.
encode(long[], long[]) - Method in interface org.openscience.cdk.hash.stereo.StereoEncoder: Encode one or more stereo elements based on the current invariants.
encode(AtomEncoder) - Method in class org.openscience.cdk.hash.HashGeneratorMaker: Add a custom encoder to the hash generator which will be built.
encode(IAtom, IAtomContainer) - Method in interface org.openscience.cdk.hash.AtomEncoder: Encode an invariant attribute of the given atom.
encodePaths(IAtomContainer, int, BitSet, int) - Method in class org.openscience.cdk.fingerprint.Fingerprinter
endColumn - Variable in class org.openscience.cdk.iupac.parser.Token: The column number of the last character of this Token.
endColumn - Variable in class org.openscience.cdk.smiles.smarts.parser.Token: The column number of the last character of this Token.
endDocument() - Method in class org.openscience.cdk.io.cml.CMLCoreModule
endDocument() - Method in class org.openscience.cdk.io.cml.CMLHandler: Calling this procedure signals the end of the XML document.
endDocument() - Method in interface org.openscience.cdk.io.cml.ICMLModule
endDocument() - Method in class org.openscience.cdk.io.cml.PDBConvention
endDocument() - Method in class org.openscience.cdk.io.inchi.INChIHandler: Deprecated.
endDocument() - Method in class org.openscience.cdk.io.iterator.event.EventCMLHandler: Procedure required by the CDOInterface.
endElement(String, String, String) - Method in class org.openscience.cdk.config.atomtypes.AtomTypeHandler
endElement(String, String, String) - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeHandler
endElement(String, String, String) - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingHandler
endElement(String, String, String) - Method in class org.openscience.cdk.config.isotopes.IsotopeHandler
endElement(String, String, String) - Method in class org.openscience.cdk.dict.DictionaryHandler
endElement(String, String, String) - Method in class org.openscience.cdk.io.cml.CMLHandler
endElement(String, String, String) - Method in class org.openscience.cdk.io.inchi.INChIHandler: Deprecated.
endElement(CMLStack, String, String, String) - Method in class org.openscience.cdk.io.cml.CMLCoreModule
endElement(CMLStack, String, String, String) - Method in class org.openscience.cdk.io.cml.CMLReactionModule
endElement(CMLStack, String, String, String) - Method in interface org.openscience.cdk.io.cml.ICMLModule
endElement(CMLStack, String, String, String) - Method in class org.openscience.cdk.io.cml.JMOLANIMATIONConvention
endElement(CMLStack, String, String, String) - Method in class org.openscience.cdk.io.cml.MDMoleculeConvention: Finish up parsing of elements in mdmolecule.
endElement(CMLStack, String, String, String) - Method in class org.openscience.cdk.io.cml.PDBConvention
endElement(CMLStack, String, String, String) - Method in class org.openscience.cdk.io.cml.QSARConvention
endFunctionalGroups() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Functional groups which occur at the end of the main chain and need a connecting "an".
endLine - Variable in class org.openscience.cdk.iupac.parser.Token: The line number of the last character of this Token.
endLine - Variable in class org.openscience.cdk.smiles.smarts.parser.Token: The line number of the last character of this Token.
endObject(String) - Method in class org.openscience.cdk.io.iterator.event.EventCMLHandler: Procedure required by the CDOInterface.
endsWith(ICMLModule) - Method in class org.openscience.cdk.io.cml.CMLModuleStack: Convenience method to check the last added elements.
endsWith(ICMLModule, ICMLModule) - Method in class org.openscience.cdk.io.cml.CMLModuleStack: Convenience method to check the last two added elements.
endsWith(ICMLModule, ICMLModule, ICMLModule) - Method in class org.openscience.cdk.io.cml.CMLModuleStack: Convenience method to check the last three added elements.
endX - Variable in class org.openscience.cdk.renderer.elements.ArrowElement: X coordinate of the point where the arrow ends.
endY - Variable in class org.openscience.cdk.renderer.elements.ArrowElement: Y coordinate of the point where the arrow ends.
ensemble() - Method in class org.openscience.cdk.hash.HashGeneratorMaker: Given the current configuration create an EnsembleHashGenerator.
EnsembleHashGenerator - Interface in org.openscience.cdk.hash: A hash function which generates a single 64-bit hash code for a set of molecules (ensemble).
enter(Permutation) - Method in class org.openscience.cdk.group.PermutationGroup: Enter the permutation g into this group.
Entry - Class in org.openscience.cdk.dict: Entry in a Dictionary.
Entry() - Constructor for class org.openscience.cdk.dict.Entry
Entry(String) - Constructor for class org.openscience.cdk.dict.Entry
Entry(String, String) - Constructor for class org.openscience.cdk.dict.Entry
EntryReact - Class in org.openscience.cdk.dict: Entry in a Dictionary for reactions.
EntryReact(String) - Constructor for class org.openscience.cdk.dict.EntryReact: Constructor of the EntryReact.
EntryReact(String, String) - Constructor for class org.openscience.cdk.dict.EntryReact: Constructor of the EntryReact.
enumeration() - Method in class org.openscience.cdk.graph.rebond.Bspt
enumHemiSphere(Bspt.Tuple, double) - Method in class org.openscience.cdk.graph.rebond.Bspt
enumNear(Bspt.Tuple, double) - Method in class org.openscience.cdk.graph.rebond.Bspt
enumSphere(Bspt.Tuple, double) - Method in class org.openscience.cdk.graph.rebond.Bspt
EnzymeResidueLocator - Class in org.openscience.cdk: Atom that represents part of an residue in an enzyme, like Arg255.
EnzymeResidueLocator(String) - Constructor for class org.openscience.cdk.EnzymeResidueLocator: Constructs an EnzymeResidueLocator from a String containing the locator.
EnzymeResidueLocator(IAtom) - Constructor for class org.openscience.cdk.EnzymeResidueLocator: Constructs an EnzymeResidueLocator from an existing Atom.
EOF - net.sf.jniinchi.INCHI_RET
EOF - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: End of File.
EOF - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: End of File.
EOL - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
EOL - Static variable in exception org.openscience.cdk.iupac.parser.ParseException: The end of line string for this machine.
EOL - Static variable in exception org.openscience.cdk.smiles.smarts.parser.ParseException: The end of line string for this machine.
EPS_FMT - Static variable in class org.openscience.cdk.depict.Depiction: Encapsulated PostScript (EPS) format key.
equalRowsCheck(int, int[][], Permutation, Permutation) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Comparing two arrays are equal.
equals(Object) - Method in class org.openscience.cdk.Atom
equals(Object) - Method in class org.openscience.cdk.AtomRef
equals(Object) - Method in class org.openscience.cdk.Bond
equals(Object) - Method in class org.openscience.cdk.BondRef
equals(Object) - Method in class org.openscience.cdk.DynamicFactory.ConstructorKey
equals(Object) - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
equals(Object) - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
equals(Object) - Method in class org.openscience.cdk.graph.invariant.GIMatrix: Verifies if two given matrix are equal or not.
equals(Object) - Method in class org.openscience.cdk.group.Partition
equals(Object) - Method in class org.openscience.cdk.group.Permutation
equals(Object) - Method in class org.openscience.cdk.io.formats.AbstractResourceFormat
equals(Object) - Method in class org.openscience.cdk.isomorphism.matchers.Expr
equals(Object) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
equals(Object) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
equals(Object) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
equals(Object) - Method in class org.openscience.cdk.isomorphism.mcss.RMap: The equals method.
equals(Object) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom
equals(Object) - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycle: Deprecated.
equals(Object) - Method in class org.openscience.cdk.silent.Atom
equals(Object) - Method in class org.openscience.cdk.silent.Bond
equals(Object) - Method in class org.openscience.cdk.smiles.InvPair: Check whether this instance equals another instance.
equals(Object) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMap: Deprecated.

The equals method.
equalSetCheck(int[], int[], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Checks two int[] arrays are equal with respect to an atom partition.
equalSetCheck2(int[], int[], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Checks two int[] arrays are equal with respect to an atom partition.
equivalenceClasses() - Method in class org.openscience.cdk.ringsearch.cyclebasis.CycleBasis: Deprecated.

Returns the connected components of this cycle basis, in regard to matroid theory.
equivalenceClasses() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis: Deprecated.
EquivalentClassPartitioner - Class in org.openscience.cdk.graph.invariant: An algorithm for topological symmetry.
EquivalentClassPartitioner() - Constructor for class org.openscience.cdk.graph.invariant.EquivalentClassPartitioner: Constructor for the TopologicalEquivalentClass object.
EquivalentClassPartitioner(IAtomContainer) - Constructor for class org.openscience.cdk.graph.invariant.EquivalentClassPartitioner: Constructor for the TopologicalEquivalentClass object.
Er - Static variable in interface org.openscience.cdk.interfaces.IElement
ER - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Erbium - org.openscience.cdk.config.Elements
ERBIUM - Static variable in enum org.openscience.cdk.config.Elements
ERBIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
error(Object) - Method in interface org.openscience.cdk.tools.ILoggingTool: Shows ERROR output for the Object.
error(Object) - Method in class org.openscience.cdk.tools.SystemOutLoggingTool: Deprecated.

Shows ERROR output for the Object.
error(Object, Object...) - Method in interface org.openscience.cdk.tools.ILoggingTool: Shows ERROR output for the given Object's.
error(Object, Object...) - Method in class org.openscience.cdk.tools.SystemOutLoggingTool: Deprecated.

Shows ERROR output for the given Object's.
error(SAXParseException) - Method in class org.openscience.cdk.io.cml.CMLErrorHandler: Outputs a SAXParseException error to the logger.
ERROR - net.sf.jniinchi.INCHI_RET
ERROR - Static variable in interface org.openscience.cdk.tools.ILoggingTool: Error, and Fatal messages will be emitted.
ERROR_MARKER - Static variable in class org.openscience.cdk.validate.ProblemMarker
errorHandler - Variable in class org.openscience.cdk.io.DefaultChemObjectReader
errorHandler - Variable in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader
Es - Static variable in interface org.openscience.cdk.interfaces.IElement
ES - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
essential() - Static method in class org.openscience.cdk.graph.Cycles: Create a cycle finder which will compute the essential cycles of a molecule.
essential(IAtomContainer) - Static method in class org.openscience.cdk.graph.Cycles: Find the essential cycles of a molecule.
ESSENTIAL_RINGS - Static variable in class org.openscience.cdk.CDKConstants: The essential rings computed for this molecule.
essentialCycles() - Method in class org.openscience.cdk.ringsearch.cyclebasis.CycleBasis: Deprecated.

Returns the essential cycles of this cycle basis.
essentialCycles() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis: Deprecated.
EssentialCycles - Class in org.openscience.cdk.graph: Determine the uniquely defined essential cycles of a graph.
EssentialCycles(int[][]) - Constructor for class org.openscience.cdk.graph.EssentialCycles: Determine the essential cycles given a graph.
EStateAtomTypeMatcher - Class in org.openscience.cdk.atomtype: Determines the EState atom types.
EStateAtomTypeMatcher() - Constructor for class org.openscience.cdk.atomtype.EStateAtomTypeMatcher
EStateFingerprinter - Class in org.openscience.cdk.fingerprint: This fingerprinter generates 79 bit fingerprints using the E-State fragments.
EStateFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.EStateFingerprinter
EStateFragments - Class in org.openscience.cdk.config.fragments: A class representing the 79 E-state atom types in terms of SMARTS.
EStateFragments() - Constructor for class org.openscience.cdk.config.fragments.EStateFragments
estimates - Variable in class org.openscience.cdk.fingerprint.model.Bayesian
ETH - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Eu - Static variable in interface org.openscience.cdk.interfaces.IElement
EU - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Europium - org.openscience.cdk.config.Elements
EUROPIUM - Static variable in enum org.openscience.cdk.config.Elements
EUROPIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
EventCMLHandler - Class in org.openscience.cdk.io.iterator.event: CDO object needed as interface with the JCFL library for reading CML in a event based manner.
EventCMLHandler(DefaultEventChemObjectReader, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.event.EventCMLHandler: Constructs an iterating-abled CDO.
EventCMLReader - Class in org.openscience.cdk.io.iterator.event: Reads a molecule in CML 1.x and 2.0 format.
EventCMLReader(Reader, IReaderListener, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.event.EventCMLReader: Define this CMLReader to take the input from a java.io.Reader class.
EX - Static variable in class org.openscience.cdk.math.Vector: Unary vector in 3 dimensional space
ExactMapping - Class in org.openscience.cdk.smsd.algorithm.mcsplus: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
ExactMapping() - Constructor for class org.openscience.cdk.smsd.algorithm.mcsplus.ExactMapping: Deprecated.
exactMass - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Exact mass of this isotope.
exactMass - Variable in class org.openscience.cdk.Isotope: Exact mass of this isotope.
exactMass - Variable in class org.openscience.cdk.silent.Isotope: Exact mass of this isotope.
exactMasses - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
exclusiveAtoms() - Method in class org.openscience.cdk.isomorphism.Mappings: Filter the mappings for those which cover an exclusive set of atoms in the target.
ExhaustiveFragmenter - Class in org.openscience.cdk.fragment: Generate fragments exhaustively.
ExhaustiveFragmenter() - Constructor for class org.openscience.cdk.fragment.ExhaustiveFragmenter: Instantiate fragmenter with default minimum fragment size.
ExhaustiveFragmenter(int) - Constructor for class org.openscience.cdk.fragment.ExhaustiveFragmenter: Instantiate fragmenter with user specified minimum fragment size.
exhaustStringTokenizer(StringTokenizer) - Method in class org.openscience.cdk.io.MDLV3000Reader
ExpandBuff(boolean) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
ExpandBuff(boolean) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
expectedTokenSequences - Variable in exception org.openscience.cdk.iupac.parser.ParseException: Each entry in this array is an array of integers.
expectedTokenSequences - Variable in exception org.openscience.cdk.smiles.smarts.parser.ParseException: Each entry in this array is an array of integers.
ExplicitAtomExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
ExplicitConnectionAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
ExplicitConnectionAtom(int, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.ExplicitConnectionAtom: Deprecated.

Create a query atom for matching the degree of an atom.
ExplicitConnectivity() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
ExplicitHighAndBond() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
ExplicitHighAndExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
exponentialDouble(double) - Static method in class org.openscience.cdk.math.RandomNumbersTool: Generates a random double from an Exponential distribution with the specified mean value.
Expr - Class in org.openscience.cdk.isomorphism.matchers: A expression stores a predicate tree for checking properties of atoms and bonds.
Expr() - Constructor for class org.openscience.cdk.isomorphism.matchers.Expr: Creates an atom expression that will always match (Expr.Type.TRUE).
Expr(Expr) - Constructor for class org.openscience.cdk.isomorphism.matchers.Expr: Copy-constructor, creates a shallow copy of the provided expression.
Expr(Expr.Type) - Constructor for class org.openscience.cdk.isomorphism.matchers.Expr: Creates an atom expression for the specified primitive.
Expr(Expr.Type, int) - Constructor for class org.openscience.cdk.isomorphism.matchers.Expr: Creates an atom expression for the specified primitive and 'value'.
Expr(Expr.Type, IAtomContainer) - Constructor for class org.openscience.cdk.isomorphism.matchers.Expr: Creates a recursive atom expression.
Expr(Expr.Type, Expr, Expr) - Constructor for class org.openscience.cdk.isomorphism.matchers.Expr: Creates a logical atom expression for the specified.
Expr.Type - Enum in org.openscience.cdk.isomorphism.matchers: Types of expression, for use in the Expr tree object.
ExtAtomContainerManipulator - Class in org.openscience.cdk.smsd.tools: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
ExtAtomContainerManipulator() - Constructor for class org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator: Deprecated.
ExtAttachOrdering - org.openscience.cdk.sgroup.SgroupType
ExtendedAtomGenerator - Class in org.openscience.cdk.renderer.generators: A generator for atoms with mass, charge, etc.
ExtendedAtomGenerator() - Constructor for class org.openscience.cdk.renderer.generators.ExtendedAtomGenerator
ExtendedAtomGenerator.ShowAtomTypeNames - Class in org.openscience.cdk.renderer.generators: Boolean that indicates if atom type names should be given instead of element symbols.
ExtendedAtomGenerator.ShowImplicitHydrogens - Class in org.openscience.cdk.renderer.generators: Boolean that indicates if implicit hydrogens should be depicted.
ExtendedCisTrans - Class in org.openscience.cdk.stereo: Extended Cis/Trans double bond configuration.
ExtendedCisTrans(IBond, IBond[], int) - Constructor for class org.openscience.cdk.stereo.ExtendedCisTrans
ExtendedFingerprinter - Class in org.openscience.cdk.fingerprint: Generates an extended fingerprint for a given IAtomContainer, that extends the Fingerprinter with additional (25) bits describing ring features and isotopic masses.
ExtendedFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.ExtendedFingerprinter: Creates a fingerprint generator of length DEFAULT_SIZE and with a search depth of DEFAULT_SEARCH_DEPTH.
ExtendedFingerprinter(int) - Constructor for class org.openscience.cdk.fingerprint.ExtendedFingerprinter
ExtendedFingerprinter(int, int) - Constructor for class org.openscience.cdk.fingerprint.ExtendedFingerprinter: Constructs a fingerprint generator that creates fingerprints of the given size, using a generation algorithm with the given search depth.
ExtendedTetrahedral - Class in org.openscience.cdk.stereo: Extended tetrahedral configuration.
ExtendedTetrahedral(IAtom, IAtom[], int) - Constructor for class org.openscience.cdk.stereo.ExtendedTetrahedral
ExtendedTetrahedral(IAtom, IAtom[], ITetrahedralChirality.Stereo) - Constructor for class org.openscience.cdk.stereo.ExtendedTetrahedral: Create an extended tetrahedral stereo element for the provided 'focus' and 'peripherals' in the given 'winding'.
extendFormula(String, int, String) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Adding new entry to the new molecular formula
ExternalHighlightColor() - Constructor for class org.openscience.cdk.renderer.RendererModel.ExternalHighlightColor
ExtMulticenter - org.openscience.cdk.sgroup.SgroupType
extractMapping(List<List<Integer>>, List<Integer>, List<Integer>) - Static method in class org.openscience.cdk.smsd.algorithm.mcsplus.ExactMapping: Deprecated.
extractSubstructure(IAtomContainer, int...) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Deprecated.
use AtomContainerManipulator.extractSubstructure(IAtomContainer, Collection) instead
extractSubstructure(IAtomContainer, Collection<IAtom>) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Extract a substructure from a 'source' molecule to the provided destination based on the collection of atoms.
extractTopReactions(IReactionScheme) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator: Extract a set of Reactions which are in top of a IReactionScheme.
extractUniqueRingSystemsFromFile(String) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor
EY - Static variable in class org.openscience.cdk.math.Vector: Unary vector in 3 dimensional space
EZ - Static variable in class org.openscience.cdk.math.Vector: Unary vector in 3 dimensional space

F

F - Static variable in interface org.openscience.cdk.interfaces.IElement
F - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
faculty(int) - Static method in class org.openscience.cdk.tools.SwissArmyKnife: Deprecated.

Calculates the faculty for a given integer.
FALSE - org.openscience.cdk.isomorphism.matchers.Expr.Type: Always returns false.
FancyBoldWedges() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.FancyBoldWedges
FancyHashedWedges() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.FancyHashedWedges
fatal(Object) - Method in interface org.openscience.cdk.tools.ILoggingTool: Shows FATAL output for the Object.
fatal(Object) - Method in class org.openscience.cdk.tools.SystemOutLoggingTool: Deprecated.

Shows FATAL output for the Object.
FATAL - net.sf.jniinchi.INCHI_RET
FATAL - Static variable in interface org.openscience.cdk.tools.ILoggingTool: Only Fatal messages will be emitted.
fatalError(SAXParseException) - Method in class org.openscience.cdk.io.cml.CMLErrorHandler: Outputs as fatal SAXParseException error to the logger.
FB - net.sf.jniinchi.INCHI_OPTION
fBlockMetals() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.
Fe - Static variable in interface org.openscience.cdk.interfaces.IElement
FE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
FenskeHall_ZMatrixFormat - Class in org.openscience.cdk.io.formats
FenskeHall_ZMatrixFormat() - Constructor for class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
Fermium - org.openscience.cdk.config.Elements
FERMIUM - Static variable in enum org.openscience.cdk.config.Elements
FERMIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
fieldVal - Variable in class org.openscience.cdk.io.VASPReader
FiguerasSSSRFinder - Class in org.openscience.cdk.ringsearch: Deprecated.
Use SSSRFinder instead (exact algorithm).
FiguerasSSSRFinder() - Constructor for class org.openscience.cdk.ringsearch.FiguerasSSSRFinder: Deprecated.
fill - Variable in class org.openscience.cdk.renderer.elements.GeneralPath: Fill the shape instead of drawing outline.
fill - Variable in class org.openscience.cdk.renderer.elements.OvalElement: If true, draw the oval as filled.
FillBuff() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
FillBuff() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
fillDegreeListHindexIsTwo(List<int[]>, List<int[]>) - Method in class org.openscience.cdk.structgen.maygen.Maygen
filled - Variable in class org.openscience.cdk.renderer.elements.RectangleElement: If true, the rectangle is drawn as filled.
filter(Predicate<int[]>) - Method in class org.openscience.cdk.isomorphism.Mappings: Filter the mappings and keep only those which match the provided predicate (Guava).
filter(List<List<Integer>>) - Static method in class org.openscience.cdk.smsd.filters.PostFilter: Deprecated.

Creates a new instance of Post Filter and removes redundant mapping(s).
filterAtoms(int, Collection<List<IAtom>>, Collection<IAtom>) - Method in class org.openscience.cdk.smsd.ring.RingFilter: Deprecated.
filterAtoms(IAtomContainer, Collection<IAtom>) - Method in class org.openscience.cdk.smsd.ring.RingFilter: Deprecated.
finalize() - Method in class org.openscience.cdk.io.random.RandomAccessReader
FinalMappings - Class in org.openscience.cdk.smsd.helper: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
FinalMappings() - Constructor for class org.openscience.cdk.smsd.helper.FinalMappings: Deprecated.
find(IAtomContainer) - Method in interface org.openscience.cdk.graph.CycleFinder: Find the cycles of the provided molecule.
find(IAtomContainer, int) - Method in interface org.openscience.cdk.graph.CycleFinder: Find the cycles of the provided molecule.
find(IAtomContainer, int[][], int) - Method in interface org.openscience.cdk.graph.CycleFinder: Find the cycles of the provided molecule when an adjacent relation (graph) is already available.
findAllRings(IAtomContainer) - Method in class org.openscience.cdk.ringsearch.AllRingsFinder: Compute all rings in the given IAtomContainer.
findAllRings(IAtomContainer, int) - Method in class org.openscience.cdk.ringsearch.AllRingsFinder: Compute all rings up to and including the maxRingSize.
findAllRingsInIsolatedRingSystem(IAtomContainer) - Method in class org.openscience.cdk.ringsearch.AllRingsFinder: Compute all rings in the given IAtomContainer.
findAllRingsInIsolatedRingSystem(IAtomContainer, int) - Method in class org.openscience.cdk.ringsearch.AllRingsFinder: Compute all rings up to an including the maxRingSize.
findBonds(IAtomContainer) - Method in class org.openscience.cdk.aromaticity.Aromaticity: Find the bonds of a molecule which this model determined were aromatic.
findCentralBond(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.stereo.ExtendedCisTrans: Locate the central double-bond in a chain of cumulated double bonds.
findChemFormats(int) - Method in class org.openscience.cdk.io.WriterFactory: Finds IChemFormats that provide a container for serialization for the given features.
findClosestByBond(IAtomContainer, IAtom, int) - Static method in class org.openscience.cdk.graph.PathTools: Returns the atoms which are closest to an atom in an AtomContainer by bonds.
findClosestInSpace(IAtomContainer, IAtom, int) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Returns the atoms which are closes to an atom in an AtomContainer by distance in 3d.
findClosestInSpace(IAtomContainer, IAtom, int) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Returns the atoms which are closes to an atom in an AtomContainer by distance in 3d.
findEquivalenceClasses() - Method in class org.openscience.cdk.ringsearch.SSSRFinder: Deprecated.

Finds the "interchangeability" equivalence classes.
findEssentialRings() - Method in class org.openscience.cdk.ringsearch.SSSRFinder: Deprecated.

Finds the Set of Essential Rings.
findGridBoundaries() - Method in class org.openscience.cdk.protein.ProteinPocketFinder: Method determines the minimum and maximum values of a coordinate space up to 3D space.
findHeavyAtomsInChain(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D: Count and find first heavy atom(s) (non Hydrogens) in a chain.
findIdentical(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.Pattern: Create a pattern which can be used to find molecules which are the same as the query structure.
findIdentical(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.VentoFoggia: Create a pattern which can be used to find molecules which are the same as the query structure.
findIdentical(IAtomContainer, AtomMatcher, BondMatcher) - Static method in class org.openscience.cdk.isomorphism.VentoFoggia: Create a pattern which can be used to find molecules which are the same as the query structure.
findIndex(int, Permutation) - Method in class org.openscience.cdk.structgen.maygen.Maygen: With the cycle permutation, mapping the row index to another row in the block.
findMappedBonds(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator: Collect the set of bonds that mapped in both a reactant and a product.
findMatch(int[], int[], int, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Find the matching entries index in compared two rows.
findMatchingAtomType(IAtomContainer, IAtom) - Method in class org.openscience.cdk.atomtype.CDKAtomTypeMatcher: Method that assigns an atom type to a given atom belonging to an atom container.
findMatchingAtomType(IAtomContainer, IAtom) - Method in class org.openscience.cdk.atomtype.EStateAtomTypeMatcher
findMatchingAtomType(IAtomContainer, IAtom) - Method in interface org.openscience.cdk.atomtype.IAtomTypeMatcher: Method that assigns an atom type to a given atom belonging to an atom container.
findMatchingAtomType(IAtomContainer, IAtom) - Method in class org.openscience.cdk.atomtype.MM2AtomTypeMatcher: Deprecated.

Assign the mm2 atom type to a given atom.
findMatchingAtomType(IAtomContainer, IAtom) - Method in class org.openscience.cdk.atomtype.MMFF94AtomTypeMatcher: Deprecated.

Assign the mmff94 atom type to a given atom.
findMatchingAtomType(IAtomContainer, IAtom) - Method in class org.openscience.cdk.atomtype.StructGenMatcher: Finds the AtomType matching the Atom's element symbol, formal charge and hybridization state.
findMatchingAtomType(IAtomContainer, IAtom) - Method in class org.openscience.cdk.atomtype.SybylAtomTypeMatcher: Sybyl atom type perception for a single atom.
findMatchingAtomTypes(IAtomContainer) - Method in class org.openscience.cdk.atomtype.CDKAtomTypeMatcher: Method that assigns atom types to atoms in the given atom container.
findMatchingAtomTypes(IAtomContainer) - Method in class org.openscience.cdk.atomtype.EStateAtomTypeMatcher
findMatchingAtomTypes(IAtomContainer) - Method in interface org.openscience.cdk.atomtype.IAtomTypeMatcher: Method that assigns atom types to atoms in the given atom container.
findMatchingAtomTypes(IAtomContainer) - Method in class org.openscience.cdk.atomtype.MM2AtomTypeMatcher: Deprecated.
findMatchingAtomTypes(IAtomContainer) - Method in class org.openscience.cdk.atomtype.MMFF94AtomTypeMatcher: Deprecated.
findMatchingAtomTypes(IAtomContainer) - Method in class org.openscience.cdk.atomtype.StructGenMatcher
findMatchingAtomTypes(IAtomContainer) - Method in class org.openscience.cdk.atomtype.SybylAtomTypeMatcher: Method that assigns atom types to atoms in the given atom container.
findMaximalIndexInComponent(int[], int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Finding the maximal index in a component to compare with other components.
findPathBetween(Graph, Object, Object) - Static method in class org.openscience.cdk.graph.BFSShortestPath: Deprecated.
findPathes(IAtomContainer, int) - Method in class org.openscience.cdk.fingerprint.Fingerprinter: Deprecated.
Use Fingerprinter.encodePaths(IAtomContainer, int, BitSet, int)
findR(int[], int[], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Finding the R index of a block
findRelevantRings() - Method in class org.openscience.cdk.ringsearch.SSSRFinder: Deprecated.

Finds the Set of Relevant Rings.
findRings(IAtomContainer) - Method in class org.openscience.cdk.smsd.ring.HanserRingFinder: Deprecated.

Returns a collection of rings.
findRings(IAtomContainer) - Method in interface org.openscience.cdk.smsd.ring.RingFinder: Deprecated.

Returns Collection of atoms in Rings based on Hanser Ring Finding method
findSSSR() - Method in class org.openscience.cdk.ringsearch.SSSRFinder: Deprecated.

Finds a Smallest Set of Smallest Rings.
findSSSR(IAtomContainer) - Method in class org.openscience.cdk.ringsearch.FiguerasSSSRFinder: Deprecated.

Finds the Smallest Set of Smallest Rings.
findSubstructure(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.DfPattern: Create a pattern which can be used to find molecules which contain the query structure.
findSubstructure(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.Pattern: Create a pattern which can be used to find molecules which contain the query structure.
findSubstructure(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.Ullmann: Create a pattern which can be used to find molecules which contain the query structure.
findSubstructure(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.VentoFoggia: Create a pattern which can be used to find molecules which contain the query structure.
findSubstructure(IAtomContainer, AtomMatcher, BondMatcher) - Static method in class org.openscience.cdk.isomorphism.VentoFoggia: Create a pattern which can be used to find molecules which contain the query structure.
findTerminalAtoms(IAtomContainer) - Method in class org.openscience.cdk.stereo.ExtendedTetrahedral: Helper method to locate two terminal atoms in a container for this extended tetrahedral element.
findTerminalAtoms(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.stereo.ExtendedTetrahedral: Helper method to locate two terminal atoms in a container for a given focus.
findTerminalAtoms(IAtomContainer, IBond) - Static method in class org.openscience.cdk.stereo.ExtendedCisTrans: Helper method to locate two terminal atoms in a container for this extended Cis/Trans element.
findTopoEquivClass(double[]) - Method in class org.openscience.cdk.graph.invariant.EquivalentClassPartitioner: Find the topological equivalent class for the given weight.
findY(int, int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: For a block index r, calculating its first row index.
findZ(int, int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: For a block index r, calculating its last row index.
findZeros(int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen
Fingerprinter - Class in org.openscience.cdk.fingerprint: Generates a fingerprint for a given AtomContainer.
Fingerprinter() - Constructor for class org.openscience.cdk.fingerprint.Fingerprinter: Creates a fingerprint generator of length DEFAULT_SIZE and with a search depth of DEFAULT_SEARCH_DEPTH.
Fingerprinter(int) - Constructor for class org.openscience.cdk.fingerprint.Fingerprinter
Fingerprinter(int, int) - Constructor for class org.openscience.cdk.fingerprint.Fingerprinter: Constructs a fingerprint generator that creates fingerprints of the given size, using a generation algorithm with the given search depth.
FingerprinterTool - Class in org.openscience.cdk.fingerprint: Tool with helper methods for IFingerprint.
FingerprinterTool() - Constructor for class org.openscience.cdk.fingerprint.FingerprinterTool
FingerprintFormat - Class in org.openscience.cdk.io.formats
FingerprintFormat() - Constructor for class org.openscience.cdk.io.formats.FingerprintFormat
fireChange() - Method in class org.openscience.cdk.renderer.RendererModel: Notifies registered listeners of certain changes that have occurred in this model.
fireFrameRead() - Method in class org.openscience.cdk.io.DefaultChemObjectReader: Sends a frame read event to the registered ReaderListeners.
fireFrameRead() - Method in class org.openscience.cdk.io.iterator.event.DefaultEventChemObjectReader: Sends a frame read event to the registered ReaderListeners.
fireIOSettingQuestion(IOSetting) - Method in class org.openscience.cdk.io.ChemObjectIO: Fires IChemObjectIOListener.processIOSettingQuestion(org.openscience.cdk.io.setting.IOSetting) for all managed listeners.
fireIOSettingQuestion(IOSetting) - Method in class org.openscience.cdk.io.random.DefaultRandomAccessChemObjectReader
first() - Method in interface org.openscience.cdk.io.random.IRandomAccessChemObjectReader
first() - Method in class org.openscience.cdk.io.random.RandomAccessReader
first() - Method in class org.openscience.cdk.isomorphism.Mappings: Obtain the first match - if there is no first match an empty array is returned.
firstIndexOfDifference(Permutation) - Method in class org.openscience.cdk.group.Permutation: Find an r such that this[r] != other[r].
firstIsIdentity() - Method in interface org.openscience.cdk.group.DiscretePartitionRefiner: Check that the first refined partition is the identity.
firstPointX - Variable in class org.openscience.cdk.renderer.elements.LineElement: The x-coordinate of the first point.
firstPointY - Variable in class org.openscience.cdk.renderer.elements.LineElement: The y-coordinate of the first point.
Fischer - org.openscience.cdk.stereo.Projection: Fischer projections are used for linear chain-form carbohydrates.
FitToScreen() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.FitToScreen
fixAromaticBondOrders(IAtomContainer) - Method in class org.openscience.cdk.smiles.DeduceBondSystemTool: Deprecated.

Added missing bond orders based on atom type information.
fixAromaticityForXLogP(IAtomContainer) - Static method in class org.openscience.cdk.tools.CDKUtilities: Deprecated.
FixBondOrdersTool - Class in org.openscience.cdk.smiles: Deprecated.
use Kekulization
FixBondOrdersTool() - Constructor for class org.openscience.cdk.smiles.FixBondOrdersTool: Deprecated.

Constructor for the FixBondOrdersTool object.
FixedH - net.sf.jniinchi.INCHI_OPTION
fixNitroGroups2(IAtomContainer) - Static method in class org.openscience.cdk.tools.CDKUtilities: Deprecated.
fixSmiles(String) - Static method in class org.openscience.cdk.tools.CDKUtilities: Deprecated.
FixSp3Bug - net.sf.jniinchi.INCHI_OPTION
fixSulphurH(IAtomContainer) - Static method in class org.openscience.cdk.tools.CDKUtilities: Deprecated.
Fl - Static variable in interface org.openscience.cdk.interfaces.IElement
FLAG_MASKS - Static variable in class org.openscience.cdk.CDKConstants
FLAVOR_CACTVS - Static variable in class org.openscience.cdk.smarts.Smarts
FLAVOR_CDK - Static variable in class org.openscience.cdk.smarts.Smarts
FLAVOR_CDK_LEGACY - Static variable in class org.openscience.cdk.smarts.Smarts
FLAVOR_DAYLIGHT - Static variable in class org.openscience.cdk.smarts.Smarts
FLAVOR_LOOSE - Static variable in class org.openscience.cdk.smarts.Smarts
FLAVOR_MOE - Static variable in class org.openscience.cdk.smarts.Smarts
FLAVOR_OECHEM - Static variable in class org.openscience.cdk.smarts.Smarts
Flerovium - org.openscience.cdk.config.Elements
FLEROVIUM - Static variable in enum org.openscience.cdk.config.Elements
flipCoin(double) - Static method in class org.openscience.cdk.math.RandomNumbersTool: Returns a boolean value based on a biased coin toss.
Fluorine - org.openscience.cdk.config.Elements
FLUORINE - Static variable in enum org.openscience.cdk.config.Elements
FLUORO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
flush() - Method in class org.openscience.cdk.io.SDFWriter
Fm - Static variable in interface org.openscience.cdk.interfaces.IElement
FM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
FMFDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: An implementation of the FMF descriptor characterizing complexity of a molecule.
FMFDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor
focus() - Method in class org.openscience.cdk.stereo.ExtendedTetrahedral: The central atom in the cumulated system.
fontManager - Variable in class org.openscience.cdk.renderer.AbstractRenderer: Font managers change the font size depending on the zoom.
FontName() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.FontName
forAny() - Static method in class org.openscience.cdk.isomorphism.AtomMatcher: Atoms are always compatible.
forAny() - Static method in class org.openscience.cdk.isomorphism.BondMatcher: All bonds are compatible.
forAtoms() - Static method in class org.openscience.cdk.group.PartitionRefinement
forBonds() - Method in class org.openscience.cdk.group.PartitionRefinement
ForceDelocalisedBondDisplay() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.ForceDelocalisedBondDisplay
ForceFieldConfigurator - Class in org.openscience.cdk.modeling.builder3d: Reads in a force field configuration file, set the atom types into a vector, and the data into a hashtable Therefore, it uses the class MM2BasedParameterSetReader.
ForceFieldConfigurator() - Constructor for class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator: Constructor for the ForceFieldConfigurator object
ForegroundColor() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ForegroundColor
forElement() - Static method in class org.openscience.cdk.isomorphism.AtomMatcher: Atoms are compatible if they are the same element.
FORMAL_CHARGE - org.openscience.cdk.hash.BasicAtomEncoder: Encode the formal charge of an atom, allowing distinction of different protonation states.
FORMAL_CHARGE - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if the formal charge (IAtomType.getFormalCharge()) of an atom equals the specified 'value'.
formalCharge - Variable in class org.openscience.cdk.AtomType: The formal charge of the atom with CDKConstants.UNSET as default.
formalCharge - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom: The formal charge of the atom with CDKConstants.UNSET as default.
formalCharge - Variable in class org.openscience.cdk.renderer.elements.AtomSymbolElement: The formal charge.
formalCharge - Variable in class org.openscience.cdk.silent.AtomType: The formal charge of the atom with CDKConstants.UNSET as default.
FormalChargeAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
FormalChargeAtom(int, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.FormalChargeAtom: Deprecated.

Creates a new instance
formalCharges - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
formalNeighbourCount - Variable in class org.openscience.cdk.AtomType: The formal number of neighbours this atom type can have with CDKConstants_UNSET as default.
formalNeighbourCount - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom: The formal number of neighbours this atom type can have with CDKConstants_UNSET as default.
formalNeighbourCount - Variable in class org.openscience.cdk.silent.AtomType: The formal number of neighbours this atom type can have with CDKConstants_UNSET as default.
format() - Method in class org.openscience.cdk.io.formats.IChemFormatMatcher.MatchResult: What was the format which matched if there was a match (IChemFormatMatcher.MatchResult.matched()).
format(char) - Method in class org.openscience.cdk.tools.FormatStringBuffer: Format a char.
format(double) - Method in class org.openscience.cdk.tools.FormatStringBuffer: Format a double.
format(float) - Method in class org.openscience.cdk.tools.FormatStringBuffer: Format a float.
format(int) - Method in class org.openscience.cdk.tools.FormatStringBuffer: Format a float.
format(long) - Method in class org.openscience.cdk.tools.FormatStringBuffer: Format a float.
format(String) - Method in class org.openscience.cdk.tools.FormatStringBuffer: Format a String.
formatCount() - Method in class org.openscience.cdk.io.WriterFactory
FormatFactory - Class in org.openscience.cdk.io: A factory for recognizing chemical file formats.
FormatFactory() - Constructor for class org.openscience.cdk.io.FormatFactory: Constructs a ReaderFactory which tries to detect the format in the first 65536 chars.
FormatFactory(int) - Constructor for class org.openscience.cdk.io.FormatFactory: Constructs a ReaderFactory which tries to detect the format in the first given number of chars.
formatMDLFloat(float) - Static method in class org.openscience.cdk.io.MDLV2000Writer: Formats a float to fit into the connectiontable and changes it to a String.
formatMDLInt(int, int) - Static method in class org.openscience.cdk.io.MDLV2000Writer: Formats an integer to fit into the connection table and changes it to a String.
formatMDLString(String, int) - Static method in class org.openscience.cdk.io.MDLV2000Writer: Formats a String to fit into the connectiontable.
FormatStringBuffer - Class in org.openscience.cdk.tools: A class for formatting output similar to the C printf command.
FormatStringBuffer(String) - Constructor for class org.openscience.cdk.tools.FormatStringBuffer: Create a new FormatStringBuffer.
formula - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
FORMULA - Static variable in class org.openscience.cdk.CDKConstants: The Molecular Formula Identifier.
formulaCounter - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
formulaGenerator - Variable in class org.openscience.cdk.formula.MolecularFormulaGenerator: The chosen implementation
forOrder() - Static method in class org.openscience.cdk.isomorphism.BondMatcher: Bonds are compatible if they are both aromatic or their orders are equal.
forQuery() - Static method in class org.openscience.cdk.isomorphism.AtomMatcher: Atoms are compatible if the second atom (atom2) is accepted by the IQueryAtom, atom1.
forQuery() - Static method in class org.openscience.cdk.isomorphism.BondMatcher: Bonds are compatible if the first bond1 (an IQueryBond) matches the second, bond2.
forStrictOrder() - Static method in class org.openscience.cdk.isomorphism.BondMatcher: Bonds are compatible if they are both aromatic or their orders are equal and they are non-aromatic.
FortranFormat - Class in org.openscience.cdk.math: Converts a String representation of a Fortran double to a double.
FortranFormat() - Constructor for class org.openscience.cdk.math.FortranFormat
forVectorGraphics(Graphics2D) - Static method in class org.openscience.cdk.renderer.visitor.AWTDrawVisitor: Create a draw visitor that will be rendering to a vector graphics output.
forward(IAtomContainer, String[], int[][], int[], int[], int[], int[][], boolean[], int[], boolean[], int[], List<ArrayList<Permutation>>, int[], int[], int[], int[], int[], int[][][], int[][][], int[][][], int[][], int[][], boolean[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Setting successor indices entry if there is a possible filling.
forward(IAtomContainer, String[], int, int, int, int, int, int[][], int[], int[], int[][], boolean[], int[], boolean[], int[], List<ArrayList<Permutation>>, int[], int[], int[], int[], int[], int[][][], int[][][], int[][][], int[][], int[][], boolean[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen
FORWARD - org.openscience.cdk.interfaces.IReaction.Direction: Reaction equilibrium which is (almost) fully on the product side.
FOUR_SHAPE - org.openscience.cdk.stereo.StereoTool.SquarePlanarShape
FourierGridBasis - Class in org.openscience.cdk.math.qm: At this time this class does not work correcly.
FourierGridBasis(int, double, double, IFunction) - Constructor for class org.openscience.cdk.math.qm.FourierGridBasis
FP(int, int, int[]) - Constructor for class org.openscience.cdk.fingerprint.CircularFingerprinter.FP
FP_SIZE - Static variable in class org.openscience.cdk.fingerprint.PubchemFingerprinter: Number of bits in this fingerprint.
Fr - Static variable in interface org.openscience.cdk.interfaces.IElement
FR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
FractionalCSP3Descriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: An implementation of the Fractional CSP3 descriptor described in [Lovering, Frank et. al.. J. Med. Chem.. 2009. 52].
FractionalCSP3Descriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.FractionalCSP3Descriptor
fractionalPoint3d - Variable in class org.openscience.cdk.Atom: A 3 point specifying the location of this atom in a crystal unit cell.
fractionalPoint3d - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom: A 3 point specifying the location of this atom in a crystal unit cell.
fractionalPoint3d - Variable in class org.openscience.cdk.silent.Atom: A 3 point specifying the location of this atom in a crystal unit cell.
FractionalPSADescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Polar surface area expressed as a ratio to molecular size.
FractionalPSADescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor
fractionalToCartesian(Vector3d, Vector3d, Vector3d, Point3d) - Static method in class org.openscience.cdk.geometry.CrystalGeometryTools
fractionalToCartesian(ICrystal) - Static method in class org.openscience.cdk.geometry.CrystalGeometryTools: Creates Cartesian coordinates for all Atoms in the Crystal.
FragmentAtom - Class in org.openscience.cdk: Class to represent an IPseudoAtom which embeds an IAtomContainer.
FragmentAtom - Class in org.openscience.cdk.silent: Class to represent an IPseudoAtom which embeds an IAtomContainer.
FragmentAtom() - Constructor for class org.openscience.cdk.FragmentAtom
FragmentAtom() - Constructor for class org.openscience.cdk.silent.FragmentAtom
FragmentComplexityDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Class that returns the complexity of a system.
FragmentComplexityDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor: Constructor for the FragmentComplexityDescriptor object.
FragmentUtils - Class in org.openscience.cdk.fragment: Helper methods for fragmentation algorithms.
FragmentUtils() - Constructor for class org.openscience.cdk.fragment.FragmentUtils
frags - Variable in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
frameRead(ReaderEvent) - Method in interface org.openscience.cdk.io.listener.IReaderListener: Indicates that a new frame has been read.
frameRead(ReaderEvent) - Method in class org.openscience.cdk.io.listener.PropertiesListener
frameRead(ReaderEvent) - Method in class org.openscience.cdk.io.listener.SwingGUIListener
frameRead(ReaderEvent) - Method in class org.openscience.cdk.io.listener.TextGUIListener
Francium - org.openscience.cdk.config.Elements
FRANCIUM - Static variable in enum org.openscience.cdk.config.Elements
FRANCIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
FREE_RADICALS - org.openscience.cdk.hash.BasicAtomEncoder: Encode the orbital hybridization of an atom.
from(int) - Method in class org.openscience.cdk.graph.AllPairsShortestPaths: Access the shortest paths object for provided start vertex.
from(IAtom) - Method in class org.openscience.cdk.graph.AllPairsShortestPaths: Access the shortest paths object for provided start atom.
fromRotationMatrix(Matrix) - Static method in class org.openscience.cdk.math.Quaternion
fromSignatureString(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.signature.MoleculeSignature: Builder for molecules (rather, for atom containers) from signature strings.
fromString(String) - Static method in class org.openscience.cdk.group.Partition: Parse a string like "[0,2|1,3]" to form the partition; cells are separated by '|' characters and elements within the cell by commas.
FULL - org.openscience.cdk.geometry.GeometryTools.CoordinateCoverage: Deprecated.

All atoms have coordinates.
FULL - org.openscience.cdk.geometry.GeometryUtil.CoordinateCoverage: All atoms have coordinates.
functionalGroupPrefix() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

The functional group part of the prefix
FURAN_RING - Static variable in class org.openscience.cdk.tools.AtomTypeTools
fused() - Method in interface org.openscience.cdk.ringsearch.CyclicVertexSearch: Construct the sets of vertices which belong to fused cycle systems (share at least one edge).
fused() - Method in class org.openscience.cdk.ringsearch.RingSearch: Construct the sets of vertices which belong to fused ring systems.
fusedRingFragments() - Method in class org.openscience.cdk.ringsearch.RingSearch: Construct a list of IAtomContainers which only contain fused rings.

G

G - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Ga - Static variable in interface org.openscience.cdk.interfaces.IElement
GA - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Gadolinium - org.openscience.cdk.config.Elements
GADOLINIUM - Static variable in enum org.openscience.cdk.config.Elements
GADOLINIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Gallium - org.openscience.cdk.config.Elements
GALLIUM - Static variable in enum org.openscience.cdk.config.Elements
GALLIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
GamessFormat - Class in org.openscience.cdk.io.formats: See here.
GamessFormat() - Constructor for class org.openscience.cdk.io.formats.GamessFormat
GamessReader - Class in org.openscience.cdk.io: A reader for GAMESS log file.
GamessReader() - Constructor for class org.openscience.cdk.io.GamessReader
GamessReader(InputStream) - Constructor for class org.openscience.cdk.io.GamessReader
GamessReader(Reader) - Constructor for class org.openscience.cdk.io.GamessReader: Constructs a new "GamessReader" object given a "Reader" object as input.
GasteigerMarsiliPartialCharges - Class in org.openscience.cdk.charges: The calculation of the Gasteiger Marsili (PEOE) partial charges is based on [Gasteiger, J. and Marsili, M.. Tetrahedron. 1980. 36].
GasteigerMarsiliPartialCharges() - Constructor for class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges: Constructor for the GasteigerMarsiliPartialCharges object.
GasteigerPEPEPartialCharges - Class in org.openscience.cdk.charges: The calculation of the Gasteiger (PEPE) partial charges is based on [Saller, H., Quantitative Emperische Modelle fur Elektronische Effekte in Pi-Systemen und fur die Chemische Reaktivitat, 1985, ?Institute?].
GasteigerPEPEPartialCharges() - Constructor for class org.openscience.cdk.charges.GasteigerPEPEPartialCharges: Constructor for the GasteigerPEPEPartialCharges object.
Gaussian03Format - Class in org.openscience.cdk.io.formats: See here.
Gaussian03Format() - Constructor for class org.openscience.cdk.io.formats.Gaussian03Format
Gaussian03Reader - Class in org.openscience.cdk.io: A reader for Gaussian03 output.
Gaussian03Reader() - Constructor for class org.openscience.cdk.io.Gaussian03Reader
Gaussian03Reader(InputStream) - Constructor for class org.openscience.cdk.io.Gaussian03Reader
Gaussian03Reader(Reader) - Constructor for class org.openscience.cdk.io.Gaussian03Reader
Gaussian90Format - Class in org.openscience.cdk.io.formats
Gaussian90Format() - Constructor for class org.openscience.cdk.io.formats.Gaussian90Format
Gaussian92Format - Class in org.openscience.cdk.io.formats
Gaussian92Format() - Constructor for class org.openscience.cdk.io.formats.Gaussian92Format
Gaussian94Format - Class in org.openscience.cdk.io.formats
Gaussian94Format() - Constructor for class org.openscience.cdk.io.formats.Gaussian94Format
Gaussian95Format - Class in org.openscience.cdk.io.formats
Gaussian95Format() - Constructor for class org.openscience.cdk.io.formats.Gaussian95Format
Gaussian98Format - Class in org.openscience.cdk.io.formats
Gaussian98Format() - Constructor for class org.openscience.cdk.io.formats.Gaussian98Format
Gaussian98Reader - Class in org.openscience.cdk.io: A reader for Gaussian98 output.
Gaussian98Reader() - Constructor for class org.openscience.cdk.io.Gaussian98Reader: Constructor for the Gaussian98Reader object
Gaussian98Reader(InputStream) - Constructor for class org.openscience.cdk.io.Gaussian98Reader
Gaussian98Reader(Reader) - Constructor for class org.openscience.cdk.io.Gaussian98Reader: Create an Gaussian98 output reader.
gaussianDouble(double) - Static method in class org.openscience.cdk.math.RandomNumbersTool: Generates a random double from a Gaussian distribution with the specified deviation.
gaussianFloat(float) - Static method in class org.openscience.cdk.math.RandomNumbersTool: Generates a random float from a Gaussian distribution with the specified deviation.
GaussianInputFormat - Class in org.openscience.cdk.io.formats: See here.
GaussianInputFormat() - Constructor for class org.openscience.cdk.io.formats.GaussianInputFormat
GaussianInputWriter - Class in org.openscience.cdk.io.program: File writer thats generates input files for Gaussian calculation jobs.
GaussianInputWriter() - Constructor for class org.openscience.cdk.io.program.GaussianInputWriter
GaussianInputWriter(OutputStream) - Constructor for class org.openscience.cdk.io.program.GaussianInputWriter
GaussianInputWriter(Writer) - Constructor for class org.openscience.cdk.io.program.GaussianInputWriter: Constructs a new writer that produces input files to run a Gaussian QM job.
GaussiansBasis - Class in org.openscience.cdk.math.qm: This class contains the information to use gauss function as a base for calculation of quantum mechanics.
GaussiansBasis() - Constructor for class org.openscience.cdk.math.qm.GaussiansBasis
GaussiansBasis(int[], int[], int[], double[], Vector[], IAtom[]) - Constructor for class org.openscience.cdk.math.qm.GaussiansBasis: Set up basis with gauss funktions f(x,y,z) = (x-rx)^nx * (y-ry)^ny * (z-rz)^nz * exp(-alpha*(r-ri)^2).
GaussJordan() - Method in class org.openscience.cdk.graph.invariant.GIMatrix: Gauss-Jordan algorithm.
Gd - Static variable in interface org.openscience.cdk.interfaces.IElement
GD - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Ge - Static variable in interface org.openscience.cdk.interfaces.IElement
GE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
GeneralPath - Class in org.openscience.cdk.renderer.elements: A path of rendering elements from the elements.path package.
GeneralPath(List<PathElement>, Color) - Constructor for class org.openscience.cdk.renderer.elements.GeneralPath: Make a path from a list of path elements.
generate() - Method in class org.openscience.cdk.structgen.SingleStructureRandomGenerator: Generates a random structure based on the atoms in the given IAtomContainer.
generate(double) - Method in class org.openscience.cdk.formula.MassToFormulaTool: Deprecated.

Method that actually does the work of extracting the molecular formula.
generate(int[]) - Method in class org.openscience.cdk.smarts.SmartsFragmentExtractor: Generate a SMARTS for the substructure formed of the provided atoms.
generate(String) - Static method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Parses the chemical name and returns the built molecule.
generate(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Parses the chemical name and returns the built molecule.
generate(Set<IAtomContainer>) - Method in interface org.openscience.cdk.hash.EnsembleHashGenerator: Generate invariant 64-bit hash code for an ensemble of molecules.
generate(IAtomContainer) - Method in class org.openscience.cdk.depict.Abbreviations: Find all enabled abbreviations in the provided molecule.
generate(IAtomContainer) - Method in interface org.openscience.cdk.hash.AtomHashGenerator: Generate invariant 64-bit hash codes for the atoms of the molecule.
generate(IAtomContainer) - Method in interface org.openscience.cdk.hash.MoleculeHashGenerator: Generate invariant 64-bit hash code for a molecule.
generate(IAtomContainer) - Static method in class org.openscience.cdk.smarts.Smarts: Generate a SMARTS string from the provided molecule.
generate(IAtomContainer, String[], int[], int[], int[][], int[], boolean[], int[], List<ArrayList<Permutation>>, int[], int[], int[], int[], int[], int[][], int[][], boolean[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Initialization of global variables for the generate of structures for given degree list.
generate(IAtomContainer, Map<IAtom, Integer>) - Method in class org.openscience.cdk.depict.Abbreviations: Find all enabled abbreviations in the provided molecule.
generate(IAtomContainer, IAtom, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator: Generate the rendering element(s) for a particular atom.
generate(IAtomContainer, IAtom, RendererModel) - Method in class org.openscience.cdk.renderer.generators.ExtendedAtomGenerator: Generate the rendering element(s) for a particular atom.
generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.AtomContainerBoundsGenerator: Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.AtomNumberGenerator: Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator: Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator: Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicGenerator: Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator: Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.HighlightGenerator: Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.LonePairGenerator: Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.RadicalGenerator: Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator: Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IAtomContainerSet) - Method in class org.openscience.cdk.structgen.stochastic.PartialFilledStructureMerger: Randomly generates a single, connected, correctly bonded structure from a number of fragments.
generate(IBond, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator: Generate rendering element(s) for the current bond, including ring elements if this bond is part of a ring.
generate(IReaction, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BoundsGenerator: Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IReaction, RendererModel) - Method in class org.openscience.cdk.renderer.generators.MappingGenerator: Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IReaction, RendererModel) - Method in class org.openscience.cdk.renderer.generators.ProductsBoxGenerator: Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IReaction, RendererModel) - Method in class org.openscience.cdk.renderer.generators.ReactantsBoxGenerator: Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IReaction, RendererModel) - Method in class org.openscience.cdk.renderer.generators.ReactionArrowGenerator: Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IReaction, RendererModel) - Method in class org.openscience.cdk.renderer.generators.ReactionBoxGenerator: Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IReaction, RendererModel) - Method in class org.openscience.cdk.renderer.generators.ReactionPlusGenerator: Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IReaction, RendererModel) - Method in class org.openscience.cdk.renderer.generators.ReactionSceneGenerator: Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(T, RendererModel) - Method in interface org.openscience.cdk.renderer.generators.IGenerator: Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate3DCoordinates(IAtomContainer, boolean) - Method in class org.openscience.cdk.modeling.builder3d.ModelBuilder3D: Generate 3D coordinates with force field information.
generateAtom(Expr) - Static method in class org.openscience.cdk.smarts.Smarts: Utility to generate an atom expression.
generateAtomContainerFromInchi(IChemObjectBuilder) - Method in class org.openscience.cdk.inchi.InChIToStructure: Gets structure from InChI, and converts InChI library data structure into an IAtomContainer.
generateBond(IBond, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator: Generate stereo or bond elements for this bond.
generateBond(Expr) - Static method in class org.openscience.cdk.smarts.Smarts: Utility to generate a bond expression.
generateBondElement(IBond, IBond.Order, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator: Generate a LineElement or an ElementGroup of LineElements for this bond.
generateBondElement(IBond, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator: Generate rendering elements for a bond, without ring elements but considering the type of the bond (single, double, triple).
generateCompactElement(IAtom, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator: Generate a compact element for an atom, such as a circle or a square, rather than text element.
GenerateCompatibilityGraph - Class in org.openscience.cdk.smsd.algorithm.mcsplus: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
GenerateCompatibilityGraph() - Constructor for class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph: Deprecated.

Default constructor added
GenerateCompatibilityGraph(IAtomContainer, IAtomContainer, boolean) - Constructor for class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph: Deprecated.

Generates a compatibility graph between two molecules
generateCoordinates() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator: The main method of this StructurDiagramGenerator.
generateCoordinates(Vector2d) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator: The main method of this StructurDiagramGenerator.
generateCoordinates(IAtomContainer) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator: Convenience method for generating 2D coordinates.
generateCoordinates(IReaction) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator: Convenience method to generate 2D coordinates for a reaction.
generateCSetCopy(int, List<String>) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks: Deprecated.
generateCTabCopy(IAtomContainer) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks: Deprecated.
generateDiagram(IAtomContainerSet) - Method in class org.openscience.cdk.renderer.MoleculeSetRenderer: The main method of the renderer, that uses each of the generators to create a different set of IRenderingElements grouped together into a tree.
generateDiagram(IReaction) - Method in class org.openscience.cdk.renderer.ReactionRenderer: The main method of the renderer, that uses each of the generators to create a different set of IRenderingElements grouped together into a tree.
generateDiagram(T) - Method in class org.openscience.cdk.renderer.AbstractRenderer: The main method of the renderer, that uses each of the generators to create a different set of IRenderingElements grouped together into a tree.
generateDiagram(T) - Method in interface org.openscience.cdk.renderer.IRenderer: Internal method to generate the intermediate format.
generateElement(IAtom, int, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator: Generate an atom symbol element.
generateExperimentalCoordinates() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator: Deprecated.
use StructureDiagramGenerator.generateCoordinates()
generateExperimentalCoordinates(Vector2d) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator: Deprecated.
use StructureDiagramGenerator.generateCoordinates()
generateFormulae(List<String>, List<String>, Map<String, Integer[]>, String, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Formulae generator for each element ranges
generateFragments(IAtomContainer) - Method in class org.openscience.cdk.fragment.ExhaustiveFragmenter: Generate fragments for the input molecule.
generateFragments(IAtomContainer) - Method in interface org.openscience.cdk.fragment.IFragmenter: Generate fragments for the input molecule.
generateFragments(IAtomContainer) - Method in class org.openscience.cdk.fragment.MurckoFragmenter: Perform the fragmentation procedure.
generateGrid() - Method in class org.openscience.cdk.tools.GridGenerator: Main method creates a grid between given boundaries (dimensions).
generateInnerElement(IBond, IRing, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator: Make the inner ring bond, which is slightly shorter than the outer bond.
generateMoments(IAtomContainer) - Static method in class org.openscience.cdk.similarity.DistanceMoment: Evaluate the 12 descriptors used to characterize the 3D shape of a molecule.
generateOnSmMat() - Method in class org.openscience.cdk.structgen.maygen.Maygen: Building an OnSm molecule for a given total number of atoms.
generateOrderEle() - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Returns the Elements ordered according to (approximate) probability of occurrence.
generateParseException() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Generate ParseException.
generateParseException() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser: Generate ParseException.
generateRingElements(IBond, IRing, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator: Generate ring elements, such as inner-ring bonds or ring stereo elements.
generateRingElements(IBond, IRing, RendererModel) - Method in class org.openscience.cdk.renderer.generators.RingGenerator: Generate ring elements, such as inner-ring bonds or ring stereo elements.
generators - Variable in class org.openscience.cdk.renderer.AbstractRenderer: Generators for diagram elements.
generic() - Static method in class org.openscience.cdk.smiles.SmilesGenerator: Create a generator for generic SMILES.
Generic - Static variable in class org.openscience.cdk.smiles.SmiFlavor: Output non-canonical SMILES without stereochemistry, atomic masses.
geometricCenterAllPlacedAtoms(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D: Calculates the geometric center of all placed atoms in the atomcontainer.
GeometricCumulativeDoubleBondFactory - Class in org.openscience.cdk.hash.stereo: Stereo encoder factory for 2D and 3D cumulative double bonds.
GeometricCumulativeDoubleBondFactory() - Constructor for class org.openscience.cdk.hash.stereo.GeometricCumulativeDoubleBondFactory
GeometricDoubleBondEncoderFactory - Class in org.openscience.cdk.hash.stereo: A stereo encoder factory encoding double bond configurations by 2D and 3D coordinates.
GeometricDoubleBondEncoderFactory() - Constructor for class org.openscience.cdk.hash.stereo.GeometricDoubleBondEncoderFactory
GeometricTetrahedralEncoderFactory - Class in org.openscience.cdk.hash.stereo: A stereo encoder factory for tetrahedral centres.
GeometricTetrahedralEncoderFactory() - Constructor for class org.openscience.cdk.hash.stereo.GeometricTetrahedralEncoderFactory
Geometry3DValidator - Class in org.openscience.cdk.validate: Validates the 3D geometry of the model.
Geometry3DValidator() - Constructor for class org.openscience.cdk.validate.Geometry3DValidator
GeometryTools - Class in org.openscience.cdk.geometry: Deprecated.
use GeometryUtil moved for dependency reorganisation
GeometryTools() - Constructor for class org.openscience.cdk.geometry.GeometryTools: Deprecated.
GeometryTools.CoordinateCoverage - Enum in org.openscience.cdk.geometry: Deprecated.

Provides the coverage of coordinates for this molecule.
GeometryUtil - Class in org.openscience.cdk.geometry: A set of static utility classes for geometric calculations and operations.
GeometryUtil.CoordinateCoverage - Enum in org.openscience.cdk.geometry: Provides the coverage of coordinates for this molecule.
GERMAINIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Germanium - org.openscience.cdk.config.Elements
GERMANIUM - Static variable in enum org.openscience.cdk.config.Elements
get(int) - Method in class org.openscience.cdk.ConformerContainer: Get the conformer at a specified position.
get(int) - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
get(int) - Method in interface org.openscience.cdk.fingerprint.IBitFingerprint: Returns the value of the bit with the specified index.
get(int) - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
get(int) - Method in class org.openscience.cdk.group.DisjointSetForest: Get the value of the forest at this index - note that this will not necessarily give the set for that element : use DisjointSetForest.getSets() after union-ing elements.
get(int) - Method in class org.openscience.cdk.group.Permutation: Get the value at this index.
get(int) - Method in class org.openscience.cdk.qsar.result.DoubleArrayResult: The first double is at index = 0;
get(int) - Method in class org.openscience.cdk.qsar.result.IntegerArrayResult: The first int is at index = 0.
get(int, int) - Method in class org.openscience.cdk.graph.GraphUtil.EdgeToBondMap: Access the bond store at the end points v and w.
get(int, int) - Method in class org.openscience.cdk.group.PermutationGroup: Get one of the permutations that make up the compact representation.
get(Class<T>) - Method in class org.openscience.cdk.renderer.RendererModel: Returns the IGeneratorParameter for the active IRenderer.
get(String) - Method in class org.openscience.cdk.io.setting.SettingManager: Access the setting stored for given name.
get(String, Class<S>) - Method in class org.openscience.cdk.io.setting.SettingManager: Convenience method that allows specification of return ISetting type so that you can nest the call to access the setting value.
get(IAtom) - Static method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom
get(IBond) - Static method in class org.openscience.cdk.pharmacophore.PharmacophoreBond
get2DCenter() - Method in class org.openscience.cdk.Bond: Returns the geometric 2D center of the bond.
get2DCenter() - Method in class org.openscience.cdk.BondRef: Returns the geometric 2D center of the bond.
get2DCenter() - Method in class org.openscience.cdk.debug.DebugBond: Returns the geometric 2D center of the bond.
get2DCenter() - Method in interface org.openscience.cdk.interfaces.IBond: Returns the geometric 2D center of the bond.
get2DCenter() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Returns the geometric 2D center of the query bond.
get2DCenter() - Method in class org.openscience.cdk.silent.Bond: Returns the geometric 2D center of the bond.
get2DCenter(Iterable<IAtom>) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Calculates the center of the given atoms and returns it as a Point2d.
get2DCenter(Iterable<IAtom>) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Calculates the center of the given atoms and returns it as a Point2d.
get2DCenter(Iterator<IAtom>) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Calculates the center of the given atoms and returns it as a Point2d.
get2DCenter(Iterator<IAtom>) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Calculates the center of the given atoms and returns it as a Point2d.
get2DCenter(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Returns the geometric center of all the atoms in the atomContainer.
get2DCenter(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Returns the geometric center of all the atoms in the atomContainer.
get2DCenter(IRingSet) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Returns the geometric center of all the rings in this ringset.
get2DCenter(IRingSet) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Returns the geometric center of all the rings in this ringset.
get2DCentreOfMass(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Calculates the center of mass for the Atoms in the AtomContainer for the 2D coordinates.
get2DCentreOfMass(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Calculates the center of mass for the Atoms in the AtomContainer for the 2D coordinates.
get2DCoordinateCoverage(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Determines the coverage of this IAtomContainer's 2D coordinates.
get2DCoordinateCoverage(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Determines the coverage of this IAtomContainer's 2D coordinates.
get2DDimension(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Returns the java.awt.Dimension of a molecule.
get2DDimension(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Returns the dimension of a molecule (width/height).
get3DCenter() - Method in class org.openscience.cdk.Bond: Returns the geometric 3D center of the bond.
get3DCenter() - Method in class org.openscience.cdk.BondRef: Returns the geometric 3D center of the bond.
get3DCenter() - Method in class org.openscience.cdk.debug.DebugBond: Returns the geometric 3D center of the bond.
get3DCenter() - Method in interface org.openscience.cdk.interfaces.IBond: Returns the geometric 3D center of the bond.
get3DCenter() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Returns the geometric 3D center of the query bond.
get3DCenter() - Method in class org.openscience.cdk.silent.Bond: Returns the geometric 3D center of the bond.
get3DCenter(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Returns the geometric center of all the atoms in this atomContainer.
get3DCenter(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Returns the geometric center of all the atoms in this atomContainer.
get3DCentreOfMass(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Calculates the center of mass for the Atoms in the AtomContainer for the 2D coordinates.
get3DCentreOfMass(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Calculates the center of mass for the Atoms in the AtomContainer.
get3DCoordinateCoverage(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Determines the coverage of this IAtomContainer's 3D coordinates.
get3DCoordinateCoverage(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Determines the coverage of this IAtomContainer's 3D coordinates.
get3DCoordinatesForLigands(IAtom, IAtomContainer, IAtomContainer, IAtom, int, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D: Adds 3D coordinates for singly-bonded ligands of a reference atom (A).
get3DCoordinatesForSP2Ligands(IAtom, IAtomContainer, IAtomContainer, IAtom, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D: Main method for the calculation of the ligand coordinates for sp2 atoms.
get3DCoordinatesForSP3Ligands(IAtom, IAtomContainer, IAtomContainer, IAtom, int, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D: Main method for the calculation of the ligand coordinates for sp3 atoms.
get3DCoordinatesForSPLigands(IAtom, IAtomContainer, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
getA() - Method in class org.openscience.cdk.Crystal: Gets the A unit cell axes in Cartesian coordinates as a three element double array.
getA() - Method in class org.openscience.cdk.debug.DebugCrystal: Gets the A unit cell axes in Cartesian coordinates as a three element double array.
getA() - Method in interface org.openscience.cdk.interfaces.ICrystal: Gets the A unit cell axes in carthesian coordinates as a three element double array.
getA() - Method in class org.openscience.cdk.silent.Crystal: Gets the A unit cell axes in Cartesian coordinates as a three element double array.
getAgents() - Method in class org.openscience.cdk.debug.DebugReaction: Returns a MoleculeSet containing the agents in this reaction.
getAgents() - Method in interface org.openscience.cdk.interfaces.IReaction: Returns a IAtomContaineSet containing the agents in this reaction.
getAgents() - Method in class org.openscience.cdk.Reaction: Returns a MoleculeSet containing the agents in this reaction.
getAgents() - Method in class org.openscience.cdk.silent.Reaction: Returns a MoleculeSet containing the agents in this reaction.
getAllAgents(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator: Returns all agents of an IReaction.
getAllAtomContainers(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator: Returns all the AtomContainer's of a MoleculeSet.
getAllAtomContainers(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator: Returns all the AtomContainer's of a MoleculeSet.
getAllAtomContainers(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator: Returns all the AtomContainer's of a ChemFile.
getAllAtomContainers(IChemModel) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator: Returns all the AtomContainer's of a ChemModel.
getAllAtomContainers(IChemSequence) - Static method in class org.openscience.cdk.tools.manipulator.ChemSequenceManipulator: Returns all the AtomContainer's of a ChemSequence.
getAllAtomContainers(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator: Returns all IAtomContainers of the given reaction.
getAllAtomContainers(IReactionScheme) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator: get all AtomContainers object from a set of Reactions.
getAllAtomContainers(IReactionScheme, IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator: Get all molecule objects from a set of Reactions given a IAtomContainerSet to add.
getAllAtomContainers(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator: Returns all the AtomContainer's of a Reaction.
getAllAtomContainers(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator: Returns all the AtomContainer's in a RingSet.
getAllAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler: Deprecated.

Returns all plausible mappings between query and target molecules.
getAllAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler: Deprecated.

Returns all plausible mappings between query and target molecules.
getAllAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler: Deprecated.

Returns all plausible mappings between query and target molecules.
getAllAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler: Deprecated.

Returns all plausible mappings between query and target molecules.
getAllAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler: Deprecated.

Returns all plausible mappings between query and target molecules.
getAllAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler: Deprecated.

Returns all plausible mappings between query and target molecules.
getAllAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler: Deprecated.

Returns all plausible mappings between query and target molecules.
getAllAtomMapping() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS: Deprecated.

Returns all plausible mappings between query and target molecules Each map in the list has atom-atom equivalence of the mappings between query and target molecule i.e.
getAllAtomMapping() - Method in interface org.openscience.cdk.smsd.interfaces.IMCSBase: Deprecated.

Returns all plausible mappings between query and target molecules.
getAllAtomMapping() - Method in class org.openscience.cdk.smsd.Isomorphism: Deprecated.

Returns all plausible mappings between query and target molecules Each map in the list has atom-atom equivalence of the mappings between query and target molecule i.e.
getAllAtomRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>, boolean) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Return the RMSD between the 2 aligned molecules.
getAllAtomRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>, boolean) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Return the RMSD between the 2 aligned molecules.
getAllAtomTypes() - Method in class org.openscience.cdk.config.AtomTypeFactory: Gets the allAtomTypes attribute of the AtomTypeFactory object.
getAllBondMaps() - Method in class org.openscience.cdk.smsd.Isomorphism: Deprecated.
getAllChemModels(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator: Get a list of all ChemModels inside an IChemFile.
getAllChemObjects(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator: Does not recursively return the contents of the AtomContainer.
getAllChemObjects(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
getAllChemObjects(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator: Returns a List of all IChemObject inside a ChemFile.
getAllChemObjects(IChemModel) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator: Retrieve a List of all ChemObject objects within an IChemModel.
getAllChemObjects(IChemSequence) - Static method in class org.openscience.cdk.tools.manipulator.ChemSequenceManipulator: Returns a List of all IChemObject inside a ChemSequence.
getAllChemObjects(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
getAllChemObjects(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
getAllConfigurations() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery: Produces all combinations of the root structure (scaffold) with the R-groups substituted in valid ways, using each R-group's definitions and conditions.
getAllConfigurations() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
getAllFormulas() - Method in class org.openscience.cdk.formula.MolecularFormulaGenerator: Generates a IMolecularFormulaSet by repeatedly calling MolecularFormulaGenerator.getNextFormula() until all possible formulas are generated.
getAllIDs(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
getAllIDs(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
getAllIDs(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
getAllIDs(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator
getAllIDs(IChemModel) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
getAllIDs(IChemSequence) - Static method in class org.openscience.cdk.tools.manipulator.ChemSequenceManipulator
getAllIDs(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
getAllIDs(IReactionScheme) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator: Get all ID of this IReactionSet.
getAllIDs(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
getAllInOneContainer(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator: Puts all rings of a ringSet in a single atomContainer
getAllMapping() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler: Deprecated.

Returns all plausible mappings between query and target molecules.
getAllMapping() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler: Deprecated.

Returns all plausible mappings between query and target molecules.
getAllMapping() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler: Deprecated.

Returns all plausible mappings between query and target molecules.
getAllMapping() - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler: Deprecated.

Returns all plausible mappings between query and target molecules.
getAllMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler: Deprecated.

Returns all plausible mappings between query and target molecules.
getAllMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler: Deprecated.

Returns all plausible mappings between query and target molecules.
getAllMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler: Deprecated.

Returns all plausible mappings between query and target molecules.
getAllMapping() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS: Deprecated.

Returns all plausible mappings between query and target molecules Each map in the list has atom-atom equivalence index of the mappings between query and target molecule i.e.
getAllMapping() - Method in interface org.openscience.cdk.smsd.interfaces.IMCSBase: Deprecated.

Returns all plausible mappings between query and target molecules.
getAllMapping() - Method in class org.openscience.cdk.smsd.Isomorphism: Deprecated.

Returns all plausible mappings between query and target molecules Each map in the list has atom-atom equivalence index of the mappings between query and target molecule i.e.
getAllMaximum(List<List<CDKRMap>>) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler: Deprecated.
getAllMolecules(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator: Returns all components of an IReaction, that is, reactants, agents and products.
getAllMolecules(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator: get all Molecules object from a set of Reactions.
getAllPaths(IAtomContainer, IAtom, IAtom) - Static method in class org.openscience.cdk.graph.PathTools: Get a list of all the paths between two atoms.
getAllProducts(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator: Returns all products of an IReaction.
getAllReactants(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator: Returns all reactants of an IReaction.
getAllReactions(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator: Get a list of all IReaction inside an IChemFile.
getAllReactions(IReactionScheme) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator: Get all IReaction's object from a given IReactionScheme.
getAllRgroupQueryAtoms() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery: Returns all R# type atoms (pseudo atoms) found in the root structure.
getAllRings() - Method in class org.openscience.cdk.graph.SpanningTree: All basic rings and the all pairs of basic rings share at least one edge combined.
getAllSurfaceAreas() - Method in class org.openscience.cdk.geometry.surface.NumericalSurface: Get an array containing the accessible surface area for each atom.
getAllSurfacePoints() - Method in class org.openscience.cdk.geometry.surface.NumericalSurface: Get an array of all the points on the molecular surface.
getAltLoc() - Method in class org.openscience.cdk.debug.DebugPDBAtom: get the Alternate location indicator of this atom.
getAltLoc() - Method in interface org.openscience.cdk.interfaces.IPDBAtom: get the Alternate location indicator of this atom.
getAltLoc() - Method in class org.openscience.cdk.protein.data.PDBAtom: get the Alternate location indicator of this atom.
getAltLoc() - Method in class org.openscience.cdk.silent.PDBAtom: get the Alternate location indicator of this atom.
getAngle(double, double) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Gets the angle attribute of the GeometryTools class.
getAngle(double, double) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Gets the angle attribute of the GeometryTools class.
getAngleData(String, String, String, String) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94ParametersCall: Gets the angle parameter set.
getAngleRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Return the variation of each angle value between the 2 aligned molecules.
getAngleRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Return the variation of each angle value between the 2 aligned molecules.
getAngleValue(String, String, String) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D: Gets the angleKey attribute of the AtomPlacer3D object.
getAngleValue(String, String, String) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D: Gets the angleKey attribute of the AtomPlacer3D object.
getArrayValue() - Method in class org.openscience.cdk.graph.invariant.GIMatrix: Returns the internal representation of the matrix, that is an array of double objects.
getAtom() - Method in class org.openscience.cdk.debug.DebugLonePair: Returns the associated Atom.
getAtom() - Method in class org.openscience.cdk.debug.DebugSingleElectron: Returns the associated Atom.
getAtom() - Method in interface org.openscience.cdk.interfaces.ILonePair: Returns the associated Atom.
getAtom() - Method in interface org.openscience.cdk.interfaces.ISingleElectron: Returns the associated Atom.
getAtom() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RingIdentifierAtom: Deprecated.
getAtom() - Method in class org.openscience.cdk.LonePair: Returns the associated Atom.
getAtom() - Method in class org.openscience.cdk.silent.LonePair: Returns the associated Atom.
getAtom() - Method in class org.openscience.cdk.silent.SingleElectron: Returns the associated Atom.
getAtom() - Method in class org.openscience.cdk.SingleElectron: Returns the associated Atom.
getAtom() - Method in class org.openscience.cdk.smiles.InvPair
getAtom(int) - Method in class org.openscience.cdk.AtomContainer: Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().
getAtom(int) - Method in class org.openscience.cdk.Bond: Returns an Atom from this bond.
getAtom(int) - Method in class org.openscience.cdk.BondRef: Returns an Atom from this bond.
getAtom(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().
getAtom(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().
getAtom(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().
getAtom(int) - Method in class org.openscience.cdk.debug.DebugBond: Returns an Atom from this bond.
getAtom(int) - Method in class org.openscience.cdk.debug.DebugCrystal: Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().
getAtom(int) - Method in class org.openscience.cdk.debug.DebugMonomer: Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().
getAtom(int) - Method in class org.openscience.cdk.debug.DebugPolymer: Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().
getAtom(int) - Method in class org.openscience.cdk.debug.DebugRing: Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().
getAtom(int) - Method in class org.openscience.cdk.debug.DebugStrand: Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().
getAtom(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().
getAtom(int) - Method in interface org.openscience.cdk.interfaces.IBond: Returns an Atom from this bond.
getAtom(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().
getAtom(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Returns an Atom from this query bond.
getAtom(int) - Method in class org.openscience.cdk.silent.AtomContainer: Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().
getAtom(int) - Method in class org.openscience.cdk.silent.Bond: Returns an Atom from this bond.
getAtom(int) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.TargetProperties: Deprecated.
getAtom(INode) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder: Deprecated.

Returns an atom associated with this node.
getAtom(INode) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQuery: Deprecated.

Returns an atom associated with this node.
getAtomArray(List<IAtom>) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Constructs an array of Atom objects from a List of Atom objects.
getAtomArray(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Constructs an array of Atom objects from an AtomContainer.
getAtomArray(IBond) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator: Constructs an array of Atom objects from Bond.
getAtomAt(int) - Method in class org.openscience.cdk.Association: Returns an Atom from this Association.
getAtomById(IAtomContainer, String) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Returns an atom in an atomcontainer identified by id
getAtomColor(IAtom) - Method in class org.openscience.cdk.renderer.color.CDK2DAtomColors: Returns the color for a certain atom type.
getAtomColor(IAtom) - Method in class org.openscience.cdk.renderer.color.CDKAtomColors: Deprecated.

Returns the CDK scheme color for the given atom's element.
getAtomColor(IAtom) - Method in class org.openscience.cdk.renderer.color.CPKAtomColors: Deprecated.

Returns the font color for atom given atom.
getAtomColor(IAtom) - Method in interface org.openscience.cdk.renderer.color.IAtomColorer: Returns the color for a certain atom type.
getAtomColor(IAtom) - Method in class org.openscience.cdk.renderer.color.JmolColors
getAtomColor(IAtom) - Method in class org.openscience.cdk.renderer.color.PartialAtomicChargeColors: Returns the a color reflecting the given atom's partial charge.
getAtomColor(IAtom) - Method in class org.openscience.cdk.renderer.color.RasmolColors: Returns the Rasmol color for the given atom's element.
getAtomColor(IAtom) - Method in class org.openscience.cdk.renderer.color.UniColor: Returns the color for a certain atom type.
getAtomColor(IAtom, Color) - Method in class org.openscience.cdk.renderer.color.CDK2DAtomColors: Returns the color for a certain atom type, and uses the given default color if it fails to identify the atom type.
getAtomColor(IAtom, Color) - Method in class org.openscience.cdk.renderer.color.CDKAtomColors: Deprecated.

Returns the CDK scheme color for the given atom's element, or defaults to the given color if no color is defined.
getAtomColor(IAtom, Color) - Method in class org.openscience.cdk.renderer.color.CPKAtomColors: Deprecated.

Returns the font color for atom given atom.
getAtomColor(IAtom, Color) - Method in interface org.openscience.cdk.renderer.color.IAtomColorer: Returns the color for a certain atom type, and uses the given default color if it fails to identify the atom type.
getAtomColor(IAtom, Color) - Method in class org.openscience.cdk.renderer.color.JmolColors
getAtomColor(IAtom, Color) - Method in class org.openscience.cdk.renderer.color.PartialAtomicChargeColors: Returns the a color reflecting the given atom's partial charge, or defaults to the given color if no color is defined.
getAtomColor(IAtom, Color) - Method in class org.openscience.cdk.renderer.color.RasmolColors: Returns the Rasmol color for the given atom's element, or defaults to the given color if no color is defined.
getAtomColor(IAtom, Color) - Method in class org.openscience.cdk.renderer.color.UniColor: Returns the color for a certain atom type, and uses the given default color if it fails to identify the atom type.
getAtomColor(IAtom, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator: Returns the drawing color of the given atom.
getAtomContainer() - Method in interface org.openscience.cdk.geometry.cip.ILigand: IAtomContainer of which this ligand is part.
getAtomContainer() - Method in class org.openscience.cdk.geometry.cip.Ligand: IAtomContainer of which this ligand is part.
getAtomContainer() - Method in class org.openscience.cdk.inchi.InChIToStructure: Returns generated molecule.
getAtomContainer() - Method in class org.openscience.cdk.io.iterator.event.EventCMLHandler
getAtomContainer() - Method in class org.openscience.cdk.io.iterator.event.EventCMLReader
getAtomContainer() - Method in interface org.openscience.cdk.io.iterator.event.IEventChemObjectReader
getAtomContainer() - Method in class org.openscience.cdk.signature.MoleculeFromSignatureBuilder: Gets the atom container.
getAtomContainer(int) - Method in class org.openscience.cdk.AtomContainerSet: Returns the AtomContainer at position number in the container.
getAtomContainer(int) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Returns the AtomContainer at position number in the container.
getAtomContainer(int) - Method in class org.openscience.cdk.debug.DebugSubstance: Returns the AtomContainer at position number in the container.
getAtomContainer(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet: Returns the AtomContainer at position number in the container.
getAtomContainer(int) - Method in class org.openscience.cdk.silent.AtomContainerSet: Returns the AtomContainer at position number in the container.
getAtomContainer(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Converts a formula string (like "C2H4") into an atom container with atoms but no bonds.
getAtomContainer(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Method that actually does the work of convert the IMolecularFormula to IAtomContainer.
getAtomContainer(IMolecularFormula, IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Method that actually does the work of convert the IMolecularFormula to IAtomContainer given a IAtomContainer.
getAtomContainerCount() - Method in class org.openscience.cdk.AtomContainerSet: Returns the number of AtomContainers in this Container.
getAtomContainerCount() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Returns the number of AtomContainers in this Container.
getAtomContainerCount() - Method in class org.openscience.cdk.debug.DebugSubstance: Returns the number of AtomContainers in this Container.
getAtomContainerCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet: Returns the number of AtomContainers in this Container.
getAtomContainerCount() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery: Return the total number of atom containers (count the root plus all substituents).
getAtomContainerCount() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
getAtomContainerCount() - Method in class org.openscience.cdk.silent.AtomContainerSet: Returns the number of AtomContainers in this Container.
getAtomContainerSet(IAtomContainer, IAtomContainer, IReactionScheme) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator: Extract the list of AtomContainers taking part in the IReactionScheme to originate a product given a reactant.
getAtomCount() - Method in class org.openscience.cdk.Association: Returns the number of Atoms in this Association.
getAtomCount() - Method in class org.openscience.cdk.AtomContainer: Returns the number of Atoms in this Container.
getAtomCount() - Method in class org.openscience.cdk.Bond: Returns the number of Atoms in this Bond.
getAtomCount() - Method in class org.openscience.cdk.BondRef: Returns the number of Atoms in this Bond.
getAtomCount() - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns the number of Atoms in this Container.
getAtomCount() - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns the number of Atoms in this Container.
getAtomCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the number of Atoms in this Container.
getAtomCount() - Method in class org.openscience.cdk.debug.DebugBond: Returns the number of Atoms in this Bond.
getAtomCount() - Method in class org.openscience.cdk.debug.DebugCrystal: Returns the number of Atoms in this Container.
getAtomCount() - Method in class org.openscience.cdk.debug.DebugMonomer: Returns the number of Atoms in this Container.
getAtomCount() - Method in class org.openscience.cdk.debug.DebugPolymer: Returns the number of Atoms in this Container.
getAtomCount() - Method in class org.openscience.cdk.debug.DebugRing: Returns the number of Atoms in this Container.
getAtomCount() - Method in class org.openscience.cdk.debug.DebugStrand: Returns the number of Atoms in this Container.
getAtomCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Returns the number of Atoms in this Container.
getAtomCount() - Method in interface org.openscience.cdk.interfaces.IBond: Returns the number of Atoms in this Bond.
getAtomCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns the number of Atoms in this Container.
getAtomCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Returns the number of Atoms in this Bond.
getAtomCount() - Method in class org.openscience.cdk.silent.AtomContainer: Returns the number of Atoms in this Container.
getAtomCount() - Method in class org.openscience.cdk.silent.Bond: Returns the number of Atoms in this Bond.
getAtomCount() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.TargetProperties: Deprecated.
getAtomCount(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
getAtomCount(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
getAtomCount(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator: Get the total number of atoms inside an IChemFile.
getAtomCount(IChemModel) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator: Get the total number of atoms inside an IChemModel.
getAtomCount(IChemSequence) - Static method in class org.openscience.cdk.tools.manipulator.ChemSequenceManipulator: Get the total number of atoms inside an IChemSequence.
getAtomCount(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Checks a set of Nodes for the occurrence of each isotopes instance in the molecular formula.
getAtomCount(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator: Returns the total number of atoms for all components of the given reaction.
getAtomCount(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
getAtomCount(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator: Return the total number of atoms over all the rings in the colllection.
getAtomicNumber() - Method in class org.openscience.cdk.AtomRef: Returns the atomic number of this element.
getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugAtom: Returns the atomic number of this element.
getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugAtomType: Returns the atomic number of this element.
getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugElement: Returns the atomic number of this element.
getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Returns the atomic number of this element.
getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugIsotope: Returns the atomic number of this element.
getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Returns the atomic number of this element.
getAtomicNumber() - Method in class org.openscience.cdk.Element: Returns the atomic number of this element.
getAtomicNumber() - Method in interface org.openscience.cdk.interfaces.IElement: Returns the atomic number of this element.
getAtomicNumber() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Returns the atomic number of this element.
getAtomicNumber() - Method in class org.openscience.cdk.silent.Element: Returns the atomic number of this element.
getAtomicNumber(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable: Get the atomic number of the element.
getAtomicSoftnessCore(IAtomContainer, int) - Method in class org.openscience.cdk.charges.InductivePartialCharges: Gets the atomicSoftnessCore attribute of the InductivePartialCharges object.
getAtomIndices() - Method in class org.openscience.cdk.signature.Orbit: Gets all the atom indices as a list.
getAtomLayers(int[][]) - Static method in class org.openscience.cdk.graph.invariant.HuLuIndexTool
getAtomMatcher() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.NodeBuilder: Deprecated.

Returns Query Atom.
getAtomMatcher() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.INode: Deprecated.

Returns Query Atom.
getAtomNumber(IAtom) - Method in class org.openscience.cdk.AtomContainer: Returns the position of a given atom in the atoms array.
getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns the position of a given atom in the atoms array.
getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the position of a given atom in the atoms array.
getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal: Returns the position of a given atom in the atoms array.
getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer: Returns the position of a given atom in the atoms array.
getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer: Returns the position of a given atom in the atoms array.
getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugRing: Returns the position of a given atom in the atoms array.
getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand: Returns the position of a given atom in the atoms array.
getAtomNumber(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Deprecated.
use IAtomContainer.indexOf(IAtom)
getAtomNumber(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns the position of a given atom in the atoms array.
getAtomNumber(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer: Returns the position of a given atom in the atoms array.
getAtomOverlapScore(IAtomContainer, Vector) - Method in class org.openscience.cdk.layout.OverlapResolver: Deprecated.

Calculates a score based on the overlap of atoms.
getAtomPlacer() - Method in class org.openscience.cdk.layout.RingPlacer
getAtoms() - Method in class org.openscience.cdk.Association: Returns the array of atoms making up this Association.
getAtoms() - Method in class org.openscience.cdk.sgroup.Sgroup: Access the atoms of this substructure group.
getAtoms() - Method in class org.openscience.cdk.smsd.ring.PathEdge: Deprecated.
getAtomSurfaceMap() - Method in class org.openscience.cdk.geometry.surface.NumericalSurface: Get the map from atom to surface points.
getAtomType(String) - Method in class org.openscience.cdk.config.AtomTypeFactory: Get an AtomType with the given ID.
getAtomTypeFactory(IChemObjectBuilder) - Method in class org.openscience.cdk.tools.SaturationChecker
getAtomTypeFactory(IChemObjectBuilder) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
getAtomTypeMappings() - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingHandler: Returns a Map with atom type mappings.
getAtomTypeName() - Method in class org.openscience.cdk.AtomRef: Gets the id attribute of the AtomType object.
getAtomTypeName() - Method in class org.openscience.cdk.AtomType: Gets the id attribute of the AtomType object.
getAtomTypeName() - Method in class org.openscience.cdk.debug.DebugAtom: Gets the id attribute of the AtomType object.
getAtomTypeName() - Method in class org.openscience.cdk.debug.DebugAtomType: Gets the id attribute of the AtomType object.
getAtomTypeName() - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Gets the id attribute of the AtomType object.
getAtomTypeName() - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Gets the id attribute of the AtomType object.
getAtomTypeName() - Method in interface org.openscience.cdk.interfaces.IAtomType: Gets the id attribute of the AtomType object.
getAtomTypeName() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Gets the id attribute of the AtomType object.
getAtomTypeName() - Method in class org.openscience.cdk.silent.AtomType: Gets the id attribute of the AtomType object.
getAtomTypePatterns() - Method in class org.openscience.cdk.modeling.builder3d.MM2BasedAtomTypePattern: Gets the atomTypePatterns attribute of the MM2BasedAtomTypePattern object
getAtomTypePatterns() - Method in class org.openscience.cdk.modeling.builder3d.MMFF94BasedAtomTypePattern: Deprecated.

Gets the atomTypePatterns attribute of the MM2BasedAtomTypePattern object
getAtomTypes() - Method in class org.openscience.cdk.config.atomtypes.AtomTypeHandler: Returns a List with read IAtomType's.
getAtomTypes() - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeHandler: Returns a List with read IAtomType's.
getAtomTypes() - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator: Gets the atomTypes attribute of the ForceFieldConfigurator object
getAtomTypes() - Method in class org.openscience.cdk.modeling.builder3d.MM2BasedParameterSetReader
getAtomTypes() - Method in class org.openscience.cdk.modeling.builder3d.MMFF94BasedParameterSetReader
getAtomTypes(String) - Method in class org.openscience.cdk.config.AtomTypeFactory: Get an array of all atomTypes known to the AtomTypeFactory for the given element symbol and atomtype class.
getAtomVector(int) - Method in class org.openscience.cdk.Vibration: Gets a atom vector at index given.
getAtomVectorCount() - Method in class org.openscience.cdk.Vibration: Gets the number of atom vectors in the vibration.
getAtomVectors() - Method in class org.openscience.cdk.Vibration: Returns an Enumeration of the atom vectors of this vibration.
getAttachPointNum() - Method in interface org.openscience.cdk.interfaces.IPseudoAtom: Access the attachment point number.
getAttachPointNum() - Method in class org.openscience.cdk.PseudoAtom: Access the attachment point number.
getAttachPointNum() - Method in class org.openscience.cdk.silent.PseudoAtom: Access the attachment point number.
getAttributeKeys() - Method in class org.openscience.cdk.sgroup.Sgroup: Access all the attribute keys of this Sgroup.
getAutomorphismGroup() - Method in interface org.openscience.cdk.group.DiscretePartitionRefiner: Get the automorphism group used to prune the search.
getAutomorphismGroup(IAtomContainer) - Method in interface org.openscience.cdk.group.AtomContainerDiscretePartitionRefiner: Gets the automorphism group of the atom container.
getAutomorphismGroup(IAtomContainer, Partition) - Method in interface org.openscience.cdk.group.AtomContainerDiscretePartitionRefiner: Get the automorphism group of the molecule given an initial partition.
getAutomorphismGroup(IAtomContainer, PermutationGroup) - Method in interface org.openscience.cdk.group.AtomContainerDiscretePartitionRefiner: Speed up the search for the automorphism group using the automorphisms in the supplied group.
getAutomorphismPartition() - Method in interface org.openscience.cdk.group.DiscretePartitionRefiner: The automorphism partition is a partition of the elements of the group.
getAutomorphismPartition(IAtomContainer) - Method in interface org.openscience.cdk.group.AtomContainerDiscretePartitionRefiner: Get the automorphism partition (equivalence classes) of the atoms.
getAuxInfo() - Method in class org.openscience.cdk.inchi.InChIGenerator: Gets auxillary information.
getAvailableDictionaryClasses() - Method in class org.openscience.cdk.qsar.DescriptorEngine: Get the all the unique dictionary classes that the descriptors belong to.
getB() - Method in class org.openscience.cdk.Crystal: Gets the B unit cell axes in Cartesian coordinates as a three element double array.
getB() - Method in class org.openscience.cdk.debug.DebugCrystal: Gets the B unit cell axes in Cartesian coordinates as a three element double array.
getB() - Method in interface org.openscience.cdk.interfaces.ICrystal: Gets the B unit cell axes in carthesian coordinates as a three element double array.
getB() - Method in class org.openscience.cdk.silent.Crystal: Gets the B unit cell axes in Cartesian coordinates as a three element double array.
getBasicRings() - Method in class org.openscience.cdk.graph.SpanningTree: The basic rings of the spanning tree.
getBasis() - Method in class org.openscience.cdk.math.qm.Orbitals: Returns the basis set of this orbitals
getBegin() - Method in class org.openscience.cdk.Bond: Access the begin (or first) atom of the bond.
getBegin() - Method in class org.openscience.cdk.BondRef: Access the begin (or first) atom of the bond.
getBegin() - Method in class org.openscience.cdk.debug.DebugBond: Access the begin (or first) atom of the bond.
getBegin() - Method in interface org.openscience.cdk.interfaces.IBond: Access the begin (or first) atom of the bond.
getBegin() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Access the begin (or first) atom of the bond.
getBegin() - Method in class org.openscience.cdk.silent.Bond: Access the begin (or first) atom of the bond.
getBeginColumn() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream: Get token beginning column number.
getBeginColumn() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Get token beginning column number.
getBeginLine() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream: Get token beginning line number.
getBeginLine() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Get token beginning line number.
getBest() - Method in interface org.openscience.cdk.group.DiscretePartitionRefiner: Get the best permutation found.
getBestAlignmentForLabel(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Determines the best alignment for the label of an atom in 2D space.
getBestAlignmentForLabel(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Determines the best alignment for the label of an atom in 2D space.
getBestAlignmentForLabelXY(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Determines the best alignment for the label of an atom in 2D space.
getBestAlignmentForLabelXY(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Determines the best alignment for the label of an atom in 2D space.
getBestCliqueSize() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.BKKCKCF: Deprecated.
getBibData() - Method in class org.openscience.cdk.tools.BremserOneSphereHOSECodePredictor
getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.AtomPairs2DFingerprinter
getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter: Calculates the circular fingerprint for the given IAtomContainer, and folds the result into a single bitset (see getSize()).
getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.EStateFingerprinter: Returns the bit fingerprint for the given IAtomContainer.
getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter: Generates a fingerprint of the default size for the given AtomContainer, using path and ring metrics.
getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.Fingerprinter: Generates a fingerprint of the default size for the given AtomContainer.
getBitFingerprint(IAtomContainer) - Method in interface org.openscience.cdk.fingerprint.IFingerprinter: Returns the bit fingerprint for the given IAtomContainer.
getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.LingoFingerprinter
getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.MACCSFingerprinter: Returns the bit fingerprint for the given IAtomContainer.
getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.PubchemFingerprinter: Calculate 881 bit Pubchem fingerprint for a molecule.
getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.ShortestPathFingerprinter: Generates a shortest path based BitSet fingerprint for the given AtomContainer.
getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.SignatureFingerprinter
getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.SubstructureFingerprinter: Returns the bit fingerprint for the given IAtomContainer.
getBitFingerprint(IAtomContainer, int) - Method in class org.openscience.cdk.fingerprint.GraphOnlyFingerprinter
getBitFingerprint(IAtomContainer, IRingSet, List<IRingSet>) - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter: Generates a fingerprint of the default size for the given AtomContainer, using path and ring metrics.
getBitFingerprint(IAtomContainer, AllRingsFinder) - Method in class org.openscience.cdk.fingerprint.Fingerprinter: Generates a fingerprint of the default size for the given AtomContainer.
getBitSet(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: Transforms an AtomContainer into a BitSet (which's size = number of bond in the atomContainer, all the bit are set to true).
getBitSet(IAtomContainer) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS: Deprecated.

Transforms an AtomContainer into atom BitSet (which's size = number of bondA1 in the atomContainer, all the bit are set to true).
getBitSetFromFile(StringTokenizer) - Static method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D
getBlocks(int[], int, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Getting a part of a int array specified by two entry indices
getBond(int) - Method in class org.openscience.cdk.AtomContainer: Get the bond at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getBondCount().
getBond(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Get the bond at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getBondCount().
getBond(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Get the bond at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getBondCount().
getBond(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Get the bond at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getBondCount().
getBond(int) - Method in class org.openscience.cdk.debug.DebugCrystal: Get the bond at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getBondCount().
getBond(int) - Method in class org.openscience.cdk.debug.DebugMonomer: Get the bond at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getBondCount().
getBond(int) - Method in class org.openscience.cdk.debug.DebugPolymer: Get the bond at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getBondCount().
getBond(int) - Method in class org.openscience.cdk.debug.DebugRing: Get the bond at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getBondCount().
getBond(int) - Method in class org.openscience.cdk.debug.DebugStrand: Get the bond at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getBondCount().
getBond(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Get the bond at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getBondCount().
getBond(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Get the bond at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getBondCount().
getBond(int) - Method in class org.openscience.cdk.silent.AtomContainer: Get the bond at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getBondCount().
getBond(IAtom) - Method in class org.openscience.cdk.Atom: Returns the bond connecting 'this' atom to the provided atom.
getBond(IAtom) - Method in class org.openscience.cdk.AtomRef: Returns the bond connecting 'this' atom to the provided atom.
getBond(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtom: Returns the bond connecting 'this' atom to the provided atom.
getBond(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Returns the bond connecting 'this' atom to the provided atom.
getBond(IAtom) - Method in class org.openscience.cdk.silent.Atom: Returns the bond connecting 'this' atom to the provided atom.
getBond(IAtom, IAtom) - Method in class org.openscience.cdk.AtomContainer: Returns the bond that connects the two given atoms.
getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns the bond that connects the two given atoms.
getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns the bond that connects the two given atoms.
getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the bond that connects the two given atoms.
getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal: Returns the bond that connects the two given atoms.
getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer: Returns the bond that connects the two given atoms.
getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer: Returns the bond that connects the two given atoms.
getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugRing: Returns the bond that connects the two given atoms.
getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugStrand: Returns the bond that connects the two given atoms.
getBond(IAtom, IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Returns the bond that connects the two given atoms.
getBond(IAtom, IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns the bond that connects the two given atoms.
getBond(IAtom, IAtom) - Method in class org.openscience.cdk.silent.AtomContainer: Returns the bond that connects the two given atoms.
getBond(IAtom, IAtom) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.TargetProperties: Deprecated.
getBondAngleInteractionData(String, String, String, String) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94ParametersCall: Gets the bond-angle interaction parameter set.
getBondArray(List<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Constructs an array of Atom objects from a List of Atom objects.
getBondArray(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Constructs an array of Bond objects from an AtomContainer.
getBondCoordinates(IBond) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Writes the coordinates of the atoms participating the given bond into an array.
getBondCoordinates(IBond) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Writes the coordinates of the atoms participating the given bond into an array.
getBondCount() - Method in class org.openscience.cdk.Atom: Get the number of explicit bonds connected to this atom.
getBondCount() - Method in class org.openscience.cdk.AtomContainer: Returns the number of Bonds in this Container.
getBondCount() - Method in class org.openscience.cdk.AtomRef
getBondCount() - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns the number of Bonds in this Container.
getBondCount() - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns the number of Bonds in this Container.
getBondCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the number of Bonds in this Container.
getBondCount() - Method in class org.openscience.cdk.debug.DebugCrystal: Returns the number of Bonds in this Container.
getBondCount() - Method in class org.openscience.cdk.debug.DebugMonomer: Returns the number of Bonds in this Container.
getBondCount() - Method in class org.openscience.cdk.debug.DebugPolymer: Returns the number of Bonds in this Container.
getBondCount() - Method in class org.openscience.cdk.debug.DebugRing: Returns the number of Bonds in this Container.
getBondCount() - Method in class org.openscience.cdk.debug.DebugStrand: Returns the number of Bonds in this Container.
getBondCount() - Method in interface org.openscience.cdk.interfaces.IAtom: Get the number of explicit bonds connected to this atom.
getBondCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Returns the number of Bonds in this Container.
getBondCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Get the number of explicit bonds connected to this atom.
getBondCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns the number of Bonds in this Container.
getBondCount() - Method in class org.openscience.cdk.silent.Atom: Get the number of explicit bonds connected to this atom.
getBondCount() - Method in class org.openscience.cdk.silent.AtomContainer: Returns the number of Bonds in this Container.
getBondCount(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
getBondCount(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
getBondCount(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator: Get the total number of bonds inside an IChemFile.
getBondCount(IChemModel) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator: Get the total number of bonds inside an IChemModel.
getBondCount(IChemSequence) - Static method in class org.openscience.cdk.tools.manipulator.ChemSequenceManipulator: Get the total number of bonds inside an IChemSequence.
getBondCount(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator: Returns the total number of atoms for all components of the given reaction.
getBondCount(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
getBondCount(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator: Return the total number of bonds over all the rings in the colllection.
getBondData(String, String, String) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94ParametersCall: Gets the bond parameter set.
getBondInSensitiveTimeOut() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS: Deprecated.

get timeout in mins for bond insensitive searches
getBondInSensitiveTimeOut() - Method in class org.openscience.cdk.smsd.Isomorphism: Deprecated.

get timeout in mins for bond insensitive searches
getBondLength() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator: Returns the bond length used for laying out the molecule.
getBondLength() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAngleBond: Get the angle between the three pharmacophore groups that make up the constraint.
getBondLength() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreBond: Get the distance between the two pharmacophore groups that make up the constraint.
getBondLengthAverage(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

An average of all 2D bond length values is produced.
getBondLengthAverage(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: An average of all 2D bond length values is produced.
getBondLengthAverage(IReaction) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.
getBondLengthAverage(IReaction) - Static method in class org.openscience.cdk.geometry.GeometryUtil
getBondLengthAverage3D(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

An average of all 3D bond length values is produced, using point3ds in atoms.
getBondLengthAverage3D(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: An average of all 3D bond length values is produced, using point3ds in atoms.
getBondLengthMedian(Iterable<IBond>, int) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Calculate the median bond length of some bonds.
getBondLengthMedian(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Calculate the median bond length of an atom container.
getBondLengthMedian(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Calculate the median bond length of an atom container.
getBondLengthRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>, boolean) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Return the RMSD of bonds length between the 2 aligned molecules.
getBondLengthRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>, boolean) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Return the RMSD of bonds length between the 2 aligned molecules.
getBondLengthValue(String, String) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D: Gets the distanceValue attribute of the parameter set.
getBondMatcher() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.EdgeBuilder: Deprecated.

Returns bond matcher.
getBondMatcher() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IEdge: Deprecated.

Returns bond matcher.
getBondNumA() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.QueryProcessor: Deprecated.
getBondNumB() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.TargetProcessor: Deprecated.
getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.AtomContainer: Returns the position of the bond between two given atoms in the electronContainers array.
getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns the position of the bond between two given atoms in the electronContainers array.
getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the position of the bond between two given atoms in the electronContainers array.
getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal: Returns the position of the bond between two given atoms in the electronContainers array.
getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer: Returns the position of the bond between two given atoms in the electronContainers array.
getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer: Returns the position of the bond between two given atoms in the electronContainers array.
getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugRing: Returns the position of the bond between two given atoms in the electronContainers array.
getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugStrand: Returns the position of the bond between two given atoms in the electronContainers array.
getBondNumber(IAtom, IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Deprecated.
use IAtomContainer.indexOf(IBond)
getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns the position of the bond between two given atoms in the electronContainers array.
getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.silent.AtomContainer: Returns the position of the bond between two given atoms in the electronContainers array.
getBondNumber(IBond) - Method in class org.openscience.cdk.AtomContainer: Returns the position of a given bond in the electronContainers array.
getBondNumber(IBond) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns the position of a given bond in the electronContainers array.
getBondNumber(IBond) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the position of a given bond in the electronContainers array.
getBondNumber(IBond) - Method in class org.openscience.cdk.debug.DebugCrystal: Returns the position of a given bond in the electronContainers array.
getBondNumber(IBond) - Method in class org.openscience.cdk.debug.DebugMonomer: Returns the position of a given bond in the electronContainers array.
getBondNumber(IBond) - Method in class org.openscience.cdk.debug.DebugPolymer: Returns the position of a given bond in the electronContainers array.
getBondNumber(IBond) - Method in class org.openscience.cdk.debug.DebugRing: Returns the position of a given bond in the electronContainers array.
getBondNumber(IBond) - Method in class org.openscience.cdk.debug.DebugStrand: Returns the position of a given bond in the electronContainers array.
getBondNumber(IBond) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Deprecated.
use IAtomContainer.indexOf(IBond)
getBondNumber(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns the position of a given bond in the electronContainers array.
getBondNumber(IBond) - Method in class org.openscience.cdk.silent.AtomContainer: Returns the position of a given bond in the electronContainers array.
getBondOrder() - Method in class org.openscience.cdk.smsd.helper.BondEnergy: Deprecated.

Returns the bond order for this bond type energy.
getBondOrderSum() - Method in class org.openscience.cdk.AtomRef: Gets the bondOrderSum attribute of the AtomType object.
getBondOrderSum() - Method in class org.openscience.cdk.AtomType: Gets the bondOrderSum attribute of the AtomType object.
getBondOrderSum() - Method in class org.openscience.cdk.debug.DebugAtom: Gets the bondOrderSum attribute of the AtomType object.
getBondOrderSum() - Method in class org.openscience.cdk.debug.DebugAtomType: Gets the bondOrderSum attribute of the AtomType object.
getBondOrderSum() - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Gets the bondOrderSum attribute of the AtomType object.
getBondOrderSum() - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Gets the bondOrderSum attribute of the AtomType object.
getBondOrderSum() - Method in class org.openscience.cdk.debug.DebugRing: Returns the sum of all bond orders in the ring.
getBondOrderSum() - Method in interface org.openscience.cdk.interfaces.IAtomType: Gets the bondOrderSum attribute of the AtomType object.
getBondOrderSum() - Method in interface org.openscience.cdk.interfaces.IRing: Returns the sum of all bond orders in the ring.
getBondOrderSum() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Gets the bondOrderSum attribute of the AtomType object.
getBondOrderSum() - Method in class org.openscience.cdk.Ring: Returns the sum of all bond orders in the ring.
getBondOrderSum() - Method in class org.openscience.cdk.silent.AtomType: Gets the bondOrderSum attribute of the AtomType object.
getBondOrderSum() - Method in class org.openscience.cdk.silent.Ring: Returns the sum of all bond orders in the ring.
getBondOrderSum(IAtom) - Method in class org.openscience.cdk.AtomContainer: Returns the sum of the bond orders for a given Atom.
getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns the sum of the bond orders for a given Atom.
getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns the sum of the bond orders for a given Atom.
getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the sum of the bond orders for a given Atom.
getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal: Returns the sum of the bond orders for a given Atom.
getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer: Returns the sum of the bond orders for a given Atom.
getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer: Returns the sum of the bond orders for a given Atom.
getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugRing: Returns the sum of the bond orders for a given Atom.
getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand: Returns the sum of the bond orders for a given Atom.
getBondOrderSum(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Returns the sum of the bond orders for a given Atom.
getBondOrderSum(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Deprecated.
Replaced by AtomContainerManipulator#getBondOrderSum(IAtomContainer, IAtom)
getBondOrderSum(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer: Returns the sum of the bond orders for a given Atom.
getBondOrderSum(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Returns the sum of the bond order equivalents for a given IAtom.
getBondOverlapScore(IAtomContainer, Vector) - Method in class org.openscience.cdk.layout.OverlapResolver: Deprecated.

Calculates a score based on the intersection of bonds.
getBonds() - Method in interface org.openscience.cdk.interfaces.IDoubleBondStereochemistry: Returns an array of ligand bonds around the double bond.
getBonds() - Method in class org.openscience.cdk.sgroup.Sgroup: Access the bonds that belong to this substructure group.
getBonds() - Method in class org.openscience.cdk.stereo.DoubleBondStereochemistry: Returns an array of ligand bonds around the double bond.
getBondsAcyclicCount() - Method in class org.openscience.cdk.graph.SpanningTree: Number of acyclic bonds.
getBondsCyclicCount() - Method in class org.openscience.cdk.graph.SpanningTree: Number of cyclic bonds.
getBondSensitiveTimeOut() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS: Deprecated.

get timeout in mins for bond sensitive searches
getBondSensitiveTimeOut() - Method in class org.openscience.cdk.smsd.Isomorphism: Deprecated.

get timeout in mins for bond sensitive searches
getBondSymbol(IBond) - Method in class org.openscience.cdk.fingerprint.Fingerprinter: Gets the bondSymbol attribute of the Fingerprinter class
getBondSymbol(IBond) - Method in class org.openscience.cdk.fingerprint.GraphOnlyFingerprinter: Gets the bondSymbol attribute of the Fingerprinter class.
getBondSymbol(IBond) - Method in class org.openscience.cdk.fingerprint.HybridizationFingerprinter: Gets the bond Symbol attribute of the Fingerprinter class.
getBounds(IRenderingElement) - Method in class org.openscience.cdk.renderer.AbstractRenderer: Given a rendering element, traverse the elements compute required bounds to full display all elements.
getBuilder() - Method in class org.openscience.cdk.ChemObject
getBuilder() - Method in class org.openscience.cdk.debug.DebugAdductFormula: Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugAtom: Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugAtomType: Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugBond: Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugChemFile: Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugChemModel: Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugChemObject: Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugChemSequence: Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugCrystal: Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugElectronContainer: Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugElement: Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugIsotope: Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugLonePair: Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugMapping: Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugMolecularFormula: Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet: Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugMonomer: Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugPolymer: Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugReaction: Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugReactionScheme: Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugReactionSet: Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugRing: Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugSingleElectron: Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugStrand: Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugSubstance: Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.formula.AdductFormula
getBuilder() - Method in class org.openscience.cdk.formula.MolecularFormula
getBuilder() - Method in class org.openscience.cdk.formula.MolecularFormulaSet
getBuilder() - Method in interface org.openscience.cdk.interfaces.ICDKObject: Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
getBuilder() - Method in class org.openscience.cdk.silent.AdductFormula
getBuilder() - Method in class org.openscience.cdk.silent.ChemObject
getBuilder() - Method in class org.openscience.cdk.silent.MolecularFormula
getBuilder() - Method in class org.openscience.cdk.silent.MolecularFormulaSet
getBuilder() - Method in class org.openscience.cdk.structgen.maygen.Maygen
getC() - Method in class org.openscience.cdk.Crystal: Gets the C unit cell axes in Cartesian coordinates as a three element double array.
getC() - Method in class org.openscience.cdk.debug.DebugCrystal: Gets the C unit cell axes in Cartesian coordinates as a three element double array.
getC() - Method in interface org.openscience.cdk.interfaces.ICrystal: Gets the C unit cell axes in carthesian coordinates as a three element double array.
getC() - Method in class org.openscience.cdk.silent.Crystal: Gets the C unit cell axes in Cartesian coordinates as a three element double array.
getCachedDescriptorValue(IAtom) - Method in class org.openscience.cdk.qsar.AbstractAtomicDescriptor: Returns the cached DescriptorValue for the given IAtom.
getCachedDescriptorValue(IBond) - Method in class org.openscience.cdk.qsar.AbstractBondDescriptor: Returns the cached DescriptorValue for the given IBond.
getCanonicalCycle(int, int, int[][], int[], Permutation) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Getting the canonical cycle of a row.
getCanonicalMolecule(IAtomContainer) - Method in class org.openscience.cdk.smsd.labelling.CanonicalLabellingAdaptor: Deprecated.
getCanonicalMolecule(IAtomContainer) - Method in interface org.openscience.cdk.smsd.labelling.ICanonicalMoleculeLabeller: Deprecated.
getCanonicalMolecule(IAtomContainer) - Method in class org.openscience.cdk.smsd.labelling.MoleculeSignatureLabellingAdaptor: Deprecated.
getCanonicalPermutation(int[], int[], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Calculating the canonical permutation of a row.
getCanonicalPermutation(IAtomContainer) - Method in class org.openscience.cdk.smsd.labelling.CanonicalLabellingAdaptor: Deprecated.
getCanonicalPermutation(IAtomContainer) - Method in interface org.openscience.cdk.smsd.labelling.ICanonicalMoleculeLabeller: Deprecated.
getCanonicalPermutation(IAtomContainer) - Method in class org.openscience.cdk.smsd.labelling.MoleculeSignatureLabellingAdaptor: Deprecated.
getCanonicalPermutation2(int[], int[], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Calculating the canonical permutation of a row.
getCanonicalReaction(IReaction) - Method in interface org.openscience.cdk.smsd.labelling.ICanonicalReactionLabeller: Deprecated.

Convert a reaction into a canonical form by canonizing each of the structures in the reaction in turn.
getCanonicalReaction(IReaction) - Method in class org.openscience.cdk.smsd.labelling.SignatureReactionCanoniser: Deprecated.

Convert a reaction into a canonical form by canonizing each of the structures in the reaction in turn.
getCanonicalReaction(IReaction) - Method in class org.openscience.cdk.smsd.labelling.SmilesReactionCanoniser: Deprecated.

Convert a reaction into a canonical form by canonizing each of the structures in the reaction in turn.
getCarbonSpecial(IAtom) - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor.JPlogPCalculator: Determines and returns the SS (subsection) portion of the atomtype integer for a Carbon Atom
getCarriers() - Method in interface org.openscience.cdk.interfaces.IStereoElement: The carriers of the stereochemistry
getCASId(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable: Get the CAS ID for an element.
getcBondNeighborsA() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper: Deprecated.
getcBondNeighborsB() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper: Deprecated.
getCBondSetA() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper: Deprecated.
getCBondSetB() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper: Deprecated.
getCDKErrorCount() - Method in class org.openscience.cdk.validate.ValidationReport: Returns the number of CDK errors.
getCDKErrors() - Method in class org.openscience.cdk.validate.ValidationReport: Returns an array of ValidationTest indicating CDK problems.
getCEdgesSize() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph: Deprecated.
getCEgdes() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph: Deprecated.
getCell(int) - Method in class org.openscience.cdk.group.Partition: Gets the cell at this index.
getCenterOfMass() - Method in class org.openscience.cdk.geometry.alignment.KabschAlignment: Returns the center of mass for the first molecule or fragment used in the calculation.
getCentralAtom() - Method in interface org.openscience.cdk.geometry.cip.ILigand: The central IAtom to which this ligand is connected via one IBond.
getCentralAtom() - Method in class org.openscience.cdk.geometry.cip.Ligand: The central IAtom to which this ligand is connected via one IBond.
getChainID() - Method in class org.openscience.cdk.debug.DebugPDBAtom: get the Chain identifier of this atom.
getChainID() - Method in class org.openscience.cdk.debug.DebugPDBMonomer: Gets the Chain ID of this monomer.
getChainID() - Method in interface org.openscience.cdk.interfaces.IPDBAtom: get the Chain identifier of this atom.
getChainID() - Method in interface org.openscience.cdk.interfaces.IPDBMonomer: Gets the Chain ID of this monomer.
getChainID() - Method in class org.openscience.cdk.protein.data.PDBAtom: get the Chain identifier of this atom.
getChainID() - Method in class org.openscience.cdk.protein.data.PDBMonomer
getChainID() - Method in class org.openscience.cdk.silent.PDBAtom: get the Chain identifier of this atom.
getChainID() - Method in class org.openscience.cdk.silent.PDBMonomer
getCharge() - Method in class org.openscience.cdk.Atom: Returns the partial charge of this atom.
getCharge() - Method in class org.openscience.cdk.AtomRef: Returns the partial charge of this atom.
getCharge() - Method in class org.openscience.cdk.debug.DebugAdductFormula: Returns the partial charge of this Adduct.
getCharge() - Method in class org.openscience.cdk.debug.DebugAtom: Returns the partial charge of this atom.
getCharge() - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Returns the partial charge of this atom.
getCharge() - Method in class org.openscience.cdk.debug.DebugMolecularFormula: Access the charge of this IMolecularFormula.
getCharge() - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Returns the partial charge of this atom.
getCharge() - Method in class org.openscience.cdk.formula.AdductFormula: Returns the partial charge of this Adduct.
getCharge() - Method in class org.openscience.cdk.formula.IsotopePattern: Get the charge in this pattern.
getCharge() - Method in class org.openscience.cdk.formula.MolecularFormula: Access the charge of this IMolecularFormula.
getCharge() - Method in interface org.openscience.cdk.interfaces.IAdductFormula: Returns the partial charge of this Adduct.
getCharge() - Method in interface org.openscience.cdk.interfaces.IAtom: Returns the partial charge of this atom.
getCharge() - Method in interface org.openscience.cdk.interfaces.IMolecularFormula: Access the charge of this IMolecularFormula.
getCharge() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Returns the partial charge of this atom.
getCharge() - Method in class org.openscience.cdk.silent.AdductFormula: Returns the partial charge of this Adduct.
getCharge() - Method in class org.openscience.cdk.silent.Atom: Returns the partial charge of this atom.
getCharge() - Method in class org.openscience.cdk.silent.MolecularFormula: Access the charge of this IMolecularFormula.
getChargeGroups() - Method in class org.openscience.cdk.libio.md.MDMolecule
getChemFile() - Method in class org.openscience.cdk.io.inchi.INChIHandler: Deprecated.
getChemicalSeries(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable: Get the chemical series for an element.
getChemModel(int) - Method in class org.openscience.cdk.ChemSequence: Returns the ChemModel at position number in the container.
getChemModel(int) - Method in class org.openscience.cdk.debug.DebugChemSequence: Returns the ChemModel at position number in the container.
getChemModel(int) - Method in interface org.openscience.cdk.interfaces.IChemSequence: Returns the ChemModel at position number in the container.
getChemModel(int) - Method in class org.openscience.cdk.silent.ChemSequence: Returns the ChemModel at position number in the container.
getChemModelCount() - Method in class org.openscience.cdk.ChemSequence: Returns the number of ChemModels in this Container.
getChemModelCount() - Method in class org.openscience.cdk.debug.DebugChemSequence: Returns the number of ChemModels in this Container.
getChemModelCount() - Method in interface org.openscience.cdk.interfaces.IChemSequence: Returns the number of ChemModels in this Container.
getChemModelCount() - Method in class org.openscience.cdk.silent.ChemSequence: Returns the number of ChemModels in this Container.
getChemObject() - Method in class org.openscience.cdk.validate.ValidationTest
getChemObject(int) - Method in class org.openscience.cdk.debug.DebugMapping: Retrieves the first or second of the related IChemObjects.
getChemObject(int) - Method in interface org.openscience.cdk.interfaces.IMapping: Retrieve the first or second of the related IChemObjects.
getChemObject(int) - Method in class org.openscience.cdk.Mapping: Retrieves the first or second of the related IChemObjects.
getChemObject(int) - Method in class org.openscience.cdk.silent.Mapping: Retrieves the first or second of the related IChemObjects.
getChemObjectReader() - Method in class org.openscience.cdk.io.random.RandomAccessReader
getChemSequence(int) - Method in class org.openscience.cdk.ChemFile: Returns the ChemSequence at position number in the container.
getChemSequence(int) - Method in class org.openscience.cdk.debug.DebugChemFile: Returns the ChemSequence at position number in the container.
getChemSequence(int) - Method in interface org.openscience.cdk.interfaces.IChemFile: Returns the ChemSequence at position number in the container.
getChemSequence(int) - Method in class org.openscience.cdk.silent.ChemFile: Returns the ChemSequence at position number in the container.
getChemSequenceCount() - Method in class org.openscience.cdk.ChemFile: Returns the number of ChemSequences in this Container.
getChemSequenceCount() - Method in class org.openscience.cdk.debug.DebugChemFile: Returns the number of ChemSequences in this Container.
getChemSequenceCount() - Method in interface org.openscience.cdk.interfaces.IChemFile: Returns the number of ChemSequences in this Container.
getChemSequenceCount() - Method in class org.openscience.cdk.silent.ChemFile: Returns the number of ChemSequences in this Container.
getChiCatHydrogen() - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges: Gets chi_cat value for hydrogen, because H poses a special problem due to lack of possible second ionisation.
getChildren() - Method in class org.openscience.cdk.tools.diff.tree.AbstractDifferenceList: Returns an Iterable of IDifference for all childs of this IDifference.
getChildren() - Method in interface org.openscience.cdk.tools.diff.tree.IDifferenceList: Returns an Iterable of IDifference for all childs of this IDifference.
getChiralAtom() - Method in interface org.openscience.cdk.interfaces.ITetrahedralChirality: Atom that is the chirality center.
getChiralAtom() - Method in class org.openscience.cdk.stereo.TetrahedralChirality
getCID(XMLStreamReader) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
getCIPChirality(LigancyFourChirality) - Static method in class org.openscience.cdk.geometry.cip.CIPTool: Returns the R or S chirality according to the CIP rules, based on the given chirality information.
getCIPChirality(IAtomContainer, IDoubleBondStereochemistry) - Static method in class org.openscience.cdk.geometry.cip.CIPTool
getCIPChirality(IAtomContainer, ITetrahedralChirality) - Static method in class org.openscience.cdk.geometry.cip.CIPTool: Returns the R or S chirality according to the CIP rules, based on the given chirality information.
getClasses() - Method in class org.openscience.cdk.renderer.elements.MarkedElement: Access the classes of the element.
getClassName() - Method in class org.openscience.cdk.dict.Entry
getClassType() - Method in class org.openscience.cdk.fingerprint.model.Bayesian: Access to the fingerprint type.
getClipboardContent() - Method in class org.openscience.cdk.renderer.RendererModel: Returns the atoms and bonds on the Renderer2D clipboard.
getClosestAtom(double, double, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Returns the atom of the given molecule that is closest to the given coordinates.
getClosestAtom(double, double, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Returns the atom of the given molecule that is closest to the given coordinates.
getClosestAtom(double, double, IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Returns the atom of the given molecule that is closest to the given coordinates and is not the atom.
getClosestAtom(double, double, IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Returns the atom of the given molecule that is closest to the given coordinates and is not the atom.
getClosestAtom(int, int, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Returns the atom of the given molecule that is closest to the given coordinates.
getClosestAtom(int, int, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Returns the atom of the given molecule that is closest to the given coordinates.
getClosestAtom(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Returns the atom of the given molecule that is closest to the given atom (excluding itself).
getClosestAtom(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Returns the atom of the given molecule that is closest to the given atom (excluding itself).
getClosestBond(double, double, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Returns the bond of the given molecule that is closest to the given coordinates.
getClosestBond(double, double, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Returns the bond of the given molecule that is closest to the given coordinates.
getClosestBond(int, int, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Returns the bond of the given molecule that is closest to the given coordinates.
getClosestBond(int, int, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Returns the bond of the given molecule that is closest to the given coordinates.
getCoefficients() - Method in class org.openscience.cdk.math.qm.Orbitals: Get the coefficient matrix
getCoeffs() - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor.JPlogPCalculator
getColorForBond(IBond, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator: Determine the color of a bond, returning either the default color, the override color or whatever is in the color hash for that bond.
getColumn() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream: Deprecated.
getColumn() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Deprecated.
getColumn(int) - Method in class org.openscience.cdk.graph.invariant.GIMatrix: Returns the column-matrix at the given line index.
getColumns() - Method in class org.openscience.cdk.math.IMatrix: Returns the count of columns
getColumns() - Method in class org.openscience.cdk.math.Matrix: Returns the number of columns.
getCompGraphNodes() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph: Deprecated.
getCompGraphNodesCZero() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph: Deprecated.
getConfidenceLimit(String) - Method in class org.openscience.cdk.tools.BremserOneSphereHOSECodePredictor
getConfig() - Method in interface org.openscience.cdk.interfaces.IStereoElement: Access the configuration order and class of the stereochemistry.
getConfigClass() - Method in interface org.openscience.cdk.interfaces.IStereoElement: The configuration class of the stereochemistry.
getConfigOrder() - Method in interface org.openscience.cdk.interfaces.IStereoElement: The configuration order of the stereochemistry.
getConnected(int) - Method in class org.openscience.cdk.signature.AtomSignature
getConnectedAtom(IAtom) - Method in class org.openscience.cdk.Bond: Returns the other atom in the bond, the atom is connected to the given atom.
getConnectedAtom(IAtom) - Method in class org.openscience.cdk.BondRef: Returns the other atom in the bond, the atom is connected to the given atom.
getConnectedAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.IBond: Deprecated.
use the method IBond.getOther(IAtom)
getConnectedAtom(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Returns the other atom in the bond, the atom is connected to the given atom.
getConnectedAtom(IAtom) - Method in class org.openscience.cdk.silent.Bond: Returns the other atom in the bond, the atom is connected to the given atom.
getConnectedAtomContainer() - Method in interface org.openscience.cdk.renderer.selection.IChemObjectSelection: Make an IAtomContainer where all the bonds only have atoms that are in the selection.
getConnectedAtoms(IAtom) - Method in class org.openscience.cdk.Bond: Returns all the atoms in the bond connected to the given atom.
getConnectedAtoms(IAtom) - Method in class org.openscience.cdk.BondRef: Returns all the atoms in the bond connected to the given atom.
getConnectedAtoms(IAtom) - Method in interface org.openscience.cdk.interfaces.IBond: Returns all the atoms in the bond connected to the given atom.
getConnectedAtoms(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Returns all the atoms in the bond connected to the given atom.
getConnectedAtoms(IAtom) - Method in class org.openscience.cdk.silent.Bond: Returns all the atoms in the bond connected to the given atom.
getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.AtomContainer: Returns the number of connected atoms (explicit degree) to the specified atom.
getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns the number of connected atoms (explicit degree) to the specified atom.
getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns the number of connected atoms (explicit degree) to the specified atom.
getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the number of connected atoms (explicit degree) to the specified atom.
getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal: Returns the number of connected atoms (explicit degree) to the specified atom.
getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer: Returns the number of connected atoms (explicit degree) to the specified atom.
getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer: Returns the number of connected atoms (explicit degree) to the specified atom.
getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugRing: Returns the number of connected atoms (explicit degree) to the specified atom.
getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand: Returns the number of connected atoms (explicit degree) to the specified atom.
getConnectedAtomsCount(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Deprecated.
use IAtomContainer.getConnectedBondsCount(IAtom)
getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns the number of atoms connected to the given atom.
getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer: Returns the number of connected atoms (explicit degree) to the specified atom.
getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.AtomContainer: Returns the atoms connected connected to the specified atom by a bond.
getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns the atoms connected connected to the specified atom by a bond.
getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns the atoms connected connected to the specified atom by a bond.
getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the atoms connected connected to the specified atom by a bond.
getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal: Returns the atoms connected connected to the specified atom by a bond.
getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer: Returns the atoms connected connected to the specified atom by a bond.
getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer: Returns the atoms connected connected to the specified atom by a bond.
getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugRing: Returns the atoms connected connected to the specified atom by a bond.
getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand: Returns the atoms connected connected to the specified atom by a bond.
getConnectedAtomsList(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Returns the atoms connected connected to the specified atom by a bond.
getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns an ArrayList of all atoms connected to the given atom.
getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer: Returns the atoms connected connected to the specified atom by a bond.
getConnectedBondsCount(int) - Method in class org.openscience.cdk.AtomContainer: Returns the number of connected bonds (explicit degree) to atom at the specified index.
getConnectedBondsCount(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Returns the number of connected bonds (explicit degree) to atom at the specified index.
getConnectedBondsCount(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns the number of connected atoms (degree) to the given atom.
getConnectedBondsCount(int) - Method in class org.openscience.cdk.silent.AtomContainer: Returns the number of connected bonds (explicit degree) to atom at the specified index.
getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.AtomContainer: Returns the number of connected bonds (explicit degree) to the specified atom.
getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns the number of connected bonds (explicit degree) to the specified atom.
getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns the number of connected bonds (explicit degree) to the specified atom.
getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the number of connected bonds (explicit degree) to the specified atom.
getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal: Returns the number of connected bonds (explicit degree) to the specified atom.
getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer: Returns the number of connected bonds (explicit degree) to the specified atom.
getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer: Returns the number of connected bonds (explicit degree) to the specified atom.
getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugRing: Returns the number of connected bonds (explicit degree) to the specified atom.
getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand: Returns the number of connected bonds (explicit degree) to the specified atom.
getConnectedBondsCount(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Returns the number of connected bonds (explicit degree) to the specified atom.
getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns the number of Bonds for a given Atom.
getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer: Returns the number of connected bonds (explicit degree) to the specified atom.
getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.AtomContainer: Returns the bonds connected connected to the specified atom.
getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns the bonds connected connected to the specified atom.
getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns the bonds connected connected to the specified atom.
getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the bonds connected connected to the specified atom.
getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal: Returns the bonds connected connected to the specified atom.
getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer: Returns the bonds connected connected to the specified atom.
getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer: Returns the bonds connected connected to the specified atom.
getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugRing: Returns the bonds connected connected to the specified atom.
getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand: Returns the bonds connected connected to the specified atom.
getConnectedBondsList(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Returns the bonds connected connected to the specified atom.
getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns an ArrayList of all Bonds connected to the given atom.
getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer: Returns the bonds connected connected to the specified atom.
getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.AtomContainer: Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.
getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.
getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.
getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.
getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal: Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.
getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer: Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.
getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer: Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.
getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugRing: Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.
getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand: Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.
getConnectedElectronContainersList(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.
getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns an ArrayList of all electronContainers connected to the given atom.
getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer: Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.
getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.AtomContainer: Returns the number of lone pairs connected to the specified atom.
getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns the number of lone pairs connected to the specified atom.
getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns the number of lone pairs connected to the specified atom.
getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the number of lone pairs connected to the specified atom.
getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal: Returns the number of lone pairs connected to the specified atom.
getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer: Returns the number of lone pairs connected to the specified atom.
getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer: Returns the number of lone pairs connected to the specified atom.
getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugRing: Returns the number of lone pairs connected to the specified atom.
getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand: Returns the number of lone pairs connected to the specified atom.
getConnectedLonePairsCount(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Returns the number of lone pairs connected to the specified atom.
getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns the number of LonePairs for a given Atom.
getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer: Returns the number of lone pairs connected to the specified atom.
getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.AtomContainer: Returns the lone pairs connected connected to the specified atom.
getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns the lone pairs connected connected to the specified atom.
getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns the lone pairs connected connected to the specified atom.
getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the lone pairs connected connected to the specified atom.
getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal: Returns the lone pairs connected connected to the specified atom.
getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer: Returns the lone pairs connected connected to the specified atom.
getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer: Returns the lone pairs connected connected to the specified atom.
getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugRing: Returns the lone pairs connected connected to the specified atom.
getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand: Returns the lone pairs connected connected to the specified atom.
getConnectedLonePairsList(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Returns the lone pairs connected connected to the specified atom.
getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns the array of lone pairs connected to an atom.
getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer: Returns the lone pairs connected connected to the specified atom.
getConnectedRings(IRing) - Method in class org.openscience.cdk.debug.DebugRingSet: Returns all the rings in the RingSet that share one or more atoms with a given ring.
getConnectedRings(IRing) - Method in interface org.openscience.cdk.interfaces.IRingSet: Returns all the rings in the RingSet that share one or more atoms with a given ring.
getConnectedRings(IRing) - Method in class org.openscience.cdk.RingSet: Returns all the rings in the RingSet that share one or more atoms with a given ring.
getConnectedRings(IRing) - Method in class org.openscience.cdk.silent.RingSet: Returns all the rings in the RingSet that share one or more atoms with a given ring.
getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.AtomContainer: Returns the number of single electrons connected to the specified atom.
getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns the number of single electrons connected to the specified atom.
getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns the number of single electrons connected to the specified atom.
getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the number of single electrons connected to the specified atom.
getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal: Returns the number of single electrons connected to the specified atom.
getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer: Returns the number of single electrons connected to the specified atom.
getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer: Returns the number of single electrons connected to the specified atom.
getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugRing: Returns the number of single electrons connected to the specified atom.
getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand: Returns the number of single electrons connected to the specified atom.
getConnectedSingleElectronsCount(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Returns the number of single electrons connected to the specified atom.
getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns the sum of the SingleElectron for a given Atom.
getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer: Returns the number of single electrons connected to the specified atom.
getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.AtomContainer: Returns the single electrons connected connected to the specified atom.
getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns the single electrons connected connected to the specified atom.
getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns the single electrons connected connected to the specified atom.
getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the single electrons connected connected to the specified atom.
getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal: Returns the single electrons connected connected to the specified atom.
getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer: Returns the single electrons connected connected to the specified atom.
getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer: Returns the single electrons connected connected to the specified atom.
getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugRing: Returns the single electrons connected connected to the specified atom.
getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand: Returns the single electrons connected connected to the specified atom.
getConnectedSingleElectronsList(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Returns the single electrons connected connected to the specified atom.
getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns an array of all SingleElectron connected to the given atom.
getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer: Returns the single electrons connected connected to the specified atom.
getConnectivity(int, int) - Method in interface org.openscience.cdk.group.Refinable: Get the connectivity between two vertices as an integer, to allow for multigraphs : so a single edge is 1, a double edge 2, etc.
getConsumer() - Method in class org.openscience.cdk.structgen.maygen.Maygen
getContainer() - Method in class org.openscience.cdk.Atom: Access the IAtomContainer of which this atom is a member of.
getContainer() - Method in class org.openscience.cdk.AtomRef: Access the IAtomContainer of which this atom is a member of.
getContainer() - Method in class org.openscience.cdk.Bond
getContainer() - Method in class org.openscience.cdk.BondRef
getContainer() - Method in class org.openscience.cdk.debug.DebugAtom: Access the IAtomContainer of which this atom is a member of.
getContainer() - Method in interface org.openscience.cdk.interfaces.IAtom: Access the IAtomContainer of which this atom is a member of.
getContainer() - Method in interface org.openscience.cdk.interfaces.IBond
getContainer() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Access the IAtomContainer of which this atom is a member of.
getContainer() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
getContainer() - Method in class org.openscience.cdk.silent.Atom: Access the IAtomContainer of which this atom is a member of.
getContainer() - Method in class org.openscience.cdk.silent.Bond
getContainer(IAtomContainer, IAtom) - Method in class org.openscience.cdk.tools.StructureResonanceGenerator: Get the container which the atom is found on resonance from a IAtomContainer.
getContainer(IAtomContainer, IBond) - Method in class org.openscience.cdk.tools.StructureResonanceGenerator: Get the container which the bond is found on resonance from a IAtomContainer.
getContainers(IAtomContainer) - Method in class org.openscience.cdk.tools.StructureResonanceGenerator: Get the container which is found resonance from a IAtomContainer.
getCoordinatesFromGridPoint(int) - Method in class org.openscience.cdk.tools.GridGenerator: Method calculates coordinates from a given grid array position.
getCoordinatesFromGridPoint(Point3d) - Method in class org.openscience.cdk.tools.GridGenerator: Method calculates coordinates from a given grid point.
getCount() - Method in class org.openscience.cdk.structgen.maygen.Maygen
getCount() - Method in class org.openscience.cdk.validate.ValidationReport: Returns the number of CDK errors.
getCount(int) - Method in interface org.openscience.cdk.fingerprint.ICountFingerprint: Returns the count value for the bin with the given index.
getCount(int) - Method in class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
getCountableMACCSSMARTS() - Static method in class org.openscience.cdk.fingerprint.StandardSubstructureSets: Subset of the MACCS fingerprint definitions.
getCountBasis() - Method in class org.openscience.cdk.math.qm.Orbitals: Set the count of bases
getCountElectrons() - Method in class org.openscience.cdk.math.qm.Orbitals: Gets the count of electrons, which occupies the orbitals
getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.AtomPairs2DFingerprinter
getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter: Calculates the circular fingerprint for the given IAtomContainer, and returns a datastructure that enumerates all of the fingerprints, and their counts (i.e.
getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.EStateFingerprinter: Returns the count fingerprint for the given IAtomContainer.
getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter: Returns the count fingerprint for the given IAtomContainer.
getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.Fingerprinter
getCountFingerprint(IAtomContainer) - Method in interface org.openscience.cdk.fingerprint.IFingerprinter: Returns the count fingerprint for the given IAtomContainer.
getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.LingoFingerprinter
getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.MACCSFingerprinter: Returns the count fingerprint for the given IAtomContainer.
getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.PubchemFingerprinter: Returns the count fingerprint for the given IAtomContainer.
getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.ShortestPathFingerprinter
getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.SignatureFingerprinter
getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.SubstructureFingerprinter: Returns the count fingerprint for the given IAtomContainer.
getCountForHash(int) - Method in interface org.openscience.cdk.fingerprint.ICountFingerprint: Get the number of times a certain hash exists in the fingerprint.
getCountForHash(int) - Method in class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
getCountOrbitals() - Method in class org.openscience.cdk.math.qm.Orbitals: Returns the count of orbitals
getCovalentRadius() - Method in class org.openscience.cdk.AtomRef: Returns the covalent radius for this AtomType.
getCovalentRadius() - Method in class org.openscience.cdk.AtomType: Returns the covalent radius for this AtomType.
getCovalentRadius() - Method in class org.openscience.cdk.debug.DebugAtom: Returns the covalent radius for this AtomType.
getCovalentRadius() - Method in class org.openscience.cdk.debug.DebugAtomType: Returns the covalent radius for this AtomType.
getCovalentRadius() - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Returns the covalent radius for this AtomType.
getCovalentRadius() - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Returns the covalent radius for this AtomType.
getCovalentRadius() - Method in interface org.openscience.cdk.interfaces.IAtomType: Returns the covalent radius for this AtomType.
getCovalentRadius() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Returns the covalent radius for this AtomType.
getCovalentRadius() - Method in class org.openscience.cdk.silent.AtomType: Returns the covalent radius for this AtomType.
getCovalentRadius(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable: Get the covalent radius for an element.
getCreatormap() - Method in class org.openscience.cdk.io.RssWriter
getCrystal() - Method in class org.openscience.cdk.ChemModel: Gets the Crystal contained in this ChemModel.
getCrystal() - Method in class org.openscience.cdk.debug.DebugChemModel: Gets the Crystal contained in this ChemModel.
getCrystal() - Method in interface org.openscience.cdk.interfaces.IChemModel: Gets the Crystal contained in this ChemModel.
getCrystal() - Method in class org.openscience.cdk.silent.ChemModel: Gets the Crystal contained in this ChemModel.
getCTab1() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.QueryProcessor: Deprecated.
getCTab1() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.TargetProcessor: Deprecated.
getCTab2() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.QueryProcessor: Deprecated.
getCTab2() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.TargetProcessor: Deprecated.
getCTerminus() - Method in class org.openscience.cdk.AminoAcid: Retrieves the C-terminus atom.
getCTerminus() - Method in class org.openscience.cdk.debug.DebugAminoAcid: Retrieves the C-terminus atom.
getCTerminus() - Method in interface org.openscience.cdk.interfaces.IAminoAcid: Retrieves the C-terminus atom.
getCTerminus() - Method in class org.openscience.cdk.silent.AminoAcid: Retrieves the C-terminus atom.
getCurr() - Method in class org.openscience.cdk.smiles.InvPair: Get the current seed.
getCurrentMaxBondOrder(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker: Returns the currently maximum formable bond order for this atom.
getCurrentPermutation() - Method in class org.openscience.cdk.graph.Permutor: Get the permutation that is currently being used.
getCurrentPermutation() - Method in class org.openscience.cdk.smsd.labelling.Permutor: Deprecated.

Get the permutation that is currently being used.
getCurrentRecord() - Method in class org.openscience.cdk.io.random.RandomAccessReader
getCyclesList(int[], int[], int, int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: For maximal and tested rows, getting the cycle lists
getCyclicFragmentsContainer() - Method in class org.openscience.cdk.graph.SpanningTree: Returns an IAtomContainer which contains all the atoms and bonds which are involved in ring systems.
getDatemap() - Method in class org.openscience.cdk.io.RssWriter
getDBE(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Returns the number of double bond equivalents in this molecule.
getDeclaringClass() - Method in class org.openscience.cdk.DynamicFactory.BasicCreator: Access the implementation of this class.
getDeclaringClass() - Method in interface org.openscience.cdk.DynamicFactory.Creator: Access the implementation of this class.
getDEdgesSize() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph: Deprecated.
getDefault() - Method in class org.openscience.cdk.renderer.generators.AtomNumberGenerator.AtomColorer: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.AtomNumberGenerator.AtomNumberTextColor: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.AtomNumberGenerator.ColorByType: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.AtomNumberGenerator.Offset: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.AtomNumberGenerator.WillDrawAtomNumbers: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.AtomColor: Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.AtomColorer: Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.AtomRadius: Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.ColorByType: Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.CompactAtom: Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.CompactShape: Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.KekuleStructure: Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.ShowEndCarbons: Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.ShowExplicitHydrogens: Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator.BondDistance: Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator.BondWidth: Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator.DefaultBondColor: Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator.TowardsRingCenterProportion: Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator.WedgeWidth: Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ArrowHeadWidth: Returns the default arrow head width.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.BackgroundColor: Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.BondLength: Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.FitToScreen: Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.FontName: Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ForegroundColor: Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.Margin: Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.Scale: Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ShowMoleculeTitle: Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ShowReactionTitle: Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ShowTooltip: Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.UseAntiAliasing: Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.UsedFontStyle: Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ZoomFactor: Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BoundsGenerator.BoundsColor: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.ExtendedAtomGenerator.ShowAtomTypeNames: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.ExtendedAtomGenerator.ShowImplicitHydrogens: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.HighlightGenerator.HighlightPalette: Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.HighlightGenerator.HighlightRadius: Returns the default value.
getDefault() - Method in interface org.openscience.cdk.renderer.generators.IGeneratorParameter: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.MappingGenerator.AtomAtomMappingLineColor: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.MappingGenerator.MappingLineWidth: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.MappingGenerator.ShowAtomAtomMapping: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.ReactionSceneGenerator.ArrowHeadWidth: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.ReactionSceneGenerator.ShowReactionBoxes: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.RingGenerator.CDKStyleAromaticity: Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.RingGenerator.MaxDrawableAromaticRing: The maximum default ring size for which an aromatic ring should be drawn.
getDefault() - Method in class org.openscience.cdk.renderer.generators.RingGenerator.RingProportion: Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.RingGenerator.ShowAromaticity: Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.AnnotationColor: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.AnnotationDistance: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.AnnotationFontScale: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.AtomColor: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.BondSeparation: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.DashSection: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.DelocalisedDonutsBondDisplay: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.DeuteriumSymbol: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.FancyBoldWedges: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.FancyHashedWedges: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.ForceDelocalisedBondDisplay: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.HashSpacing: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.Highlighting: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.OmitMajorIsotopes: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.OuterGlowWidth: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.PseudoFontStyle: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.SgroupBracketDepth: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.SgroupFontScale: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.StrokeRatio: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.SymbolMarginRatio: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.Visibility: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.WaveSpacing: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.WedgeRatio: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.RendererModel.ColorHash: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.RendererModel.ExternalHighlightColor: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.RendererModel.MarkedOutput: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.RendererModel.Padding: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.RendererModel.SelectionColor: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.RendererModel.TitleColor: Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.RendererModel.TitleFontScale: Gets the default value for this parameter.
getDefault(Class<T>) - Method in class org.openscience.cdk.renderer.RendererModel: Returns the default value for the IGeneratorParameter for the active IRenderer.
getDefaultSetting() - Method in class org.openscience.cdk.io.setting.IOSetting
getDefaultSpecial(IAtom) - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor.JPlogPCalculator: Determines and returns the SS (subsection) portion of the atomtype integer for a "Default" ie not C,N,O,H,F Atom
getDefaultStretchBendData(int, int, int) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94ParametersCall: Gets the bond-angle interaction parameter set.
getDefinition() - Method in class org.openscience.cdk.dict.Entry
getDEgdes() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph: Deprecated.
getDegree() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom: Deprecated.
getDescription() - Method in class org.openscience.cdk.dict.Entry
getDescriptorClassNameByInterface(String, String[]) - Static method in class org.openscience.cdk.qsar.DescriptorEngine: Returns a list containing the classes that implement a specific interface.
getDescriptorClassNameByPackage(String, String[]) - Static method in class org.openscience.cdk.qsar.DescriptorEngine: Returns a list containing the classes found in the specified descriptor package.
getDescriptorClassNames() - Method in class org.openscience.cdk.qsar.DescriptorEngine: Returns a list containing the names of the classes implementing the descriptors.
getDescriptorInstances() - Method in class org.openscience.cdk.qsar.DescriptorEngine: Returns a List containing the instantiated descriptor classes.
getDescriptorMetadata() - Method in class org.openscience.cdk.dict.Entry
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor: Deprecated.
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInConjugatedPiSystemDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor: Deprecated.
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor: Returns an array of names for each descriptor value calculated.
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor: Returns an array of names for each descriptor value calculated.
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor: Returns an array of names for each descriptor value calculated.
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalCSP3Descriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor: Deprecated.
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor: Returns the names of the descriptors made available by this class.
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.SpiroAtomCountDescriptor: Returns an array of names for each descriptor value calculated.
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.substance.OxygenAtomCountDescriptor: Returns an array of names for each descriptor value calculated.
getDescriptorNames() - Method in interface org.openscience.cdk.qsar.IDescriptor: Returns an array of names for each descriptor value calculated.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor: Returns the specific type of the FMF descriptor value.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalCSP3Descriptor: Returns the specific type of the Fsp3 descriptor value.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor: Deprecated.

Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor: Returns a type of return value calculated by this descriptor.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor: Returns a placeholder with the descriptor size and type.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.SpiroAtomCountDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in interface org.openscience.cdk.qsar.descriptors.substance.ISubstanceDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.substance.OxygenAtomCountDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in interface org.openscience.cdk.qsar.IMolecularDescriptor: Returns the specific type of the DescriptorResult object.
getDescriptorSpecifications() - Method in class org.openscience.cdk.qsar.DescriptorEngine: Returns the DescriptorSpecification objects for all available descriptors.
getDetails() - Method in class org.openscience.cdk.validate.ValidationTest
getDictionary() - Method in class org.openscience.cdk.dict.DictionaryHandler
getDictionary(String) - Method in class org.openscience.cdk.dict.DictionaryDatabase
getDictionaryClass(String) - Method in class org.openscience.cdk.qsar.DescriptorEngine: Returns the class(es) of the decsriptor as defined in the descriptor dictionary.
getDictionaryClass(IImplementationSpecification) - Method in class org.openscience.cdk.qsar.DescriptorEngine: Returns the class(es) of the descriptor as defined in the descriptor dictionary.
getDictionaryDefinition(String) - Method in class org.openscience.cdk.qsar.DescriptorEngine: Gets the definition of the descriptor.
getDictionaryDefinition(DescriptorSpecification) - Method in class org.openscience.cdk.qsar.DescriptorEngine: Gets the definition of the descriptor.
getDictionaryEntries(String) - Method in class org.openscience.cdk.dict.DictionaryDatabase: Returns a String[] with the id's of all entries in the specified database.
getDictionaryEntry(String) - Method in class org.openscience.cdk.dict.DictionaryDatabase
getDictionaryNames() - Method in class org.openscience.cdk.dict.DictionaryDatabase: Returns a String[] with the names of the known dictionaries.
getDictionaryTitle(String) - Method in class org.openscience.cdk.qsar.DescriptorEngine: Gets the label (title) of the descriptor.
getDictionaryTitle(DescriptorSpecification) - Method in class org.openscience.cdk.qsar.DescriptorEngine: Gets the label (title) of the descriptor.
getDictionaryType(String) - Method in class org.openscience.cdk.qsar.DescriptorEngine: Returns the type of the descriptor as defined in the descriptor dictionary.
getDictionaryType(IImplementationSpecification) - Method in class org.openscience.cdk.qsar.DescriptorEngine: Returns the type of the descriptor as defined in the descriptor dictionary.
getDim() - Method in class org.openscience.cdk.tools.GridGenerator
getDimValue(int) - Method in interface org.openscience.cdk.graph.rebond.Bspt.Tuple
getDimValue(int) - Method in class org.openscience.cdk.graph.rebond.Point
getDirection() - Method in class org.openscience.cdk.debug.DebugReaction: Returns the direction of the reaction.
getDirection() - Method in interface org.openscience.cdk.interfaces.IReaction: Returns the IReaction.Direction of the reaction.
getDirection() - Method in class org.openscience.cdk.Reaction: Returns the direction of the reaction.
getDirection() - Method in class org.openscience.cdk.silent.Reaction: Returns the direction of the reaction.
getDisplay() - Method in class org.openscience.cdk.Bond: Access the bond display style.
getDisplay() - Method in class org.openscience.cdk.BondRef: Access the bond display style.
getDisplay() - Method in interface org.openscience.cdk.interfaces.IBond: Access the bond display style.
getDisplay() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Not used for query bonds.
getDisplay() - Method in class org.openscience.cdk.silent.Bond: Access the bond display style.
getDisplayMode() - Method in class org.openscience.cdk.renderer.GraphRendererModel: Get the display mode
getDrawCenter() - Method in class org.openscience.cdk.renderer.AbstractRenderer: Get the position on screen that the diagram will be drawn.
getDuration(long) - Static method in class org.openscience.cdk.tools.SwissArmyKnife: Deprecated.

Returns a String reporting the time passed during a given number of milliseconds.
getDuration(long, long) - Static method in class org.openscience.cdk.tools.SwissArmyKnife: Deprecated.

Returns a string reporting the time passed between startTime and endTime, both given in milliseconds, in hours, minutes, seconds and milliseconds.
getEAIDNumber(IAtomContainer) - Static method in class org.openscience.cdk.graph.invariant.HuLuIndexTool: Calculates the extended adjacency matrix index.
getEdge(int) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder: Deprecated.

Returns an edge of the query mol at a given position.
getEdge(int) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQuery: Deprecated.

Returns an edge of the query mol at a given position.
getEdge(INode, INode) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder: Deprecated.

Returns an edge associated between two nodes.
getEdge(INode, INode) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQuery: Deprecated.

Returns an edge associated between two nodes.
getEdgeLabel(int, int) - Method in class org.openscience.cdk.signature.AtomSignature
getEdges() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.NodeBuilder: Deprecated.

Returns List of Edges.
getEdges() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.INode: Deprecated.

Returns List of Edges.
getElapsedTimeInHours() - Method in class org.openscience.cdk.smsd.tools.TimeManager: Deprecated.

Returns Elapsed Time In Hours
getElapsedTimeInMilliSeconds() - Method in class org.openscience.cdk.smsd.tools.TimeManager: Deprecated.

Returns Elapsed Time In Mill Seconds
getElapsedTimeInMinutes() - Method in class org.openscience.cdk.smsd.tools.TimeManager: Deprecated.

Returns Elapsed Time In Minutes
getElapsedTimeInSeconds() - Method in class org.openscience.cdk.smsd.tools.TimeManager: Deprecated.

Return Elapsed Time In Seconds
getElectronContainer(int) - Method in class org.openscience.cdk.AtomContainer: Returns the ElectronContainer at position number in the container.
getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns the ElectronContainer at position number in the container.
getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns the ElectronContainer at position number in the container.
getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the ElectronContainer at position number in the container.
getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugCrystal: Returns the ElectronContainer at position number in the container.
getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugMonomer: Returns the ElectronContainer at position number in the container.
getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugPolymer: Returns the ElectronContainer at position number in the container.
getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugRing: Returns the ElectronContainer at position number in the container.
getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugStrand: Returns the ElectronContainer at position number in the container.
getElectronContainer(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Returns the ElectronContainer at position number in the container.
getElectronContainer(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns the ElectronContainer at position number in the container.
getElectronContainer(int) - Method in class org.openscience.cdk.silent.AtomContainer: Returns the ElectronContainer at position number in the container.
getElectronContainerArray(List<IElectronContainer>) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Constructs an array of Atom objects from a List of Atom objects.
getElectronContainerArray(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Constructs an array of Bond objects from an AtomContainer.
getElectronContainerCount() - Method in class org.openscience.cdk.AtomContainer: Returns the number of ElectronContainers in this Container.
getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns the number of ElectronContainers in this Container.
getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns the number of ElectronContainers in this Container.
getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the number of ElectronContainers in this Container.
getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugCrystal: Returns the number of ElectronContainers in this Container.
getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugMonomer: Returns the number of ElectronContainers in this Container.
getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugPolymer: Returns the number of ElectronContainers in this Container.
getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugRing: Returns the number of ElectronContainers in this Container.
getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugStrand: Returns the number of ElectronContainers in this Container.
getElectronContainerCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Returns the number of ElectronContainers in this Container.
getElectronContainerCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns the number of ElectronContainers in this Container.
getElectronContainerCount() - Method in class org.openscience.cdk.silent.AtomContainer: Returns the number of ElectronContainers in this Container.
getElectronCount() - Method in class org.openscience.cdk.Association: Returns the number of electrons in a Association.
getElectronCount() - Method in class org.openscience.cdk.BondRef: Returns the number of electrons in this electron container.
getElectronCount() - Method in class org.openscience.cdk.debug.DebugBond: Returns the number of electrons in this electron container.
getElectronCount() - Method in class org.openscience.cdk.debug.DebugElectronContainer: Returns the number of electrons in this electron container.
getElectronCount() - Method in class org.openscience.cdk.debug.DebugLonePair: Returns the number of electrons in a LonePair.
getElectronCount() - Method in class org.openscience.cdk.debug.DebugSingleElectron: Returns the number of electrons in this SingleElectron.
getElectronCount() - Method in class org.openscience.cdk.ElectronContainer: Returns the number of electrons in this electron container.
getElectronCount() - Method in interface org.openscience.cdk.interfaces.IElectronContainer: Returns the number of electrons in this electron container.
getElectronCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Returns the number of electrons in this bond
getElectronCount() - Method in class org.openscience.cdk.LonePair: Returns the number of electrons in a LonePair.
getElectronCount() - Method in class org.openscience.cdk.silent.ElectronContainer: Returns the number of electrons in this electron container.
getElectronCount() - Method in class org.openscience.cdk.silent.LonePair: Returns the number of electrons in a LonePair.
getElectronCount() - Method in class org.openscience.cdk.silent.SingleElectron: Returns the number of electrons in this SingleElectron.
getElectronCount() - Method in class org.openscience.cdk.SingleElectron: Returns the number of electrons in this SingleElectron.
getElectronegativity(String) - Method in class org.openscience.cdk.tools.AtomicProperties
getElement(int) - Method in class org.openscience.cdk.config.IsotopeFactory: Returns an element according to a given atomic number.
getElement(String) - Method in class org.openscience.cdk.config.IsotopeFactory: Returns an Element with a given element symbol.
getElementCount() - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable: Return the number of elements currently considered in the periodic table.
getElementCount(IMolecularFormula, String) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Occurrences of a given element in a molecular formula.
getElementCount(IMolecularFormula, IElement) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Checks a set of Nodes for the occurrence of the isotopes in the molecular formula from a particular IElement.
getElementCount(IMolecularFormula, IIsotope) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Occurrences of a given element from an isotope in a molecular formula.
getElements(String) - Static method in class org.openscience.cdk.tools.HOSECodeAnalyser
getElementSymbol(int) - Method in class org.openscience.cdk.config.IsotopeFactory: Returns the symbol matching the element with the given atomic number.
getEnd() - Method in class org.openscience.cdk.Bond: Access the end (or second) atom of the bond.
getEnd() - Method in class org.openscience.cdk.BondRef: Access the end (or second) atom of the bond.
getEnd() - Method in class org.openscience.cdk.debug.DebugBond: Access the end (or second) atom of the bond.
getEnd() - Method in interface org.openscience.cdk.interfaces.IBond: Access the end (or second) atom of the bond.
getEnd() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Access the end (or second) atom of the bond.
getEnd() - Method in class org.openscience.cdk.silent.Bond: Access the end (or second) atom of the bond.
getEndChainID() - Method in class org.openscience.cdk.debug.DebugPDBStructure: get the ending Chain identifier of this structure.
getEndChainID() - Method in interface org.openscience.cdk.interfaces.IPDBStructure: get the ending Chain identifier of this structure.
getEndChainID() - Method in class org.openscience.cdk.protein.data.PDBStructure: get the ending Chain identifier of this structure.
getEndChainID() - Method in class org.openscience.cdk.silent.PDBStructure: get the ending Chain identifier of this structure.
getEndColumn() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream: Get token end column number.
getEndColumn() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Get token end column number.
getEndInsertionCode() - Method in class org.openscience.cdk.debug.DebugPDBStructure: get the ending Code for insertion of residues of this structure.
getEndInsertionCode() - Method in interface org.openscience.cdk.interfaces.IPDBStructure: get the ending Code for insertion of residues of this structure.
getEndInsertionCode() - Method in class org.openscience.cdk.protein.data.PDBStructure: get the ending Code for insertion of residues of this structure.
getEndInsertionCode() - Method in class org.openscience.cdk.silent.PDBStructure: get the ending Code for insertion of residues of this structure.
getEndLine() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream: Get token end line number.
getEndLine() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Get token end line number.
getEndSequenceNumber() - Method in class org.openscience.cdk.debug.DebugPDBStructure: get the ending sequence number of this structure.
getEndSequenceNumber() - Method in interface org.openscience.cdk.interfaces.IPDBStructure: get the ending sequence number of this structure.
getEndSequenceNumber() - Method in class org.openscience.cdk.protein.data.PDBStructure: get the ending sequence number of this structure.
getEndSequenceNumber() - Method in class org.openscience.cdk.silent.PDBStructure: get the ending sequence number of this structure.
getEnergies() - Method in class org.openscience.cdk.math.qm.ClosedShellJob
getEnergies() - Method in class org.openscience.cdk.math.qm.OneElectronJob: Returns the energies of the orbitals
getEnergies(String, String, IBond.Order) - Method in class org.openscience.cdk.smsd.tools.BondEnergies: Deprecated.

Returns bond energy for a bond type, given atoms and bond type
getEnergies(IAtom, IAtom, IBond.Order) - Method in class org.openscience.cdk.smsd.tools.BondEnergies: Deprecated.

Returns bond energy for a bond type, given atoms and bond type
getEnergies(IBond) - Method in class org.openscience.cdk.smsd.tools.BondEnergies: Deprecated.

Returns bond energy for a bond type, given atoms and bond type
getEnergy() - Method in class org.openscience.cdk.smsd.helper.BondEnergy: Deprecated.

Returns the energy for this bond type.
getEnergyScore(int) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS: Deprecated.

Returns summation energy score of the disorder if the MCS is removed from the target and query graph.
getEnergyScore(int) - Method in class org.openscience.cdk.smsd.Isomorphism: Deprecated.

Returns summation energy score of the disorder if the MCS is removed from the target and query graph.
getEntries() - Method in class org.openscience.cdk.dict.Dictionary
getEntry(String) - Method in class org.openscience.cdk.dict.Dictionary
getEqual() - Method in class org.openscience.cdk.smsd.helper.BinaryTree: Deprecated.

Returns equal node
getEqualPerm(Permutation, int, int[][], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Getting the permutation making two rows identical.
getEquivalenceClassesSizeVector() - Method in class org.openscience.cdk.ringsearch.SSSRFinder: Deprecated.

Returns a vector containing the size of the "interchangeability" equivalence classes.
getEquivalentClass(double[]) - Method in class org.openscience.cdk.graph.invariant.EquivalentClassPartitioner: Get the final equivalent class.
getError() - Method in class org.openscience.cdk.validate.ValidationTest
getErrorCount() - Method in class org.openscience.cdk.validate.ValidationReport: Returns the number of failed tests.
getErrors() - Method in class org.openscience.cdk.validate.ValidationReport: Returns an array of ValidationTest errors.
getEuclideanDistance() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS: Deprecated.

Returns Euclidean Distance between query and target molecule.
getEuclideanDistance() - Method in class org.openscience.cdk.smsd.Isomorphism: Deprecated.

Returns Euclidean Distance between query and target molecule.
getExactMass() - Method in class org.openscience.cdk.AtomRef: Gets the ExactMass attribute of the Isotope object.
getExactMass() - Method in class org.openscience.cdk.debug.DebugAtom: Gets the ExactMass attribute of the Isotope object.
getExactMass() - Method in class org.openscience.cdk.debug.DebugAtomType: Gets the ExactMass attribute of the Isotope object.
getExactMass() - Method in class org.openscience.cdk.debug.DebugFragmentAtom: The exact mass of an FragmentAtom is defined as the sum of exact masses of the IAtom's in the fragment.
getExactMass() - Method in class org.openscience.cdk.debug.DebugIsotope: Gets the ExactMass attribute of the Isotope object.
getExactMass() - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Gets the ExactMass attribute of the Isotope object.
getExactMass() - Method in class org.openscience.cdk.FragmentAtom: The exact mass of an FragmentAtom is defined as the sum of exact masses of the IAtom's in the fragment.
getExactMass() - Method in interface org.openscience.cdk.interfaces.IIsotope: Gets the ExactMass attribute of the Isotope object.
getExactMass() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Gets the ExactMass attribute of the Isotope object.
getExactMass() - Method in class org.openscience.cdk.Isotope: Gets the ExactMass attribute of the Isotope object.
getExactMass() - Method in class org.openscience.cdk.silent.FragmentAtom: The exact mass of an FragmentAtom is defined as the sum of exact masses of the IAtom's in the fragment.
getExactMass() - Method in class org.openscience.cdk.silent.Isotope: Gets the ExactMass attribute of the Isotope object.
getExactMass(Integer, Integer) - Method in class org.openscience.cdk.config.IsotopeFactory: Get the exact mass of a specified isotope for an atom.
getExampleReactions() - Method in class org.openscience.cdk.dict.EntryReact
getException() - Method in class org.openscience.cdk.qsar.DescriptorValue
getExplicitHydrogenCount(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.normalize.SMSDNormalizer: Deprecated.

Returns The number of explicit hydrogens for a given IAtom.
getExplicitHydrogenCount(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator: Deprecated.

Returns The number of explicit hydrogens for a given IAtom.
getExpression() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Get the atom-expression predicate for this query atom.
getExpression() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Access the bond expression predicate associated with this query bond.
getExtendedAdjacencyMatrix(IAtomContainer) - Static method in class org.openscience.cdk.graph.invariant.HuLuIndexTool: Compute the extended adjacency matrix as described in [Chang-Yu Hu and Lu Xu. J. Chem. Inf. Comput. Sci.. 1996. 36].
getExtendGrid() - Method in class org.openscience.cdk.tools.GridGenerator
getExtension() - Method in class org.openscience.cdk.isomorphism.mcss.RNode: Gets the extension attribute of the RNode object.
getExtension() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode: Deprecated.

Gets the extension attribute of the RNode object
getExternalSelectedPart() - Method in class org.openscience.cdk.renderer.RendererModel: Get externally selected atoms.
getExternalSubset(String, String) - Method in class org.openscience.cdk.io.cml.CMLResolver: Not implemented: always returns null.
getFarthestAtom(Point3d, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D: Gets the farthestAtom attribute of the AtomPlacer3D object.
getFfTypes() - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator: gives a list of possible force field types
getFfTypes() - Method in class org.openscience.cdk.modeling.builder3d.ModelBuilder3D: Gives a list of possible force field types.
getFinalMapping() - Method in class org.openscience.cdk.smsd.helper.FinalMappings: Deprecated.

Returns the stored mappings
getFinalMapping() - Method in interface org.openscience.cdk.smsd.interfaces.IFinalMapping: Deprecated.

Returns the stored mappings
getFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.AbstractFingerprinter: Generate a binary fingerprint as a bit.
getFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter
getFingerprint(IAtomContainer) - Method in interface org.openscience.cdk.fingerprint.IFingerprinter: Generate a binary fingerprint as a bit.
getFingerprintAsBytes() - Method in class org.openscience.cdk.fingerprint.PubchemFingerprinter: Returns the fingerprint generated for a molecule as a byte[].
getFinishedPercentage() - Method in class org.openscience.cdk.formula.MolecularFormulaGenerator: Returns a value between 0.0 and 1.0 indicating what portion of the search space has been examined so far by this MolecularFormulaGenerator.
getFirst() - Method in interface org.openscience.cdk.group.DiscretePartitionRefiner: Get the first permutation reached by the search.
getFirstAtom() - Method in class org.openscience.cdk.AtomContainer: Returns the atom at position 0 in the container.
getFirstAtom() - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns the atom at position 0 in the container.
getFirstAtom() - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns the atom at position 0 in the container.
getFirstAtom() - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the atom at position 0 in the container.
getFirstAtom() - Method in class org.openscience.cdk.debug.DebugCrystal: Returns the atom at position 0 in the container.
getFirstAtom() - Method in class org.openscience.cdk.debug.DebugMonomer: Returns the atom at position 0 in the container.
getFirstAtom() - Method in class org.openscience.cdk.debug.DebugPolymer: Returns the atom at position 0 in the container.
getFirstAtom() - Method in class org.openscience.cdk.debug.DebugRing: Returns the atom at position 0 in the container.
getFirstAtom() - Method in class org.openscience.cdk.debug.DebugStrand: Returns the atom at position 0 in the container.
getFirstAtom() - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Deprecated.
use IAtomContainer.getAtom(int)
getFirstAtom() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns the atom at position 0 in the container.
getFirstAtom() - Method in class org.openscience.cdk.signature.Orbit: Gets the first atom index of the orbit.
getFirstAtom() - Method in class org.openscience.cdk.silent.AtomContainer: Returns the atom at position 0 in the container.
getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler: Deprecated.

Returns one of the best matches with atoms mapped.
getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler: Deprecated.

Returns one of the best matches with atoms mapped.
getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler: Deprecated.

Returns one of the best matches with atoms mapped.
getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler: Deprecated.

Returns one of the best matches with atoms mapped.
getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler: Deprecated.

Returns one of the best matches with atoms mapped.
getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler: Deprecated.

Returns one of the best matches with atoms mapped.
getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler: Deprecated.

Returns one of the best matches with atoms mapped.
getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS: Deprecated.

Returns one of the best matches with atoms mapped.
getFirstAtomMapping() - Method in interface org.openscience.cdk.smsd.interfaces.IMCSBase: Deprecated.

Returns one of the best matches with atoms mapped.
getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.Isomorphism: Deprecated.

Returns one of the best matches with atoms mapped.
getFirstAttachmentPoint() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroup: Get the first attachment point of the RGroup.
getFirstAttachmentPoint() - Method in class org.openscience.cdk.isomorphism.matchers.RGroup
getFirstBondMap() - Method in class org.openscience.cdk.smsd.Isomorphism: Deprecated.
getFirstGraphSize() - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Returns the size of the first of the two compared graphs.
getFirstGraphSize() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph: Deprecated.

Returns the size of the first of the two compared graphs.
getFirstInCell(int) - Method in class org.openscience.cdk.group.Partition: Gets the first element in the specified cell.
getFirstMap(IAtomContainer) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper: Deprecated.

Returns first solution map.
getFirstMap(IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper: Deprecated.

Returns first solution map.
getFirstMap(IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper: Deprecated.

Returns first solution map.
getFirstMap(TargetProperties) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper: Deprecated.

Returns first solution map.
getFirstMap(TargetProperties) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper: Deprecated.

Returns first solution map.
getFirstMap(TargetProperties) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper: Deprecated.

Returns first solution map.
getFirstMapping() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler: Deprecated.

Returns one of the best matches with atom indexes mapped.
getFirstMapping() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler: Deprecated.

Returns one of the best matches with atom indexes mapped.
getFirstMapping() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler: Deprecated.

Returns one of the best matches with atom indexes mapped.
getFirstMapping() - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler: Deprecated.

Returns one of the best matches with atom indexes mapped.
getFirstMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler: Deprecated.

Returns one of the best matches with atom indexes mapped.
getFirstMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler: Deprecated.

Returns one of the best matches with atom indexes mapped.
getFirstMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler: Deprecated.

Returns one of the best matches with atom indexes mapped.
getFirstMapping() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS: Deprecated.

Returns one of the best matches with atom indexes mapped.
getFirstMapping() - Method in interface org.openscience.cdk.smsd.interfaces.IMCSBase: Deprecated.

Returns one of the best matches with atom indexes mapped.
getFirstMapping() - Method in class org.openscience.cdk.smsd.Isomorphism: Deprecated.

Returns one of the best matches with atom indexes mapped.
getFirstPoint() - Method in class org.openscience.cdk.sgroup.SgroupBracket: First point of the bracket (x1,y1).
getFlag(int) - Method in class org.openscience.cdk.ChemObject: Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugAtom: Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugAtomType: Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugBond: Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugChemFile: Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugChemModel: Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugChemObject: Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugChemSequence: Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugCrystal: Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugElectronContainer: Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugElement: Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugIsotope: Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugLonePair: Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugMapping: Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugMonomer: Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugPolymer: Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugReaction: Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugReactionScheme: Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugReactionSet: Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugRing: Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugSingleElectron: Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugStrand: Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugSubstance: Returns the value of a given flag.
getFlag(int) - Method in interface org.openscience.cdk.interfaces.IChemObject: Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject: Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom: Deprecated.
getFlag(int) - Method in class org.openscience.cdk.silent.ChemObject: Returns the value of a given flag.
getFlags() - Method in class org.openscience.cdk.ChemObject: Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugAtom: Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugAtomType: Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugBond: Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugChemFile: Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugChemModel: Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugChemObject: Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugChemSequence: Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugCrystal: Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugElectronContainer: Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugElement: Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugIsotope: Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugLonePair: Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugMapping: Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugMonomer: Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugPolymer: Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugReaction: Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugReactionScheme: Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugReactionSet: Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugRing: Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugSingleElectron: Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugStrand: Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugSubstance: Returns the whole set of flags.
getFlags() - Method in interface org.openscience.cdk.interfaces.IChemObject: Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject: Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.silent.ChemObject: Returns the whole set of flags.
getFlagValue() - Method in class org.openscience.cdk.ChemObject: Access the internal value used to store the flags.
getFlagValue() - Method in interface org.openscience.cdk.interfaces.IChemObject: Access the internal value used to store the flags.
getFlagValue() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject: Access the internal value used to store the flags.
getFlagValue() - Method in class org.openscience.cdk.silent.ChemObject: Access the internal value used to store the flags.
getFluorineSpecial(IAtom) - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor.JPlogPCalculator: Determines and returns the SS (subsection) portion of the atomtype integer for a Fluorine Atom
getFocus() - Method in interface org.openscience.cdk.interfaces.IStereoElement: The focus atom or bond at the 'centre' of the stereo-configuration.
getFolding() - Method in class org.openscience.cdk.fingerprint.model.Bayesian: Access to the fingerprint folding extent.
getFont() - Method in class org.openscience.cdk.renderer.font.AWTFontManager: Get the current font.
getFontName() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager: Get the font family name used in this font manager.
getFontSizeForZoom(double) - Method in class org.openscience.cdk.renderer.font.AbstractFontManager: For a particular zoom, get the appropriate font size.
getFontStyle() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager: Get the font style, defined in the IFontManager interface.
getForbidden() - Method in class org.openscience.cdk.isomorphism.mcss.RNode: Gets the forbidden attribute of the RNode object.
getForbidden() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode: Deprecated.

Gets the forbidden attribute of the RNode object
getFormalCharge() - Method in class org.openscience.cdk.AtomRef: Returns the formal charge of this atom.
getFormalCharge() - Method in class org.openscience.cdk.AtomType: Returns the formal charge of this atom.
getFormalCharge() - Method in class org.openscience.cdk.debug.DebugAtom: Returns the formal charge of this atom.
getFormalCharge() - Method in class org.openscience.cdk.debug.DebugAtomType: Returns the formal charge of this atom.
getFormalCharge() - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Returns the formal charge of this atom.
getFormalCharge() - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Returns the formal charge of this atom.
getFormalCharge() - Method in interface org.openscience.cdk.interfaces.IAtomType: Returns the formal charge of this atom.
getFormalCharge() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Returns the formal charge of this atom.
getFormalCharge() - Method in class org.openscience.cdk.silent.AtomType: Returns the formal charge of this atom.
getFormalNeighbourCount() - Method in class org.openscience.cdk.AtomRef: Returns the formal neighbour count of this atom.
getFormalNeighbourCount() - Method in class org.openscience.cdk.AtomType: Returns the formal neighbour count of this atom.
getFormalNeighbourCount() - Method in class org.openscience.cdk.debug.DebugAtom: Returns the formal neighbour count of this atom.
getFormalNeighbourCount() - Method in class org.openscience.cdk.debug.DebugAtomType: Returns the formal neighbour count of this atom.
getFormalNeighbourCount() - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Returns the formal neighbour count of this atom.
getFormalNeighbourCount() - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Returns the formal neighbour count of this atom.
getFormalNeighbourCount() - Method in interface org.openscience.cdk.interfaces.IAtomType: Returns the formal neighbour count of this atom.
getFormalNeighbourCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Returns the formal neighbour count of this atom.
getFormalNeighbourCount() - Method in class org.openscience.cdk.silent.AtomType: Returns the formal neighbour count of this atom.
getFormat() - Method in class org.openscience.cdk.io.CDKSourceCodeWriter
getFormat() - Method in class org.openscience.cdk.io.CIFReader
getFormat() - Method in class org.openscience.cdk.io.CMLReader
getFormat() - Method in class org.openscience.cdk.io.CMLWriter
getFormat() - Method in class org.openscience.cdk.io.CrystClustReader
getFormat() - Method in class org.openscience.cdk.io.CrystClustWriter
getFormat() - Method in class org.openscience.cdk.io.CTXReader
getFormat() - Method in class org.openscience.cdk.io.GamessReader
getFormat() - Method in class org.openscience.cdk.io.Gaussian03Reader
getFormat() - Method in class org.openscience.cdk.io.Gaussian98Reader
getFormat() - Method in class org.openscience.cdk.io.GhemicalMMReader
getFormat() - Method in class org.openscience.cdk.io.HINReader
getFormat() - Method in class org.openscience.cdk.io.HINWriter
getFormat() - Method in interface org.openscience.cdk.io.IChemObjectIO: Returns the IResourceFormat class for this IO class.
getFormat() - Method in class org.openscience.cdk.io.INChIPlainTextReader
getFormat() - Method in class org.openscience.cdk.io.INChIReader
getFormat() - Method in class org.openscience.cdk.io.iterator.event.EventCMLReader
getFormat() - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundASNReader
getFormat() - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader
getFormat() - Method in class org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader
getFormat() - Method in class org.openscience.cdk.io.iterator.IteratingSDFReader
getFormat() - Method in class org.openscience.cdk.io.iterator.IteratingSMILESReader: Get the format for this reader.
getFormat() - Method in class org.openscience.cdk.io.MDLReader: Deprecated.
getFormat() - Method in class org.openscience.cdk.io.MDLRXNReader: Deprecated.
getFormat() - Method in class org.openscience.cdk.io.MDLRXNV2000Reader
getFormat() - Method in class org.openscience.cdk.io.MDLRXNV3000Reader
getFormat() - Method in class org.openscience.cdk.io.MDLRXNWriter
getFormat() - Method in class org.openscience.cdk.io.MDLV2000Reader
getFormat() - Method in class org.openscience.cdk.io.MDLV2000Writer
getFormat() - Method in class org.openscience.cdk.io.MDLV3000Reader
getFormat() - Method in class org.openscience.cdk.io.MDLV3000Writer: Returns the IResourceFormat class for this IO class.
getFormat() - Method in class org.openscience.cdk.io.Mol2Reader
getFormat() - Method in class org.openscience.cdk.io.Mol2Writer
getFormat() - Method in class org.openscience.cdk.io.Mopac7Reader
getFormat() - Method in class org.openscience.cdk.io.MoSSOutputReader: Returns the IResourceFormat class for this IO class.
getFormat() - Method in class org.openscience.cdk.io.PCCompoundASNReader
getFormat() - Method in class org.openscience.cdk.io.PCCompoundXMLReader
getFormat() - Method in class org.openscience.cdk.io.PCSubstanceXMLReader
getFormat() - Method in class org.openscience.cdk.io.PDBReader
getFormat() - Method in class org.openscience.cdk.io.PDBWriter
getFormat() - Method in class org.openscience.cdk.io.PMPReader
getFormat() - Method in class org.openscience.cdk.io.program.GaussianInputWriter
getFormat() - Method in class org.openscience.cdk.io.program.Mopac7Writer
getFormat() - Method in class org.openscience.cdk.io.random.RandomAccessSDFReader
getFormat() - Method in class org.openscience.cdk.io.rdf.CDKOWLReader: Returns the IResourceFormat for this reader.
getFormat() - Method in class org.openscience.cdk.io.rdf.CDKOWLWriter: Returns the IResourceFormat for this writer.
getFormat() - Method in class org.openscience.cdk.io.RGroupQueryReader
getFormat() - Method in class org.openscience.cdk.io.RGroupQueryWriter: Returns output format.
getFormat() - Method in class org.openscience.cdk.io.RssWriter
getFormat() - Method in class org.openscience.cdk.io.SDFWriter
getFormat() - Method in class org.openscience.cdk.io.ShelXReader
getFormat() - Method in class org.openscience.cdk.io.ShelXWriter
getFormat() - Method in class org.openscience.cdk.io.SMILESReader
getFormat() - Method in class org.openscience.cdk.io.SMILESWriter
getFormat() - Method in class org.openscience.cdk.io.VASPReader
getFormat() - Method in class org.openscience.cdk.io.XYZReader
getFormat() - Method in class org.openscience.cdk.io.XYZWriter
getFormat() - Method in class org.openscience.cdk.io.ZMatrixReader
getFormatName() - Method in class org.openscience.cdk.io.formats.ABINITFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.Aces2Format: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.ADFFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.AlchemyFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.BGFFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.BSFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
getFormatName() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.CACheFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
getFormatName() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.CIFFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.CMLFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.CRK2DFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.CRK3DFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.CrystClustFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.CTXFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.DaltonFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.DMol3Format: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.DOCK5Format: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.FingerprintFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.GamessFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian03Format: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian90Format: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian92Format: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian94Format: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian95Format: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian98Format: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat
getFormatName() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.GROMOS96Format: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.HINFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.INChIFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat: Returns a one-lined format name of the format.
getFormatName() - Method in interface org.openscience.cdk.io.formats.IResourceFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.JaguarFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.JMEFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MacroModelFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MDLFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MDLRXNV2000Format: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MDLV2000Format: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MDLV3000Format: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MMODFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.Mol2Format: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC7Format: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC93Format: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC97Format: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MPQCFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.NWChemFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.PCModelFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.PDBFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.PDBMLFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.PMPFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.POVRayFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.PQSChemFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.QChemFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.RawCopyFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.SDFFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.ShelXFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.SMARTSFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.SMILESFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.SpartanFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.SVGFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.VASPFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.ViewmolFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.XEDFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.XYZFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.YasaraFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.ZindoFormat: Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat: Returns a one-lined format name of the format.
getFormats() - Method in class org.openscience.cdk.io.FormatFactory: Returns the list of recognizable formats.
getFormats() - Method in class org.openscience.cdk.io.ReaderFactory
getFormula() - Method in class org.openscience.cdk.formula.IsotopeContainer: Get the IMolecularFormula object of this container.
getFormula() - Method in class org.openscience.cdk.structgen.maygen.Maygen
getFormulaList(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Generating list of formulae for the input fuzzy formula
getFormulas() - Method in class org.openscience.cdk.formula.IsotopeContainer: Access the formulas of this isotope container.
getFP(int) - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter: Returns the requested fingerprint.
getFPCount() - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter: Returns the number of fingerprints generated.
getFractionalPoint3d() - Method in class org.openscience.cdk.Atom: Returns a point specifying the location of this atom in a Crystal unit cell.
getFractionalPoint3d() - Method in class org.openscience.cdk.AtomRef: Returns a point specifying the location of this atom in a Crystal unit cell.
getFractionalPoint3d() - Method in class org.openscience.cdk.debug.DebugAtom: Returns a point specifying the location of this atom in a Crystal unit cell.
getFractionalPoint3d() - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Returns a point specifying the location of this atom in a Crystal unit cell.
getFractionalPoint3d() - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Returns a point specifying the location of this atom in a Crystal unit cell.
getFractionalPoint3d() - Method in interface org.openscience.cdk.interfaces.IAtom: Returns a point specifying the location of this atom in a Crystal unit cell.
getFractionalPoint3d() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Returns a point specifying the location of this atom in a Crystal unit cell.
getFractionalPoint3d() - Method in class org.openscience.cdk.silent.Atom: Returns a point specifying the location of this atom in a Crystal unit cell.
getFragment() - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Returns the fully expended form of the IFragmentAtom.
getFragment() - Method in class org.openscience.cdk.FragmentAtom
getFragment() - Method in interface org.openscience.cdk.interfaces.IFragmentAtom: Returns the fully expended form of the IFragmentAtom.
getFragment() - Method in class org.openscience.cdk.silent.FragmentAtom
getFragments() - Method in class org.openscience.cdk.fragment.ExhaustiveFragmenter: Get the fragments generated as SMILES strings.
getFragments() - Method in interface org.openscience.cdk.fragment.IFragmenter: Get the fragments generated as SMILES strings.
getFragments() - Method in class org.openscience.cdk.fragment.MurckoFragmenter: This returns the frameworks and ring systems from a Murcko fragmentation.
getFragmentsAsContainers() - Method in class org.openscience.cdk.fragment.ExhaustiveFragmenter: Get the fragments generated as IAtomContainer objects..
getFragmentsAsContainers() - Method in interface org.openscience.cdk.fragment.IFragmenter: Get fragments generated as IAtomContainer objects.
getFragmentsAsContainers() - Method in class org.openscience.cdk.fragment.MurckoFragmenter: Get all frameworks and ring systems as IAtomContainer objects.
getFragmentSize(int) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS: Deprecated.

Returns number of fragment generated in the solution space, if the MCS is removed from the target and query graph.
getFragmentSize(int) - Method in class org.openscience.cdk.smsd.Isomorphism: Deprecated.

Returns number of fragment generated in the solution space, if the MCS is removed from the target and query graph.
getFrameworks() - Method in class org.openscience.cdk.fragment.MurckoFragmenter: Get frameworks as SMILES strings.
getFrameworksAsContainers() - Method in class org.openscience.cdk.fragment.MurckoFragmenter: Get frameworks as IAtomContainer as objects.
getFunction(int) - Method in class org.openscience.cdk.renderer.GraphRendererModel: Get a function from this set
getFunctionalGroupSMARTS() - Static method in class org.openscience.cdk.fingerprint.StandardSubstructureSets: The functional groups.
getFunctionColor(int) - Method in class org.openscience.cdk.renderer.GraphRendererModel: Get a color from a function in this set
getFunctionsSize() - Method in class org.openscience.cdk.renderer.GraphRendererModel: Get the count of functions in this set
getFuzzyCount() - Method in class org.openscience.cdk.structgen.maygen.Maygen
getFuzzyFormula() - Method in class org.openscience.cdk.structgen.maygen.Maygen
getFuzzyFormulaRanges(String, List<String>) - Method in class org.openscience.cdk.structgen.maygen.Maygen: To get the fuzzy formula ranges for each element type in the molecular formula
getFuzzyFormulaRangesWithNewElements(String, List<String>) - Method in class org.openscience.cdk.structgen.maygen.Maygen
getGenerators() - Method in class org.openscience.cdk.renderer.AtomContainerRenderer: Returns a List of IGenerators for this renderer.
getGenerators() - Method in class org.openscience.cdk.renderer.ChemModelRenderer: Returns a List of IGenerators for this renderer.
getGenerators() - Method in interface org.openscience.cdk.renderer.IRenderer: Returns a List of IGenerators for this renderer.
getGenerators() - Method in class org.openscience.cdk.renderer.MoleculeSetRenderer: Returns a List of IGenerators for this renderer.
getGenerators() - Method in class org.openscience.cdk.renderer.ReactionRenderer: Returns a List of IGenerators for this renderer.
getGenerators() - Method in class org.openscience.cdk.renderer.ReactionSetRenderer: Returns a List of IGenerators for this renderer.
getGraph() - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Returns the graph object of this RGraph.
getGraph() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph: Deprecated.

Returns the graph object of this CDKRGraph.
getGraphics() - Method in class org.openscience.cdk.renderer.visitor.AWTDrawVisitor: Returns the Graphics2D for for this visitor.
getGrid() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
getGrid() - Method in class org.openscience.cdk.tools.GridGenerator
getGridArray() - Method in class org.openscience.cdk.tools.GridGenerator
getGridPointFrom3dCoordinates(Point3d) - Method in class org.openscience.cdk.tools.GridGenerator: Method calculates the nearest grid point from given coordinates.
getGroup() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroup: Get the connection table of atoms/bonds for this Rgroup.
getGroup() - Method in class org.openscience.cdk.isomorphism.matchers.RGroup
getGroup(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable: Get the group of the element.
getGroupInfo() - Method in interface org.openscience.cdk.interfaces.IStereoElement: Access the stereo group information - see class doc.
getHandedness(IAtom, IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.stereo.StereoTool: Gets the tetrahedral handedness of four atoms - three of which form the 'base' of the tetrahedron, and the other the apex.
getHash(int) - Method in interface org.openscience.cdk.fingerprint.ICountFingerprint: Returns the hash corresponding to the given index in the fingerprint.
getHash(int) - Method in class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
getHashMapBySingleCharCode() - Static method in class org.openscience.cdk.templates.AminoAcids: Returns a HashMap where the key is one of G, A, V, L, I, S, T, C, M, D, N, E, Q, R, K, H, F, Y, W and P.
getHashMapByThreeLetterCode() - Static method in class org.openscience.cdk.templates.AminoAcids: Returns a HashMap where the key is one of GLY, ALA, VAL, LEU, ILE, SER, THR, CYS, MET, ASP, ASN, GLU, GLN, ARG, LYS, HIS, PHE, TYR, TRP AND PRO.
getHeaviestRing(IRingSet, IBond) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator: We define the heaviest ring as the one with the highest number of double bonds.
getHeavyAtomRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>, boolean, boolean) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Return the RMSD of the heavy atoms between the 2 aligned molecules.
getHeavyAtomRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>, boolean, boolean) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Return the RMSD of the heavy atoms between the 2 aligned molecules.
getHeavyAtoms(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Returns a set of nodes excluding all the hydrogens.
getHeavyElements(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Returns a set of nodes excluding all the hydrogens.
getHeight() - Method in class org.openscience.cdk.signature.Orbit: Gets the height of the signature label.
getHetAtom() - Method in class org.openscience.cdk.debug.DebugPDBAtom: Determine whether this is a heteroatom or not.
getHetAtom() - Method in interface org.openscience.cdk.interfaces.IPDBAtom: Determine whether this is a heteroatom or not.
getHetAtom() - Method in class org.openscience.cdk.protein.data.PDBAtom
getHetAtom() - Method in class org.openscience.cdk.silent.PDBAtom
getHigherValences(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Reading the molecular formula and setting the higher valences.
getHighlightedAtom() - Method in class org.openscience.cdk.renderer.RendererModel: Returns the atom currently highlighted.
getHighlightedBond() - Method in class org.openscience.cdk.renderer.RendererModel: Returns the Bond currently highlighted.
getHillString(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Deprecated.
Use MolecularFormulaManipulator.getString(org.openscience.cdk.interfaces.IMolecularFormula)
getHOSECode(IAtomContainer, IAtom, int) - Method in class org.openscience.cdk.tools.HOSECodeGenerator: Produces a HOSE code for Atom root in the IAtomContainer ac.
getHOSECode(IAtomContainer, IAtom, int, boolean) - Method in class org.openscience.cdk.tools.HOSECodeGenerator: Produces a HOSE code for Atom root in the IAtomContainer ac.
getHTML(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Returns the string representation of the molecular formula based on Hill System with numbers wrapped in tags.
getHTML(IMolecularFormula, boolean, boolean) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Returns the string representation of the molecular formula based on Hill System with numbers wrapped in tags and the isotope of each Element in tags and the total charge of IMolecularFormula in tags.
getHTML(IMolecularFormula, String[], boolean, boolean) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Returns the string representation of the molecular formula with numbers wrapped in tags and the isotope of each Element in tags and the total showCharge of IMolecularFormula in tags.
getHybridization() - Method in class org.openscience.cdk.AtomRef: Returns the hybridization of this atom.
getHybridization() - Method in class org.openscience.cdk.AtomType: Returns the hybridization of this atom.
getHybridization() - Method in class org.openscience.cdk.debug.DebugAtom: Returns the hybridization of this atom.
getHybridization() - Method in class org.openscience.cdk.debug.DebugAtomType: Returns the hybridization of this atom.
getHybridization() - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Returns the hybridization of this atom.
getHybridization() - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Returns the hybridization of this atom.
getHybridization() - Method in interface org.openscience.cdk.interfaces.IAtomType: Returns the hybridization of this atom.
getHybridization() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Returns the hybridization of this atom.
getHybridization() - Method in class org.openscience.cdk.silent.AtomType: Returns the hybridization of this atom.
getHydrogenCount(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.normalize.SMSDNormalizer: Deprecated.

The summed implicit + explicit hydrogens of the given IAtom.
getHydrogenCount(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator: Deprecated.

The summed implicit + explicit hydrogens of the given IAtom.
getHydrogensInfoLengthIsOne(List<String>, String[], int) - Method in class org.openscience.cdk.structgen.maygen.Maygen
getHydrogenSpecial(IAtom) - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor.JPlogPCalculator: Determines and returns the SS (subsection) portion of the atomtype integer for a Hydrogen Atom
getiBondNeighborAtomsA() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper: Deprecated.
getiBondNeighborAtomsB() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper: Deprecated.
getIBondSetA() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper: Deprecated.
getIBondSetB() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper: Deprecated.
getICode() - Method in class org.openscience.cdk.debug.DebugPDBAtom: get Code for insertion of residues of this atom.
getICode() - Method in class org.openscience.cdk.debug.DebugPDBMonomer: Gets the ICode of this monomer.
getICode() - Method in interface org.openscience.cdk.interfaces.IPDBAtom: get Code for insertion of residues of this atom.
getICode() - Method in interface org.openscience.cdk.interfaces.IPDBMonomer: Gets the ICode of this monomer.
getICode() - Method in class org.openscience.cdk.protein.data.PDBAtom: get Code for insertion of residues of this atom.
getICode() - Method in class org.openscience.cdk.protein.data.PDBMonomer
getICode() - Method in class org.openscience.cdk.silent.PDBAtom: get Code for insertion of residues of this atom.
getICode() - Method in class org.openscience.cdk.silent.PDBMonomer
getId() - Method in class org.openscience.cdk.renderer.elements.MarkedElement: Access the id of the element.
getID() - Method in class org.openscience.cdk.ChemObject: Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugAtom: Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugAtomType: Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugBond: Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugChemFile: Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugChemModel: Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugChemObject: Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugChemSequence: Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugCrystal: Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugElectronContainer: Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugElement: Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugIsotope: Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugLonePair: Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugMapping: Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugMonomer: Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugPolymer: Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugReaction: Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugReactionScheme: Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugReactionSet: Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugRing: Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugSingleElectron: Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugStrand: Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugSubstance: Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.dict.Entry
getID() - Method in interface org.openscience.cdk.interfaces.IChemObject: Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject: Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.silent.ChemObject: Returns the identifier (ID) of this object.
getId1() - Method in class org.openscience.cdk.isomorphism.mcss.RMap: Gets the id1 attribute of the RMap object.
getId1() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMap: Deprecated.

Gets the id1 attribute of the CDKRMap object
getId2() - Method in class org.openscience.cdk.isomorphism.mcss.RMap: Gets the id2 attribute of the RMap object.
getId2() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMap: Deprecated.

Gets the id2 attribute of the CDKRMap object
getIgnoreAromaticBonds() - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory: Deprecated.
GetImage() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream: Get token literal value.
GetImage() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Get token literal value.
getImaginaryPart() - Method in class org.openscience.cdk.math.Complex: Gets the imaginary part of this value
getIminus() - Method in class org.openscience.cdk.math.qm.AngularMomentum: Calculates the I- operator
getImplementationIdentifier() - Method in interface org.openscience.cdk.IImplementationSpecification: Identifier for this implementation which must include version information.
getImplementationIdentifier() - Method in class org.openscience.cdk.qsar.DescriptorSpecification
getImplementationIdentifier() - Method in class org.openscience.cdk.reaction.ReactionSpecification
getImplementationTitle() - Method in interface org.openscience.cdk.IImplementationSpecification: Human-readable name for the implementation for the algorithm specified by the reference.
getImplementationTitle() - Method in class org.openscience.cdk.qsar.DescriptorSpecification
getImplementationTitle() - Method in class org.openscience.cdk.reaction.ReactionSpecification
getImplementationVendor() - Method in interface org.openscience.cdk.IImplementationSpecification: Human-readable name for the vendor that holds copyright for this implementation.
getImplementationVendor() - Method in class org.openscience.cdk.qsar.DescriptorSpecification
getImplementationVendor() - Method in class org.openscience.cdk.reaction.ReactionSpecification
getImplicitHydrogenCount() - Method in class org.openscience.cdk.Atom: Returns the hydrogen count of this atom.
getImplicitHydrogenCount() - Method in class org.openscience.cdk.AtomRef: Returns the implicit hydrogen count of this atom.
getImplicitHydrogenCount() - Method in class org.openscience.cdk.debug.DebugAtom: Returns the hydrogen count of this atom.
getImplicitHydrogenCount() - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Returns the hydrogen count of this atom.
getImplicitHydrogenCount() - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Returns the hydrogen count of this atom.
getImplicitHydrogenCount() - Method in interface org.openscience.cdk.interfaces.IAtom: Returns the implicit hydrogen count of this atom.
getImplicitHydrogenCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Returns the hydrogen count of this atom.
getImplicitHydrogenCount() - Method in class org.openscience.cdk.silent.Atom: Returns the hydrogen count of this atom.
getImplicitHydrogenCount(IAtom) - Static method in class org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator: Deprecated.

Returns The number of Implicit Hydrogen Count for a given IAtom.
getImplicitHydrogenCount(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Counts the number of implicit hydrogens on the provided IAtomContainer.
getImplicitHydrogenCount(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.normalize.SMSDNormalizer: Deprecated.

Returns The number of Implicit Hydrogen Count for a given IAtom.
getInchi() - Method in class org.openscience.cdk.inchi.InChIGenerator: Gets generated InChI string.
getInChIGenerator(IAtomContainer) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory: Gets an Standard InChI generator for a IAtomContainer.
getInChIGenerator(IAtomContainer, InchiFlag...) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory: Get an InChI generator providing flags to customise the generation.
getInChIGenerator(IAtomContainer, InchiOptions) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory: Get an InChI generator providing flags to customise the generation.
getInChIGenerator(IAtomContainer, String) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory: Gets InChI generator for CDK IAtomContainer.
getInChIGenerator(IAtomContainer, List<INCHI_OPTION>) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory: Deprecated.
use InChIGeneratorFactory.getInChIGenerator(org.openscience.cdk.interfaces.IAtomContainer, io.github.dan2097.jnainchi.InchiOptions)
getInchiKey() - Method in class org.openscience.cdk.inchi.InChIGenerator: Gets generated InChIKey string.
getInchimap() - Method in class org.openscience.cdk.io.RssWriter
getInChIToStructure(String, IChemObjectBuilder) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory: Gets structure generator for an InChI string.
getInChIToStructure(String, IChemObjectBuilder, String) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory: Gets structure generator for an InChI string.
getInChIToStructure(String, IChemObjectBuilder, List<String>) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory: Gets structure generator for an InChI string.
getIndex() - Method in class org.openscience.cdk.Atom: Acces the index of an atom in the context of an IAtomContainer.
getIndex() - Method in class org.openscience.cdk.AtomRef: Acces the index of an atom in the context of an IAtomContainer.
getIndex() - Method in class org.openscience.cdk.Bond
getIndex() - Method in class org.openscience.cdk.BondRef
getIndex() - Method in class org.openscience.cdk.debug.DebugAtom: Acces the index of an atom in the context of an IAtomContainer.
getIndex() - Method in interface org.openscience.cdk.interfaces.IAtom: Acces the index of an atom in the context of an IAtomContainer.
getIndex() - Method in interface org.openscience.cdk.interfaces.IBond
getIndex() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Acces the index of an atom in the context of an IAtomContainer.
getIndex() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
getIndex() - Method in class org.openscience.cdk.silent.Atom: Acces the index of an atom in the context of an IAtomContainer.
getIndex() - Method in class org.openscience.cdk.silent.Bond
getIndexFile(String) - Static method in class org.openscience.cdk.io.random.RandomAccessReader: Opens the file index file _cdk.index in a temporary folder, as specified by "java.io.tmpdir" property.
getIndexOfFirstNonDiscreteCell() - Method in class org.openscience.cdk.group.Partition: Gets the index of the first cell in the partition that is discrete.
getInitialLongestChain(IAtomContainer) - Static method in class org.openscience.cdk.layout.AtomPlacer: Search an aliphatic molecule for the longest chain.
getInitialPartition() - Method in interface org.openscience.cdk.group.Refinable: Get an initial partition of the vertices of the refinable - for example, by color.
getInstance() - Static method in class org.openscience.cdk.config.Isotopes: Returns a singleton instance of this class.
getInstance() - Static method in class org.openscience.cdk.debug.DebugChemObjectBuilder: Access the singleton instance of this DebugChemObjectBuilder.
getInstance() - Static method in class org.openscience.cdk.DefaultChemObjectBuilder: Access the singleton instance of this DefaultChemObjectBuilder.
getInstance() - Static method in class org.openscience.cdk.inchi.InChIGeneratorFactory: Gives the one InChIGeneratorFactory instance, if needed also creates it.
getInstance() - Static method in class org.openscience.cdk.io.formats.ABINITFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.Aces2Format
getInstance() - Static method in class org.openscience.cdk.io.formats.ADFFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.AlchemyFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.BGFFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.BSFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.CacaoInternalFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.CACheFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.CDKOWLFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
getInstance() - Static method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
getInstance() - Static method in class org.openscience.cdk.io.formats.ChemDrawFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.ChemtoolFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.CIFFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.CMLFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.CMLRSSFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.CRK2DFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.CRK3DFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.CrystClustFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.CTXFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.DaltonFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.DMol3Format
getInstance() - Static method in class org.openscience.cdk.io.formats.DOCK5Format
getInstance() - Static method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.FingerprintFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.GamessFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.Gaussian03Format
getInstance() - Static method in class org.openscience.cdk.io.formats.Gaussian90Format
getInstance() - Static method in class org.openscience.cdk.io.formats.Gaussian92Format
getInstance() - Static method in class org.openscience.cdk.io.formats.Gaussian94Format
getInstance() - Static method in class org.openscience.cdk.io.formats.Gaussian95Format
getInstance() - Static method in class org.openscience.cdk.io.formats.Gaussian98Format
getInstance() - Static method in class org.openscience.cdk.io.formats.GaussianInputFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.GhemicalMMFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.GhemicalSPMFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.GROMOS96Format
getInstance() - Static method in class org.openscience.cdk.io.formats.HINFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.INChIFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.INChIPlainTextFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.JaguarFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.JMEFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.MacroModelFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.MDLFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.MDLRXNFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.MDLRXNV2000Format
getInstance() - Static method in class org.openscience.cdk.io.formats.MDLRXNV3000Format
getInstance() - Static method in class org.openscience.cdk.io.formats.MDLV2000Format
getInstance() - Static method in class org.openscience.cdk.io.formats.MDLV3000Format
getInstance() - Static method in class org.openscience.cdk.io.formats.MMODFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.Mol2Format
getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC2002Format
getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC2007Format
getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC2009Format
getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC2012Format
getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC7Format
getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC7InputFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC93Format
getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC97Format
getInstance() - Static method in class org.openscience.cdk.io.formats.MoSSOutputFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.MPQCFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.NWChemFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.PCModelFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.PDBFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.PDBMLFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.PMPFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.POVRayFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.PQSChemFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemASNFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.QChemFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.RawCopyFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.RGroupQueryFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.SDFFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.ShelXFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.SMARTSFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.SMILESFIXFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.SMILESFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.SpartanFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.SVGFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.SybylDescriptorFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.TinkerMM2Format
getInstance() - Static method in class org.openscience.cdk.io.formats.TinkerXYZFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.TurboMoleFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.UniChemXYZFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.VASPFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.ViewmolFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.XEDFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.XYZFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.YasaraFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.ZindoFormat
getInstance() - Static method in class org.openscience.cdk.io.formats.ZMatrixFormat
getInstance() - Static method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D
getInstance() - Static method in class org.openscience.cdk.silent.SilentChemObjectBuilder: Access the singleton instance of this SilentChemObjectBuilder.
getInstance() - Static method in class org.openscience.cdk.smsd.global.TimeOut: Deprecated.

Get Instance of the timeout.
getInstance() - Static method in class org.openscience.cdk.smsd.helper.FinalMappings: Deprecated.

Stores mapping solutions
getInstance() - Static method in class org.openscience.cdk.smsd.helper.LabelContainer: Deprecated.

Create ids from atom labels
getInstance() - Static method in class org.openscience.cdk.smsd.tools.BondEnergies: Deprecated.

Returns Singleton pattern instance for the Bond Energy class
getInstance() - Static method in class org.openscience.cdk.tools.AtomicProperties
getInstance(InputStream, String, IChemObjectBuilder) - Static method in class org.openscience.cdk.config.AtomTypeFactory: Method to create a default AtomTypeFactory, using the given InputStream.
getInstance(String) - Static method in class org.openscience.cdk.atomtype.mapper.AtomTypeMapper: Instantiates an atom type to atom type mapping, based on the given mapping file.
getInstance(String, InputStream) - Static method in class org.openscience.cdk.atomtype.mapper.AtomTypeMapper: Instantiates an atom type to atom type mapping, based on the given InputStream.
getInstance(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.config.AtomTypeFactory: Method to create a specialized AtomTypeFactory.
getInstance(IChemObjectBuilder) - Static method in class org.openscience.cdk.atomtype.CDKAtomTypeMatcher
getInstance(IChemObjectBuilder) - Static method in class org.openscience.cdk.atomtype.SybylAtomTypeMatcher: Returns an instance of this atom typer.
getInstance(IChemObjectBuilder) - Static method in class org.openscience.cdk.config.AtomTypeFactory: Method to create a default AtomTypeFactory, using the structgen atom type list.
getInstance(IChemObjectBuilder) - Static method in class org.openscience.cdk.config.XMLIsotopeFactory: Returns an IsotopeFactory instance.
getInstance(IChemObjectBuilder) - Static method in class org.openscience.cdk.modeling.builder3d.ModelBuilder3D
getInstance(IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.CDKHydrogenAdder
getInstance(IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.CDKValencyChecker
getInstance(IChemObjectBuilder, int) - Static method in class org.openscience.cdk.atomtype.CDKAtomTypeMatcher
getInstance(TemplateHandler3D, String, IChemObjectBuilder) - Static method in class org.openscience.cdk.modeling.builder3d.ModelBuilder3D
getInt2DColumnSum(int[][]) - Static method in class org.openscience.cdk.graph.PathTools: Sums up the columns in a 2D int matrix.
getIntensity() - Method in class org.openscience.cdk.formula.IsotopeContainer: Get the intensity value of this container.
getInterfaces(Class<?>) - Method in class org.openscience.cdk.DynamicFactory.DefaultInterfaceProvider: Access the interfaces for a given class.
getInterfaces(Class<?>) - Method in interface org.openscience.cdk.DynamicFactory.InterfaceProvider: Access the interfaces for a given class.
getIntersection(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Compares this AtomContainer with another given AtomContainer and returns the Intersection between them.
getIntLabel(int) - Method in class org.openscience.cdk.signature.AtomSignature
getIOSettings() - Method in class org.openscience.cdk.io.ChemObjectIO: Returns an array of IOSettings defined by this IChemObjectIO class.
getIOSettings() - Method in interface org.openscience.cdk.io.IChemObjectIO: Returns an array of IOSettings defined by this IChemObjectIO class.
getIOSettings() - Method in class org.openscience.cdk.io.random.DefaultRandomAccessChemObjectReader
getIplus() - Method in class org.openscience.cdk.math.qm.AngularMomentum: Calculates the I+ operator
getIsobutane(IChemObjectBuilder) - Static method in class org.openscience.cdk.templates.saturatedhydrocarbons.IsoAlkanes
getIsohexane(IChemObjectBuilder) - Static method in class org.openscience.cdk.templates.saturatedhydrocarbons.IsoAlkanes
getIsomorphAtomsMap(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: Returns the first isomorph 'atom mapping' found for g2 in g1.
getIsomorphAtomsMap(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS: Deprecated.

Returns the first isomorph 'atom mapping' found for targetGraph in sourceGraph.
getIsomorphMap(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: Returns the first isomorph mapping found or null.
getIsomorphMap(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS: Deprecated.

Returns the first isomorph mapping found or null.
getIsomorphMaps(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: Returns all the isomorph 'mappings' found between two atom containers.
getIsomorphMaps(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS: Deprecated.

Returns all the isomorph 'mappings' found between two atom containers.
getIsopentane(IChemObjectBuilder) - Static method in class org.openscience.cdk.templates.saturatedhydrocarbons.IsoAlkanes
getIsotope(int) - Method in class org.openscience.cdk.formula.IsotopePattern: Returns the a isotopes given a specific position.
getIsotope(String, double, double) - Method in class org.openscience.cdk.config.IsotopeFactory: Get an isotope based on the element symbol and exact mass.
getIsotope(String, int) - Method in class org.openscience.cdk.config.IsotopeFactory: Get isotope based on element symbol and mass number.
getIsotopeCount() - Method in class org.openscience.cdk.debug.DebugAdductFormula: Checks a set of Nodes for the number of different isotopes in the adduct formula.
getIsotopeCount() - Method in class org.openscience.cdk.debug.DebugMolecularFormula: Checks a set of Nodes for the number of different isotopes in the IMolecularFormula.
getIsotopeCount() - Method in class org.openscience.cdk.formula.AdductFormula: Checks a set of Nodes for the number of different isotopes in the adduct formula.
getIsotopeCount() - Method in class org.openscience.cdk.formula.MolecularFormula: Checks a set of Nodes for the number of different isotopes in the IMolecularFormula.
getIsotopeCount() - Method in class org.openscience.cdk.formula.MolecularFormulaRange: Checks a set of Nodes for the number of different isotopes in the MolecularFormulaExpand.
getIsotopeCount() - Method in interface org.openscience.cdk.interfaces.IAdductFormula: Checks a set of Nodes for the number of different isotopes in the adduct formula.
getIsotopeCount() - Method in interface org.openscience.cdk.interfaces.IMolecularFormula: Checks a set of Nodes for the number of different isotopes in the IMolecularFormula.
getIsotopeCount() - Method in class org.openscience.cdk.silent.AdductFormula: Checks a set of Nodes for the number of different isotopes in the adduct formula.
getIsotopeCount() - Method in class org.openscience.cdk.silent.MolecularFormula: Checks a set of Nodes for the number of different isotopes in the IMolecularFormula.
getIsotopeCount(IIsotope) - Method in class org.openscience.cdk.debug.DebugAdductFormula: Checks a set of Nodes for the occurrence of the isotope in the adduct formula from a particular isotope.
getIsotopeCount(IIsotope) - Method in class org.openscience.cdk.debug.DebugMolecularFormula: Checks a set of Nodes for the occurrence of the isotope in the IMolecularFormula from a particular isotope.
getIsotopeCount(IIsotope) - Method in class org.openscience.cdk.formula.AdductFormula: Checks a set of Nodes for the occurrence of the isotope in the adduct formula from a particular isotope.
getIsotopeCount(IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormula: Checks a set of Nodes for the occurrence of the isotope in the IMolecularFormula from a particular isotope.
getIsotopeCount(IIsotope) - Method in interface org.openscience.cdk.interfaces.IAdductFormula: Checks a set of Nodes for the occurrence of the isotope in the adduct formula from a particular isotope.
getIsotopeCount(IIsotope) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula: Checks a set of Nodes for the occurrence of the isotope in the IMolecularFormula from a particular isotope.
getIsotopeCount(IIsotope) - Method in class org.openscience.cdk.silent.AdductFormula: Checks a set of Nodes for the occurrence of the isotope in the adduct formula from a particular isotope.
getIsotopeCount(IIsotope) - Method in class org.openscience.cdk.silent.MolecularFormula: Checks a set of Nodes for the occurrence of the isotope in the IMolecularFormula from a particular isotope.
getIsotopeCountMax(IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormulaRange: Checks a set of Nodes for the maximal occurrence of the isotope in the MolecularFormulaExpand from a particular isotope.
getIsotopeCountMin(IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormulaRange: Checks a set of Nodes for the minimal occurrence of the isotope in the MolecularFormulaExpand from a particular isotope.
getIsotopes() - Method in class org.openscience.cdk.config.IsotopeFactory: Gets a array of all isotopes known to the IsotopeFactory.
getIsotopes() - Method in class org.openscience.cdk.config.isotopes.IsotopeHandler: Returns the isotopes read from the XML file.
getIsotopes() - Method in class org.openscience.cdk.formula.IsotopePattern: Returns the all isotopes that form this isotope pattern.
getIsotopes(double, double) - Method in class org.openscience.cdk.config.IsotopeFactory: Gets an array of all isotopes matching the searched exact mass within a certain difference.
getIsotopes(int) - Method in class org.openscience.cdk.config.IsotopeFactory: Gets an array of all isotopes known to the IsotopeFactory for the given element symbol.
getIsotopes(String) - Method in class org.openscience.cdk.config.IsotopeFactory: Gets an array of all isotopes known to the IsotopeFactory for the given element symbol.
getIsotopes(IMolecularFormula) - Method in class org.openscience.cdk.formula.IsotopePatternGenerator: Get all combinatorial chemical isotopes given a structure.
getIsotopes(IMolecularFormula, IElement) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Get a list of IIsotope from a given IElement which is contained molecular.
getIterator() - Method in class org.openscience.cdk.smsd.helper.FinalMappings: Deprecated.

Returns a mapping Iterator
getIterator() - Method in interface org.openscience.cdk.smsd.interfaces.IFinalMapping: Deprecated.

Returns a mapping Iterator
getIx() - Method in class org.openscience.cdk.math.qm.AngularMomentum: Calculates the Ix operator
getIy() - Method in class org.openscience.cdk.math.qm.AngularMomentum: Calculates the Iy operator
getIz() - Method in class org.openscience.cdk.math.qm.AngularMomentum: Calculates the Iz operator
getKey() - Method in enum org.openscience.cdk.sgroup.SgroupType
getLabel() - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Returns the label of this PseudoAtom.
getLabel() - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Returns the label of this PseudoAtom.
getLabel() - Method in class org.openscience.cdk.dict.Entry
getLabel() - Method in interface org.openscience.cdk.interfaces.IPseudoAtom: Returns the label of this PseudoAtom.
getLabel() - Method in class org.openscience.cdk.PseudoAtom: Returns the label of this PseudoAtom.
getLabel() - Method in class org.openscience.cdk.signature.Orbit: Gets the label of the orbit.
getLabel() - Method in class org.openscience.cdk.silent.PseudoAtom: Returns the label of this PseudoAtom.
getLabel() - Method in class org.openscience.cdk.Vibration: Gets the label identifying this vibration.
getLabel(Integer) - Method in class org.openscience.cdk.smsd.helper.LabelContainer: Deprecated.

Returns Label of a given ID
getLabelID(String) - Method in class org.openscience.cdk.smsd.helper.LabelContainer: Deprecated.

Returns label ID
getLargestRingSet(List<IRingSet>) - Method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D: Returns the largest (number of atoms) ring set in a molecule.
getLargestRingSet(List<IRingSet>) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator: Returns the largest (number of atoms) ring set in a molecule
getLast() - Method in class org.openscience.cdk.smiles.InvPair
getLastAtom() - Method in class org.openscience.cdk.AtomContainer: Returns the atom at the last position in the container.
getLastAtom() - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns the atom at the last position in the container.
getLastAtom() - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns the atom at the last position in the container.
getLastAtom() - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the atom at the last position in the container.
getLastAtom() - Method in class org.openscience.cdk.debug.DebugCrystal: Returns the atom at the last position in the container.
getLastAtom() - Method in class org.openscience.cdk.debug.DebugMonomer: Returns the atom at the last position in the container.
getLastAtom() - Method in class org.openscience.cdk.debug.DebugPolymer: Returns the atom at the last position in the container.
getLastAtom() - Method in class org.openscience.cdk.debug.DebugRing: Returns the atom at the last position in the container.
getLastAtom() - Method in class org.openscience.cdk.debug.DebugStrand: Returns the atom at the last position in the container.
getLastAtom() - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Deprecated.
use IAtomContainer.getAtom(int)
getLastAtom() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns the atom at the last position in the container.
getLastAtom() - Method in class org.openscience.cdk.silent.AtomContainer: Returns the atom at the last position in the container.
getLastErrorLocation() - Static method in class org.openscience.cdk.smarts.Smarts: Access a display of the error position from previously parsed SMARTS (when Smarts.parse(org.openscience.cdk.interfaces.IAtomContainer, java.lang.String, int)=false).
getLastErrorMesg() - Static method in class org.openscience.cdk.smarts.Smarts: Access the error message from previously parsed SMARTS (when Smarts.parse(org.openscience.cdk.interfaces.IAtomContainer, java.lang.String, int)=false).
getLatticeConstant() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
getLatticeConstant() - Method in class org.openscience.cdk.tools.GridGenerator
getLeft() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom: Deprecated.
getLeft() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond: Deprecated.
getLeftTransversal(int) - Method in class org.openscience.cdk.group.PermutationGroup: Get the traversal U_i from the list of transversals.
getLength() - Method in class org.openscience.cdk.iupac.parser.AttachedGroup: Getter for property length.
getLength(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.stereo.ExtendedTetrahedral
getLength2D(IBond) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Returns the geometric length of this bond in 2D space.
getLength2D(IBond) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Returns the geometric length of this bond in 2D space.
getLernenIndices(int, int[][], List<Permutation>, int[], int[], boolean[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Get indices from "learning from canonical test" method.
getLevel() - Method in class org.openscience.cdk.io.setting.IOSetting
getLevel() - Method in interface org.openscience.cdk.tools.ILoggingTool: Get the current level of this logger.
getLevel() - Method in class org.openscience.cdk.tools.SystemOutLoggingTool: Deprecated.

Get the current level of this logger.
getLigandAtom() - Method in interface org.openscience.cdk.geometry.cip.ILigand: IAtom of the ligand that is connected to the central IAtom via one IBond.
getLigandAtom() - Method in class org.openscience.cdk.geometry.cip.Ligand: IAtom of the ligand that is connected to the chiral IAtom via one IBond.
getLigandLigands(ILigand) - Static method in class org.openscience.cdk.geometry.cip.CIPTool: Returns a CIP-expanded array of side chains of a ligand.
getLigands() - Method in interface org.openscience.cdk.interfaces.ITetrahedralChirality: Returns an array of ligand atoms around the chiral atom.
getLigands() - Method in class org.openscience.cdk.stereo.TetrahedralChirality
getLimitedPathsOfLengthUpto(IAtomContainer, IAtom, int, int) - Static method in class org.openscience.cdk.graph.PathTools: Get all the paths starting from an atom of length 0 up to the specified length.
getLine() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream: Deprecated.
getLine() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Deprecated.
getLine(int) - Method in class org.openscience.cdk.graph.invariant.GIMatrix: Returns the line-matrix at the given line index.
getLinkageRadius() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
getLinkmap() - Method in class org.openscience.cdk.io.RssWriter
getListenerCount() - Method in class org.openscience.cdk.ChemObject: Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugAtom: Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugAtomType: Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugBond: Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugChemFile: Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugChemModel: Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugChemObject: Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugChemSequence: Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugCrystal: Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugElectronContainer: Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugElement: Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugIsotope: Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugLonePair: Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugMapping: Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugMonomer: Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugPolymer: Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugReaction: Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugReactionScheme: Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugReactionSet: Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugRing: Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugSingleElectron: Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugStrand: Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugSubstance: Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in interface org.openscience.cdk.interfaces.IChemObject: Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject: Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.silent.ChemObject: Returns the number of ChemObjectListeners registered with this object.
getListeners() - Method in class org.openscience.cdk.io.ChemObjectIO: Access all the listeners for this ChemObject Reader or Writer.
getListeners() - Method in interface org.openscience.cdk.io.IChemObjectIO: Access all the listeners for this ChemObject Reader or Writer.
getLocations() - Method in class org.openscience.cdk.iupac.parser.AttachedGroup: Getter for property locations.
getLog() - Method in class org.openscience.cdk.inchi.InChIGenerator: Gets generated log.
getLog() - Method in class org.openscience.cdk.inchi.InChIToStructure: Gets generated log.
getLoggingToolClass() - Static method in class org.openscience.cdk.tools.LoggingToolFactory: Gets the currently used ILoggingTool implementation.
getLonePair(int) - Method in class org.openscience.cdk.AtomContainer: Get the lone pair at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getLonePairCount().
getLonePair(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Get the lone pair at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getLonePairCount().
getLonePair(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Get the lone pair at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getLonePairCount().
getLonePair(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Get the lone pair at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getLonePairCount().
getLonePair(int) - Method in class org.openscience.cdk.debug.DebugCrystal: Get the lone pair at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getLonePairCount().
getLonePair(int) - Method in class org.openscience.cdk.debug.DebugMonomer: Get the lone pair at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getLonePairCount().
getLonePair(int) - Method in class org.openscience.cdk.debug.DebugPolymer: Get the lone pair at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getLonePairCount().
getLonePair(int) - Method in class org.openscience.cdk.debug.DebugRing: Get the lone pair at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getLonePairCount().
getLonePair(int) - Method in class org.openscience.cdk.debug.DebugStrand: Get the lone pair at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getLonePairCount().
getLonePair(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Get the lone pair at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getLonePairCount().
getLonePair(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Get the lone pair at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getLonePairCount().
getLonePair(int) - Method in class org.openscience.cdk.silent.AtomContainer: Get the lone pair at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getLonePairCount().
getLonePairCount() - Method in class org.openscience.cdk.AtomContainer: Returns the number of LonePairs in this Container.
getLonePairCount() - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns the number of LonePairs in this Container.
getLonePairCount() - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns the number of LonePairs in this Container.
getLonePairCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the number of LonePairs in this Container.
getLonePairCount() - Method in class org.openscience.cdk.debug.DebugCrystal: Returns the number of LonePairs in this Container.
getLonePairCount() - Method in class org.openscience.cdk.debug.DebugMonomer: Returns the number of LonePairs in this Container.
getLonePairCount() - Method in class org.openscience.cdk.debug.DebugPolymer: Returns the number of LonePairs in this Container.
getLonePairCount() - Method in class org.openscience.cdk.debug.DebugRing: Returns the number of LonePairs in this Container.
getLonePairCount() - Method in class org.openscience.cdk.debug.DebugStrand: Returns the number of LonePairs in this Container.
getLonePairCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Returns the number of LonePairs in this Container.
getLonePairCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns the number of LonePairs in this Container.
getLonePairCount() - Method in class org.openscience.cdk.silent.AtomContainer: Returns the number of LonePairs in this Container.
getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.AtomContainer: Returns the position of a given lone pair in the lone pair array.
getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns the position of a given lone pair in the lone pair array.
getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the position of a given lone pair in the lone pair array.
getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugCrystal: Returns the position of a given lone pair in the lone pair array.
getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugMonomer: Returns the position of a given lone pair in the lone pair array.
getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugPolymer: Returns the position of a given lone pair in the lone pair array.
getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugRing: Returns the position of a given lone pair in the lone pair array.
getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugStrand: Returns the position of a given lone pair in the lone pair array.
getLonePairNumber(ILonePair) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Deprecated.
use IAtomContainer.indexOf(ILonePair)
getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns the position of a given lone pair in the lone pair array.
getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.silent.AtomContainer: Returns the position of a given lone pair in the lone pair array.
getLongestUnplacedChain(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.layout.AtomPlacer: Search a molecule for the longest unplaced, aliphatic chain in it.
getLower() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryAngleBond
getLower() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryBond
getMajorIsotope(int) - Method in class org.openscience.cdk.config.IsotopeFactory: Returns the most abundant (major) isotope with a given atomic number.
getMajorIsotope(String) - Method in class org.openscience.cdk.config.IsotopeFactory: Returns the most abundant (major) isotope whose symbol equals element.
getMajorIsotopeMass(int) - Method in class org.openscience.cdk.config.IsotopeFactory: Get the mass of the most abundant (major) isotope, if there is no major isotopes 2*elem is returned.
getMajorIsotopeMass(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Deprecated.
use MolecularFormulaManipulator.getMass(IMolecularFormula, int) with option MolecularFormulaManipulator.MonoIsotopic.
getMajorIsotopeMolecularFormula(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Construct an instance of IMolecularFormula, initialized with a molecular formula string.
getMap() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IState: Deprecated.

Returns the current mapping of query atoms onto target atoms.
getMap() - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFState: Deprecated.

Returns the current mapping of query atoms onto target atoms.
getMapIdx() - Method in class org.openscience.cdk.Atom
getMapIdx() - Method in class org.openscience.cdk.AtomRef
getMapIdx() - Method in interface org.openscience.cdk.interfaces.IAtom: Access the map index for this atom.
getMapIdx() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Access the map index for this atom.
getMapIdx() - Method in class org.openscience.cdk.silent.Atom
getMappedAtomCount() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper: Deprecated.
getMappedAtomsOrg() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper: Deprecated.
getMappedChemObject(IReaction, IChemObject) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator: Returns the IAtom that is mapped.
getMappedHologram(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor.JPlogPCalculator: Used in Training the model
getMappedSubstructures(IAtomContainer) - Method in class org.openscience.cdk.layout.TemplateHandler: Checks if one of the loaded templates is a substructure in the given Molecule and returns all matched substructures in a IAtomContainerSet.
getMapping() - Method in class org.openscience.cdk.atomtype.mapper.AtomTypeMapper: Returns the name of this mapping.
getMapping(int) - Method in interface org.openscience.cdk.interfaces.IReaction: Retrieves a mapping between the reactant and product side to this Reaction.
getMapping(int) - Method in class org.openscience.cdk.Reaction: Retrieves a mapping between the reactant and product side to this Reaction.
getMapping(int) - Method in class org.openscience.cdk.silent.Reaction: Retrieves a mapping between the reactant and product side to this Reaction.
getMappingCount() - Method in interface org.openscience.cdk.interfaces.IReaction: Get the number of mappings between the reactant and product side to this Reaction.
getMappingCount() - Method in class org.openscience.cdk.Reaction: Get the number of mappings between the reactant and product side to this Reaction.
getMappingCount() - Method in class org.openscience.cdk.silent.Reaction: Get the number of mappings between the reactant and product side to this Reaction.
getMappings() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregor: Deprecated.

Returns computed mappings.
getMappings() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler: Deprecated.

Returns mapping solutions
getMaps(IAtomContainer) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper: Deprecated.

Returns all solution map.
getMaps(IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper: Deprecated.

Returns all solution map.
getMaps(IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper: Deprecated.

Returns all solution map.
getMaps(TargetProperties) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper: Deprecated.

Returns all solution map.
getMaps(TargetProperties) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper: Deprecated.

Returns all solution map.
getMaps(TargetProperties) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper: Deprecated.

Returns all solution map.
getMass() - Method in class org.openscience.cdk.formula.IsotopeContainer: Get the mass value of this container.
getMass(String) - Method in class org.openscience.cdk.tools.AtomicProperties
getMass(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Calculate the mass of a molecule, this function takes an optional 'mass flavour' that switches the computation type.
getMass(IAtomContainer, int) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Calculate the mass of a molecule, this function takes an optional 'mass flavour' that switches the computation type.
getMass(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Calculate the mass of a formula, this function takes an optional 'mass flavour' that switches the computation type.
getMass(IMolecularFormula, int) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Calculate the mass of a formula, this function takes an optional 'mass flavour' that switches the computation type.
getMassNumber() - Method in class org.openscience.cdk.AtomRef: Returns the atomic mass of this element.
getMassNumber() - Method in class org.openscience.cdk.debug.DebugAtom: Returns the atomic mass of this element.
getMassNumber() - Method in class org.openscience.cdk.debug.DebugAtomType: Returns the atomic mass of this element.
getMassNumber() - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Returns the atomic mass of this element.
getMassNumber() - Method in class org.openscience.cdk.debug.DebugIsotope: Returns the atomic mass of this element.
getMassNumber() - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Returns the atomic mass of this element.
getMassNumber() - Method in interface org.openscience.cdk.interfaces.IIsotope: Returns the atomic mass of this element.
getMassNumber() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Returns the atomic mass of this element.
getMassNumber() - Method in class org.openscience.cdk.Isotope: Returns the atomic mass of this element.
getMassNumber() - Method in class org.openscience.cdk.silent.Isotope: Returns the atomic mass of this element.
getMatchingAtoms() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom: Get the atoms of a target molecule that correspond to this group.
getMatchingAtoms() - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool: Deprecated.

Get the atoms in the target molecule that match the query pattern.
getMatchingPharmacophoreAtoms() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher: Get the matching pharmacophore groups.
getMatchingPharmacophoreBonds() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher: Get the matching pharmacophore constraints.
getMatrix(IAtomContainer) - Static method in class org.openscience.cdk.graph.matrix.AdjacencyMatrix: Returns the adjacency matrix for the given AtomContainer.
getMatrix(IAtomContainer) - Static method in class org.openscience.cdk.graph.matrix.ConnectionMatrix: Returns the connection matrix representation of this AtomContainer.
getMatrix(IAtomContainer) - Static method in class org.openscience.cdk.graph.matrix.TopologicalMatrix: Returns the topological matrix for the given AtomContainer.
getMaxBondOrder() - Method in class org.openscience.cdk.AtomRef: Gets the MaxBondOrder attribute of the AtomType object.
getMaxBondOrder() - Method in class org.openscience.cdk.AtomType: Gets the MaxBondOrder attribute of the AtomType object.
getMaxBondOrder() - Method in class org.openscience.cdk.debug.DebugAtom: Gets the MaxBondOrder attribute of the AtomType object.
getMaxBondOrder() - Method in class org.openscience.cdk.debug.DebugAtomType: Gets the MaxBondOrder attribute of the AtomType object.
getMaxBondOrder() - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Gets the MaxBondOrder attribute of the AtomType object.
getMaxBondOrder() - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Gets the MaxBondOrder attribute of the AtomType object.
getMaxBondOrder() - Method in interface org.openscience.cdk.interfaces.IAtomType: Gets the MaxBondOrder attribute of the AtomType object.
getMaxBondOrder() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Gets the MaxBondOrder attribute of the AtomType object.
getMaxBondOrder() - Method in class org.openscience.cdk.silent.AtomType: Gets the MaxBondOrder attribute of the AtomType object.
getMaxCliqueSet() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.BKKCKCF: Deprecated.
getMaxGasteigerDamp() - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges: Gets the maxGasteigerDamp attribute of the GasteigerMarsiliPartialCharges object.
getMaxGasteigerIters() - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges: Gets the maxGasteigerIters attribute of the GasteigerMarsiliPartialCharges object.
getMaxGasteigerIters() - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges: Gets the maxGasteigerIters attribute of the GasteigerPEPEPartialCharges object.
getMaximalFormula(MolecularFormulaRange, IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaRangeManipulator: Returns the maximal occurrence of the IIsotope into IMolecularFormula from this MolelecularFormulaRange.
getMaximalStructures() - Method in class org.openscience.cdk.tools.StructureResonanceGenerator: Get the number maximal of resonance structures to be found.
getMaximum(List) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler: Deprecated.
getMaximumBondOrder(Iterator<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator: Returns the maximum bond order for a List of bonds, given an iterator to the list.
getMaximumBondOrder(List<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator: Returns the maximum bond order for a List of bonds.
getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.AtomContainer: Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal: Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer: Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer: Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugRing: Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand: Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
getMaximumBondOrder(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer: Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
getMaximumBondOrder(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
getMaximumBondOrder(IBond.Order, IBond.Order) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator: Returns the maximum bond order for the two bond orders.
getMaximumBondOrder(IBond, IBond) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator: Returns the maximum bond order for the two bonds.
getMaximumPair(int[], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Between two index pairs, getting the bigger indices.
getMaxIterations() - Method in class org.openscience.cdk.charges.Electronegativity: get the maximum number of Iterations.
getMaxIterations() - Method in class org.openscience.cdk.charges.PiElectronegativity: get the maximum number of Iterations.
getMaxNoOfBonds(IAtom) - Method in class org.openscience.cdk.tools.AtomTypeAwareSaturationChecker: This method calculates the number of bonds that an IAtom can have.
getMaxOccurrenceElements(IMolecularFormulaSet) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaSetManipulator: Extract from a set of MolecularFormula the maximum occurrence of each element found and put the element and occurrence in a new IMolecularFormula.
getMaxResonStruc() - Method in class org.openscience.cdk.charges.Electronegativity: get the maximum number of resonance structures.
getMaxResonStruc() - Method in class org.openscience.cdk.charges.PiElectronegativity: get the maximum number of resonance structures.
getMaxResoStruc() - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges: Gets the maximum resonance structures to be searched.
getMaxx() - Method in class org.openscience.cdk.tools.GridGenerator
getMaxX() - Method in class org.openscience.cdk.math.qm.FourierGridBasis
getMaxX() - Method in class org.openscience.cdk.math.qm.GaussiansBasis: Gets the dimension of the volume, which describes the base.
getMaxX() - Method in interface org.openscience.cdk.math.qm.IBasis: Gets the dimension of the volume, which describes the base.
getMaxy() - Method in class org.openscience.cdk.tools.GridGenerator
getMaxY() - Method in class org.openscience.cdk.math.qm.FourierGridBasis
getMaxY() - Method in class org.openscience.cdk.math.qm.GaussiansBasis: Gets the dimension of the volume, which describes the base.
getMaxY() - Method in interface org.openscience.cdk.math.qm.IBasis: Gets the dimension of the volume, which describes the base.
getMaxz() - Method in class org.openscience.cdk.tools.GridGenerator
getMaxZ() - Method in class org.openscience.cdk.math.qm.FourierGridBasis
getMaxZ() - Method in class org.openscience.cdk.math.qm.GaussiansBasis: Gets the dimension of the volume, which describes the base.
getMaxZ() - Method in interface org.openscience.cdk.math.qm.IBasis: Gets the dimension of the volume, which describes the base.
getMCSSize() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregor: Deprecated.

Returns MCS size.
getMechanism() - Method in class org.openscience.cdk.dict.EntryReact: Get the mechanism of this reaction.
getMerge() - Method in class org.openscience.cdk.renderer.RendererModel: This is the central facility for handling "merges" of atoms.
getMessage() - Method in class org.openscience.cdk.inchi.InChIGenerator: Gets generated (error/warning) messages.
getMessage() - Method in class org.openscience.cdk.inchi.InChIToStructure: Gets generated (error/warning) messages.
getMessage() - Method in error org.openscience.cdk.iupac.parser.TokenMgrError: You can also modify the body of this method to customize your error messages.
getMessage() - Method in class org.openscience.cdk.smarts.SmartsResult: The error/warning message.
getMessage() - Method in error org.openscience.cdk.smiles.smarts.parser.TokenMgrError: You can also modify the body of this method to customize your error messages.
getMIMEType() - Method in class org.openscience.cdk.io.formats.ABINITFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.Aces2Format: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.ADFFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.AlchemyFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.BGFFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.BSFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
getMIMEType() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.CACheFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
getMIMEType() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.CIFFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.CMLFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.CRK2DFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.CRK3DFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.CrystClustFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.CTXFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.DaltonFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.DMol3Format: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.DOCK5Format: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.FingerprintFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.GamessFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian03Format: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian90Format: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian92Format: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian94Format: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian95Format: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian98Format: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat
getMIMEType() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.GROMOS96Format: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.HINFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.INChIFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in interface org.openscience.cdk.io.formats.IResourceFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.JaguarFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.JMEFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MacroModelFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MDLFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MDLRXNV2000Format: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MDLV2000Format: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MDLV3000Format: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MMODFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.Mol2Format: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC7Format: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC93Format: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC97Format: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MPQCFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.NWChemFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.PCModelFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.PDBFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.PDBMLFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.PMPFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.POVRayFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.PQSChemFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.QChemFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.RawCopyFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.SDFFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.ShelXFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.SMARTSFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.SMILESFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.SpartanFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.SVGFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.VASPFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.ViewmolFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.XEDFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.XYZFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.YasaraFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.ZindoFormat: Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat: Returns the accepted MIME type for this format.
getMinimalFormula(MolecularFormulaRange, IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaRangeManipulator: Returns the minimal occurrence of the IIsotope into IMolecularFormula from this MolelecularFormulaRange.
getMinimumBondOrder(Iterator<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator: Returns the minimum bond order for a List of bonds, given an iterator to the list.
getMinimumBondOrder(List<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator: Returns the minimum bond order for a List of bonds.
getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.AtomContainer: Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal: Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer: Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer: Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugRing: Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand: Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
getMinimumBondOrder(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer: Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
getMinMax(Iterable<IAtom>) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Returns the minimum and maximum X and Y coordinates of the atoms.
getMinMax(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Returns the minimum and maximum X and Y coordinates of the atoms in the AtomContainer.
getMinMax(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Returns the minimum and maximum X and Y coordinates of the atoms in the AtomContainer.
getMinOccurrenceElements(IMolecularFormulaSet) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaSetManipulator: Extract from a set of MolecularFormula the minimal occurrence of each element found and put the element and occurrence in a new IMolecularFormula.
getMinPSCluster() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
getMinPSPocket() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
getMinx() - Method in class org.openscience.cdk.tools.GridGenerator
getMinX() - Method in class org.openscience.cdk.math.qm.FourierGridBasis
getMinX() - Method in class org.openscience.cdk.math.qm.GaussiansBasis: Gets the dimension of the volume, which describes the base.
getMinX() - Method in interface org.openscience.cdk.math.qm.IBasis: Gets the dimension of the volume, which describes the base.
getMiny() - Method in class org.openscience.cdk.tools.GridGenerator
getMinY() - Method in class org.openscience.cdk.math.qm.FourierGridBasis
getMinY() - Method in class org.openscience.cdk.math.qm.GaussiansBasis: Gets the dimension of the volume, which describes the base.
getMinY() - Method in interface org.openscience.cdk.math.qm.IBasis: Gets the dimension of the volume, which describes the base.
getMinz() - Method in class org.openscience.cdk.tools.GridGenerator
getMinZ() - Method in class org.openscience.cdk.math.qm.FourierGridBasis
getMinZ() - Method in class org.openscience.cdk.math.qm.GaussiansBasis: Gets the dimension of the volume, which describes the base.
getMinZ() - Method in interface org.openscience.cdk.math.qm.IBasis: Gets the dimension of the volume, which describes the base.
getModelCenter() - Method in class org.openscience.cdk.renderer.AbstractRenderer: Get the center of the model.
getMolecularFormula(int) - Method in class org.openscience.cdk.debug.DebugAdductFormula: Returns the MolecularFormula at position number in the chemObject.
getMolecularFormula(int) - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet: Returns the MolecularFormula at position number in the chemObject.
getMolecularFormula(int) - Method in class org.openscience.cdk.formula.AdductFormula: Returns the MolecularFormula at position number in the chemObject.
getMolecularFormula(int) - Method in class org.openscience.cdk.formula.MolecularFormulaSet: Returns the MolecularFormula at position number in the chemObject.
getMolecularFormula(int) - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet: Returns the IMolecularFormula at position number in the chemObject.
getMolecularFormula(int) - Method in class org.openscience.cdk.silent.AdductFormula: Returns the MolecularFormula at position number in the chemObject.
getMolecularFormula(int) - Method in class org.openscience.cdk.silent.MolecularFormulaSet: Returns the MolecularFormula at position number in the chemObject.
getMolecularFormula(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Construct an instance of IMolecularFormula, initialized with a molecular formula string.
getMolecularFormula(String, IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: add in a instance of IMolecularFormula the elements extracts form molecular formula string.
getMolecularFormula(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Method that actually does the work of convert the atomContainer to IMolecularFormula.
getMolecularFormula(IAtomContainer, IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Method that actually does the work of convert the atomContainer to IMolecularFormula given a IMolecularFormula.
getMolecularGraphDiameter(IAtomContainer) - Static method in class org.openscience.cdk.graph.PathTools: Returns the diameter of the molecular graph.
getMolecularGraphRadius(IAtomContainer) - Static method in class org.openscience.cdk.graph.PathTools: Returns the radius of the molecular graph.
getMolecularWeight(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Deprecated.
use AtomContainerManipulator.getMass(IAtomContainer, int) and AtomContainerManipulator.MolWeight
getMolecule() - Method in class org.openscience.cdk.layout.AtomPlacer: Return the molecule the AtomPlacer currently works with
getMolecule() - Method in class org.openscience.cdk.layout.RingPlacer
getMolecule() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator: Returns the molecule, usually used after a call of generateCoordinates()
getMolecule() - Method in class org.openscience.cdk.smsd.tools.MolHandler: Deprecated.

Returns the modified container
getMolecule() - Method in class org.openscience.cdk.structgen.RandomGenerator: Returns the molecule which reflects the current state of this stochastic structure generator.
getMoleculeGraph(IAtomContainer) - Static method in class org.openscience.cdk.graph.MoleculeGraphs: Deprecated.

Creates a molecule graph for use with jgrapht.
getMoleculeSet() - Method in class org.openscience.cdk.ChemModel: Returns the MoleculeSet of this ChemModel.
getMoleculeSet() - Method in class org.openscience.cdk.debug.DebugChemModel: Returns the MoleculeSet of this ChemModel.
getMoleculeSet() - Method in interface org.openscience.cdk.interfaces.IChemModel: Returns the IAtomContainerSet of this ChemModel.
getMoleculeSet() - Method in class org.openscience.cdk.silent.ChemModel: Returns the MoleculeSet of this ChemModel.
getMonoIsotope() - Method in class org.openscience.cdk.formula.IsotopePattern: Returns the mono-isotope peak that form this isotope pattern.
getMonomer(String) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Retrieves a Monomer object by specifying its name.
getMonomer(String) - Method in class org.openscience.cdk.debug.DebugPolymer: Retrieves a Monomer object by specifying its name.
getMonomer(String) - Method in class org.openscience.cdk.debug.DebugStrand: Retrieves a Monomer object by specifying its name.
getMonomer(String) - Method in interface org.openscience.cdk.interfaces.IPolymer: Retrieve a Monomer object by specifying its name.
getMonomer(String) - Method in interface org.openscience.cdk.interfaces.IStrand: Retrieve a Monomer object by specifying its name.
getMonomer(String) - Method in class org.openscience.cdk.Polymer: Retrieves a Monomer object by specifying its name.
getMonomer(String) - Method in class org.openscience.cdk.silent.Polymer: Retrieves a Monomer object by specifying its name.
getMonomer(String) - Method in class org.openscience.cdk.silent.Strand: Retrieves a Monomer object by specifying its name.
getMonomer(String) - Method in class org.openscience.cdk.Strand: Retrieves a Monomer object by specifying its name.
getMonomer(String, String) - Method in class org.openscience.cdk.BioPolymer: Retrieves a Monomer object by specifying its name.
getMonomer(String, String) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Retrieves a Monomer object by specifying its name.
getMonomer(String, String) - Method in interface org.openscience.cdk.interfaces.IBioPolymer: Retrieve a Monomer object by specifying its name.
getMonomer(String, String) - Method in class org.openscience.cdk.silent.BioPolymer: Retrieves a Monomer object by specifying its name.
getMonomerCount() - Method in class org.openscience.cdk.BioPolymer: Returns the number of monomers present in BioPolymer.
getMonomerCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the number of monomers present in BioPolymer.
getMonomerCount() - Method in class org.openscience.cdk.debug.DebugPolymer: Returns the number of monomers present in the Polymer.
getMonomerCount() - Method in class org.openscience.cdk.debug.DebugStrand: Returns the number of monomers present in the Strand.
getMonomerCount() - Method in interface org.openscience.cdk.interfaces.IBioPolymer: Return the number of monomers present in BioPolymer.
getMonomerCount() - Method in interface org.openscience.cdk.interfaces.IPolymer: Return the number of monomers present in the Polymer.
getMonomerCount() - Method in interface org.openscience.cdk.interfaces.IStrand: Return the number of monomers present in the Strand.
getMonomerCount() - Method in class org.openscience.cdk.Polymer: Returns the number of monomers present in the Polymer.
getMonomerCount() - Method in class org.openscience.cdk.silent.BioPolymer: Returns the number of monomers present in BioPolymer.
getMonomerCount() - Method in class org.openscience.cdk.silent.Polymer: Returns the number of monomers present in the Polymer.
getMonomerCount() - Method in class org.openscience.cdk.silent.Strand: Returns the number of monomers present in the Strand.
getMonomerCount() - Method in class org.openscience.cdk.Strand: Returns the number of monomers present in the Strand.
getMonomerName() - Method in class org.openscience.cdk.debug.DebugAminoAcid: Retrieves the monomer name.
getMonomerName() - Method in class org.openscience.cdk.debug.DebugMonomer: Retrieves the monomer name.
getMonomerName() - Method in interface org.openscience.cdk.interfaces.IMonomer: Retrieve the monomer name.
getMonomerName() - Method in class org.openscience.cdk.Monomer: Retrieves the monomer name.
getMonomerName() - Method in class org.openscience.cdk.silent.Monomer: Retrieves the monomer name.
getMonomerNames() - Method in class org.openscience.cdk.BioPolymer: Returns a collection of the names of all Monomers in this BioPolymer.
getMonomerNames() - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns a collection of the names of all Monomers in this BioPolymer.
getMonomerNames() - Method in class org.openscience.cdk.debug.DebugPolymer: Returns a collection of the names of all Monomers in this polymer.
getMonomerNames() - Method in class org.openscience.cdk.debug.DebugStrand: Returns a collection of the names of all Monomers in this polymer.
getMonomerNames() - Method in interface org.openscience.cdk.interfaces.IBioPolymer: Returns a collection of the names of all Monomers in this BioPolymer.
getMonomerNames() - Method in interface org.openscience.cdk.interfaces.IPolymer: Returns a collection of the names of all Monomers in this polymer.
getMonomerNames() - Method in interface org.openscience.cdk.interfaces.IStrand: Returns a collection of the names of all Monomers in this polymer.
getMonomerNames() - Method in class org.openscience.cdk.Polymer: Returns a collection of the names of all Monomers in this polymer.
getMonomerNames() - Method in class org.openscience.cdk.silent.BioPolymer: Returns a collection of the names of all Monomers in this BioPolymer.
getMonomerNames() - Method in class org.openscience.cdk.silent.Polymer: Returns a collection of the names of all Monomers in this polymer.
getMonomerNames() - Method in class org.openscience.cdk.silent.Strand: Returns a collection of the names of all Monomers in this polymer.
getMonomerNames() - Method in class org.openscience.cdk.Strand: Returns a collection of the names of all Monomers in this polymer.
getMonomerNamesInSequentialOrder() - Method in class org.openscience.cdk.protein.data.PDBPolymer: Returns the monomer names in the order in which they were added.
getMonomerNamesInSequentialOrder() - Method in class org.openscience.cdk.protein.data.PDBStrand: Returns the monomer names in the order in which they were added.
getMonomerNamesInSequentialOrder() - Method in class org.openscience.cdk.silent.PDBPolymer: Returns the monomer names in the order in which they were added.
getMonomers() - Method in class org.openscience.cdk.debug.DebugStrand: Returns a hashtable containing the monomers in the strand.
getMonomers() - Method in interface org.openscience.cdk.interfaces.IStrand: Returns the monomers in this strand.
getMonomers() - Method in class org.openscience.cdk.silent.Strand: Returns a hashtable containing the monomers in the strand.
getMonomers() - Method in class org.openscience.cdk.Strand: Returns a hashtable containing the monomers in the strand.
getMonomerType() - Method in class org.openscience.cdk.debug.DebugAminoAcid: Retrieves the monomer type.
getMonomerType() - Method in class org.openscience.cdk.debug.DebugMonomer: Retrieves the monomer type.
getMonomerType() - Method in interface org.openscience.cdk.interfaces.IMonomer: Retrieve the monomer type.
getMonomerType() - Method in class org.openscience.cdk.Monomer: Retrieves the monomer type.
getMonomerType() - Method in class org.openscience.cdk.silent.Monomer: Retrieves the monomer type.
getMorganNumbers(IAtomContainer) - Static method in class org.openscience.cdk.graph.invariant.MorganNumbersTools: Makes an array containing the morgan numbers of the atoms of atomContainer.
getMorganNumbersWithElementSymbol(IAtomContainer) - Static method in class org.openscience.cdk.graph.invariant.MorganNumbersTools: Makes an array containing the morgan numbers+element symbol of the atoms of atomContainer.
getMostAbundant(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Compute the most abundant MF.
getMostAbundant(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Compute the most abundant MF.
getMostComplexRing(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator: Returns the ring with the highest numbers of other rings attached to it.
getMultiMap() - Method in class org.openscience.cdk.io.RssWriter
getMultiplier(int) - Method in class org.openscience.cdk.AtomContainerSet: Returns the multiplier for the AtomContainer at position number in the container.
getMultiplier(int) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Returns the multiplier for the AtomContainer at position number in the container.
getMultiplier(int) - Method in class org.openscience.cdk.debug.DebugSubstance: Returns the multiplier for the AtomContainer at position number in the container.
getMultiplier(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet: Returns the multiplier for the AtomContainer at position number in the container.
getMultiplier(int) - Method in class org.openscience.cdk.silent.AtomContainerSet: Returns the multiplier for the AtomContainer at position number in the container.
getMultiplier(IAtomContainer) - Method in class org.openscience.cdk.AtomContainerSet: Returns the multiplier of the given AtomContainer.
getMultiplier(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Returns the multiplier of the given AtomContainer.
getMultiplier(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugSubstance: Returns the multiplier of the given AtomContainer.
getMultiplier(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet: Returns the multiplier of the given AtomContainer.
getMultiplier(IAtomContainer) - Method in class org.openscience.cdk.silent.AtomContainerSet: Returns the multiplier of the given AtomContainer.
getMultipliers() - Method in class org.openscience.cdk.AtomContainerSet: Returns an array of double with the stoichiometric coefficients of the products.
getMultipliers() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Returns an array of double with the stoichiometric coefficients of the products.
getMultipliers() - Method in class org.openscience.cdk.debug.DebugSubstance: Returns an array of double with the stoichiometric coefficients of the products.
getMultipliers() - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet: Returns an array of double with the stoichiometric coefficients of the products.
getMultipliers() - Method in class org.openscience.cdk.silent.AtomContainerSet: Returns an array of double with the stoichiometric coefficients of the products.
getName() - Method in class org.openscience.cdk.debug.DebugPDBAtom: get the Atom name of this atom.
getName() - Method in interface org.openscience.cdk.interfaces.IPDBAtom: get the Atom name of this atom.
getName() - Method in interface org.openscience.cdk.interfaces.ISetting: Access the name of the setting.
getName() - Method in class org.openscience.cdk.io.setting.IOSetting
getName() - Method in class org.openscience.cdk.iupac.parser.AttachedGroup: Getter for property name.
getName() - Method in class org.openscience.cdk.libio.md.Residue
getName() - Method in class org.openscience.cdk.protein.data.PDBAtom: get the Atom name of this atom.
getName() - Method in class org.openscience.cdk.silent.PDBAtom: get the Atom name of this atom.
getName(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable: Get the name of the element.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.ABINITFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.Aces2Format: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.ADFFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.AlchemyFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.BGFFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.BSFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
getNameExtensions() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.CACheFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
getNameExtensions() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.CIFFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.CMLFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.CRK2DFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.CRK3DFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.CrystClustFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.CTXFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.DaltonFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.DMol3Format: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.DOCK5Format: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.FingerprintFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.GamessFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian03Format: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian90Format: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian92Format: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian94Format: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian95Format: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian98Format: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat
getNameExtensions() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.GROMOS96Format: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.HINFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.INChIFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in interface org.openscience.cdk.io.formats.IResourceFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.JaguarFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.JMEFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MacroModelFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MDLFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MDLRXNV2000Format: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MDLV2000Format: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MDLV3000Format: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MMODFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.Mol2Format: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC7Format: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC93Format: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC97Format: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MPQCFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.NWChemFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.PCModelFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.PDBFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.PDBMLFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.PMPFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.POVRayFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.PQSChemFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.QChemFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.RawCopyFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.SDFFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.ShelXFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.SMARTSFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.SMILESFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.SpartanFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.SVGFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.VASPFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.ViewmolFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.XEDFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.XYZFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.YasaraFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.ZindoFormat: Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat: Returns an array of common resource name extensions.
getNames() - Static method in class org.openscience.cdk.config.fragments.EStateFragments: Get the fragment names.
getNames() - Method in class org.openscience.cdk.qsar.DescriptorValue: Returns an array of names for each descriptor value calculated.
getNativeRingRadius(IRing, double) - Method in class org.openscience.cdk.layout.RingPlacer: Returns the ring radius of a perfect polygons of size ring.getAtomCount() The ring radius is the distance of each atom to the ringcenter.
getNaturalAbundance() - Method in class org.openscience.cdk.AtomRef: Gets the NaturalAbundance attribute of the Isotope object.
getNaturalAbundance() - Method in class org.openscience.cdk.debug.DebugAtom: Gets the NaturalAbundance attribute of the Isotope object.
getNaturalAbundance() - Method in class org.openscience.cdk.debug.DebugAtomType: Gets the NaturalAbundance attribute of the Isotope object.
getNaturalAbundance() - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Gets the NaturalAbundance attribute of the Isotope object.
getNaturalAbundance() - Method in class org.openscience.cdk.debug.DebugIsotope: Gets the NaturalAbundance attribute of the Isotope object.
getNaturalAbundance() - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Gets the NaturalAbundance attribute of the Isotope object.
getNaturalAbundance() - Method in interface org.openscience.cdk.interfaces.IIsotope: Gets the NaturalAbundance attribute of the Isotope object.
getNaturalAbundance() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Gets the NaturalAbundance attribute of the Isotope object.
getNaturalAbundance() - Method in class org.openscience.cdk.Isotope: Gets the NaturalAbundance attribute of the Isotope object.
getNaturalAbundance() - Method in class org.openscience.cdk.silent.Isotope: Gets the NaturalAbundance attribute of the Isotope object.
getNaturalExactMass(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Deprecated.
uses AtomContainerManipulator.getMass(IAtomContainer, int) and AtomContainerManipulator.MolWeightIgnoreSpecified. You probably want AtomContainerManipulator.MolWeight!
getNaturalExactMass(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Deprecated.
use MolecularFormulaManipulator.getMass(IMolecularFormula, int) with option MolecularFormulaManipulator.MolWeightIgnoreSpecified.
getNaturalMass(int) - Method in class org.openscience.cdk.config.IsotopeFactory: Gets the natural mass of this element, defined as average of masses of isotopes, weighted by abundance.
getNaturalMass(IElement) - Method in class org.openscience.cdk.config.IsotopeFactory: Gets the natural mass of this element, defined as average of masses of isotopes, weighted by abundance.
getNeighborBondNumA() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper: Deprecated.
getNeighborBondNumA() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.QueryProcessor: Deprecated.
getNeighborBondNumB() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper: Deprecated.
getNeighborBondNumB() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.TargetProcessor: Deprecated.
getNeighbors(int) - Method in class org.openscience.cdk.geometry.surface.NeighborList: Get the neighbors that are with the given radius of atom i.
getNeighbors(IAtom) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.TargetProperties: Deprecated.
getNextBond(IBond, IAtom) - Method in class org.openscience.cdk.debug.DebugRing: Returns the next bond in order, relative to a given bond and atom.
getNextBond(IBond, IAtom) - Method in interface org.openscience.cdk.interfaces.IRing: Returns the next bond in order, relative to a given bond and atom.
getNextBond(IBond, IAtom) - Method in class org.openscience.cdk.Ring: Returns the next bond in order, relative to a given bond and atom.
getNextBond(IBond, IAtom) - Method in class org.openscience.cdk.silent.Ring: Returns the next bond in order, relative to a given bond and atom.
getNextBondVector(IAtom, IAtom, Point2d, boolean) - Method in class org.openscience.cdk.layout.AtomPlacer: Returns the next bond vector needed for drawing an extended linear chain of atoms.
getNextFormula() - Method in class org.openscience.cdk.formula.MolecularFormulaGenerator: Returns next generated formula or null in case no new formula was found (search is finished).
getNextPermutation() - Method in class org.openscience.cdk.graph.Permutor: Get the next permutation in the list.
getNextPermutation() - Method in class org.openscience.cdk.smsd.labelling.Permutor: Deprecated.

Get the next permutation in the list.
getNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D: Gets the nextPlacedHeavyAtomWithAliphaticPlacedNeigbor from an atom container or molecule.
getNextPlacedHeavyAtomWithUnplacedRingNeighbour(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D: Gets the nextPlacedHeavyAtomWithUnplacedRingNeighbour attribute of the AtomPlacer3D object.
getNextToken() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Get the next Token.
getNextToken() - Method in class org.openscience.cdk.iupac.parser.NomParserTokenManager: Get the next Token.
getNextToken() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser: Get the next Token.
getNextToken() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager: Get the next Token.
getNextUnplacedHeavyAtomWithAliphaticPlacedNeighbour(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D: Gets the nextUnplacedHeavyAtomWithAliphaticPlacedNeighbour from an atom container or molecule.
getNitrogenSpecial(IAtom) - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor.JPlogPCalculator: Determines and returns the SS (subsection) portion of the atomtype integer for a Nitrogen Atom
getNode(int) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder: Deprecated.

Returns a node of the query mol at a given position.
getNode(int) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQuery: Deprecated.

Returns a node of the query mol at a given position.
getNode(IAtom) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder: Deprecated.

Return a node for a given atom else return null
getNodesInSphere(int) - Method in class org.openscience.cdk.tools.HOSECodeGenerator
getNonCanonicalMakerPermutation(int[], Permutation, int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Calculating the permutation, permuting the second row and making first row non maximal.
getNormal(Point3d, Point3d, Point3d) - Static method in class org.openscience.cdk.stereo.StereoTool: Given three points (A, B, C), makes the vectors A-B and A-C, and makes the cross product of these two vectors; this has the effect of making a third vector at right angles to AB and AC.
getNormalizationFactor(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Calculates the normalization factor in order to get an average bond length of 1.5.
getNormalizationFactor(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Calculates the normalization factor in order to get an average bond length of 1.5.
getNormalizedElectronegativity(String) - Method in class org.openscience.cdk.tools.AtomicProperties
getNormalizedMass(String) - Method in class org.openscience.cdk.tools.AtomicProperties
getNormalizedPolarizability(String) - Method in class org.openscience.cdk.tools.AtomicProperties
getNormalizedVdWVolume(String) - Method in class org.openscience.cdk.tools.AtomicProperties
getNoteComments() - Method in class org.openscience.cdk.fingerprint.model.Bayesian: Returns the optional comments, which is a list of arbitrary text strings.
getNoteOrigin() - Method in class org.openscience.cdk.fingerprint.model.Bayesian: Returns the optional description of the source for the model.
getNotEqual() - Method in class org.openscience.cdk.smsd.helper.BinaryTree: Deprecated.

Returns not equal node
getNoteTitle() - Method in class org.openscience.cdk.fingerprint.model.Bayesian: Returns the optional title used to describe the model.
getNotification() - Method in class org.openscience.cdk.ChemObject
getNotification() - Method in class org.openscience.cdk.debug.DebugChemObject: Returns the flag that indicates whether notification messages are sent around.
getNotification() - Method in interface org.openscience.cdk.interfaces.IChemObject: Returns the flag that indicates whether notification messages are sent around.
getNotification() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
getNotification() - Method in class org.openscience.cdk.renderer.RendererModel: Determines if the model sends around change notifications.
getNotification() - Method in class org.openscience.cdk.silent.ChemObject
getNS() - Method in class org.openscience.cdk.dict.Dictionary
getNTerminus() - Method in class org.openscience.cdk.AminoAcid: Retrieves the N-terminus atom.
getNTerminus() - Method in class org.openscience.cdk.debug.DebugAminoAcid: Retrieves the N-terminus atom.
getNTerminus() - Method in interface org.openscience.cdk.interfaces.IAminoAcid: Retrieves the N-terminus atom.
getNTerminus() - Method in class org.openscience.cdk.silent.AminoAcid: Retrieves the N-terminus atom.
getNumAtoms() - Method in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
getNumber() - Method in class org.openscience.cdk.libio.md.ChargeGroup
getNumber() - Method in class org.openscience.cdk.libio.md.Residue
getNumberOfFontSizes() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager: Get the number of font sizes used.
getNumberOfIsotopes() - Method in class org.openscience.cdk.formula.IsotopePattern: Returns the number of isotopes in this pattern.
getNumberOfNeighbors(int) - Method in class org.openscience.cdk.geometry.surface.NeighborList
getNumberOfTriangles() - Method in class org.openscience.cdk.geometry.surface.Tessellate
getNumbers(IAtomContainer) - Static method in class org.openscience.cdk.graph.invariant.InChINumbersTools: Makes an array containing the InChI atom numbers of the non-hydrogen atoms in the atomContainer.
getNumMoreElectronegativethanCarbon(IAtom) - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor.JPlogPCalculator
getOccupancy() - Method in class org.openscience.cdk.debug.DebugPDBAtom: get the Occupancy of this atom.
getOccupancy() - Method in interface org.openscience.cdk.interfaces.IPDBAtom: get the Occupancy of this atom.
getOccupancy() - Method in class org.openscience.cdk.protein.data.PDBAtom: get the Occupancy of this atom.
getOccupancy() - Method in class org.openscience.cdk.silent.PDBAtom: get the Occupancy of this atom.
getOccurrence() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupList: Occurrence required: n : exactly n ; n - m : n through m ; > n : greater than n ; < n : fewer than n ; default (blank) is > 0 ; Any non-contradictory combination of the preceding values is also allowed; for example "1, 3-7, 9, >11".
getOccurrence() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList: Returns the occurrence value.
getOccurrences() - Method in class org.openscience.cdk.structgen.maygen.Maygen
getOKCount() - Method in class org.openscience.cdk.validate.ValidationReport: Returns the number of tests without errors.
getOKs() - Method in class org.openscience.cdk.validate.ValidationReport: Returns an array of ValidationTest which did not find problems.
getOperator() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom: Deprecated.
getOperator() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond: Deprecated.
getOptions() - Method in class org.openscience.cdk.io.setting.OptionIOSetting: Returns a Vector of Strings containing all possible options.
getOrbit(int) - Method in class org.openscience.cdk.group.Permutation: Get all the elements in the same orbit in the permutation (unsorted).
getOrder() - Method in class org.openscience.cdk.Bond: Returns the bond order of this bond.
getOrder() - Method in class org.openscience.cdk.BondRef: Returns the bond order of this bond.
getOrder() - Method in class org.openscience.cdk.debug.DebugBond: Returns the bond order of this bond.
getOrder() - Method in interface org.openscience.cdk.interfaces.IBond: Returns the bond order of this bond.
getOrder() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Returns the query bond order of this query bond.
getOrder() - Method in class org.openscience.cdk.silent.Bond: Returns the bond order of this bond.
getOther(IAtom) - Method in class org.openscience.cdk.Bond: Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correct IBond.getConnectedAtoms(IAtom) should be used.
getOther(IAtom) - Method in class org.openscience.cdk.BondRef: Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correct IBond.getConnectedAtoms(IAtom) should be used.
getOther(IAtom) - Method in class org.openscience.cdk.debug.DebugBond: Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correct IBond.getConnectedAtoms(IAtom) should be used.
getOther(IAtom) - Method in interface org.openscience.cdk.interfaces.IBond: Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correct IBond.getConnectedAtoms(IAtom) should be used.
getOther(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correct IBond.getConnectedAtoms(IAtom) should be used.
getOther(IAtom) - Method in class org.openscience.cdk.silent.Bond: Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correct IBond.getConnectedAtoms(IAtom) should be used.
getOtherBondAtom(IAtom, IBond) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator: Returns the other atom of the bond.
getOverlaps(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: Returns all the maximal common substructure between two atom containers.
getOverlaps(IAtomContainer, IAtomContainer, boolean) - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlus: Deprecated.
getOverlaps(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS: Deprecated.

Returns all the maximal common substructure between 2 atom containers.
getOverLaps(IAtomContainer, IAtomContainer, boolean) - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMapping: Deprecated.

Returns single mapping solutions.
getOverLaps(IQueryAtomContainer, IAtomContainer, boolean) - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMapping: Deprecated.

Returns single mapping solutions.
getOverlapScore(IAtomContainer, Vector, Vector) - Method in class org.openscience.cdk.layout.OverlapResolver: Deprecated.

Calculates a score based on the overlap of atoms and intersection of bonds.
getOxt() - Method in class org.openscience.cdk.debug.DebugPDBAtom: Returns true of this atom is a PDB OXT atom.
getOxt() - Method in interface org.openscience.cdk.interfaces.IPDBAtom: Returns true of this atom is a PDB OXT atom.
getOxt() - Method in class org.openscience.cdk.protein.data.PDBAtom
getOxt() - Method in class org.openscience.cdk.silent.PDBAtom
getOxygenSpecial(IAtom) - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor.JPlogPCalculator: Determines and returns the SS (subsection) portion of the atomtype integer for an Oxygen Atom
getOxygenSulfur() - Method in class org.openscience.cdk.structgen.maygen.Maygen
getParameter(Class<T>) - Method in class org.openscience.cdk.renderer.RendererModel: Returns the IGeneratorParameter for the active IRenderer.
getParameterClass() - Method in class org.openscience.cdk.dict.EntryReact: Get the IParameterReact's of the reaction.
getParameterClass(Class<?>) - Method in interface org.openscience.cdk.reaction.IReactionProcess: Return the IParameterReact if it exists given the class.
getParameterClass(Class<?>) - Method in class org.openscience.cdk.reaction.ReactionEngine: Return the IParameterReact if it exists given the class.
getParameterList() - Method in interface org.openscience.cdk.reaction.IReactionProcess: Returns the current parameter values.
getParameterList() - Method in class org.openscience.cdk.reaction.ReactionEngine: Returns the current parameter values.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor: Gets the parameterNames attribute of the AtomDegreeDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor: Gets the parameterNames attribute of the VdWRadiusDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor: Gets the parameterNames attribute of the AtomHybridizationVSEPRDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor: Gets the parameterNames attribute of the VdWRadiusDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor: Gets the parameterNames attribute of the BondsToAtomDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor: Gets the parameterNames attribute of the VdWRadiusDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor: Gets the parameterNames attribute of the DistanceToAtomDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor: Gets the parameterNames attribute of the EffectiveAtomPolarizabilityDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor: Gets the parameterNames attribute of the InductiveAtomicHardnessDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor: Gets the parameterNames attribute of the InductiveAtomicSoftnessDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor: Gets the parameterNames attribute of the IPAtomicHOSEDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor: Deprecated.

Gets the parameterNames attribute of the IPAtomicLearningDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor: Gets the parameterNames attribute of the IsProtonInAromaticSystemDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInConjugatedPiSystemDescriptor: Gets the parameterNames attribute of the IsProtonInConjugatedPiSystemDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor: Gets the parameterNames attribute of the PartialPiChargeDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor: Gets the parameterNames attribute of the PartialSigmaChargeDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor: Gets the parameterNames attribute of the PartialTChargeMMFF94Descriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor: Gets the parameterNames attribute of the PartialTChargePEOEDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor: Gets the parameterNames attribute of the PeriodicTablePositionDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor: Gets the parameterNames attribute of the SigmaElectronegativityDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor: Gets the parameterNames attribute of the ProtonAffinityDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor: Gets the parameterNames attribute of the ProtonTotalPartialChargeDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R: Gets the parameterNames attribute of the RDFProtonDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR: Gets the parameterNames attribute of the RDFProtonDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol: Gets the parameterNames attribute of the RDFProtonDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR: Gets the parameterNames attribute of the RDFProtonDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR: Gets the parameterNames attribute of the RDFProtonDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor: Gets the parameterNames attribute of the SigmaElectronegativityDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor: Gets the parameterNames attribute of the StabilizationPlusChargeDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor: Gets the parameterNames attribute of the VdWRadiusDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor: Gets the parameterNames attribute of the PiContactDetectionDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptor
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor: Gets the parameterNames attribute of the BondPartialPiChargeDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor: Gets the parameterNames attribute of the BondPartialSigmaChargeDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor: Gets the parameterNames attribute of the BondPartialTChargeDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor: Gets the parameterNames attribute of the BondSigmaElectronegativityDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor: Deprecated.

Gets the parameterNames attribute of the IPBondLearningDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor: Returns the names of the parameters for this descriptor.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor: Gets the parameterNames attribute of the AromaticAtomsCountDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor: Gets the parameterNames attribute of the APolDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor: Gets the parameterNames attribute of the AromaticAtomsCountDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor: Gets the parameterNames attribute of the AromaticBondsCountDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor: Gets the parameterNames attribute of the AtomCountDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor: Returns the names of the parameters for this descriptor.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor: Gets the parameterNames attribute of the BCUTDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor: Gets the parameterNames attribute of the BondCountDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor: Gets the parameterNames attribute of the BPolDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor: Gets the parameterNames attribute of the GravitationalIndexDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor: Gets the parameterNames attribute of the CPSADescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor: Gets the parameterNames attribute of the EccentricConnectivityIndexDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor: Returns the names of the parameters for this descriptor.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalCSP3Descriptor: Returns the names of the parameters for this descriptor.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor: Returns the names of the parameters for this descriptor.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor: Gets the parameterNames attribute of the FragmentComplexityDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor: Gets the parameterNames attribute of the GravitationalIndexDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor: Gets the parameterNames attribute of the HBondAcceptorCountDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor: Gets the parameterNames of the HBondDonorCountDescriptor.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor: Gets the parameterNames attribute of the HybridizationRatioDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor: Deprecated.

Gets the parameterNames attribute of the IPMolecularLearningDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor: Gets the parameterNames attribute of the KappaShapeIndicesDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor: Gets the parameterNames attribute of the descriptor.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor: Gets the parameterNames attribute of the LargestPiSystemDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor: Gets the parameterNames attribute of the LargestPiSystemDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor: Gets the parameterNames attribute of the PetitjeanNumberDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor: Gets the parameterNames attribute of the LongestAliphaticChainDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor: Gets the parameterNames attribute for this descriptor.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor: Gets the parameterNames attribute of the WeightDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor: Gets the parameterNames attribute of the MomentOfInertiaDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor: Gets the parameterNames attribute of the PetitjeanNumberDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor: Gets the parameterNames attribute of the PetitjeanShapeIndexDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor: Gets the parameterNames attribute of the RotatableBondsCountDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor: Gets the parameterNames attribute of the RuleOfFiveDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor: Get parameters: empty, there are none.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.SpiroAtomCountDescriptor: Returns the names of the parameters for this descriptor.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor: Gets the parameterNames attribute of the TPSADescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor: Returns the names of the parameters for this descriptor.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor: Gets the parameterNames attribute of the VAdjMaDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor: Gets the parameterNames attribute of the WeightDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor: Gets the parameterNames attribute of the WeightedPathDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor: Gets the parameterNames attribute of the WHIMDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor: Gets the parameterNames attribute of the WienerNumbersDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor: Gets the parameterNames attribute of the XLogPDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor: Gets the parameterNames attribute of the ZagrebIndexDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor: Gets the parameterNames attribute of the TaeAminOAcidDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.substance.OxygenAtomCountDescriptor: Returns the names of the parameters for this descriptor.
getParameterNames() - Method in class org.openscience.cdk.qsar.DescriptorValue
getParameterNames() - Method in interface org.openscience.cdk.qsar.IDescriptor: Returns the names of the parameters for this descriptor.
getParameters() - Method in class org.openscience.cdk.dict.EntryReact: Get the parameters of the reaction.
getParameters() - Method in class org.openscience.cdk.fingerprint.AbstractFingerprinter: Base classes should override this method to report the parameters they are configured with.
getParameters() - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter
getParameters() - Method in class org.openscience.cdk.fingerprint.Fingerprinter
getParameters() - Method in class org.openscience.cdk.fingerprint.LingoFingerprinter
getParameters() - Method in class org.openscience.cdk.fingerprint.SignatureFingerprinter
getParameters() - Method in class org.openscience.cdk.formula.rules.ChargeRule: Gets the parameters attribute of the ChargeRule object.
getParameters() - Method in class org.openscience.cdk.formula.rules.ElementRule: Gets the parameters attribute of the ElementRule object.
getParameters() - Method in interface org.openscience.cdk.formula.rules.IRule: Returns the current parameter values.
getParameters() - Method in class org.openscience.cdk.formula.rules.IsotopePatternRule: Gets the parameters attribute of the IsotopePatternRule object.
getParameters() - Method in class org.openscience.cdk.formula.rules.MMElementRule: Gets the parameters attribute of the MMElementRule object.
getParameters() - Method in class org.openscience.cdk.formula.rules.NitrogenRule: Gets the parameters attribute of the NitrogenRule object.
getParameters() - Method in class org.openscience.cdk.formula.rules.RDBERule: Gets the parameters attribute of the RDBRule object.
getParameters() - Method in class org.openscience.cdk.formula.rules.ToleranceRangeRule: Gets the parameters attribute of the ToleranceRangeRule object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor: Gets the parameters attribute of the AtomDegreeDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor: Gets the parameters attribute of the VdWRadiusDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor: Gets the parameters attribute of the AtomHybridizationVSEPRDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor: Gets the parameters attribute of the VdWRadiusDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor: Gets the parameters attribute of the BondsToAtomDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor: Gets the parameters attribute of the VdWRadiusDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor: Gets the parameters attribute of the DistanceToAtomDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor: Gets the parameters attribute of the EffectiveAtomPolarizabilityDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor: Gets the parameters attribute of the InductiveAtomicHardnessDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor: Gets the parameters attribute of the InductiveAtomicSoftnessDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor: Gets the parameters attribute of the IPAtomicHOSEDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor: Deprecated.

Gets the parameters attribute of the IPAtomicLearningDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor: Gets the parameters attribute of the IsProtonInAromaticSystemDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInConjugatedPiSystemDescriptor: Gets the parameters attribute of the IsProtonInConjugatedPiSystemDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor: Gets the parameters attribute of the PartialPiChargeDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor: Gets the parameters attribute of the PartialSigmaChargeDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor: Gets the parameters attribute of the PartialTChargeMMFF94Descriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor: Gets the parameters attribute of the PartialTChargePEOEDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor: Gets the parameters attribute of the PeriodicTablePositionDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor: Gets the parameters attribute of the PiElectronegativityDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor: Gets the parameters attribute of the ProtonAffinityDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor: Gets the parameters attribute of the ProtonTotalPartialChargeDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R: Gets the parameters attribute of the RDFProtonDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR: Gets the parameters attribute of the RDFProtonDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol: Gets the parameters attribute of the RDFProtonDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR: Gets the parameters attribute of the RDFProtonDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR: Gets the parameters attribute of the RDFProtonDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor: Gets the parameters attribute of the SigmaElectronegativityDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor: Gets the parameters attribute of the StabilizationPlusChargeDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor: Gets the parameters attribute of the VdWRadiusDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor: Gets the parameters attribute of the PiContactDetectionDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptor
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor: Gets the parameters attribute of the BondPartialPiChargeDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor: Gets the parameters attribute of the BondPartialSigmaChargeDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor: Gets the parameters attribute of the BondPartialTChargeDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor: Gets the parameters attribute of the BondSigmaElectronegativityDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor: Deprecated.

Gets the parameters attribute of the IPBondLearningDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor: Returns the current parameter values.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor: Gets the parameters attribute of the AminoAcidsCountDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor: Gets the parameters attribute of the APolDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor: Gets the parameters attribute of the AromaticAtomsCountDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor: Gets the parameters attribute of the AromaticBondsCountDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor: Gets the parameters attribute of the AtomCountDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor: Returns the current parameter values.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor: Gets the parameters attribute of the BCUTDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor: Gets the parameters attribute of the BondCountDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor: Gets the parameters attribute of the BPolDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor: Gets the parameters attribute of the GravitationalIndexDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor: Gets the parameters attribute of the CPSADescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor: Gets the parameters attribute of the EccentricConnectivityIndexDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor: Returns the current parameter values.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalCSP3Descriptor: Returns the current parameter values.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor: Returns the current parameter values.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor: Gets the parameters attribute of the FragmentComplexityDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor: Gets the parameters attribute of the GravitationalIndexDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor: Gets the parameters attribute of the HBondAcceptorCountDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor: Gets the parameters of the HBondDonorCountDescriptor instance.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor: Gets the parameters attribute of the HybridizationRatioDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor: Deprecated.

Gets the parameters attribute of the IPMolecularLearningDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor: Gets the parameters attribute of the KappaShapeIndicesDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor: Gets the parameters attribute of the descriptor.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor: Gets the parameters attribute of the LargestChainDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor: Gets the parameters attribute of the LargestPiSystemDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor: Gets the parameters attribute of the PetitjeanNumberDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor: Gets the parameters attribute of the LongestAliphaticChainDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor: Gets the parameters attribute of the MannholdLogPDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor: Gets the parameters attribute of the WeightDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor: Gets the parameters attribute of the MomentOfInertiaDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor: Gets the parameters attribute of the PetitjeanNumberDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor: Gets the parameters attribute of the PetitjeanShapeIndexDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor: Gets the parameters attribute of the RotatableBondsCountDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor: Gets the parameters attribute of the RuleOfFiveDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor: Get parameters: returns empty array, there are none.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.SpiroAtomCountDescriptor: Returns the current parameter values.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor: Gets the parameters attribute of the TPSADescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor: Returns the current parameter values.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor: Gets the parameters attribute of the VAdjMaDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor: Gets the parameters attribute of the WeightDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor: Gets the parameters attribute of the WeightedPathDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor: Gets the parameters attribute of the WHIMDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor: Gets the parameters attribute of the WienerNumbersDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor: Gets the parameters attribute of the XLogPDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor: Gets the parameters attribute of the ZagrebIndexDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor: Gets the parameters attribute of the TaeAminoAcidDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.substance.OxygenAtomCountDescriptor: Returns the current parameter values.
getParameters() - Method in class org.openscience.cdk.qsar.DescriptorValue
getParameters() - Method in interface org.openscience.cdk.qsar.IDescriptor: Returns the current parameter values.
getParameters() - Method in class org.openscience.cdk.renderer.generators.AtomContainerBoundsGenerator: Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.AtomNumberGenerator: Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator: Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator: Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.BasicGenerator: Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator: Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.BoundsGenerator: Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.ExtendedAtomGenerator: Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.HighlightGenerator: Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in interface org.openscience.cdk.renderer.generators.IGenerator: Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.LonePairGenerator: Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.MappingGenerator: Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.ProductsBoxGenerator: Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.RadicalGenerator: Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.ReactantsBoxGenerator: Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.ReactionArrowGenerator: Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.ReactionBoxGenerator: Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.ReactionPlusGenerator: Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.ReactionSceneGenerator: Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.RingGenerator: Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator: Returns the list of IGeneratorParameter for this particular generator.
getParameterSet() - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator: Gets the parameterSet attribute of the ForceFieldConfigurator object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor: Gets the parameterType attribute of the AtomDegreeDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor: Gets the parameterType attribute of the VdWRadiusDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor: Gets the parameterType attribute of the AtomHybridizationVSEPRDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor: Gets the parameterType attribute of the VdWRadiusDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor: Gets the parameterType attribute of the BondsToAtomDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor: Gets the parameterType attribute of the VdWRadiusDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor: Gets the parameterType attribute of the DistanceToAtomDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor: Gets the parameterType attribute of the EffectiveAtomPolarizabilityDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor: Gets the parameterType attribute of the InductiveAtomicHardnessDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor: Gets the parameterType attribute of the InductiveAtomicSoftnessDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor: Gets the parameterType attribute of the IPAtomicHOSEDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor: Deprecated.

Gets the parameterType attribute of the IPAtomicLearningDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor: Gets the parameterType attribute of the IsProtonInAromaticSystemDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInConjugatedPiSystemDescriptor: Gets the parameterType attribute of the IsProtonInConjugatedPiSystemDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor: Gets the parameterType attribute of the PartialPiChargeDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor: Gets the parameterType attribute of the PartialSigmaChargeDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor: Gets the parameterType attribute of the PartialTChargeMMFF94Descriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor: Gets the parameterType attribute of the PartialTChargePEOEDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor: Gets the parameterType attribute of the PeriodicTablePositionDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor: Gets the parameterType attribute of the SigmaElectronegativityDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor: Gets the parameterType attribute of the ProtonAffinityDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor: Gets the parameterType attribute of the ProtonTotalPartialChargeDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R: Gets the parameterType attribute of the RDFProtonDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR: Gets the parameterType attribute of the RDFProtonDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol: Gets the parameterType attribute of the RDFProtonDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR: Gets the parameterType attribute of the RDFProtonDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR: Gets the parameterType attribute of the RDFProtonDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor: Gets the parameterType attribute of the SigmaElectronegativityDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor: Gets the parameterType attribute of the StabilizationPlusChargeDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor: Gets the parameterType attribute of the VdWRadiusDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor: Gets the parameterType attribute of the PiContactDetectionDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptor
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor: Gets the parameterType attribute of the BondPartialPiChargeDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor: Gets the parameterType attribute of the BondPartialSigmaChargeDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor: Gets the parameterType attribute of the BondPartialTChargeDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor: Gets the parameterType attribute of the BondSigmaElectronegativityDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor: Deprecated.

Gets the parameterType attribute of the IPBondLearningDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor: Returns a class matching that of the parameter with the given name.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor: Gets the parameterType attribute of the AromaticAtomsCountDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor: Gets the parameterType attribute of the APolDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor: Gets the parameterType attribute of the AromaticAtomsCountDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor: Gets the parameterType attribute of the AromaticBondsCountDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor: Gets the parameterType attribute of the AtomCountDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor: Returns a class matching that of the parameter with the given name.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor: Gets the parameterType attribute of the BCUTDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor: Gets the parameterType attribute of the BondCountDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor: Gets the parameterType attribute of the BPolDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor: Gets the parameterType attribute of the GravitationalIndexDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor: Gets the parameterType attribute of the CPSADescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor: Gets the parameterType attribute of the EccentricConnectivityIndexDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor: Returns a class matching that of the parameter with the given name.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalCSP3Descriptor: Returns a class matching that of the parameter with the given name.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor: Returns a class matching that of the parameter with the given name.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor: Gets the parameterType attribute of the FragmentComplexityDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor: Gets the parameterType attribute of the GravitationalIndexDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor: Gets the parameterType attribute of the HBondAcceptorCountDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor: Gets the parameterType of the HBondDonorCountDescriptor.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor: Gets the parameterType attribute of the HybridizationRatioDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor: Deprecated.

Gets the parameterType attribute of the IPMolecularLearningDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor: Gets the parameterType attribute of the KappaShapeIndicesDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor: Gets the parameterType attribute of the descriptor.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor: Gets the parameterType attribute of the LargestChainDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor: Gets the parameterType attribute of the LargestPiSystemDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor: Gets the parameterType attribute of the PetitjeanNumberDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor: Gets the parameterType attribute of the LongestAliphaticChainDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor: Gets the parameterType attribute for a given parameter name.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor: Gets the parameterType attribute of the WeightDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor: Gets the parameterType attribute of the MomentOfInertiaDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor: Gets the parameterType attribute of the PetitjeanNumberDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor: Gets the parameterType attribute of the PetitjeanShapeIndexDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor: Gets the parameterType attribute of the RotatableBondsCountDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor: Gets the parameterType attribute of the RuleOfFiveDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor: Parameter types: there aren't any.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.SpiroAtomCountDescriptor: Returns a class matching that of the parameter with the given name.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor: Gets the parameterType attribute of the TPSADescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor: Returns a class matching that of the parameter with the given name.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor: Gets the parameterType attribute of the VAdjMaDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor: Gets the parameterType attribute of the WeightDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor: Gets the parameterType attribute of the WeightedPathDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor: Gets the parameterType attribute of the WHIMDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor: Gets the parameterType attribute of the WienerNumbersDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor: Gets the parameterType attribute of the XLogPDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor: Gets the parameterType attribute of the ZagrebIndexDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor: Gets the parameterType attribute of the TaeAminoAcidDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.substance.OxygenAtomCountDescriptor: Returns a class matching that of the parameter with the given name.
getParameterType(String) - Method in interface org.openscience.cdk.qsar.IDescriptor: Returns a class matching that of the parameter with the given name.
getParameterValue() - Method in class org.openscience.cdk.dict.EntryReact: Get the parameter value of the reaction.
getParamterSet() - Method in class org.openscience.cdk.modeling.builder3d.MM2BasedParameterSetReader
getParamterSet() - Method in class org.openscience.cdk.modeling.builder3d.MMFF94BasedParameterSetReader
getParentMolecule() - Method in class org.openscience.cdk.libio.md.ChargeGroup
getParentMolecule() - Method in class org.openscience.cdk.libio.md.Residue
getParents() - Method in class org.openscience.cdk.sgroup.Sgroup: Access the parents of this Sgroup.
getPartition(int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Based on the new degrees and the former partition, getting the new atom partition.
getPartition(List<String>) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Getting the partition of symbols
getPath(IAtomContainer, IAtom, IAtom) - Method in class org.openscience.cdk.graph.SpanningTree: Find a path connected a1 and a2 in the tree.
getPathsOfLength(IAtomContainer, IAtom, int) - Static method in class org.openscience.cdk.graph.PathTools: Get the paths starting from an atom of specified length.
getPathsOfLengthUpto(IAtomContainer, IAtom, int) - Static method in class org.openscience.cdk.graph.PathTools: Get all the paths starting from an atom of length 0 upto the specified length.
getPatterns() - Static method in class org.openscience.cdk.config.fragments.EStateFragments
getPaulingElectronegativities(IAtomContainer, boolean) - Method in class org.openscience.cdk.charges.InductivePartialCharges: Gets the paulingElectronegativities attribute of the InductivePartialCharges object.
getPaulingElectronegativity(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable: Get the Pauling electronegativity of an element.
getPeriod(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable: Get the period of the element.
getPermutedIndex(Permutation, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: By a given permutation, checking which entry is mapped to the index.
getPharmacophoreQuery() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher: Get the query pharmacophore.
getPhase(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable: Get the phase of the element.
getPlacedAtoms(IAtomContainer) - Static method in class org.openscience.cdk.layout.AtomPlacer: Get all the placed atoms in an AtomContainer
getPlacedAtomsInAtomContainer(IAtom, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D: Gets all placed neighbouring atoms of a atom.
getPlacedHeavyAtom(IAtomContainer, IAtom) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D: Returns a placed atom connected to a given atom.
getPlacedHeavyAtom(IAtomContainer, IAtom, IAtom) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D: Gets the first placed Heavy Atom around atomA which is not atomB.
getPlacedHeavyAtomInAtomContainer(IAtom, IAtom, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D: Returns a placed neighbouring atom of a central atom atomA, which is not atomB.
getPlacedHeavyAtoms(IAtomContainer, IAtom) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D: Gets the placed Heavy Atoms connected to an atom.
getPockets() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
getPocketSize() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
getPoint2d() - Method in class org.openscience.cdk.Atom: Returns a point specifying the location of this atom in a 2D space.
getPoint2d() - Method in class org.openscience.cdk.AtomRef: Returns a point specifying the location of this atom in a 2D space.
getPoint2d() - Method in class org.openscience.cdk.debug.DebugAtom: Returns a point specifying the location of this atom in a 2D space.
getPoint2d() - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Returns a point specifying the location of this atom in a 2D space.
getPoint2d() - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Returns a point specifying the location of this atom in a 2D space.
getPoint2d() - Method in interface org.openscience.cdk.interfaces.IAtom: Returns a point specifying the location of this atom in a 2D space.
getPoint2d() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Returns a point specifying the location of this atom in a 2D space.
getPoint2d() - Method in class org.openscience.cdk.silent.Atom: Returns a point specifying the location of this atom in a 2D space.
getPoint3d() - Method in class org.openscience.cdk.Atom: Returns a point specifying the location of this atom in a 3D space.
getPoint3d() - Method in class org.openscience.cdk.AtomRef: Returns a point specifying the location of this atom in a 3D space.
getPoint3d() - Method in class org.openscience.cdk.debug.DebugAtom: Returns a point specifying the location of this atom in a 3D space.
getPoint3d() - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Returns a point specifying the location of this atom in a 3D space.
getPoint3d() - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Returns a point specifying the location of this atom in a 3D space.
getPoint3d() - Method in interface org.openscience.cdk.interfaces.IAtom: Returns a point specifying the location of this atom in a 3D space.
getPoint3d() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Returns a point specifying the location of this atom in a 3D space.
getPoint3d() - Method in class org.openscience.cdk.silent.Atom: Returns a point specifying the location of this atom in a 3D space.
getPolarBondArray(IAtom) - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor.JPlogPCalculator
getPolarizabilitiyFactorForAtom(IAtomContainer, IAtom) - Method in class org.openscience.cdk.charges.Polarizability: Gets the polarizabilitiyFactorForAtom.
getPolarizability(String) - Method in class org.openscience.cdk.tools.AtomicProperties
getPosition() - Method in class org.openscience.cdk.smarts.SmartsResult: The position (string index) in the input that was interpreted.
getPosition(int) - Method in class org.openscience.cdk.math.qm.GaussiansBasis: Gets the position of a base.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ABINITFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Aces2Format: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ADFFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.AlchemyFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.BGFFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.BSFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CACheFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CIFFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CMLFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CRK2DFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CRK3DFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CrystClustFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CTXFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.DaltonFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.DMol3Format: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.DOCK5Format: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.FingerprintFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.GamessFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian03Format: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian90Format: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian92Format: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian94Format: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian95Format: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian98Format: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.GROMOS96Format: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.HINFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.INChIFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in interface org.openscience.cdk.io.formats.IResourceFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.JaguarFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.JMEFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MacroModelFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MDLFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MDLRXNV2000Format: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MDLV2000Format: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MDLV3000Format: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MMODFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Mol2Format: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC7Format: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC93Format: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC97Format: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MPQCFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.NWChemFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PCModelFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PDBFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PDBMLFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PMPFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.POVRayFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PQSChemFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.QChemFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.RawCopyFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SDFFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ShelXFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SMARTSFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SMILESFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SpartanFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SVGFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.VASPFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ViewmolFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.XEDFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.XYZFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.YasaraFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ZindoFormat: Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat: Returns the preferred resource name extension.
getPrime() - Method in class org.openscience.cdk.smiles.InvPair: Get the current prime number.
getPrimeAt(int) - Static method in class org.openscience.cdk.math.Primes: Deprecated.

Returns the i-th prime number in the sequence of all prime numbers below 19700.
getProductCoefficient(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugReaction: Returns the stoichiometry coefficient of the given product.
getProductCoefficient(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IReaction: Returns the stoichiometry coefficient of the given product.
getProductCoefficient(IAtomContainer) - Method in class org.openscience.cdk.Reaction: Returns the stoichiometry coefficient of the given product.
getProductCoefficient(IAtomContainer) - Method in class org.openscience.cdk.silent.Reaction: Returns the stoichiometry coefficient of the given product.
getProductCoefficients() - Method in class org.openscience.cdk.debug.DebugReaction: Returns an array of double with the stoichiometric coefficients of the products.
getProductCoefficients() - Method in interface org.openscience.cdk.interfaces.IReaction: Returns an array of double with the stoichiometric coefficients of the products.
getProductCoefficients() - Method in class org.openscience.cdk.Reaction: Returns an array of double with the stoichiometric coefficients of the products.
getProductCoefficients() - Method in class org.openscience.cdk.silent.Reaction: Returns an array of double with the stoichiometric coefficients of the products.
getProductCount() - Method in class org.openscience.cdk.debug.DebugReaction: Returns the number of products in this reaction.
getProductCount() - Method in interface org.openscience.cdk.interfaces.IReaction: Returns the number of products in this reaction.
getProductCount() - Method in class org.openscience.cdk.Reaction: Returns the number of products in this reaction.
getProductCount() - Method in class org.openscience.cdk.silent.Reaction: Returns the number of products in this reaction.
getProductMolecule() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS: Deprecated.

Returns modified target molecule on which mapping was performed.
getProductMolecule() - Method in class org.openscience.cdk.smsd.Isomorphism: Deprecated.

Returns modified target molecule on which mapping was performed.
getProducts() - Method in class org.openscience.cdk.debug.DebugReaction: Returns a MoleculeSet containing the products of this reaction.
getProducts() - Method in interface org.openscience.cdk.interfaces.IReaction: Returns a IAtomContaineSet containing the products of this reaction.
getProducts() - Method in class org.openscience.cdk.Reaction: Returns a MoleculeSet containing the products of this reaction.
getProducts() - Method in class org.openscience.cdk.silent.Reaction: Returns a MoleculeSet containing the products of this reaction.
getProperties() - Method in class org.openscience.cdk.ChemObject: Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugAtom: Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugAtomType: Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugBond: Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugChemFile: Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugChemModel: Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugChemObject: Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugChemSequence: Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugCrystal: Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugElectronContainer: Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugElement: Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugIsotope: Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugLonePair: Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugMapping: Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugMolecularFormula: Returns a Map with the IChemObject's properties.I should integrate into ChemObject.
getProperties() - Method in class org.openscience.cdk.debug.DebugMonomer: Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugPolymer: Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugReaction: Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugReactionScheme: Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugReactionSet: Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugRing: Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugSingleElectron: Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugStrand: Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugSubstance: Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.formula.MolecularFormula: Returns a Map with the IChemObject's properties.I should integrate into ChemObject.
getProperties() - Method in interface org.openscience.cdk.interfaces.IChemObject: Returns a Map with the IChemObject's properties.
getProperties() - Method in interface org.openscience.cdk.interfaces.IMolecularFormula: Returns a Map with the IChemObject's properties.I should integrate into ChemObject.
getProperties() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject: Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.silent.ChemObject: Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.silent.MolecularFormula: Returns a Map with the IChemObject's properties.I should integrate into ChemObject.
getProperty(Object) - Method in class org.openscience.cdk.ChemObject: Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugAtom: Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugAtomType: Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugBond: Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugChemFile: Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugChemModel: Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugChemObject: Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugChemSequence: Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugCrystal: Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugElectronContainer: Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugElement: Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugIsotope: Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugLonePair: Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugMapping: Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugMolecularFormula: Returns a property for the IChemObject - the object is automatically cast to the required type.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugMonomer: Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugPolymer: Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugReaction: Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugReactionScheme: Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugReactionSet: Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugRing: Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugSingleElectron: Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugStrand: Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugSubstance: Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.formula.MolecularFormula: Returns a property for the IChemObject - the object is automatically cast to the required type.
getProperty(Object) - Method in interface org.openscience.cdk.interfaces.IChemObject: Returns a property for the IChemObject - the object is automatically cast to the required type.
getProperty(Object) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula: Returns a property for the IChemObject - the object is automatically cast to the required type.
getProperty(Object) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject: Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.silent.ChemObject: Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.silent.MolecularFormula: Returns a property for the IChemObject - the object is automatically cast to the required type.
getProperty(Object, Class<T>) - Method in class org.openscience.cdk.ChemObject: Access a property of the given description and cast the specified class.
getProperty(Object, Class<T>) - Method in class org.openscience.cdk.debug.DebugChemObject: Access a property of the given description and cast the specified class.
getProperty(Object, Class<T>) - Method in class org.openscience.cdk.formula.MolecularFormula: Access a property of the given description and cast the specified class.
getProperty(Object, Class<T>) - Method in interface org.openscience.cdk.interfaces.IChemObject: Access a property of the given description and cast the specified class.
getProperty(Object, Class<T>) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula: Access a property of the given description and cast the specified class.
getProperty(Object, Class<T>) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject: Access a property of the given description and cast the specified class.
getProperty(Object, Class<T>) - Method in class org.openscience.cdk.silent.ChemObject: Access a property of the given description and cast the specified class.
getProperty(Object, Class<T>) - Method in class org.openscience.cdk.silent.MolecularFormula: Access a property of the given description and cast the specified class.
getProtein() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
getProteinInterior() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
getQSARs(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.tools.IonizationPotentialTool: Deprecated.

Get the results of 7 qsar descriptors been applied.
getQSARs(IAtomContainer, IBond) - Static method in class org.openscience.cdk.tools.IonizationPotentialTool: Deprecated.

Get the results of 7 qsar descriptors been applied.
getQueryNode() - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.Match: Deprecated.

Return query node
getQuestion() - Method in class org.openscience.cdk.io.setting.IOSetting
getRandom() - Static method in class org.openscience.cdk.math.RandomNumbersTool: Returns the instance of Random used by this class.
getRandomNextPermutation() - Method in class org.openscience.cdk.graph.Permutor: Randomly skip ahead in the list of permutations.
getRandomNextPermutation() - Method in class org.openscience.cdk.smsd.labelling.Permutor: Deprecated.

Randomly skip ahead in the list of permutations.
getRandomSeed() - Static method in class org.openscience.cdk.math.RandomNumbersTool: Returns the seed being used by this random number generator.
getRange(IMolecularFormulaSet) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaRangeManipulator: Extract from a set of MolecularFormula the range of each each element found and put the element and occurrence in a new MolecularFormulaRange.
getRank() - Method in class org.openscience.cdk.graph.Permutor: Get the current rank.
getRank() - Method in class org.openscience.cdk.smsd.labelling.Permutor: Deprecated.
getRAtom() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
getRawContent() - Method in class org.openscience.cdk.dict.Entry
getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.AtomPairs2DFingerprinter
getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter: Invalid: it is not appropriate to convert the integer hash codes into strings.
getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.EStateFingerprinter: Returns the raw representation of the fingerprint for the given IAtomContainer.
getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter: Returns the raw representation of the fingerprint for the given IAtomContainer.
getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.Fingerprinter: Returns the raw representation of the fingerprint for the given IAtomContainer.
getRawFingerprint(IAtomContainer) - Method in interface org.openscience.cdk.fingerprint.IFingerprinter: Returns the raw representation of the fingerprint for the given IAtomContainer.
getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.LingoFingerprinter
getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.MACCSFingerprinter: Returns the raw representation of the fingerprint for the given IAtomContainer.
getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.PubchemFingerprinter: Returns the raw representation of the fingerprint for the given IAtomContainer.
getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.ShortestPathFingerprinter: Returns the raw representation of the fingerprint for the given IAtomContainer.
getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.SignatureFingerprinter
getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.SubstructureFingerprinter: Returns the raw representation of the fingerprint for the given IAtomContainer.
getRDBEValue(IMolecularFormula) - Method in class org.openscience.cdk.formula.rules.RDBERule: Method to extract the Ring Double Bond Equivalents (RDB) value.
getReactantCoefficient(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugReaction: Returns the stoichiometry coefficient of the given reactant.
getReactantCoefficient(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IReaction: Returns the stoichiometry coefficient of the given reactant.
getReactantCoefficient(IAtomContainer) - Method in class org.openscience.cdk.Reaction: Returns the stoichiometry coefficient of the given reactant.
getReactantCoefficient(IAtomContainer) - Method in class org.openscience.cdk.silent.Reaction: Returns the stoichiometry coefficient of the given reactant.
getReactantCoefficients() - Method in class org.openscience.cdk.debug.DebugReaction: Returns an array of double with the stoichiometric coefficients of the reactants.
getReactantCoefficients() - Method in interface org.openscience.cdk.interfaces.IReaction: Returns an array of double with the stoichiometric coefficients of the reactants.
getReactantCoefficients() - Method in class org.openscience.cdk.Reaction: Returns an array of double with the stoichiometric coefficients of the reactants.
getReactantCoefficients() - Method in class org.openscience.cdk.silent.Reaction: Returns an array of double with the stoichiometric coefficients of the reactants.
getReactantCount() - Method in class org.openscience.cdk.debug.DebugReaction: Returns the number of reactants in this reaction.
getReactantCount() - Method in interface org.openscience.cdk.interfaces.IReaction: Returns the number of reactants in this reaction.
getReactantCount() - Method in class org.openscience.cdk.Reaction: Returns the number of reactants in this reaction.
getReactantCount() - Method in class org.openscience.cdk.silent.Reaction: Returns the number of reactants in this reaction.
getReactantMolecule() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS: Deprecated.

Returns modified query molecule on which mapping was performed.
getReactantMolecule() - Method in class org.openscience.cdk.smsd.Isomorphism: Deprecated.

Returns modified query molecule on which mapping was performed.
getReactants() - Method in class org.openscience.cdk.debug.DebugReaction: Returns a MoleculeSet containing the reactants in this reaction.
getReactants() - Method in interface org.openscience.cdk.interfaces.IReaction: Returns a IAtomContaineSet containing the reactants in this reaction.
getReactants() - Method in class org.openscience.cdk.Reaction: Returns a MoleculeSet containing the reactants in this reaction.
getReactants() - Method in class org.openscience.cdk.silent.Reaction: Returns a MoleculeSet containing the reactants in this reaction.
getReaction(int) - Method in class org.openscience.cdk.debug.DebugReactionSet: Returns the Reaction at position number in the container.
getReaction(int) - Method in interface org.openscience.cdk.interfaces.IReactionSet: Returns the Reaction at position number in the container.
getReaction(int) - Method in class org.openscience.cdk.reaction.ReactionChain: Get the reaction of this chain reaction object at the position.
getReaction(int) - Method in class org.openscience.cdk.ReactionSet: Returns the Reaction at position number in the container.
getReaction(int) - Method in class org.openscience.cdk.silent.ReactionSet: Returns the Reaction at position number in the container.
getReactionByAtomContainerID(IReactionSet, String) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator: Gets a reaction from a ReactionSet by ID of any product or reactant.
getReactionByReactionID(IReactionSet, String) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator: Gets a reaction from a ReactionSet by ID.
getReactionCount() - Method in class org.openscience.cdk.debug.DebugReactionSet: Returns the number of Reactions in this Container.
getReactionCount() - Method in interface org.openscience.cdk.interfaces.IReactionSet: Returns the number of Reactions in this Container.
getReactionCount() - Method in class org.openscience.cdk.ReactionSet: Returns the number of Reactions in this Container.
getReactionCount() - Method in class org.openscience.cdk.silent.ReactionSet: Returns the number of Reactions in this Container.
getReactionMetadata() - Method in class org.openscience.cdk.dict.EntryReact
getReactions() - Method in class org.openscience.cdk.tools.StructureResonanceGenerator: Get the reactions that must be presents in the generation of the resonance.
getReactionSchemeCount() - Method in class org.openscience.cdk.debug.DebugReactionScheme: Returns the number of ReactionScheme in this Scheme.
getReactionSchemeCount() - Method in interface org.openscience.cdk.interfaces.IReactionScheme: Returns the number of ReactionScheme in this Scheme.
getReactionSchemeCount() - Method in class org.openscience.cdk.ReactionScheme: Returns the number of ReactionScheme in this Scheme.
getReactionSchemeCount() - Method in class org.openscience.cdk.silent.ReactionScheme: Returns the number of ReactionScheme in this Scheme.
getReactionSet() - Method in class org.openscience.cdk.ChemModel: Gets the ReactionSet contained in this ChemModel.
getReactionSet() - Method in class org.openscience.cdk.debug.DebugChemModel: Gets the ReactionSet contained in this ChemModel.
getReactionSet() - Method in interface org.openscience.cdk.interfaces.IChemModel: Gets the ReactionSet contained in this ChemModel.
getReactionSet() - Method in class org.openscience.cdk.silent.ChemModel: Gets the ReactionSet contained in this ChemModel.
getReactionStep(IReaction) - Method in class org.openscience.cdk.reaction.ReactionChain: Get the position of the reaction into this chain reaction object.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.ABINITFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.Aces2Format: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.ADFFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.AlchemyFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.BGFFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.BSFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
getReaderClassName() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.CACheFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
getReaderClassName() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.CIFFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.CMLFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.CRK2DFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.CRK3DFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.CrystClustFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.CTXFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.DaltonFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.DMol3Format: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.DOCK5Format: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.FingerprintFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.GamessFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian03Format: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian90Format: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian92Format: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian94Format: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian95Format: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian98Format: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat
getReaderClassName() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.GROMOS96Format: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.HINFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in interface org.openscience.cdk.io.formats.IChemFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.INChIFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.JaguarFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.JMEFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MacroModelFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MDLFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MDLRXNV2000Format: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MDLV2000Format: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MDLV3000Format: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MMODFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.Mol2Format: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC7Format: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC93Format: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC97Format: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MPQCFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.NWChemFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.PCModelFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.PDBFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.PDBMLFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.PMPFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.PQSChemFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.QChemFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.RawCopyFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.SDFFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.ShelXFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.SMARTSFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.SMILESFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.SpartanFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.VASPFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.ViewmolFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.XEDFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.XYZFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.YasaraFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.ZindoFormat: Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat: Returns the class name of the CDK Reader for this format.
getRealPart() - Method in class org.openscience.cdk.math.Complex: Gets the real part of this complex value
getRecord() - Method in class org.openscience.cdk.debug.DebugPDBAtom: get one entire line from the PDB entry file which describe the IPDBAtom.
getRecord() - Method in interface org.openscience.cdk.interfaces.IPDBAtom: Get one entire line from the PDB entry file which describe the IPDBAtom.
getRecord() - Method in class org.openscience.cdk.protein.data.PDBAtom: get one entire line from the PDB entry file which describe the IPDBAtom.
getRecord() - Method in class org.openscience.cdk.silent.PDBAtom: get one entire line from the PDB entry file which describe the IPDBAtom.
getRectangle2D(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Returns the 2D rectangle spanning the space occupied by the atom container.
getReference() - Method in class org.openscience.cdk.dict.DictRef
getRelevantAtomContainer(IAtomContainerSet, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
getRelevantAtomContainer(IAtomContainerSet, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
getRelevantAtomContainer(IAtomContainerSet, IBond) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
getRelevantAtomContainer(IAtomContainerSet, IBond) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
getRelevantAtomContainer(IChemModel, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator: This badly named methods tries to determine which AtomContainer in the ChemModel is best suited to contain added Atom's and Bond's.
getRelevantAtomContainer(IChemModel, IBond) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator: Retrieves the first IAtomContainer containing a given IBond from an IChemModel.
getRelevantAtomContainer(IReaction, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
getRelevantAtomContainer(IReaction, IBond) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
getRelevantAtomContainer(IReactionSet, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
getRelevantAtomContainer(IReactionSet, IBond) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
getRelevantReaction(IChemModel, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator: Retrieves the first IReaction containing a given IAtom from an IChemModel.
getRelevantReaction(IReactionSet, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
getRelevantReaction(IReactionSet, IBond) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
getRelevantReactions(IReactionSet, IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator: Get all Reactions object containing a Molecule from a set of Reactions.
getRelevantReactionsAsProduct(IReactionSet, IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator: Get all Reactions object containing a Molecule as a Product from a set of Reactions.
getRelevantReactionsAsReactant(IReactionSet, IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator: Get all Reactions object containing a Molecule as a Reactant from a set of Reactions.
getRemoveHydrogenFlag() - Method in class org.openscience.cdk.smsd.tools.MolHandler: Deprecated.

Returns true if hydrogens were made implicit else return false
getRenderer2DModel() - Method in class org.openscience.cdk.renderer.AbstractRenderer: Get the RendererModel used by this renderer, which provides access to the various parameters used to generate and draw the diagram.
getRenderer2DModel() - Method in interface org.openscience.cdk.renderer.IRenderer: Returns the drawing model, giving access to drawing parameters.
getRendererModel() - Method in class org.openscience.cdk.renderer.visitor.AWTDrawVisitor: Returns the current RendererModel.
getRenderingParameters() - Method in class org.openscience.cdk.renderer.RendererModel: Returns all IGeneratorParameters for the current RendererModel.
getRepresentations() - Method in class org.openscience.cdk.dict.EntryReact: Get the Representation of the reaction.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.CDKSourceCodeWriter
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ABINITFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Aces2Format: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ADFFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.AlchemyFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.BGFFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.BSFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CACheFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CIFFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CMLFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CRK2DFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CRK3DFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CrystClustFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CTXFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.DaltonFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.DMol3Format: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.DOCK5Format: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.FingerprintFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.GamessFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian03Format: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian90Format: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian92Format: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian94Format: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian95Format: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian98Format: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.GROMOS96Format: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.HINFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in interface org.openscience.cdk.io.formats.IChemFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.INChIFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.JaguarFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.JMEFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MacroModelFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLRXNV2000Format: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLV2000Format: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLV3000Format: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MMODFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Mol2Format: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC7Format: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC93Format: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC97Format: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MPQCFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.NWChemFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PCModelFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PDBFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PDBMLFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PMPFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PQSChemFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.QChemFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.RawCopyFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SDFFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ShelXFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SMARTSFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SMILESFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SpartanFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.VASPFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ViewmolFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.XEDFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.XYZFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.YasaraFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ZindoFormat: Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat: Returns an integer indicating the data features that this format requires.
getRequiredRGroupNumber() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupList: Access the dependant Rgroup number if R1 then R2.
getRequiredRGroupNumber() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
getResidues() - Method in class org.openscience.cdk.libio.md.MDMolecule
getResName() - Method in class org.openscience.cdk.debug.DebugPDBAtom: get the Residue name of this atom.
getResName() - Method in interface org.openscience.cdk.interfaces.IPDBAtom: get the Residue name of this atom.
getResName() - Method in class org.openscience.cdk.protein.data.PDBAtom: get the Residue name of this atom.
getResName() - Method in class org.openscience.cdk.silent.PDBAtom: get the Residue name of this atom.
getResSeq() - Method in class org.openscience.cdk.debug.DebugPDBAtom: get the Residue sequence number of this atom.
getResSeq() - Method in interface org.openscience.cdk.interfaces.IPDBAtom: get the Residue sequence number of this atom.
getResSeq() - Method in interface org.openscience.cdk.interfaces.IPDBMonomer: Gets the sequence identifier of this monomer.
getResSeq() - Method in class org.openscience.cdk.protein.data.PDBAtom: get the Residue sequence number of this atom.
getResSeq() - Method in class org.openscience.cdk.protein.data.PDBMonomer
getResSeq() - Method in class org.openscience.cdk.silent.PDBAtom: get the Residue sequence number of this atom.
getResSeq() - Method in class org.openscience.cdk.silent.PDBMonomer
getRestrictions() - Method in class org.openscience.cdk.formula.MassToFormulaTool: Deprecated.

Get the restrictions that must be presents in the molecular formula.
getReturnStatus() - Method in class org.openscience.cdk.inchi.InChIGenerator: Deprecated.
use getStatus
getReturnStatus() - Method in class org.openscience.cdk.inchi.InChIToStructure: Deprecated.
use getStatus
getRGroupDefinitions() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery: Getter for the R-group definitions (substituents).
getRGroupDefinitions() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
getRGroupNumber() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupList: Get the Rgroup number, for example R1 => 1.
getRGroupNumber() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
getRgroupQueryAtoms(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery: Returns all R# type atoms (pseudo atoms) found in the root structure for a certain provided RGgroup number.
getRGroups() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupList: Access the list of possible RGroups.
getRGroups() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
getRight() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom: Deprecated.
getRight() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond: Deprecated.
getRingBond() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RingIdentifierAtom: Deprecated.
getRings(IAtom) - Method in class org.openscience.cdk.debug.DebugRingSet: Returns a vector of all rings that this atom is part of.
getRings(IAtom) - Method in interface org.openscience.cdk.interfaces.IRingSet: Returns a vector of all rings that this atom is part of.
getRings(IAtom) - Method in class org.openscience.cdk.RingSet: Returns a vector of all rings that this atom is part of.
getRings(IAtom) - Method in class org.openscience.cdk.silent.RingSet: Returns a vector of all rings that this atom is part of.
getRings(IBond) - Method in class org.openscience.cdk.debug.DebugRingSet: Returns a vector of all rings that this bond is part of.
getRings(IBond) - Method in interface org.openscience.cdk.interfaces.IRingSet: Returns a vector of all rings that this bond is part of.
getRings(IBond) - Method in class org.openscience.cdk.RingSet: Returns a vector of all rings that this bond is part of.
getRings(IBond) - Method in class org.openscience.cdk.silent.RingSet: Returns a vector of all rings that this bond is part of.
getRingSet() - Method in class org.openscience.cdk.ChemModel: Returns the RingSet of this ChemModel.
getRingSet() - Method in class org.openscience.cdk.debug.DebugChemModel: Returns the RingSet of this ChemModel.
getRingSet() - Method in interface org.openscience.cdk.interfaces.IChemModel: Returns the RingSet of this ChemModel.
getRingSet() - Method in class org.openscience.cdk.silent.ChemModel: Returns the RingSet of this ChemModel.
getRingSet(IAtomContainer) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator: Determine the ring set for this atom container.
getRingSet(IAtomContainer) - Method in class org.openscience.cdk.smsd.ring.HanserRingFinder: Deprecated.

Returns Ring set based on Hanser Ring Finding method
getRingSet(IAtomContainer) - Method in interface org.openscience.cdk.smsd.ring.RingFinder: Deprecated.

Returns CDK object Ring set based on Hanser Ring Finding method
getRingSize() - Method in class org.openscience.cdk.debug.DebugRing: Returns the number of atoms\edges in this ring.
getRingSize() - Method in interface org.openscience.cdk.interfaces.IRing: Returns the number of atoms/bonds in this ring.
getRingSize() - Method in class org.openscience.cdk.Ring: Returns the number of atoms\edges in this ring.
getRingSize() - Method in class org.openscience.cdk.silent.Ring: Returns the number of atoms\edges in this ring.
getRingSystems() - Method in class org.openscience.cdk.fragment.MurckoFragmenter: Get the ring system fragments as SMILES strings.
getRingSystemsAsContainers() - Method in class org.openscience.cdk.fragment.MurckoFragmenter: Get rings systems as IAtomContainer objects.
getrMap() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode: Deprecated.

Returns resolution Map
getRMap() - Method in class org.openscience.cdk.isomorphism.mcss.RNode: Gets the rMap attribute of the RNode object.
getRMap() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode: Deprecated.

Gets the rMap attribute of the RNode object
getRMSD() - Method in class org.openscience.cdk.geometry.alignment.KabschAlignment: Returns the RMSD from the alignment.
getROCAUC() - Method in class org.openscience.cdk.fingerprint.model.Bayesian: Returns the integral of the area-under-the-curve of the receiver-operator-characteristic.
getROCType() - Method in class org.openscience.cdk.fingerprint.model.Bayesian: Returns a string description of the method used to create the ROC curve (e.g.
getRocX() - Method in class org.openscience.cdk.fingerprint.model.Bayesian: Returns X-values that can be used to plot the ROC-curve.
getRocY() - Method in class org.openscience.cdk.fingerprint.model.Bayesian: Returns Y-values that can be used to plot the ROC-curve.
getRoot(int) - Method in class org.openscience.cdk.group.DisjointSetForest: Travel up the tree that this element is in, until the root of the set is found, and return that root.
getRoot(Node) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
getRootAttachmentPoints() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery: Getter for root attachment points = bonds that connect R pseudo-atoms to the scaffold.
getRootAttachmentPoints() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
getRootStructure() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery: Getter for the root structure of this R-Group.
getRootStructure() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
getRotationMatrix() - Method in class org.openscience.cdk.geometry.alignment.KabschAlignment: Returns the rotation matrix (u).
getRows() - Method in class org.openscience.cdk.math.IMatrix: Returns the count of rows
getRows() - Method in class org.openscience.cdk.math.Matrix: Returns the number of rows.
getRSolvent() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
getRules() - Method in class org.openscience.cdk.formula.MolecularFormulaChecker: Get the IRules to be applied to validate the IMolecularFormula.
getScaleFactor(IAtomContainer, double) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Determines the scale factor for displaying a structure loaded from disk in a frame.
getScaleFactor(IAtomContainer, double) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Determines the scale factor for displaying a structure loaded from disk in a frame.
getSearchDepth() - Method in class org.openscience.cdk.fingerprint.Fingerprinter
getSecondAttachmentPoint() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroup: Get the optional second attachment point of the RGroup.
getSecondAttachmentPoint() - Method in class org.openscience.cdk.isomorphism.matchers.RGroup
getSecondGraphSize() - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Returns the size of the second of the two compared graphs.
getSecondGraphSize() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph: Deprecated.

Returns the size of the second of the two compared graphs.
getSecondPoint() - Method in class org.openscience.cdk.sgroup.SgroupBracket: Second point of the bracket (x2,y2).
getSegID() - Method in class org.openscience.cdk.debug.DebugPDBAtom: get the Segment identifier, left-justified of this atom.
getSegID() - Method in interface org.openscience.cdk.interfaces.IPDBAtom: get the Segment identifier, left-justified of this atom.
getSegID() - Method in class org.openscience.cdk.protein.data.PDBAtom: get the Segment identifier, left-justified of this atom.
getSegID() - Method in class org.openscience.cdk.silent.PDBAtom: get the Segment identifier, left-justified of this atom.
getSelection() - Method in class org.openscience.cdk.renderer.RendererModel: Returns an IChemObjectSelection with the currently selected IChemObjects.
getSerial() - Method in class org.openscience.cdk.debug.DebugPDBAtom: get the Atom serial number of this atom.
getSerial() - Method in interface org.openscience.cdk.interfaces.IPDBAtom: get the Atom serial number of this atom.
getSerial() - Method in class org.openscience.cdk.protein.data.PDBAtom: get the Atom serial number of this atom.
getSerial() - Method in class org.openscience.cdk.silent.PDBAtom: get the Atom serial number of this atom.
getSetbits() - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
getSetbits() - Method in interface org.openscience.cdk.fingerprint.IBitFingerprint: Returns a listing of the bits in the fingerprint that are set to true.
getSetbits() - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
getSetNumA() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper: Deprecated.
getSets() - Method in class org.openscience.cdk.group.DisjointSetForest: Retrieve the sets as 2D-array of ints.
getSetting() - Method in class org.openscience.cdk.io.setting.IOSetting: Sets the setting for a certain question.
getSetting(String) - Method in class org.openscience.cdk.io.ChemObjectIO: Access a named setting managed by this reader/writer.
getSetting(String) - Method in interface org.openscience.cdk.io.IChemObjectIO: Access a named setting managed by this reader/writer.
getSetting(String, Class<S>) - Method in class org.openscience.cdk.io.ChemObjectIO: Access a named setting managed by this reader/writer.
getSetting(String, Class<S>) - Method in interface org.openscience.cdk.io.IChemObjectIO: Access a named setting managed by this reader/writer.
getSettings() - Method in class org.openscience.cdk.io.ChemObjectIO: Access a collection of IOSettings for this reader/writer.
getSettings() - Method in interface org.openscience.cdk.io.IChemObjectIO: Access a collection of IOSettings for this reader/writer.
getSettings() - Method in class org.openscience.cdk.io.setting.SettingManager: Access a collection of all settings in the manager.
getSettingValue() - Method in class org.openscience.cdk.io.setting.IntegerIOSetting
getShortestPath(IAtomContainer, IAtom, IAtom) - Static method in class org.openscience.cdk.graph.PathTools: Deprecated.
This implementation recalculates all shortest paths from the start atom for each method call and does not indicate if there are equally short paths from the start to the end. Replaced by ShortestPaths.atomsTo(IAtom)
getSID(XMLStreamReader) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
getSingleAtomVariables(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen
getSingleBondEquivalentSum(Iterator<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator: Get the single bond equivalent (SBE) of a list of bonds, given an iterator to the list.
getSingleBondEquivalentSum(List<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator: Get the single bond equivalent (SBE) of a list of bonds.
getSingleBondEquivalentSum(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Returns the sum of bond orders, where a single bond counts as one single bond equivalent, a double as two, etc.
getSingleElectron(int) - Method in class org.openscience.cdk.AtomContainer: Get the single electron at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getSingleElectronCount().
getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Get the single electron at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getSingleElectronCount().
getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Get the single electron at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getSingleElectronCount().
getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Get the single electron at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getSingleElectronCount().
getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugCrystal: Get the single electron at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getSingleElectronCount().
getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugMonomer: Get the single electron at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getSingleElectronCount().
getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugPolymer: Get the single electron at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getSingleElectronCount().
getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugRing: Get the single electron at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getSingleElectronCount().
getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugStrand: Get the single electron at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getSingleElectronCount().
getSingleElectron(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Get the single electron at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getSingleElectronCount().
getSingleElectron(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Get the single electron at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getSingleElectronCount().
getSingleElectron(int) - Method in class org.openscience.cdk.silent.AtomContainer: Get the single electron at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getSingleElectronCount().
getSingleElectronCount() - Method in class org.openscience.cdk.AtomContainer: Returns the number of the single electrons in this container.
getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns the number of the single electrons in this container.
getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns the number of the single electrons in this container.
getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the number of the single electrons in this container.
getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugCrystal: Returns the number of the single electrons in this container.
getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugMonomer: Returns the number of the single electrons in this container.
getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugPolymer: Returns the number of the single electrons in this container.
getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugRing: Returns the number of the single electrons in this container.
getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugStrand: Returns the number of the single electrons in this container.
getSingleElectronCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Returns the number of the single electrons in this container.
getSingleElectronCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns the number of the single electrons in this container,
getSingleElectronCount() - Method in class org.openscience.cdk.silent.AtomContainer: Returns the number of the single electrons in this container.
getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.AtomContainer: Returns the position of a given single electron in the single electron array.
getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns the position of a given single electron in the single electron array.
getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the position of a given single electron in the single electron array.
getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugCrystal: Returns the position of a given single electron in the single electron array.
getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugMonomer: Returns the position of a given single electron in the single electron array.
getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugPolymer: Returns the position of a given single electron in the single electron array.
getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugRing: Returns the position of a given single electron in the single electron array.
getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugStrand: Returns the position of a given single electron in the single electron array.
getSingleElectronNumber(ISingleElectron) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Deprecated.
use IAtomContainer.indexOf(ISingleElectron)
getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns the position of a given single electron in the single electron array.
getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.silent.AtomContainer: Returns the position of a given single electron in the single electron array.
getSingleElectrons() - Method in enum org.openscience.cdk.io.MDLV2000Writer.SPIN_MULTIPLICITY: The number of single electrons that correspond to the spin multiplicity.
getSize() - Method in class org.openscience.cdk.config.AtomTypeFactory: Returns the number of atom types in this list.
getSize() - Method in class org.openscience.cdk.config.IsotopeFactory: Returns the number of isotopes defined by this class.
getSize() - Method in class org.openscience.cdk.fingerprint.AtomPairs2DFingerprinter
getSize() - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter: Returns the extent of the folded fingerprints.
getSize() - Method in class org.openscience.cdk.fingerprint.EStateFingerprinter: Returns the size (or length) of the fingerprint.
getSize() - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter: Returns the size (or length) of the fingerprint.
getSize() - Method in class org.openscience.cdk.fingerprint.Fingerprinter
getSize() - Method in interface org.openscience.cdk.fingerprint.IFingerprinter: Returns the size (or length) of the fingerprint.
getSize() - Method in class org.openscience.cdk.fingerprint.LingoFingerprinter
getSize() - Method in class org.openscience.cdk.fingerprint.MACCSFingerprinter: Returns the size (or length) of the fingerprint.
getSize() - Method in class org.openscience.cdk.fingerprint.PubchemFingerprinter: Get the size of the fingerprint.
getSize() - Method in class org.openscience.cdk.fingerprint.ShortestPathFingerprinter
getSize() - Method in class org.openscience.cdk.fingerprint.SignatureFingerprinter
getSize() - Method in class org.openscience.cdk.fingerprint.SubstructureFingerprinter: Returns the size (or length) of the fingerprint.
getSize() - Method in class org.openscience.cdk.group.PermutationGroup: Get the number of elements in each permutation in the group.
getSize() - Method in class org.openscience.cdk.math.IVector: Return the size from this vector
getSize() - Method in class org.openscience.cdk.math.qm.FourierGridBasis
getSize() - Method in class org.openscience.cdk.math.qm.GaussiansBasis: Gets the number of base vectors.
getSize() - Method in interface org.openscience.cdk.math.qm.IBasis: Gets the number of base vectors
getSize() - Method in class org.openscience.cdk.math.Vector: Returns the size of this vector
getSize() - Method in class org.openscience.cdk.smsd.helper.FinalMappings: Deprecated.

Returns number of stored mappings
getSize() - Method in class org.openscience.cdk.smsd.helper.LabelContainer: Deprecated.

Returns label count
getSize() - Method in interface org.openscience.cdk.smsd.interfaces.IFinalMapping: Deprecated.

Returns number of stored mappings
getSize() - Method in class org.openscience.cdk.structgen.maygen.Maygen
getSmarts() - Static method in class org.openscience.cdk.config.fragments.EStateFragments: Get the SMARTS patterns.
getSmarts() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom: Get the SMARTS for the group.
getSmarts() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryAtom: Get the SMARTS pattern for this pharmacophore group.
getSmarts() - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool: Deprecated.

Returns the current SMARTS pattern being used.
getSolutions() - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Returns the list of solutions.
getSolutions() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph: Deprecated.

Returns the list of solutions.
getSolvantValue() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
getSortedEnergy() - Method in class org.openscience.cdk.smsd.filters.ChemicalFilters: Deprecated.

Return sorted energy in ascending order.
getSortedFragment() - Method in class org.openscience.cdk.smsd.filters.ChemicalFilters: Deprecated.

Return sorted fragment in ascending order of the size.
getSource() - Method in interface org.openscience.cdk.interfaces.IChemObjectChangeEvent: IChemObject that fired the event.
getSource() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler: Deprecated.

Returns source molecule
getSource() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.EdgeBuilder: Deprecated.

Returns source Node.
getSource() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IEdge: Deprecated.

Returns source Node.
getSource() - Method in class org.openscience.cdk.smsd.ring.PathEdge: Deprecated.
getSpaceGroup() - Method in class org.openscience.cdk.Crystal: Gets the space group of this crystal.
getSpaceGroup() - Method in class org.openscience.cdk.debug.DebugCrystal: Gets the space group of this crystal.
getSpaceGroup() - Method in interface org.openscience.cdk.interfaces.ICrystal: Gets the space group of this crystal.
getSpaceGroup() - Method in class org.openscience.cdk.silent.Crystal: Gets the space group of this crystal.
getSpanningTree() - Method in class org.openscience.cdk.graph.SpanningTree: Access the computed spanning tree of the input molecule.
getSpanningTreeSize() - Method in class org.openscience.cdk.graph.SpanningTree: Size of the spanning tree specified as the number of edges in the tree.
getSpatproduct(Vector3d, Vector3d, Vector3d) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D: Gets the spatproduct of three vectors.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor: Gets the specification attribute of the AtomHybridizationDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor: Gets the specification attribute of the AtomHybridizationVSEPRDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor: Gets the specification attribute of the AtomValenceDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor: Gets the specification attribute of the BondsToAtomDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor: Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor: Gets the specification attribute of the DistanceToAtomDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor: Gets the specification attribute of the EffectiveAtomPolarizabilityDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor: Gets the specification attribute of the InductiveAtomicHardnessDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor: Gets the specification attribute of the InductiveAtomicSoftnessDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor: Gets the specification attribute of the IPAtomicHOSEDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor: Deprecated.

Gets the specification attribute of the IPAtomicLearningDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor: Gets the specification attribute of the IsProtonInAromaticSystemDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInConjugatedPiSystemDescriptor: Gets the specification attribute of the IsProtonInConjugatedPiSystemDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor: Gets the specification attribute of the PartialPiChargeDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor: Gets the specification attribute of the PartialSigmaChargeDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor: Gets the specification attribute of the PartialTChargeMMFF94Descriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor: Gets the specification attribute of the PartialTChargePEOEDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor: Gets the specification attribute of the PeriodicTablePositionDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor: Gets the specification attribute of the PiElectronegativityDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor: Gets the specification attribute of the ProtonAffinityDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor: Gets the specification attribute of the ProtonTotalPartialChargeDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R: Gets the specification attribute of the RDFProtonDescriptor_G3R object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR: Gets the specification attribute of the RDFProtonDescriptor_GDR object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol: Gets the specification attribute of the RDFProtonDescriptor_GHR_topol object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR: Gets the specification attribute of the RDFProtonDescriptor_GHR object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR: Gets the specification attribute of the RDFProtonDescriptor_GSR object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor: Gets the specification attribute of the SigmaElectronegativityDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor: Gets the specification attribute of the StabilizationPlusChargeDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor: Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor: Gets the specification attribute of the PiContactDetectionDescriptor object.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptor
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor: Gets the specification attribute of the BondPartialPiChargeDescriptor object.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor: Gets the specification attribute of the BondPartialSigmaChargeDescriptor object.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor: Gets the specification attribute of the BondPartialTChargeDescriptor object.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor: Gets the specification attribute of the BondSigmaElectronegativityDescriptor object.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor: Deprecated.

Gets the specification attribute of the IPBondLearningDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor: Returns a IImplementationSpecification which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor: Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor: Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor: Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor: Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor: Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor: Returns a IImplementationSpecification which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor: Gets the specification attribute of the BondCountDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor: Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalCSP3Descriptor: Returns a IImplementationSpecification which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor: Returns a IImplementationSpecification which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor: Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor: Gets the specification attribute of the HBondAcceptorCountDescriptor object.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor: Gets the specification attribute of the HBondDonorCountDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor: Returns a DescriptorSpecification which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor: Deprecated.

Gets the specification attribute of the IPMolecularLearningDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor: Gets the specification attribute of the KappaShapeIndicesDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor: Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor: Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor: Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor: Gets the specification attribute of the PetitjeanNumberDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor: Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor: Gets the specification attribute of the MannholdLogPDescriptor object.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor: Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor: Gets the specification attribute of the PetitjeanNumberDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor: Gets the specification attribute of the RotatableBondsCountDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor: Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor: Fetch descriptor specification.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.SpiroAtomCountDescriptor: Returns a IImplementationSpecification which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor: Gets the specification attribute of the TPSADescriptor object.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor: Returns a IImplementationSpecification which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor: Gets the specification attribute of the VAdjMaDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor: Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor: Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor: Gets the specification attribute of the XLogPDescriptor object.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor: Gets the specification attribute of the ZagrebIndexDescriptor object.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.substance.OxygenAtomCountDescriptor: Returns a IImplementationSpecification which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.DescriptorValue
getSpecification() - Method in interface org.openscience.cdk.qsar.IDescriptor: Returns a IImplementationSpecification which specifies which descriptor is implemented by this class.
getSpecification() - Method in interface org.openscience.cdk.reaction.IReactionProcess: Returns a Map which specifies which reaction is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.reaction.type.AdductionProtonLPReaction: Gets the specification attribute of the AdductionProtonLPReaction object.
getSpecification() - Method in class org.openscience.cdk.reaction.type.AdductionProtonPBReaction: Gets the specification attribute of the AdductionProtonPBReaction object.
getSpecification() - Method in class org.openscience.cdk.reaction.type.AdductionSodiumLPReaction: Gets the specification attribute of the AdductionSodiumLPReaction object.
getSpecification() - Method in class org.openscience.cdk.reaction.type.CarbonylEliminationReaction: Gets the specification attribute of the CarbonylEliminationReaction object.
getSpecification() - Method in class org.openscience.cdk.reaction.type.ElectronImpactNBEReaction: Gets the specification attribute of the ElectronImpactNBEReaction object.
getSpecification() - Method in class org.openscience.cdk.reaction.type.ElectronImpactPDBReaction: Gets the specification attribute of the ElectronImpactPDBReaction object.
getSpecification() - Method in class org.openscience.cdk.reaction.type.ElectronImpactSDBReaction: Gets the specification attribute of the ElectronImpactSDBReaction object.
getSpecification() - Method in class org.openscience.cdk.reaction.type.HeterolyticCleavagePBReaction: Gets the specification attribute of the HeterolyticCleavagePBReaction object.
getSpecification() - Method in class org.openscience.cdk.reaction.type.HeterolyticCleavageSBReaction: Gets the specification attribute of the HeterolyticCleavageSBReaction object.
getSpecification() - Method in class org.openscience.cdk.reaction.type.HomolyticCleavageReaction: Gets the specification attribute of the HomolyticCleavageReaction object.
getSpecification() - Method in class org.openscience.cdk.reaction.type.HyperconjugationReaction: Gets the specification attribute of the HyperconjugationReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.PiBondingMovementReaction: Gets the specification attribute of the PiBondingMovementReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalChargeSiteInitiationHReaction: Gets the specification attribute of the RadicalChargeSiteInitiationHReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalChargeSiteInitiationReaction: Gets the specification attribute of the RadicalChargeSiteInitiationReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrAlphaReaction: Gets the specification attribute of the RadicalSiteHrAlphaReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrBetaReaction: Gets the specification attribute of the RadicalSiteHrBetaReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrDeltaReaction: Gets the specification attribute of the RadicalSiteHrDeltaReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrGammaReaction: Gets the specification attribute of the RadicalSiteHrGammaReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteInitiationHReaction: Gets the specification attribute of the RadicalSiteInitiationHReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteInitiationReaction: Gets the specification attribute of the RadicalSiteInitiationReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrAlphaReaction: Gets the specification attribute of the RadicalSiteRrAlphaReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrBetaReaction: Gets the specification attribute of the RadicalSiteRrBetaReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrDeltaReaction: Gets the specification attribute of the RadicalSiteRrDeltaReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrGammaReaction: Gets the specification attribute of the RadicalSiteRrGammaReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.RearrangementAnionReaction: Gets the specification attribute of the RearrangementAnionReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.RearrangementCationReaction: Gets the specification attribute of the RearrangementCationReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.RearrangementLonePairReaction: Gets the specification attribute of the RearrangementLonePairReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.RearrangementRadicalReaction: Gets the specification attribute of the RearrangementRadicalReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.SharingAnionReaction: Gets the specification attribute of the SharingAnionReaction object.
getSpecification() - Method in class org.openscience.cdk.reaction.type.SharingChargeDBReaction: Gets the specification attribute of the SharingChargeDBReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.SharingChargeSBReaction: Gets the specification attribute of the SharingChargeSBReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.SharingLonePairReaction: Gets the specification attribute of the SharingLonePairReaction object.
getSpecification() - Method in class org.openscience.cdk.reaction.type.TautomerizationReaction: Gets the specification attribute of the TautomerizationReaction object.
getSpecificationReference() - Method in interface org.openscience.cdk.IImplementationSpecification: Pointer to a dictionary or ontology describing a unique algorithm.
getSpecificationReference() - Method in class org.openscience.cdk.qsar.DescriptorSpecification
getSpecificationReference() - Method in class org.openscience.cdk.reaction.ReactionSpecification
getSpheres(IAtomContainer, IAtom, int, boolean) - Method in class org.openscience.cdk.tools.HOSECodeGenerator: This method is intended to be used to get the atoms around an atom in spheres.
getSpinVector(double, double) - Method in class org.openscience.cdk.math.qm.AngularMomentum: Calculates a spin vector by a direction specified by theta and phi
getSqrtRadii(IAtom) - Static method in class org.openscience.cdk.graph.invariant.HuLuIndexTool
getSquarePlanarShape(IAtom, IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.stereo.StereoTool: Given four atoms (assumed to be in the same plane), returns the arrangement of those atoms in that plane.
getSSSRWeightVector() - Method in class org.openscience.cdk.ringsearch.SSSRFinder: Deprecated.

Returns a vector containing the lengths of the rings in a SSSR.
getStartChainID() - Method in class org.openscience.cdk.debug.DebugPDBStructure: get start Chain identifier of this structure.
getStartChainID() - Method in interface org.openscience.cdk.interfaces.IPDBStructure: get start Chain identifier of this structure.
getStartChainID() - Method in class org.openscience.cdk.protein.data.PDBStructure: get start Chain identifier of this structure.
getStartChainID() - Method in class org.openscience.cdk.silent.PDBStructure: get start Chain identifier of this structure.
getStartInsertionCode() - Method in class org.openscience.cdk.debug.DebugPDBStructure: get start Code for insertion of residues of this structure.
getStartInsertionCode() - Method in interface org.openscience.cdk.interfaces.IPDBStructure: get start Code for insertion of residues of this structure.
getStartInsertionCode() - Method in class org.openscience.cdk.protein.data.PDBStructure: get start Code for insertion of residues of this structure.
getStartInsertionCode() - Method in class org.openscience.cdk.silent.PDBStructure: get start Code for insertion of residues of this structure.
getStartSequenceNumber() - Method in class org.openscience.cdk.debug.DebugPDBStructure: get the start sequence number of this structure.
getStartSequenceNumber() - Method in interface org.openscience.cdk.interfaces.IPDBStructure: get the start sequence number of this structure.
getStartSequenceNumber() - Method in class org.openscience.cdk.protein.data.PDBStructure: get the start sequence number of this structure.
getStartSequenceNumber() - Method in class org.openscience.cdk.silent.PDBStructure: get the start sequence number of this structure.
getStatus() - Method in class org.openscience.cdk.inchi.InChIGenerator: Access the status of the InChI output.
getStatus() - Method in class org.openscience.cdk.inchi.InChIToStructure: Access the status of the InChI output.
getStepSize() - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges: Get the StepSize attribute of the GasteigerMarsiliPartialCharges object.
getStepSize() - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges: Get the StepSize attribute of the GasteigerMarsiliPartialCharges object.
getStereo() - Method in class org.openscience.cdk.Bond: Returns the stereo descriptor for this bond.
getStereo() - Method in class org.openscience.cdk.BondRef: Returns the stereo descriptor for this bond.
getStereo() - Method in class org.openscience.cdk.debug.DebugBond: Returns the stereo descriptor for this bond.
getStereo() - Method in interface org.openscience.cdk.interfaces.IBond: Returns the stereo descriptor for this bond.
getStereo() - Method in interface org.openscience.cdk.interfaces.IDoubleBondStereochemistry: Defines the stereochemistry around the double bond.
getStereo() - Method in interface org.openscience.cdk.interfaces.ITetrahedralChirality: Defines the stereochemistry around the chiral atom.
getStereo() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Returns the stereo descriptor for this query bond.
getStereo() - Method in class org.openscience.cdk.silent.Bond: Returns the stereo descriptor for this bond.
getStereo() - Method in class org.openscience.cdk.stereo.DoubleBondStereochemistry: Defines the stereochemistry around the double bond.
getStereo() - Method in class org.openscience.cdk.stereo.TetrahedralChirality
getStereo(IAtom, IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.stereo.StereoTool: Take four atoms, and return Stereo.CLOCKWISE or Stereo.ANTI_CLOCKWISE.
getStereoBond() - Method in interface org.openscience.cdk.interfaces.IDoubleBondStereochemistry: IBond that is the stereo center.
getStereoBond() - Method in class org.openscience.cdk.stereo.DoubleBondStereochemistry: IBond that is the stereo center.
getStereoMatches() - Method in class org.openscience.cdk.smsd.filters.ChemicalFilters: Deprecated.

Return Stereo matches in descending order.
getStereoParity() - Method in class org.openscience.cdk.Atom: Returns the stereo parity of this atom.
getStereoParity() - Method in class org.openscience.cdk.AtomRef: Returns the stereo parity of this atom.
getStereoParity() - Method in class org.openscience.cdk.debug.DebugAtom: Returns the stereo parity of this atom.
getStereoParity() - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Returns the stereo parity of this atom.
getStereoParity() - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Returns the stereo parity of this atom.
getStereoParity() - Method in interface org.openscience.cdk.interfaces.IAtom: Deprecated.
use IStereoElements for storing stereochemistry
getStereoParity() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Returns the stereo parity of this atom.
getStereoParity() - Method in class org.openscience.cdk.silent.Atom: Returns the stereo parity of this atom.
getStereoScore(int) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS: Deprecated.

Returns a number which denotes the quality of the mcs.
getStereoScore(int) - Method in class org.openscience.cdk.smsd.Isomorphism: Deprecated.

Returns a number which denotes the quality of the mcs.
getStrand(String) - Method in class org.openscience.cdk.BioPolymer: Retrieves a Monomer object by specifying its name.
getStrand(String) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Retrieves a Monomer object by specifying its name.
getStrand(String) - Method in interface org.openscience.cdk.interfaces.IBioPolymer: Retrieve a Monomer object by specifying its name.
getStrand(String) - Method in class org.openscience.cdk.silent.BioPolymer: Retrieves a Monomer object by specifying its name.
getStrandCount() - Method in class org.openscience.cdk.BioPolymer: Returns the number of strands present in the BioPolymer.
getStrandCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the number of strands present in the BioPolymer.
getStrandCount() - Method in interface org.openscience.cdk.interfaces.IBioPolymer: Return the number of strands present in the BioPolymer.
getStrandCount() - Method in class org.openscience.cdk.silent.BioPolymer: Returns the number of strands present in the BioPolymer.
getStrandName() - Method in class org.openscience.cdk.debug.DebugStrand: Retrieves the strand name.
getStrandName() - Method in interface org.openscience.cdk.interfaces.IStrand: Retrieve the strand name.
getStrandName() - Method in class org.openscience.cdk.silent.Strand: Retrieves the strand name.
getStrandName() - Method in class org.openscience.cdk.Strand: Retrieves the strand name.
getStrandNames() - Method in class org.openscience.cdk.BioPolymer: Returns a collection of the names of all Strands in this BioPolymer.
getStrandNames() - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns a collection of the names of all Strands in this BioPolymer.
getStrandNames() - Method in interface org.openscience.cdk.interfaces.IBioPolymer: Returns a collection of the names of all Strands in this BioPolymer.
getStrandNames() - Method in class org.openscience.cdk.silent.BioPolymer: Returns a collection of the names of all Strands in this BioPolymer.
getStrands() - Method in class org.openscience.cdk.BioPolymer
getStrands() - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns a Map containing the strands in the Polymer.
getStrands() - Method in interface org.openscience.cdk.interfaces.IBioPolymer: Returns a Map containing the strands in the Polymer.
getStrands() - Method in class org.openscience.cdk.silent.BioPolymer
getStrandType() - Method in class org.openscience.cdk.debug.DebugStrand: Retrieves the strand type.
getStrandType() - Method in interface org.openscience.cdk.interfaces.IStrand: Retrieve the strand type.
getStrandType() - Method in class org.openscience.cdk.silent.Strand: Retrieves the strand type.
getStrandType() - Method in class org.openscience.cdk.Strand: Retrieves the strand type.
getString(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Returns the string representation of the molecular formula.
getString(IMolecularFormula, boolean) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Returns the string representation of the molecular formula.
getString(IMolecularFormula, boolean, boolean) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Returns the string representation of the molecular formula.
getString(IMolecularFormula, String[], boolean) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Returns the string representation of the molecular formula.
getString(IMolecularFormula, String[], boolean, boolean) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Returns the string representation of the molecular formula.
getStrokeMap() - Method in class org.openscience.cdk.renderer.visitor.AWTDrawVisitor: Returns the current stroke map.
getStructures() - Method in class org.openscience.cdk.debug.DebugPDBPolymer: Returns a Collection containing the PDBStructure in the PDBPolymer.
getStructures() - Method in interface org.openscience.cdk.interfaces.IPDBPolymer: Returns a Collection containing the PDBStructure in the PDBPolymer.
getStructures() - Method in class org.openscience.cdk.protein.data.PDBPolymer
getStructures() - Method in class org.openscience.cdk.silent.PDBPolymer
getStructures(IAtomContainer) - Method in class org.openscience.cdk.tools.StructureResonanceGenerator: Get the resonance structures from an IAtomContainer.
getStructureType() - Method in class org.openscience.cdk.debug.DebugPDBStructure: get Structure Type of this structure.
getStructureType() - Method in interface org.openscience.cdk.interfaces.IPDBStructure: get Structure Type of this structure.
getStructureType() - Method in class org.openscience.cdk.protein.data.PDBStructure: get Structure Type of this structure.
getStructureType() - Method in class org.openscience.cdk.silent.PDBStructure: get Structure Type of this structure.
getSubgraph() - Method in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
getSubgraphAtomsMap(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: Returns the first subgraph 'atom mapping' found for g2 in g1, where g2 must be a substructure of g1.
getSubgraphAtomsMap(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS: Deprecated.

Returns the first subgraph 'atom mapping' found for targetGraph in sourceGraph.
getSubgraphAtomsMaps(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: Returns all subgraph 'atom mappings' found for g2 in g1, where g2 must be a substructure of g1.
getSubgraphAtomsMaps(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS: Deprecated.

Returns all subgraph 'atom mappings' found for targetGraph in sourceGraph.
getSubgraphMap(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: Returns the first subgraph 'bond mapping' found for g2 in g1.
getSubgraphMap(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS: Deprecated.

Returns the first subgraph 'bondA1 mapping' found for targetGraph in sourceGraph.
getSubgraphMaps(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: Returns all the subgraph 'bond mappings' found for g2 in g1.
getSubgraphMaps(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS: Deprecated.

Returns all the subgraph 'bondA1 mappings' found for targetGraph in sourceGraph.
getSubPartition(int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Calculating the sub partitions for a given group of degrees.
getSubscript() - Method in class org.openscience.cdk.sgroup.Sgroup: Access the subscript value.
getSubstituents() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery: Return all the substituent atom containers, in other words the atom containers defined in this RGroupQuery except for the root structure.
getSubstituents() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
getSubstructure(int) - Method in class org.openscience.cdk.fingerprint.SubstructureFingerprinter: Retrieves the SMARTS representation of a substructure for a given bit in the fingerprint.
GetSuffix(int) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream: Get the suffix.
GetSuffix(int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Get the suffix.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.CDKSourceCodeWriter
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ABINITFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Aces2Format: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ADFFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.AlchemyFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.BGFFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.BSFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CACheFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CIFFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CMLFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CRK2DFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CRK3DFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CrystClustFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CTXFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.DaltonFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.DMol3Format: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.DOCK5Format: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.FingerprintFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.GamessFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian03Format: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian90Format: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian92Format: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian94Format: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian95Format: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian98Format: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.GROMOS96Format: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.HINFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in interface org.openscience.cdk.io.formats.IChemFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.INChIFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.JaguarFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.JMEFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MacroModelFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLRXNV2000Format: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLV2000Format: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLV3000Format: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MMODFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Mol2Format: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC7Format: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC93Format: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC97Format: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MPQCFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.NWChemFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PCModelFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PDBFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PDBMLFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PMPFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PQSChemFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.QChemFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.RawCopyFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SDFFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ShelXFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SMARTSFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SMILESFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SpartanFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.VASPFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ViewmolFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.XEDFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.XYZFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.YasaraFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ZindoFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat: Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures(IAtomContainer) - Static method in class org.openscience.cdk.tools.DataFeaturesTool: Determines the features present in the given IAtomContainer.
getSurfaceArea(int) - Method in class org.openscience.cdk.geometry.surface.NumericalSurface: Get the surface area for the specified atom.
getSurfacePoints(int) - Method in class org.openscience.cdk.geometry.surface.NumericalSurface: Get an array of the points on the accessible surface of a specific atom.
getSwitchingAtom() - Method in class org.openscience.cdk.libio.md.ChargeGroup
getSymbol() - Method in class org.openscience.cdk.AtomRef: Returns the element symbol of this element.
getSymbol() - Method in class org.openscience.cdk.debug.DebugAtom: Returns the element symbol of this element.
getSymbol() - Method in class org.openscience.cdk.debug.DebugAtomType: Returns the element symbol of this element.
getSymbol() - Method in class org.openscience.cdk.debug.DebugElement: Returns the element symbol of this element.
getSymbol() - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Returns the element symbol of this element.
getSymbol() - Method in class org.openscience.cdk.debug.DebugIsotope: Returns the element symbol of this element.
getSymbol() - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Returns the element symbol of this element.
getSymbol() - Method in class org.openscience.cdk.Element: Returns the element symbol of this element.
getSymbol() - Method in interface org.openscience.cdk.interfaces.IElement: Returns the element symbol of this element.
getSymbol() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Returns the element symbol of this element.
getSymbol() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom
getSymbol() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryAtom: Returns the element symbol of this element.
getSymbol() - Method in class org.openscience.cdk.silent.Element: Returns the element symbol of this element.
getSymbol(int) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable: Get the symbol for the specified atomic number.
getSymbol(String[], Integer[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen
getSymbolArray() - Method in class org.openscience.cdk.structgen.maygen.Maygen
getSymbolFirstAtom() - Method in class org.openscience.cdk.smsd.helper.BondEnergy: Deprecated.

Returns the element symbol of the first atom.
getSymbolOccurrences(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Getting the symbol occurrences from the input local formula.
getSymbols() - Method in class org.openscience.cdk.structgen.maygen.Maygen
getSymbolSecondAtom() - Method in class org.openscience.cdk.smsd.helper.BondEnergy: Deprecated.

Returns the element symbol of the second atom.
getSymbolSet() - Method in class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom: Deprecated.

Retrieve the Set of symbols
getSymbolSet() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom: Deprecated.

Retrieve the Set of symbols
getTabSize() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
getTabSize() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
getTanimotoAtomSimilarity() - Method in class org.openscience.cdk.smsd.Isomorphism: Deprecated.
getTanimotoBondSimilarity() - Method in class org.openscience.cdk.smsd.Isomorphism: Deprecated.
getTanimotoSimilarity() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS: Deprecated.

Returns Tanimoto similarity between query and target molecules (Score is between 0-min and 1-max).
getTanimotoSimilarity() - Method in class org.openscience.cdk.smsd.Isomorphism: Deprecated.

Returns Tanimoto similarity between query and target molecules (Score is between 0-min and 1-max).
getTarget() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler: Deprecated.

Returns target molecule
getTarget() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.EdgeBuilder: Deprecated.

Returns target Node.
getTarget() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IEdge: Deprecated.

Returns target Node.
getTarget() - Method in class org.openscience.cdk.smsd.ring.PathEdge: Deprecated.
getTargetAtom() - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.Match: Deprecated.

Return Target Atom
getTargetQueryBondMappings() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher: Return a list of HashMap's that allows one to get the query constraint for a given pharmacophore bond.
getTautomers(IAtomContainer) - Method in class org.openscience.cdk.tautomers.InChITautomerGenerator: Public method to get tautomers for an input molecule, based on the InChI which will be calculated by JNI-InChI.
getTautomers(IAtomContainer, String) - Method in class org.openscience.cdk.tautomers.InChITautomerGenerator: Deprecated.
use InChITautomerGenerator.getTautomers(IAtomContainer) directly
getTempFactor() - Method in class org.openscience.cdk.debug.DebugPDBAtom: get the Temperature factor of this atom.
getTempFactor() - Method in interface org.openscience.cdk.interfaces.IPDBAtom: get the Temperature factor of this atom.
getTempFactor() - Method in class org.openscience.cdk.protein.data.PDBAtom: get the Temperature factor of this atom.
getTempFactor() - Method in class org.openscience.cdk.silent.PDBAtom: get the Temperature factor of this atom.
getTemplateAt(int) - Method in class org.openscience.cdk.layout.TemplateHandler: Gets the templateAt attribute of the TemplateHandler object
getTemplateAt(int) - Method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D: Gets the templateAt attribute of the TemplateHandler object.
getTemplateCount() - Method in class org.openscience.cdk.layout.TemplateHandler: Gets the templateCount attribute of the TemplateHandler object
getTemplateCount() - Method in class org.openscience.cdk.modeling.builder3d.ModelBuilder3D: Returns the number of loaded templates.
getTemplateCount() - Method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D: Gets the templateCount attribute of the TemplateHandler object.
getTemplateHandler() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator: Deprecated.
always null, substructure templates are not used anymore
getTessAsPoint3ds() - Method in class org.openscience.cdk.geometry.surface.Tessellate
getTessAsTriangles() - Method in class org.openscience.cdk.geometry.surface.Tessellate
getTextBasePoint(String, double, double, Graphics2D) - Method in class org.openscience.cdk.renderer.visitor.AbstractAWTDrawVisitor: Calculates the base point where text should be rendered, as text in Java is typically placed using the left-lower corner point in screen coordinates.
getTextBounds(String, double, double, Graphics2D) - Method in class org.openscience.cdk.renderer.visitor.AbstractAWTDrawVisitor: Calculates the boundaries of a text string in screen coordinates.
getTextBounds(String, Graphics2D) - Method in class org.openscience.cdk.renderer.visitor.AbstractAWTDrawVisitor: Obtain the exact bounding box of the text in the provided graphics environment.
getTimeManager() - Static method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlus: Deprecated.
getTimeManager() - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS: Deprecated.
getTimeManager() - Static method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper: Deprecated.
getTimeManager() - Static method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper: Deprecated.
getTimeout() - Method in class org.openscience.cdk.ringsearch.AllRingsFinder: Deprecated.
timeout not used
getTimeout() - Static method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlus: Deprecated.
getTimeout() - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS: Deprecated.
getTimeout() - Static method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper: Deprecated.
getTimeout() - Static method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper: Deprecated.
getTimeOut() - Method in class org.openscience.cdk.smsd.global.TimeOut: Deprecated.

Return cutoff value for time out.
getTitle() - Method in class org.openscience.cdk.AtomContainer: Access the title of the record.
getTitle() - Method in class org.openscience.cdk.ConformerContainer: Get the title of the conformers.
getTitle() - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Access the title of the record.
getTitle() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Access the title of the record.
getTitle() - Method in class org.openscience.cdk.renderer.GraphRendererModel: Get the main title
getTitle() - Method in class org.openscience.cdk.silent.AtomContainer: Access the title of the record.
getTitlemap() - Method in class org.openscience.cdk.io.RssWriter
getToken(int) - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Get the specific Token.
getToken(int) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser: Get the specific Token.
getTolerance() - Method in class org.openscience.cdk.formula.IsotopePatternSimilarity: Get the tolerance of the mass accuracy.
getToolTipText(IAtom) - Method in class org.openscience.cdk.renderer.RendererModel: Gets the toolTipText for atom certain atom.
getToolTipTextMap() - Method in class org.openscience.cdk.renderer.RendererModel: Gets the toolTipTextMap.
getTopoEquivClassbyHuXu(IAtomContainer) - Method in class org.openscience.cdk.graph.invariant.EquivalentClassPartitioner: Get the topological equivalent class of the molecule.
getTorsionAngle(Point3d, Point3d, Point3d, Point3d) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D: Calculates the torsionAngle of a-b-c-d.
getTorsionData(String, String, String, String, String) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94ParametersCall: Gets the bond parameter set.
getTotal() - Method in class org.openscience.cdk.structgen.maygen.Maygen
getTotalCharge(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Get the summed charge of all atoms in an AtomContainer
getTotalCharge(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
getTotalCharge(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
getTotalExactMass(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Deprecated.
uses AtomContainerManipulator.getMass(IAtomContainer, int) and AtomContainerManipulator.MonoIsotopic
getTotalExactMass(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Deprecated.
calls MolecularFormulaManipulator.getMass(IMolecularFormula, int) with option MolecularFormulaManipulator.MonoIsotopic and adjusts for charge with MolecularFormulaManipulator.correctMass(double, Integer). These functions should be used directly.
getTotalFormalCharge(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Get the total formal charge on a molecule.
getTotalFormalCharge(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
getTotalFormalCharge(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
getTotalHydrogen() - Method in class org.openscience.cdk.structgen.maygen.Maygen
getTotalHydrogenCount(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Counts the number of hydrogens on the provided IAtomContainer.
getTotalHydrogenCount(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
getTotalHydrogenCount(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
getTotalMassNumber(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Get the summed mass number of all isotopes from an MolecularFormula.
getTotalNaturalAbundance(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Get the summed natural abundance of all atoms in an AtomContainer
getTotalNaturalAbundance(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Get the summed natural abundance of all isotopes from an MolecularFormula.
getTotalNegativeFormalCharge(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Get the total formal negative charge on a molecule.
getTotalPositiveFormalCharge(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Get the total positive formal charge on a molecule.
getTotalSurfaceArea() - Method in class org.openscience.cdk.geometry.surface.NumericalSurface: Get the total surface area for the AtomContainer.
getTrainingActives() - Method in class org.openscience.cdk.fingerprint.model.Bayesian: Returns the number of actives in the training set that was used to create the model.
getTrainingSize() - Method in class org.openscience.cdk.fingerprint.model.Bayesian: Returns the size of the training set, i.e.
getTranspose(int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: For an index pair, getting its transpose.
getType() - Method in class org.openscience.cdk.dict.DictRef
getType() - Method in class org.openscience.cdk.isomorphism.matchers.CTFileQueryBond: Deprecated.

Getter for type
getType() - Method in class org.openscience.cdk.sgroup.Sgroup: Access the type of the Sgroup.
getUncommon(IAtomContainer, IAtomContainer, boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler: Deprecated.
getUncommon(IAtomContainer, IAtomContainer, boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler: Deprecated.
getUniqueMatchingAtoms() - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool: Deprecated.

Get the atoms in the target molecule that match the query pattern.
getUniqueMatchingPharmacophoreAtoms() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher: Get the uniue matching pharmacophore groups.
getUnplacedRingHeavyAtom(IAtomContainer, IAtom) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D: Gets the unplacedRingHeavyAtom attribute of the AtomPlacer3D object.
getUnsetAtomsInAtomContainer(IAtom, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D: Gets the unsetAtomsInAtomContainer attribute of the AtomTetrahedralLigandPlacer3D object.
getUpper() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryAngleBond
getUpper() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryBond
getUseTemplates() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator: Deprecated.
always false, substructure templates are not used anymore
getUSmilesNumbers(IAtomContainer) - Static method in class org.openscience.cdk.graph.invariant.InChINumbersTools: Obtain the InChI numbers for the input container to be used to order atoms in Universal SMILES [O'Boyle, Noel. Journal of Cheminformatics. 2012. 4].
getValence(IAtom) - Static method in class org.openscience.cdk.qsar.AtomValenceTool
getValency() - Method in class org.openscience.cdk.AtomRef: Gets the the exact electron valency of the AtomType object.
getValency() - Method in class org.openscience.cdk.AtomType: Gets the the exact electron valency of the AtomType object.
getValency() - Method in class org.openscience.cdk.debug.DebugAtom: Gets the the exact electron valency of the AtomType object.
getValency() - Method in class org.openscience.cdk.debug.DebugAtomType: Gets the the exact electron valency of the AtomType object.
getValency() - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Gets the the exact electron valency of the AtomType object.
getValency() - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Gets the the exact electron valency of the AtomType object.
getValency() - Method in interface org.openscience.cdk.interfaces.IAtomType: Gets the the exact electron valency of the AtomType object.
getValency() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Gets the the exact electron valency of the AtomType object.
getValency() - Method in class org.openscience.cdk.silent.AtomType: Gets the the exact electron valency of the AtomType object.
getValue() - Method in enum org.openscience.cdk.io.MDLV2000Writer.SPIN_MULTIPLICITY: Radical value for the spin multiplicity in the properties block.
getValue() - Method in class org.openscience.cdk.iupac.parser.Token: An optional attribute value of the Token.
getValue() - Method in class org.openscience.cdk.qsar.DescriptorValue
getValue() - Method in interface org.openscience.cdk.reaction.type.parameters.IParameterReact: Get the value of the parameter.
getValue() - Method in class org.openscience.cdk.reaction.type.parameters.ParameterReact: Get the value of the parameter.
getValue() - Method in interface org.openscience.cdk.renderer.generators.IGeneratorParameter: Gets the value for this parameter.
getValue() - Method in class org.openscience.cdk.renderer.generators.parameter.AbstractGeneratorParameter: Gets the value for this parameter.
getValue() - Method in class org.openscience.cdk.smiles.smarts.parser.Token: An optional attribute value of the Token.
getValue() - Method in class org.openscience.cdk.smsd.helper.BinaryTree: Deprecated.

Return value of the node
getValue(double, double, double) - Method in interface org.openscience.cdk.math.IFunction: Return the function value at (x,y,z)
getValue(int, double, double, double) - Method in class org.openscience.cdk.math.qm.FourierGridBasis
getValue(int, double, double, double) - Method in class org.openscience.cdk.math.qm.GaussiansBasis: Calculates the function value an (x,y,z).
getValue(int, double, double, double) - Method in interface org.openscience.cdk.math.qm.IBasis: Calculates the function value an (x,y,z).
getValue(int, double, double, double) - Method in class org.openscience.cdk.math.qm.Orbitals: Get the function value of a orbital at the position (x,y,z)
getValue(SgroupKey) - Method in class org.openscience.cdk.sgroup.Sgroup: Access an attribute for the Sgroup.
getValueAt(int, int) - Method in class org.openscience.cdk.graph.invariant.GIMatrix: Returns the value of the given element.
getValues() - Method in class org.openscience.cdk.group.Permutation: Get all the values as an array.
getValues(int, Matrix) - Method in class org.openscience.cdk.math.qm.FourierGridBasis
getValues(int, Matrix) - Method in class org.openscience.cdk.math.qm.GaussiansBasis: Calculates the function values.
getValues(int, Matrix) - Method in interface org.openscience.cdk.math.qm.IBasis: Calculates the function values.
getValues(int, Matrix) - Method in class org.openscience.cdk.math.qm.Orbitals: Get the function value of a orbital
getValues(Matrix) - Method in interface org.openscience.cdk.math.IFunction: Return the function value The rows of the matrix x are the Parameters like x,y,z and the columns are the values which must calculated.
getVanDerWaalsFile() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
getVdwRadius(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable: Get the Van der Waals radius for the element in question.
getVdWVolume(String) - Method in class org.openscience.cdk.tools.AtomicProperties
getVectorFromColumn(int) - Method in class org.openscience.cdk.math.IMatrix: Creates a vector with the content of a column from this matrix
getVectorFromColumn(int) - Method in class org.openscience.cdk.math.Matrix: Creates a Vector with the content of a column from this Matrix.
getVectorFromDiagonal() - Method in class org.openscience.cdk.math.IMatrix: Creates a vector with the content of the diagonal elements from this matrix
getVectorFromDiagonal() - Method in class org.openscience.cdk.math.Matrix: Creates a Vector with the content of the diagonal elements from this Matrix.
getVectorFromRow(int) - Method in class org.openscience.cdk.math.IMatrix: Creates a vector with the content of a row from this matrix
getVectorFromRow(int) - Method in class org.openscience.cdk.math.Matrix: Creates a Vector with the content of a row from this Matrix.
getVerbose() - Method in class org.openscience.cdk.structgen.maygen.Maygen
getVersion() - Static method in class org.openscience.cdk.CDK: Returns the version of this CDK library.
getVersionDescription() - Method in class org.openscience.cdk.fingerprint.AbstractFingerprinter
getVersionDescription() - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter
getVersionDescription() - Method in interface org.openscience.cdk.fingerprint.IFingerprinter: Generate a fingerprint type version description in chemfp's FPS format.
getVertexCount() - Method in interface org.openscience.cdk.group.Refinable: Get the number of vertices in the graph to be refined.
getVertexCount() - Method in class org.openscience.cdk.signature.MoleculeSignature
getVertexCountAtDistance(IAtomContainer, int) - Static method in class org.openscience.cdk.graph.PathTools: Returns the number of vertices that are a distance 'd' apart.
getVertexSymbol(int) - Method in class org.openscience.cdk.signature.AtomSignature
getVisitedAtoms() - Method in interface org.openscience.cdk.geometry.cip.ILigand: Returns a list of visitedAtoms.
getVisitedAtoms() - Method in class org.openscience.cdk.geometry.cip.Ligand: Returns a list of visitedAtoms.
getWarningCount() - Method in class org.openscience.cdk.validate.ValidationReport: Returns the number of tests which gave warnings.
getWarningFlags() - Method in class org.openscience.cdk.inchi.InChIToStructure: Returns warning flags, see INCHIDIFF in inchicmp.h.
getWarnings() - Method in class org.openscience.cdk.validate.ValidationReport: Returns an array of ValidationTest warnings.
getWidthForBond(IBond, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator: Determine the width of a bond, returning either the width defined in the model, or the override width.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.ABINITFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.Aces2Format: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.ADFFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.AlchemyFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.BGFFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.BSFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
getWriterClassName() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.CACheFormat
getWriterClassName() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
getWriterClassName() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat
getWriterClassName() - Method in class org.openscience.cdk.io.formats.CIFFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.CMLFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.CRK2DFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.CRK3DFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.CrystClustFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.CTXFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.DaltonFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.DMol3Format: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.DOCK5Format: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.FingerprintFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.GamessFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.Gaussian03Format: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.Gaussian90Format: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.Gaussian92Format: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.Gaussian94Format: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.Gaussian95Format: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.Gaussian98Format: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat
getWriterClassName() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.GROMOS96Format: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.HINFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in interface org.openscience.cdk.io.formats.IChemFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.INChIFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.JaguarFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.JMEFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MacroModelFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MDLFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MDLRXNV2000Format: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MDLV2000Format: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MDLV3000Format: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MMODFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.Mol2Format: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC7Format: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC93Format: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC97Format: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MPQCFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.NWChemFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.PCModelFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.PDBFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.PDBMLFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.PMPFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.PQSChemFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.QChemFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.RawCopyFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.SDFFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.ShelXFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.SMARTSFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.SMILESFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.SpartanFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.VASPFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.ViewmolFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.XEDFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.XYZFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.YasaraFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.ZindoFormat: Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat: Returns the class name of the CDK Writer for this format.
getXMax() - Method in class org.openscience.cdk.renderer.GraphRendererModel: Sets the function area, which will painted
getXMin() - Method in class org.openscience.cdk.renderer.GraphRendererModel: Gets the function area, which will painted
getXTitle() - Method in class org.openscience.cdk.renderer.GraphRendererModel: Get the title of the x axis
getYMax() - Method in class org.openscience.cdk.renderer.GraphRendererModel: Sets the function area, which will painted
getYMin() - Method in class org.openscience.cdk.renderer.GraphRendererModel: Sets the function area, which will painted
getYTitle() - Method in class org.openscience.cdk.renderer.GraphRendererModel: Get the title of the y axis
getZ() - Method in class org.openscience.cdk.Crystal: Gets the number of asymmetric parts in the unit cell.
getZ() - Method in class org.openscience.cdk.debug.DebugCrystal: Gets the number of asymmetric parts in the unit cell.
getZ() - Method in interface org.openscience.cdk.interfaces.ICrystal: Gets the number of asymmetric parts in the unit cell.
getZ() - Method in class org.openscience.cdk.silent.Crystal: Gets the number of asymmetric parts in the unit cell.
GhemicalMMFormat - Class in org.openscience.cdk.io.formats: See here.
GhemicalMMFormat() - Constructor for class org.openscience.cdk.io.formats.GhemicalMMFormat
GhemicalMMReader - Class in org.openscience.cdk.io: Reads Ghemical ( http://www.uku.fi/~thassine/ghemical/) molecular mechanics (*.mm1gp) files.
GhemicalMMReader() - Constructor for class org.openscience.cdk.io.GhemicalMMReader
GhemicalMMReader(InputStream) - Constructor for class org.openscience.cdk.io.GhemicalMMReader
GhemicalMMReader(Reader) - Constructor for class org.openscience.cdk.io.GhemicalMMReader
GhemicalSPMFormat - Class in org.openscience.cdk.io.formats
GhemicalSPMFormat() - Constructor for class org.openscience.cdk.io.formats.GhemicalSPMFormat
GIF_FMT - Static variable in class org.openscience.cdk.depict.Depiction: Graphics Interchange Format (GIF) format key.
GIMatrix - Class in org.openscience.cdk.graph.invariant: This class is intended to provide the user an efficient way of implementing matrix of double number and using normal operations (linear operations, addition, subtraction, multiplication, inversion, concatenation) on them.
GIMatrix(double[][]) - Constructor for class org.openscience.cdk.graph.invariant.GIMatrix: Class constructor.
GIMatrix(int[][]) - Constructor for class org.openscience.cdk.graph.invariant.GIMatrix: Class constructor.
GIMatrix(int, int) - Constructor for class org.openscience.cdk.graph.invariant.GIMatrix: Class constructor.
GIMatrix(GIMatrix) - Constructor for class org.openscience.cdk.graph.invariant.GIMatrix: Class constructor.
GIMatrix(GIMatrix[][]) - Constructor for class org.openscience.cdk.graph.invariant.GIMatrix: Class constructor.
giveAngle(IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.geometry.BondTools: Calls giveAngleBothMethods with bool = true.
giveAngleBothMethods(Point2d, Point2d, Point2d, boolean) - Static method in class org.openscience.cdk.geometry.BondTools
giveAngleBothMethods(IAtom, IAtom, IAtom, boolean) - Static method in class org.openscience.cdk.geometry.BondTools: Gives the angle between two lines starting at atom from and going to to1 and to2.
giveAngleFromMiddle(IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.geometry.BondTools: Calls giveAngleBothMethods with bool = false.
Gold - org.openscience.cdk.config.Elements
GOLD - Static variable in enum org.openscience.cdk.config.Elements
GOLD - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
graph - Variable in class org.openscience.cdk.stereo.StereoElementFactory: Adjacency list graph representation.
GraphOnlyFingerprinter - Class in org.openscience.cdk.fingerprint: Specialized version of the Fingerprinter which does not take bond orders into account.
GraphOnlyFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.GraphOnlyFingerprinter: Creates a fingerprint generator of length defaultSize and with a search depth of defaultSearchDepth.
GraphOnlyFingerprinter(int) - Constructor for class org.openscience.cdk.fingerprint.GraphOnlyFingerprinter
GraphOnlyFingerprinter(int, int) - Constructor for class org.openscience.cdk.fingerprint.GraphOnlyFingerprinter
GraphRendererModel - Class in org.openscience.cdk.renderer: This class handles a set of function for the GraphRenderer
GraphRendererModel() - Constructor for class org.openscience.cdk.renderer.GraphRendererModel
GraphUtil - Class in org.openscience.cdk.graph: Collection of static utilities for manipulating adjacency list representations stored as a int[][].
GraphUtil.EdgeToBondMap - Class in org.openscience.cdk.graph: Utility for storing IBonds indexed by vertex end points.
GravitationalIndexDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: IDescriptor characterizing the mass distribution of the molecule.
GravitationalIndexDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor
GridGenerator - Class in org.openscience.cdk.tools: Generates a grid of points in 3D space within given boundaries.
GridGenerator() - Constructor for class org.openscience.cdk.tools.GridGenerator
GridGenerator(double[], double, boolean) - Constructor for class org.openscience.cdk.tools.GridGenerator
GridGenerator(double, double) - Constructor for class org.openscience.cdk.tools.GridGenerator
GridGenerator(double, double, double) - Constructor for class org.openscience.cdk.tools.GridGenerator
gridToGridArray(double[][][]) - Method in class org.openscience.cdk.tools.GridGenerator: Method transforms the grid to an array.
gridToPmesh(String) - Method in class org.openscience.cdk.protein.ProteinPocketFinder: Method writes the grid to pmesh format.
GROMOS96Format - Class in org.openscience.cdk.io.formats: See here.
GROMOS96Format() - Constructor for class org.openscience.cdk.io.formats.GROMOS96Format
group() - Method in enum org.openscience.cdk.config.Elements: Return the group in the periodic table this element belongs to.
GroupExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
groupOneMetals() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.
groupTwoMetals() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.
growArraySize - Variable in class org.openscience.cdk.AtomContainer: Amount by which the bond and atom arrays grow when elements are added and the arrays are not large enough for that.
growArraySize - Variable in class org.openscience.cdk.AtomContainerSet: Amount by which the AtomContainers array grows when elements are added and the array is not large enough for that.
growArraySize - Variable in class org.openscience.cdk.ChemFile: Amount by which the chemsequence array grows when elements are added and the array is not large enough for that.
growArraySize - Variable in class org.openscience.cdk.ChemSequence: Amount by which the chemModels array grows when elements are added and the array is not large enough for that.
growArraySize - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Amount by which the bond and atom arrays grow when elements are added and the arrays are not large enough for that.
growArraySize - Variable in class org.openscience.cdk.Reaction
growArraySize - Variable in class org.openscience.cdk.silent.AtomContainer: Amount by which the bond and atom arrays grow when elements are added and the arrays are not large enough for that.
growArraySize - Variable in class org.openscience.cdk.silent.AtomContainerSet: Amount by which the AtomContainers array grows when elements are added and the array is not large enough for that.
growArraySize - Variable in class org.openscience.cdk.silent.ChemFile: Amount by which the chemsequence array grows when elements are added and the array is not large enough for that.
growArraySize - Variable in class org.openscience.cdk.silent.ChemSequence: Amount by which the chemModels array grows when elements are added and the array is not large enough for that.
growArraySize - Variable in class org.openscience.cdk.silent.Reaction
growAtomContainerArray() - Method in class org.openscience.cdk.AtomContainerSet: Grows the atomContainer array by a given size.
growAtomContainerArray() - Method in class org.openscience.cdk.silent.AtomContainerSet: Grows the atomContainer array by a given size.
growChemModelArray() - Method in class org.openscience.cdk.ChemSequence: Grows the chemModel array by a given size.
growChemModelArray() - Method in class org.openscience.cdk.silent.ChemSequence: Grows the chemModel array by a given size.
growChemSequenceArray() - Method in class org.openscience.cdk.ChemFile: Grows the ChemSequence array by a given size.
growChemSequenceArray() - Method in class org.openscience.cdk.silent.ChemFile: Grows the ChemSequence array by a given size.
GRP_ABS - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Absolute stereo group, the exact stereo configuration of this atom is known.
GRP_MASK - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Mask for the stereo group information
GRP_NUM_MASK - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Mask for the stereo group number information, 0x0 ..
GRP_NUM_SHIFT - Static variable in interface org.openscience.cdk.interfaces.IStereoElement
GRP_RAC - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Racemic stereo group type, the stereo configuration of this atom is a mixture of R/S.
GRP_RAC1 - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Convenience field for testing if the stereo is group RAC1 (&1).
GRP_RAC2 - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Convenience field for testing if the stereo is group RAC2 (&2).
GRP_RAC3 - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Convenience field for testing if the stereo is group RAC3 (&3).
GRP_RAC4 - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Convenience field for testing if the stereo is group RAC4 (&4).
GRP_RAC5 - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Convenience field for testing if the stereo is group RAC5 (&5).
GRP_REL - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Relative stereo group type, the stereo configuration of this atom is unknown but is relative to another atom in the same group.
GRP_REL1 - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Convenience field for testing if the stereo is group OR1 (&1).
GRP_REL2 - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Convenience field for testing if the stereo is group OR2 (&2).
GRP_REL3 - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Convenience field for testing if the stereo is group OR3 (&3).
GRP_REL4 - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Convenience field for testing if the stereo is group OR4 (&4).
GRP_REL5 - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Convenience field for testing if the stereo is group OR5 (&5).
GRP_TYPE_MASK - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Mask for the stereo group type information, GRP_ABS, GRP_AND, GRP_OR
guessFormat(InputStream) - Method in class org.openscience.cdk.io.FormatFactory
guessFormat(Reader) - Method in class org.openscience.cdk.io.FormatFactory: Creates a String of the Class name of the IChemObject reader for this file format.

H

h - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
H - Static variable in interface org.openscience.cdk.interfaces.IElement: Hydrogen atomic number
H - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
H_AND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Hafnium - org.openscience.cdk.config.Elements
HAFNIUM - Static variable in enum org.openscience.cdk.config.Elements
HAFNIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
handleError(String) - Method in class org.openscience.cdk.io.DefaultChemObjectReader: Redirects an error message to the IChemObjectReaderErrorHandler.
handleError(String) - Method in interface org.openscience.cdk.io.IChemObjectReader: Redirects an error message to the IChemObjectReaderErrorHandler.
handleError(String) - Method in interface org.openscience.cdk.io.IChemObjectReaderErrorHandler: Method that should react on an error message send by an IChemObjectReader.
handleError(String) - Method in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader: Redirects an error message to the IChemObjectReaderErrorHandler.
handleError(String, int, int, int) - Method in class org.openscience.cdk.io.DefaultChemObjectReader: Redirects an error message to the IChemObjectReaderErrorHandler.
handleError(String, int, int, int) - Method in interface org.openscience.cdk.io.IChemObjectReader: Redirects an error message to the IChemObjectReaderErrorHandler.
handleError(String, int, int, int) - Method in interface org.openscience.cdk.io.IChemObjectReaderErrorHandler: Method that should react on an error message send by an IChemObjectReader.
handleError(String, int, int, int) - Method in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader: Redirects an error message to the IChemObjectReaderErrorHandler.
handleError(String, int, int, int, Exception) - Method in class org.openscience.cdk.io.DefaultChemObjectReader: Redirects an error message to the IChemObjectReaderErrorHandler.
handleError(String, int, int, int, Exception) - Method in interface org.openscience.cdk.io.IChemObjectReader: Redirects an error message to the IChemObjectReaderErrorHandler.
handleError(String, int, int, int, Exception) - Method in interface org.openscience.cdk.io.IChemObjectReaderErrorHandler: Method that should react on an error message send by an IChemObjectReader.
handleError(String, int, int, int, Exception) - Method in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader: Redirects an error message to the IChemObjectReaderErrorHandler.
handleError(String, Exception) - Method in class org.openscience.cdk.io.DefaultChemObjectReader: Redirects an error message to the IChemObjectReaderErrorHandler.
handleError(String, Exception) - Method in interface org.openscience.cdk.io.IChemObjectReader: Redirects an error message to the IChemObjectReaderErrorHandler.
handleError(String, Exception) - Method in interface org.openscience.cdk.io.IChemObjectReaderErrorHandler: Method that should react on an error message send by an IChemObjectReader.
handleError(String, Exception) - Method in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader: Redirects an error message to the IChemObjectReaderErrorHandler.
HanserRingFinder - Class in org.openscience.cdk.smsd.ring: Deprecated.
Use CDK AllRingsFinder. A more recent version of SMSD is available at http://github.com/asad/smsd.
HanserRingFinder() - Constructor for class org.openscience.cdk.smsd.ring.HanserRingFinder: Deprecated.
has(String) - Method in class org.openscience.cdk.io.setting.SettingManager: Determines whether the manager currently holds a setting of the provided name.
HAS_2D_COORDINATES - Static variable in class org.openscience.cdk.tools.DataFeatures
HAS_3D_COORDINATES - Static variable in class org.openscience.cdk.tools.DataFeatures
HAS_ALIPHATIC_HETERO_SUBSTITUENT - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if the atom is adjacent to an aliphatic hetero atom.
HAS_ATOM_ELEMENT_SYMBOL - Static variable in class org.openscience.cdk.tools.DataFeatures
HAS_ATOM_FORMAL_CHARGES - Static variable in class org.openscience.cdk.tools.DataFeatures
HAS_ATOM_HYBRIDIZATIONS - Static variable in class org.openscience.cdk.tools.DataFeatures: FIXME: NOT YET IN BODF !!!
HAS_ATOM_ISOTOPE_NUMBERS - Static variable in class org.openscience.cdk.tools.DataFeatures
HAS_ATOM_MASS_NUMBERS - Static variable in class org.openscience.cdk.tools.DataFeatures
HAS_ATOM_PARTIAL_CHARGES - Static variable in class org.openscience.cdk.tools.DataFeatures
HAS_DIETZ_REPRESENTATION - Static variable in class org.openscience.cdk.tools.DataFeatures
HAS_FRACTIONAL_CRYSTAL_COORDINATES - Static variable in class org.openscience.cdk.tools.DataFeatures
HAS_GRAPH_REPRESENTATION - Static variable in class org.openscience.cdk.tools.DataFeatures
HAS_HETERO_SUBSTITUENT - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if the atom is adjacent to a hetero atom.
HAS_IMPLICIT_HYDROGEN - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if the hydrogen count (IAtom.getImplicitHydrogenCount()) is > 0.
HAS_ISOTOPE - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if the atom mass (IIsotope.getMassNumber()) is non-null.
HAS_REACTIONS - Static variable in class org.openscience.cdk.tools.DataFeatures: FIXME: NOT YET IN BODF !!!
HAS_UNITCELL_PARAMETERS - Static variable in class org.openscience.cdk.tools.DataFeatures: FIXME: NOT YET IN BODF !!!
HAS_UNSPEC_ISOTOPE - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if the atom mass (IIsotope.getMassNumber()) is null (unspecified).
has2DCoordinates(IAtom) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Determines if this Atom contains 2D coordinates.
has2DCoordinates(IAtom) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Determines if this Atom contains 2D coordinates.
has2DCoordinates(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Determines if all this IAtomContainer's atoms contain 2D coordinates.
has2DCoordinates(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Determines if all this IAtomContainer's atoms contain 2D coordinates.
has2DCoordinates(IBond) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Determines if this Bond contains 2D coordinates.
has2DCoordinates(IBond) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Determines if this Bond contains 2D coordinates.
has2DCoordinates(IReaction) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Determine if all parts of a reaction have coodinates
has2DCoordinatesNew(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.
use GeometryTools.get2DCoordinateCoverage(org.openscience.cdk.interfaces.IAtomContainer) for determining partial coordinates
has2DCoordinatesNew(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Deprecated.
use GeometryUtil.get2DCoordinateCoverage(org.openscience.cdk.interfaces.IAtomContainer) for determining partial coordinates
has3DCoordinates(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Determines if all this IAtomContainer's atoms contain 3D coordinates.
has3DCoordinates(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Determines if all this IAtomContainer's atoms contain 3D coordinates.
has3DCoordinates(IChemModel) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Determines if this model contains 3D coordinates for all atoms.
has3DCoordinates(IChemModel) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Determines if this model contains 3D coordinates for all atoms.
HASATOM - Static variable in class org.openscience.cdk.libio.jena.CDK
HASATOMICNUMBER - Static variable in class org.openscience.cdk.libio.jena.CDK
HASATOMTYPENAME - Static variable in class org.openscience.cdk.libio.jena.CDK
HASBOND - Static variable in class org.openscience.cdk.libio.jena.CDK
hasCoordinates(IAtom) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator: Checks an atom to see if it has 2D coordinates.
hasCrystalCoordinates(IAtomContainer) - Static method in class org.openscience.cdk.geometry.CrystalGeometryTools: Determines if this model contains fractional (crystal) coordinates.
hasDictionary(String) - Method in class org.openscience.cdk.dict.DictionaryDatabase: Returns true if the database contains the dictionary.
HASELECTRONCOUNT - Static variable in class org.openscience.cdk.libio.jena.CDK
hasElementSymbols(IAtomContainer) - Static method in class org.openscience.cdk.tools.features.MoleculeFeaturesTool
hasEntry(String) - Method in class org.openscience.cdk.dict.Dictionary
hasEntry(String, String) - Method in class org.openscience.cdk.dict.DictionaryDatabase: Returns true if the given dictionary contains the given entry.
HASEXACTMASS - Static variable in class org.openscience.cdk.libio.jena.CDK
HASFORMALCHARGE - Static variable in class org.openscience.cdk.libio.jena.CDK
hasFormalCharges(IAtomContainer) - Static method in class org.openscience.cdk.tools.features.MoleculeFeaturesTool
hasGraphRepresentation(IAtomContainer) - Static method in class org.openscience.cdk.tools.features.MoleculeFeaturesTool: Checks whether all bonds have exactly two atoms.
Hash - org.openscience.cdk.interfaces.IBond.Display: A hashed line (bold dashed).
hasHash(int) - Method in interface org.openscience.cdk.fingerprint.ICountFingerprint: Whether the fingerprint contains the given hash.
hasHash(int) - Method in class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
hashCode - Variable in class org.openscience.cdk.fingerprint.CircularFingerprinter.FP
hashCode() - Method in class org.openscience.cdk.Atom
hashCode() - Method in class org.openscience.cdk.AtomRef
hashCode() - Method in class org.openscience.cdk.Bond
hashCode() - Method in class org.openscience.cdk.BondRef
hashCode() - Method in class org.openscience.cdk.DynamicFactory.ConstructorKey
hashCode() - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
hashCode() - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
hashCode() - Method in class org.openscience.cdk.graph.invariant.GIMatrix
hashCode() - Method in class org.openscience.cdk.group.Partition
hashCode() - Method in class org.openscience.cdk.group.Permutation
hashCode() - Method in class org.openscience.cdk.io.formats.AbstractResourceFormat
hashCode() - Method in class org.openscience.cdk.isomorphism.matchers.Expr
hashCode() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
hashCode() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
hashCode() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
hashCode() - Method in class org.openscience.cdk.isomorphism.mcss.RMap
hashCode() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom
hashCode() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycle: Deprecated.
hashCode() - Method in class org.openscience.cdk.silent.Atom
hashCode() - Method in class org.openscience.cdk.silent.Bond
hashCode() - Method in class org.openscience.cdk.smiles.InvPair
hashCode() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMap: Deprecated.

Returns a hash code for object comparison.
HashGeneratorMaker - Class in org.openscience.cdk.hash: Fluent API for creating hash generators.
HashGeneratorMaker() - Constructor for class org.openscience.cdk.hash.HashGeneratorMaker
HashSpacing() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.HashSpacing
HASHYBRIDIZATION - Static variable in class org.openscience.cdk.libio.jena.CDK
hasLabel(String) - Method in class org.openscience.cdk.signature.Orbit: Checks to see if the orbit has this string as a label.
HASLABEL - Static variable in class org.openscience.cdk.libio.jena.CDK
hasMap(IAtomContainer) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper: Deprecated.

checks if a map exits for a molecule.
hasMap(IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper: Deprecated.

checks if a map exits for a molecule.
hasMap(IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper: Deprecated.

checks if a map exits for a molecule.
hasMap(TargetProperties) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper: Deprecated.

checks if a map exits for a molecule.
hasMap(TargetProperties) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper: Deprecated.

checks if a map exits for a molecule.
hasMap(TargetProperties) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper: Deprecated.

checks if a map exits for a molecule.
HASMASSNUMBER - Static variable in class org.openscience.cdk.libio.jena.CDK
HASMAXBONDORDER - Static variable in class org.openscience.cdk.libio.jena.CDK
hasMoreElements() - Method in class org.openscience.cdk.formula.rules.RDBERule.Combinations
HASNATURALABUNDANCE - Static variable in class org.openscience.cdk.libio.jena.CDK
hasNext() - Method in class org.openscience.cdk.graph.MinimalPathIterator: Deprecated.
hasNext() - Method in class org.openscience.cdk.graph.Permutor
hasNext() - Method in class org.openscience.cdk.io.iterator.IteratingMDLConformerReader
hasNext() - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundASNReader
hasNext() - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader
hasNext() - Method in class org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader
hasNext() - Method in class org.openscience.cdk.io.iterator.IteratingSDFReader: Returns true if another IAtomContainer can be read.
hasNext() - Method in class org.openscience.cdk.io.iterator.IteratingSMILESReader: Checks whether there is another molecule to read.
hasNext() - Method in class org.openscience.cdk.io.random.RandomAccessReader
hasNext() - Method in class org.openscience.cdk.smsd.labelling.Permutor: Deprecated.
hasNextCandidate() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IState: Deprecated.

Returns true if another candidate match can be found or false otherwise.
hasNextCandidate() - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFState: Deprecated.

Returns true if another candidate match can be found or false otherwise.
HASORDER - Static variable in class org.openscience.cdk.libio.jena.CDK
hasParameter(Class<T>) - Method in class org.openscience.cdk.renderer.RendererModel: Returns true if the passed IGeneratorParameters has been registered.
hasPartialCharges(IAtomContainer) - Static method in class org.openscience.cdk.tools.features.MoleculeFeaturesTool
hasPerfectConfiguration(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker
hasPrevious() - Method in class org.openscience.cdk.io.random.RandomAccessReader
hasSetting(String) - Method in class org.openscience.cdk.io.ChemObjectIO: Determine whether this reader/writer has a setting of the provided name.
hasSetting(String) - Method in interface org.openscience.cdk.io.IChemObjectIO: Determine whether this reader/writer has a setting of the provided name.
Hassium - org.openscience.cdk.config.Elements
HASSIUM - Static variable in enum org.openscience.cdk.config.Elements
HASSIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
hasSymbol(String) - Method in class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom: Deprecated.

Check whether a symbol is already registered
hasSymbol(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom: Deprecated.

Check whether a symbol is already registered
hasUnsetNeighbour(IAtom, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
Haworth - org.openscience.cdk.stereo.Projection: Haworth projection are used to depict ring-form carbohydrates.
HBondAcceptorCountDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: This descriptor calculates the number of hydrogen bond acceptors using a slightly simplified version of the PHACIR atom types.
HBondAcceptorCountDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor: Constructor for the HBondAcceptorCountDescriptor object
HBondDonorCountDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: This descriptor calculates the number of hydrogen bond donors using a slightly simplified version of the PHACIR atom types.
HBondDonorCountDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor: Constructor for the HBondDonorCountDescriptor object
HBPY8 - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Hexagonal Bipyramidal (HBPY-8)
HBPY9 - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Heptagonal Bipyramidal (HBPY-9)
hCounts - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
He - Static variable in interface org.openscience.cdk.interfaces.IElement
HE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
headerOptions - Variable in class org.openscience.cdk.io.random.RandomAccessReader
HEAVY_DEGREE - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if the degree (IAtom.getBondCount()) - any hydrogen atoms x* equals the specified 'value'.
height - Variable in class org.openscience.cdk.renderer.elements.RectangleElement: The height of the rectangle.
height() - Method in class org.openscience.cdk.graph.invariant.GIMatrix: Returns the number of lines of the matrix.
height() - Method in class org.openscience.cdk.renderer.elements.Bounds: Specifies the height of the bounding box.
Helium - org.openscience.cdk.config.Elements
HELIUM - Static variable in enum org.openscience.cdk.config.Elements
HELIX - Static variable in class org.openscience.cdk.protein.data.PDBStructure
HELIX - Static variable in class org.openscience.cdk.silent.PDBStructure
HEN - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
HENICOS - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
HEPT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
HeptagonalBipyramidal - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Heptagonal Bipyramidal (HBPY-9)
HETERO_SUBSTITUENT_COUNT - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if the number hetero atoms (see Expr.Type.IS_HETERO) this atom is next to is equal to the specified value.
HeterolyticCleavageMechanism - Class in org.openscience.cdk.reaction.mechanism: This mechanism displaces the chemical bond to an Atom.
HeterolyticCleavageMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.HeterolyticCleavageMechanism
HeterolyticCleavagePBReaction - Class in org.openscience.cdk.reaction.type: IReactionProcess which a bond is broken displacing the electron to one of the atoms.
HeterolyticCleavagePBReaction() - Constructor for class org.openscience.cdk.reaction.type.HeterolyticCleavagePBReaction: Constructor of the HeterolyticCleavagePBReaction object.
HeterolyticCleavageSBReaction - Class in org.openscience.cdk.reaction.type: IReactionProcess which a bond is broken displacing the electron to one of the atoms.
HeterolyticCleavageSBReaction() - Constructor for class org.openscience.cdk.reaction.type.HeterolyticCleavageSBReaction: Constructor of the HeterolyticCleavageSBReaction object.
HEX - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
HexagonalBipyramidal - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Hexagonal Bipyramidal (HBPY-8)
Hf - Static variable in interface org.openscience.cdk.interfaces.IElement
HF - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Hg - Static variable in interface org.openscience.cdk.interfaces.IElement
HG - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
HIDDEN - Static variable in class org.openscience.cdk.renderer.generators.standard.StandardGenerator: Marks atoms and bonds as being hidden from the actual depiction.
HIDDEN_FULLY - Static variable in class org.openscience.cdk.renderer.generators.standard.StandardGenerator
HIGH - org.openscience.cdk.io.setting.IOSetting.Importance
HIGHLIGHT_COLOR - Static variable in class org.openscience.cdk.renderer.generators.standard.StandardGenerator: Defines that a chem object should be highlighted in a depiction.
HighlightGenerator - Class in org.openscience.cdk.renderer.generators: Generate an under/overlaid highlight in structure depictions.
HighlightGenerator() - Constructor for class org.openscience.cdk.renderer.generators.HighlightGenerator
HighlightGenerator.HighlightPalette - Class in org.openscience.cdk.renderer.generators: Defines the color palette used to provide the highlight colors.
HighlightGenerator.HighlightRadius - Class in org.openscience.cdk.renderer.generators: Magic number with unknown units that defines the radius around an atom, e.g.
HighlightGenerator.Palette - Interface in org.openscience.cdk.renderer.generators: Defines a color palette, the palette should provide a color the specified identifier (id).
Highlighting() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.Highlighting
HighlightPalette() - Constructor for class org.openscience.cdk.renderer.generators.HighlightGenerator.HighlightPalette
HighlightRadius() - Constructor for class org.openscience.cdk.renderer.generators.HighlightGenerator.HighlightRadius
highThresh - Variable in class org.openscience.cdk.fingerprint.model.Bayesian
HINFormat - Class in org.openscience.cdk.io.formats: See here.
HINFormat() - Constructor for class org.openscience.cdk.io.formats.HINFormat
HINReader - Class in org.openscience.cdk.io: Reads an object from HIN formated input.
HINReader() - Constructor for class org.openscience.cdk.io.HINReader
HINReader(InputStream) - Constructor for class org.openscience.cdk.io.HINReader
HINReader(Reader) - Constructor for class org.openscience.cdk.io.HINReader: Construct a new reader from a Reader type object
HINWriter - Class in org.openscience.cdk.io: Writer that outputs in the HIN format.
HINWriter() - Constructor for class org.openscience.cdk.io.HINWriter
HINWriter(OutputStream) - Constructor for class org.openscience.cdk.io.HINWriter
HINWriter(Writer) - Constructor for class org.openscience.cdk.io.HINWriter: Constructor.
Ho - Static variable in interface org.openscience.cdk.interfaces.IElement
HO - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Holmium - org.openscience.cdk.config.Elements
HOLMIUM - Static variable in enum org.openscience.cdk.config.Elements
HOLMIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
HomolyticCleavageMechanism - Class in org.openscience.cdk.reaction.mechanism: This mechanism breaks the chemical bond between atoms.
HomolyticCleavageMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.HomolyticCleavageMechanism
HomolyticCleavageReaction - Class in org.openscience.cdk.reaction.type: IReactionProcess which breaks the bond homogeneously leading to radical ions.
HomolyticCleavageReaction() - Constructor for class org.openscience.cdk.reaction.type.HomolyticCleavageReaction: Constructor of the HomolyticCleavageReaction object.
HOSECode - Variable in class org.openscience.cdk.tools.HOSECodeGenerator: The HOSECode string that we assemble
HOSECodeAnalyser - Class in org.openscience.cdk.tools: Analyses a molecular formula given in String format and builds an AtomContainer with the Atoms in the molecular formula.
HOSECodeAnalyser() - Constructor for class org.openscience.cdk.tools.HOSECodeAnalyser
HOSECodeGenerator - Class in org.openscience.cdk.tools: Generates HOSE codes [Bremser, W.. Analytica Chimica Acta. 1978. 103].
HOSECodeGenerator() - Constructor for class org.openscience.cdk.tools.HOSECodeGenerator: Constructor for the HOSECodeGenerator.
HOSECodeGenerator(int) - Constructor for class org.openscience.cdk.tools.HOSECodeGenerator: Constructor for the HOSECodeGenerator.
Hs - Static variable in interface org.openscience.cdk.interfaces.IElement
HuLuIndexTool - Class in org.openscience.cdk.graph.invariant: Collection of methods for the calculation of topological indices of a molecular graph as described in [Chang-Yu Hu and Lu Xu. J. Chem. Inf. Comput. Sci.. 1996. 36].
HuLuIndexTool() - Constructor for class org.openscience.cdk.graph.invariant.HuLuIndexTool
HX - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
HYBRID_PLANAR3 - Static variable in class org.openscience.cdk.libio.jena.CDK
HYBRID_S - Static variable in class org.openscience.cdk.libio.jena.CDK
HYBRID_SP1 - Static variable in class org.openscience.cdk.libio.jena.CDK
HYBRID_SP2 - Static variable in class org.openscience.cdk.libio.jena.CDK
HYBRID_SP3 - Static variable in class org.openscience.cdk.libio.jena.CDK
HYBRID_SP3D1 - Static variable in class org.openscience.cdk.libio.jena.CDK
HYBRID_SP3D2 - Static variable in class org.openscience.cdk.libio.jena.CDK
HYBRID_SP3D3 - Static variable in class org.openscience.cdk.libio.jena.CDK
HYBRID_SP3D4 - Static variable in class org.openscience.cdk.libio.jena.CDK
HYBRID_SP3D5 - Static variable in class org.openscience.cdk.libio.jena.CDK
HYBRIDISATION_NUMBER - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if the this atom hybridisation (IAtomType.getHybridization()) is equal to the specified 'value'.
hybridization - Variable in class org.openscience.cdk.AtomType: The hybridization state of this atom with CDKConstants.HYBRIDIZATION_UNSET as default.
hybridization - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom: The hybridization state of this atom with CDKConstants.HYBRIDIZATION_UNSET as default.
hybridization - Variable in class org.openscience.cdk.silent.AtomType: The hybridization state of this atom with CDKConstants.HYBRIDIZATION_UNSET as default.
HYBRIDIZATION_SP1 - Static variable in class org.openscience.cdk.CDKConstants: A geometry of neighboring atoms when an s orbital is hybridized with one p orbital.
HYBRIDIZATION_SP2 - Static variable in class org.openscience.cdk.CDKConstants: A geometry of neighboring atoms when an s orbital is hybridized with two p orbitals.
HYBRIDIZATION_SP3 - Static variable in class org.openscience.cdk.CDKConstants: A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals.
HYBRIDIZATION_SP3D1 - Static variable in class org.openscience.cdk.CDKConstants: A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals with one d orbital.
HYBRIDIZATION_SP3D2 - Static variable in class org.openscience.cdk.CDKConstants: A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals with two d orbitals.
HYBRIDIZATION_SP3D3 - Static variable in class org.openscience.cdk.CDKConstants: A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals with three d orbitals.
HYBRIDIZATION_SP3D4 - Static variable in class org.openscience.cdk.CDKConstants: A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals with four d orbitals.
HYBRIDIZATION_SP3D5 - Static variable in class org.openscience.cdk.CDKConstants: A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals with five d orbitals.
HYBRIDIZATION_UNSET - Static variable in class org.openscience.cdk.CDKConstants: A undefined hybridization.
HybridizationFingerprinter - Class in org.openscience.cdk.fingerprint: Generates a fingerprint for a given IAtomContainer.
HybridizationFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.HybridizationFingerprinter: Creates a fingerprint generator of length DEFAULT_SIZE and with a search depth of DEFAULT_SEARCH_DEPTH.
HybridizationFingerprinter(int) - Constructor for class org.openscience.cdk.fingerprint.HybridizationFingerprinter
HybridizationFingerprinter(int, int) - Constructor for class org.openscience.cdk.fingerprint.HybridizationFingerprinter: Constructs a fingerprint generator that creates fingerprints of the given size, using a generation algorithm with the given search depth.
HybridizationNumber() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
HybridizationNumberAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
HybridizationNumberAtom(int, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.HybridizationNumberAtom: Deprecated.

Creates a new instance
HybridizationRatioDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: IMolecularDescriptor that reports the fraction of sp3 carbons to sp2 carbons.
HybridizationRatioDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor: Constructor for the HybridizationRatioDescriptor object.
Hydrogen - org.openscience.cdk.config.Elements
HYDROGEN - Static variable in enum org.openscience.cdk.config.Elements
HYDROGEN - Static variable in class org.openscience.cdk.geometry.cip.CIPTool: IAtom index to indicate an implicit hydrogen, not present in the chemical graph.
HydrogenAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
HydrogenAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.HydrogenAtom: Deprecated.

Creates a new instance.
hydrogenCount - Variable in class org.openscience.cdk.Atom: The number of implicitly bound hydrogen atoms for this atom.
hydrogenCount - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom: The number of implicitly bound hydrogen atoms for this atom.
hydrogenCount - Variable in class org.openscience.cdk.renderer.elements.AtomSymbolElement: The hydrogen count.
hydrogenCount - Variable in class org.openscience.cdk.silent.Atom: The number of implicitly bound hydrogen atoms for this atom.
HydrogenPlacer - Class in org.openscience.cdk.layout: This is a wrapper class for some existing methods in AtomPlacer.
HydrogenPlacer() - Constructor for class org.openscience.cdk.layout.HydrogenPlacer
HYDROXY - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
HyperconjugationReaction - Class in org.openscience.cdk.reaction.type: HyperconjugationReaction is the stabilizing interaction that results from the interaction of the electrons in a s-bond (for our case only C-H) with an adjacent empty (or partially filled) p-orbital.
HyperconjugationReaction() - Constructor for class org.openscience.cdk.reaction.type.HyperconjugationReaction: Constructor of the HyperconjugationReaction object

I

I - Static variable in interface org.openscience.cdk.interfaces.IElement
I - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
IAdductFormula - Interface in org.openscience.cdk.interfaces: Class defining an adduct object in a MolecularFormula.
IAminoAcid - Interface in org.openscience.cdk.interfaces: A AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.
IAtom - Interface in org.openscience.cdk.interfaces: Represents the idea of an chemical atom.
IAtomColorer - Interface in org.openscience.cdk.renderer.color: Interface to a class for coloring atoms.
IAtomContainer - Interface in org.openscience.cdk.interfaces: Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.
IAtomContainerSet - Interface in org.openscience.cdk.interfaces: A set of AtomContainers.
IAtomicDescriptor - Interface in org.openscience.cdk.qsar: Classes that implement this interface are QSAR descriptor calculators.
IAtomPairDescriptor - Interface in org.openscience.cdk.qsar: Classes that implement this interface are QSAR descriptor calculators.
IAtomType - Interface in org.openscience.cdk.interfaces: The base class for atom types.
IAtomType.Hybridization - Enum in org.openscience.cdk.interfaces: An enum for the different hybridization states.
IAtomTypeConfigurator - Interface in org.openscience.cdk.config: Interface that allows reading atom type configuration data from some source.
IAtomTypeGuesser - Interface in org.openscience.cdk.atomtype: Classes that implement this interface are atom type guessers.
IAtomTypeMatcher - Interface in org.openscience.cdk.atomtype: Classes that implement this interface are atom type matchers.
IBasis - Interface in org.openscience.cdk.math.qm: A basis set must implement this class.
IBioPolymer - Interface in org.openscience.cdk.interfaces: A BioPolymer is a subclass of a Polymer which is supposed to store additional informations about the Polymer which are connected to BioPolymers.
IBitFingerprint - Interface in org.openscience.cdk.fingerprint: Interface for bit fingerprint representations.
IBond - Interface in org.openscience.cdk.interfaces: Implements the concept of a covalent bond between two or more atoms.
IBond.Display - Enum in org.openscience.cdk.interfaces: Bond display style, controlling how bonds appear in a 2D depiction.
IBond.Order - Enum in org.openscience.cdk.interfaces: A list of permissible bond orders.
IBond.Stereo - Enum in org.openscience.cdk.interfaces: Enumeration of possible stereo types of two-atom bonds.
IBondDescriptor - Interface in org.openscience.cdk.qsar: Classes that implement this interface are QSAR descriptor calculators.
ICanonicalMoleculeLabeller - Interface in org.openscience.cdk.smsd.labelling: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
ICanonicalReactionLabeller - Interface in org.openscience.cdk.smsd.labelling: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
ICDKChangeListener - Interface in org.openscience.cdk.event: A ChangeListener for the CDK, to be independent from the Swing package.
ICDKObject - Interface in org.openscience.cdk.interfaces: The base class for all data objects in this CDK.
ICDKSelectionChangeListener - Interface in org.openscience.cdk.event: A ChangeListener for the CDK, to be independent from the Swing package.
IChargeCalculator - Interface in org.openscience.cdk.charges: Interface for classes that calculate (partial) charges centered on atom nuclei.
IChemFile - Interface in org.openscience.cdk.interfaces: An IChemObject containing a number of ChemSequences.
IChemFormat - Interface in org.openscience.cdk.io.formats: This class is the interface that all ChemFormat's should implement.
IChemFormatMatcher - Interface in org.openscience.cdk.io.formats: This interface is used for classes that are able to match a certain chemical file format.
IChemFormatMatcher.MatchResult - Class in org.openscience.cdk.io.formats: Simple class holds whether a format matcher matched, when it matched and what the format was.
IChemModel - Interface in org.openscience.cdk.interfaces: An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.
IChemObject - Interface in org.openscience.cdk.interfaces: The base class for all chemical objects in this cdk.
IChemObjectBuilder - Interface in org.openscience.cdk.interfaces: A helper class to instantiate a ICDKObject instance for a specific implementation.
IChemObjectChangeEvent - Interface in org.openscience.cdk.interfaces: Event fired by CDK IChemObject classes to their registered listeners in case something changed within them.
IChemObjectIO - Interface in org.openscience.cdk.io: This class is the interface that all IO readers should implement.
IChemObjectIOListener - Interface in org.openscience.cdk.io.listener: Allows monitoring of progress of file reader activities.
IChemObjectListener - Interface in org.openscience.cdk.interfaces: Classes implementing this interface must implement this method such that they react appropriately to changes in the object they are interested in.
IChemObjectReader - Interface in org.openscience.cdk.io: This interface specifies the common functionality all IO readers should provide.
IChemObjectReader.Mode - Enum in org.openscience.cdk.io
IChemObjectReaderErrorHandler - Interface in org.openscience.cdk.io: Interface for classes aimed to handle IChemObjectReader errors.
IChemObjectSelection - Interface in org.openscience.cdk.renderer.selection: A selection of some atoms and bonds from an IAtomContainer or IChemModel.
IChemObjectWriter - Interface in org.openscience.cdk.io: This class is the interface that all IO writers should implement.
IChemSequence - Interface in org.openscience.cdk.interfaces: A sequence of ChemModels, which can, for example, be used to store the course of a reaction.
ICMLConvention - Interface in org.openscience.cdk.io.cml: This interface describes the procedures classes must implement to be plugable into the CMLHandler.
ICMLCustomizer - Interface in org.openscience.cdk.libio.cml: Interface for classes that allow the Convertor to be customized for certain features.
ICMLModule - Interface in org.openscience.cdk.io.cml: This interface describes the procedures classes must implement to be plugable into the CMLHandler.
ICountFingerprint - Interface in org.openscience.cdk.fingerprint: Interface for count fingerprint representations.
ICrystal - Interface in org.openscience.cdk.interfaces: Class representing a molecular crystal.
ID - Static variable in class org.openscience.cdk.templates.AminoAcids
ID_KEY - Static variable in class org.openscience.cdk.renderer.elements.MarkedElement
ID_MAP - Static variable in class org.openscience.cdk.renderer.generators.HighlightGenerator: Property key.
IDCreator - Class in org.openscience.cdk.tools: Class that provides methods to give unique IDs to ChemObjects.
IDCreator() - Constructor for class org.openscience.cdk.tools.IDCreator
IDeduceBondOrderTool - Interface in org.openscience.cdk.tools: A common interface for tools that deduce bond orders from connectivity and optionally additional information, like number of implicit or explicit hydrogens, or hybridization states.
IDENTIFIER - Static variable in class org.openscience.cdk.libio.jena.CDK
identifyMatchedParts(List<List<CDKRMap>>, IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler: Deprecated.
identifySingleAtomsMatchedParts(List<CDKRMap>, IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler: Deprecated.
identity(int) - Static method in class org.openscience.cdk.graph.invariant.GIMatrix: Returns the identity matrix.
IDescriptor - Interface in org.openscience.cdk.qsar: Classes that implement this interface are QSAR descriptor calculators.
IDescriptorResult - Interface in org.openscience.cdk.qsar.result: Object that provides access to the calculated descriptor value.
IDifference - Interface in org.openscience.cdk.tools.diff.tree: Object that describes the difference between two Objects.
IDifferenceList - Interface in org.openscience.cdk.tools.diff.tree: IDifference between two Objects which contains one or more child IDifference objects.
IDoubleBondStereochemistry - Interface in org.openscience.cdk.interfaces: Stereochemistry specification for double bond stereochemistry.
IDoubleBondStereochemistry.Conformation - Enum in org.openscience.cdk.interfaces: Enumeration that defines the two possible values for this stereochemistry type.
idPermutation(int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Builds id permutation.
IDrawVisitor - Interface in org.openscience.cdk.renderer.visitor: An IDrawVisitor is an IRenderingVisitor that can be customized and knows about fonts and other rendering parameters.
idValues(int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Values for an id permutation for a given localSize
IEdge - Interface in org.openscience.cdk.smsd.algorithm.vflib.interfaces: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
IElectronContainer - Interface in org.openscience.cdk.interfaces: Base class for entities containing electrons, like bonds, orbitals, lone-pairs.
IElectronicPropertyCalculator - Interface in org.openscience.cdk.charges: Interface for classes that calculate (partial) charges centered on atom nuclei.
IElement - Interface in org.openscience.cdk.interfaces: Implements the idea of an element in the periodic table.
IEventChemObjectReader - Interface in org.openscience.cdk.io.iterator.event: Interface for an iterating molecule reader.
IFinalMapping - Interface in org.openscience.cdk.smsd.interfaces: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
IFingerprinter - Interface in org.openscience.cdk.fingerprint: Interface for fingerprint calculators.
IFontManager - Interface in org.openscience.cdk.renderer.font: An interface for managing the drawing of fonts at different zoom levels.
IFontManager.FontStyle - Enum in org.openscience.cdk.renderer.font: Style of the font to use to draw text.
IFragmentAtom - Interface in org.openscience.cdk.interfaces: Class to represent an IPseudoAtom which embeds an IAtomContainer.
IFragmenter - Interface in org.openscience.cdk.fragment: An interface for classes implementing fragmentation algorithms.
IFunction - Interface in org.openscience.cdk.math: A class, which has a function value should implement this interface.
IGenerator<T extends IChemObject> - Interface in org.openscience.cdk.renderer.generators: An IGenerator converts chemical entities into parts of the chemical drawing expressed as IRenderingElements.
IGeneratorParameter<T> - Interface in org.openscience.cdk.renderer.generators: Parameter from some rendering of the 2D diagram.
ignoringAtomTypes() - Method in class org.openscience.cdk.group.PartitionRefinement.AtomRefinerBuilder
ignoringBondOrders() - Method in class org.openscience.cdk.group.PartitionRefinement.AtomRefinerBuilder
ignoringBondOrders() - Method in class org.openscience.cdk.group.PartitionRefinement.BondRefinerBuilder
IGraphMatrix - Interface in org.openscience.cdk.graph.matrix: Interface describing a molecular graph matrix calculator.
IImplementationSpecification - Interface in org.openscience.cdk: Interface that is used to describe the specification of a certain implementation of an algorithm.
IIsotope - Interface in org.openscience.cdk.interfaces: Used to store and retrieve data of a particular isotope.
IIteratingChemObjectReader<T extends IChemObject> - Interface in org.openscience.cdk.io.iterator: Interface for an iterating molecule reader.
ILigand - Interface in org.openscience.cdk.geometry.cip: Concept of a ligand in CIP terms, reflecting a side chain of a central atom that can have precedence over another.
ILoggingTool - Interface in org.openscience.cdk.tools: Useful for logging messages.
ILonePair - Interface in org.openscience.cdk.interfaces: A LonePair is an orbital primarily located with one Atom, containing two electrons.
imag - Variable in class org.openscience.cdk.math.Complex: The imaginary part of this value
image - Variable in class org.openscience.cdk.iupac.parser.Token: The string image of the token.
image - Variable in class org.openscience.cdk.smiles.smarts.parser.Token: The string image of the token.
imagmatrix - Variable in class org.openscience.cdk.math.IMatrix: the imaginary part of the content
imagvector - Variable in class org.openscience.cdk.math.IVector: The imaginary part of this vector
IMapper - Interface in org.openscience.cdk.smsd.algorithm.vflib.interfaces: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
IMapping - Interface in org.openscience.cdk.interfaces: Represents a mapping of two atoms.
IMatrix - Class in org.openscience.cdk.math: This class contains a complex matrix.
IMatrix(int, int) - Constructor for class org.openscience.cdk.math.IMatrix: Creates a complex matrix
IMatrix(Matrix) - Constructor for class org.openscience.cdk.math.IMatrix: Creates a complex copy of a matrix
IMCSBase - Interface in org.openscience.cdk.smsd.interfaces: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
IMolecularDescriptor - Interface in org.openscience.cdk.qsar: Classes that implement this interface are QSAR descriptor calculators for IAtomContainer objects.
IMolecularFormula - Interface in org.openscience.cdk.interfaces: Class defining a molecular formula object.
IMolecularFormulaSet - Interface in org.openscience.cdk.interfaces: Class defining a molecular formula object.
IMonomer - Interface in org.openscience.cdk.interfaces: A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.
IMouseEventRelay - Interface in org.openscience.cdk.controller: Widget toolkit-independent interface to relay for mouse events.
IMPL_H_COUNT - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if the hydrogen count (IAtom.getImplicitHydrogenCount()) of an atom equals the specified 'value'.
implementorsOf(Class<T>) - Method in class org.openscience.cdk.DynamicFactory: Access the registered implementations for a given interface.
ImplicitHCount() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
ImplicitHCountAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
ImplicitHCountAtom(int, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.ImplicitHCountAtom: Deprecated.

Creates a new instance
ImplicitHighAndBond() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
ImplicitHighAndExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
ImplicitHydrogenLigand - Class in org.openscience.cdk.geometry.cip: Subclass of Ligand to which no further recursion must be applied.
ImplicitHydrogenLigand(IAtomContainer, VisitedAtoms, IAtom) - Constructor for class org.openscience.cdk.geometry.cip.ImplicitHydrogenLigand
In - Static variable in interface org.openscience.cdk.interfaces.IElement
IN - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
inBuf - Variable in class org.openscience.cdk.iupac.parser.SimpleCharStream
inBuf - Variable in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
inchi - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
INCHI - Static variable in class org.openscience.cdk.CDKConstants: The IUPAC International Chemical Identifier.
INCHI_OPTION - Enum in net.sf.jniinchi: This class provides backwards compatibility of JNA-INCHI with JNI-INCHI, this enum was exposed in the CDK API.
INCHI_RET - Enum in net.sf.jniinchi: This class provides backwards compatibility of JNA-INCHI with JNI-INCHI, this enum was exposed in the CDK API.
INChIContentProcessorTool - Class in org.openscience.cdk.io.inchi: Deprecated.
INChIContentProcessorTool() - Constructor for class org.openscience.cdk.io.inchi.INChIContentProcessorTool: Deprecated.
INChIFormat - Class in org.openscience.cdk.io.formats: See here.
INChIFormat() - Constructor for class org.openscience.cdk.io.formats.INChIFormat
InChIGenerator - Class in org.openscience.cdk.inchi: This class generates the IUPAC International Chemical Identifier (InChI) for a CDK IAtomContainer.
InChIGenerator(IAtomContainer, boolean) - Constructor for class org.openscience.cdk.inchi.InChIGenerator: Constructor.
InChIGenerator(IAtomContainer, InchiOptions, boolean) - Constructor for class org.openscience.cdk.inchi.InChIGenerator
InChIGenerator(IAtomContainer, String, boolean) - Constructor for class org.openscience.cdk.inchi.InChIGenerator: Constructor.
InChIGenerator(IAtomContainer, List<INCHI_OPTION>, boolean) - Constructor for class org.openscience.cdk.inchi.InChIGenerator: Deprecated.
InChIGeneratorFactory - Class in org.openscience.cdk.inchi: Factory providing access to InChIGenerator and InChIToStructure.
INChIHandler - Class in org.openscience.cdk.io.inchi: Deprecated.
INChIHandler() - Constructor for class org.openscience.cdk.io.inchi.INChIHandler: Deprecated.

Constructor for the IChIHandler.
InChILabelling - Static variable in class org.openscience.cdk.smiles.SmiFlavor: Output SMILES in a canonical order using the InChI labelling algorithm.
InChINumbersTools - Class in org.openscience.cdk.graph.invariant: Tool for calculating atom numbers using the InChI algorithm.
InChINumbersTools() - Constructor for class org.openscience.cdk.graph.invariant.InChINumbersTools
INChIPlainTextFormat - Class in org.openscience.cdk.io.formats
INChIPlainTextFormat() - Constructor for class org.openscience.cdk.io.formats.INChIPlainTextFormat
INChIPlainTextReader - Class in org.openscience.cdk.io: Reads the content of a IUPAC/NIST Chemical Identifier (INChI) plain text document.
INChIPlainTextReader() - Constructor for class org.openscience.cdk.io.INChIPlainTextReader
INChIPlainTextReader(InputStream) - Constructor for class org.openscience.cdk.io.INChIPlainTextReader
INChIPlainTextReader(Reader) - Constructor for class org.openscience.cdk.io.INChIPlainTextReader: Construct a INChI reader from a Reader object.
INChIReader - Class in org.openscience.cdk.io: Reads the content of a IUPAC/NIST Chemical Identifier (INChI) document.
INChIReader() - Constructor for class org.openscience.cdk.io.INChIReader
INChIReader(InputStream) - Constructor for class org.openscience.cdk.io.INChIReader: Construct a INChI reader from a InputStream object.
InChITautomerGenerator - Class in org.openscience.cdk.tautomers: Creates tautomers for a given input molecule, based on the mobile H atoms listed in the InChI.
InChITautomerGenerator() - Constructor for class org.openscience.cdk.tautomers.InChITautomerGenerator: Create a tautomer generator, keto-enol (-KET) and 1,5-shifts (-15T) are disabled.
InChITautomerGenerator(int) - Constructor for class org.openscience.cdk.tautomers.InChITautomerGenerator: Create a tautomer generator specifygin whether to enable, keto-enol (-KET) and 1,5-shifts (-15T).
InChIToStructure - Class in org.openscience.cdk.inchi: This class generates a CDK IAtomContainer from an InChI string.
InChIToStructure(String, IChemObjectBuilder) - Constructor for class org.openscience.cdk.inchi.InChIToStructure: Constructor.
InChIToStructure(String, IChemObjectBuilder, InchiOptions) - Constructor for class org.openscience.cdk.inchi.InChIToStructure: Constructor.
InChIToStructure(String, IChemObjectBuilder, String) - Constructor for class org.openscience.cdk.inchi.InChIToStructure: Constructor.
InChIToStructure(String, IChemObjectBuilder, List<String>) - Constructor for class org.openscience.cdk.inchi.InChIToStructure: Constructor.
IncorrectUseOfCDKCoreClassError - Error in org.openscience.cdk.exception: Error that is thrown by debug implementations of the core CDK classes.
IncorrectUseOfCDKCoreClassError(String) - Constructor for error org.openscience.cdk.exception.IncorrectUseOfCDKCoreClassError
increaseBondOrder(IBond) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator: Increment the bond order of this bond.
increaseBondOrder(IBond.Order) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator: Returns the IBond.Order one higher.
increaseFontSize() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager: Move the font size pointer up.
index - Variable in class org.openscience.cdk.io.random.RandomAccessReader
indexCreated - Variable in class org.openscience.cdk.io.random.RandomAccessReader
indexOf(Object) - Method in class org.openscience.cdk.ConformerContainer: Returns the lowest index at which the specific IAtomContainer appears in the list or -1 if is not found.
indexOf(IAtom) - Method in class org.openscience.cdk.AtomContainer: Access the storage index of an atom.
indexOf(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Access the storage index of an atom.
indexOf(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Access the storage index of an atom.
indexOf(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
indexOf(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer: Access the storage index of an atom.
indexOf(IBond) - Method in class org.openscience.cdk.AtomContainer: Access the storage index of a bond.
indexOf(IBond) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Access the storage index of a bond.
indexOf(IBond) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Access the storage index of a bond.
indexOf(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
indexOf(IBond) - Method in class org.openscience.cdk.silent.AtomContainer: Access the storage index of a bond.
indexOf(ILonePair) - Method in class org.openscience.cdk.AtomContainer: Access the storage index of a long pair.
indexOf(ILonePair) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Access the storage index of a long pair.
indexOf(ILonePair) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Access the storage index of a long pair.
indexOf(ILonePair) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
indexOf(ILonePair) - Method in class org.openscience.cdk.silent.AtomContainer: Access the storage index of a long pair.
indexOf(ISingleElectron) - Method in class org.openscience.cdk.AtomContainer: Access the storage index of a single electron (radical).
indexOf(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Access the storage index of a single electron (radical).
indexOf(ISingleElectron) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Access the storage index of a single electron (radical).
indexOf(ISingleElectron) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
indexOf(ISingleElectron) - Method in class org.openscience.cdk.silent.AtomContainer: Access the storage index of a single electron (radical).
IndexOutOfBoundsException - Exception in org.openscience.cdk.graph.invariant.exception
IndexOutOfBoundsException() - Constructor for exception org.openscience.cdk.graph.invariant.exception.IndexOutOfBoundsException
indexVersion - Variable in class org.openscience.cdk.io.random.RandomAccessReader
indexYZ(int[], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Based on the molecules automorphisms, testing an adjacency matrix is canonical or not.
INDIFF - org.openscience.cdk.renderer.elements.WedgeLineElement.TYPE
Indium - org.openscience.cdk.config.Elements
INDIUM - Static variable in enum org.openscience.cdk.config.Elements
INDIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
InductiveAtomicHardnessDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic: Inductive atomic hardness of an atom in a polyatomic system can be defined as the "resistance" to a change of the atomic charge.
InductiveAtomicHardnessDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor: Constructor for the InductiveAtomicHardnessDescriptor object
InductiveAtomicSoftnessDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic: Inductive atomic softness of an atom in a polyatomic system can be defined as charge delocalizing ability.
InductiveAtomicSoftnessDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor: Constructor for the InductiveAtomicSoftnessDescriptor object
InductivePartialCharges - Class in org.openscience.cdk.charges: The calculation of the inductive partial atomic charges and equalization of effective electronegativities is based on [Cherkasov, A.. J. Chem. Inf. Comput. Sci.. 2003. 43].
InductivePartialCharges() - Constructor for class org.openscience.cdk.charges.InductivePartialCharges: Constructor for the InductivePartialCharges object.
info(Object) - Method in interface org.openscience.cdk.tools.ILoggingTool: Shows INFO output for the Object.
info(Object) - Method in class org.openscience.cdk.tools.SystemOutLoggingTool: Deprecated.

Shows INFO output for the Object.
info(Object, Object...) - Method in interface org.openscience.cdk.tools.ILoggingTool: Shows INFO output for the given Object's.
info(Object, Object...) - Method in class org.openscience.cdk.tools.SystemOutLoggingTool: Deprecated.

Shows INFO output for the given Object's.
INFO - Static variable in interface org.openscience.cdk.tools.ILoggingTool: Info, Warn, Error, and Fatal messages will be emitted.
inHash - Variable in class org.openscience.cdk.fingerprint.model.Bayesian
inherit(ICMLModule) - Method in class org.openscience.cdk.io.cml.CMLCoreModule
inherit(ICMLModule) - Method in interface org.openscience.cdk.io.cml.ICMLModule
init(String, String, boolean, boolean) - Method in class org.openscience.cdk.smsd.Isomorphism: Deprecated.

Initialize the query and targetAtomCount mol via mol files
init(IAtomContainer, IAtomContainer, boolean, boolean) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS: Deprecated.

initialize query and target molecules.
init(IAtomContainer, IAtomContainer, boolean, boolean) - Method in class org.openscience.cdk.smsd.Isomorphism: Deprecated.

initialize query and target molecules.
init(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS: Deprecated.

initialize query and target molecules.
init(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.Isomorphism: Deprecated.
initAC(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Building an atom container from a string of atom-implicit hydrogen information.
initAC(IAtomContainer, String[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Building an atom container from a string of atom-implicit hydrogen information.
initialDegrees() - Method in class org.openscience.cdk.structgen.maygen.Maygen: Initial degree arrays are set based on the molecular formula.
initialise(IChemObjectBuilder) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor
initialise(IChemObjectBuilder) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor
initialise(IChemObjectBuilder) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor
initialise(IChemObjectBuilder) - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor
initialise(IChemObjectBuilder) - Method in class org.openscience.cdk.qsar.descriptors.molecular.SpiroAtomCountDescriptor
initialise(IChemObjectBuilder) - Method in class org.openscience.cdk.qsar.descriptors.substance.OxygenAtomCountDescriptor: Initialise the descriptor with the specified chem object builder.
initialise(IChemObjectBuilder) - Method in interface org.openscience.cdk.qsar.IDescriptor: Initialise the descriptor with the specified chem object builder.
initialize(Map<String, List>) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94ParametersCall: Initialize the AtomOrder class.
initializeGrid(double) - Method in class org.openscience.cdk.tools.GridGenerator: Method initialise the given grid points with a value.
initializeGrid(double[][][], double) - Method in class org.openscience.cdk.tools.GridGenerator: Method initialise the given grid points with a value.
initializeSpecifications(List<IDescriptor>) - Method in class org.openscience.cdk.qsar.DescriptorEngine
initialKList(int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Initializing the first connectivity partition.
initialPartition(int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Initial atom partition of the input molecular formula
initiate(IAtomContainerSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in interface org.openscience.cdk.reaction.IReactionMechanism: Initiates the process for the given mechanism.
initiate(IAtomContainerSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.AdductionLPMechanism: Initiates the process for the given mechanism.
initiate(IAtomContainerSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.AdductionPBMechanism: Initiates the process for the given mechanism.
initiate(IAtomContainerSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.HeterolyticCleavageMechanism: Initiates the process for the given mechanism.
initiate(IAtomContainerSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.HomolyticCleavageMechanism: Initiates the process for the given mechanism.
initiate(IAtomContainerSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.RadicalSiteIonizationMechanism: Initiates the process for the given mechanism.
initiate(IAtomContainerSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.RadicalSiteRearrangementMechanism: Initiates the process for the given mechanism.
initiate(IAtomContainerSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.RearrangementChargeMechanism: Initiates the process for the given mechanism.
initiate(IAtomContainerSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.RemovingSEofBMechanism: Initiates the process for the given mechanism.
initiate(IAtomContainerSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.RemovingSEofNBMechanism: Initiates the process for the given mechanism.
initiate(IAtomContainerSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.SharingElectronMechanism: Initiates the process for the given mechanism.
initiate(IAtomContainerSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.TautomerizationMechanism: Initiates the process for the given mechanism.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in interface org.openscience.cdk.reaction.IReactionProcess: Initiates the process for the given Reaction.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.AdductionProtonLPReaction: Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.AdductionProtonPBReaction: Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.AdductionSodiumLPReaction: Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.CarbonylEliminationReaction: Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.ElectronImpactNBEReaction: Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.ElectronImpactPDBReaction: Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.ElectronImpactSDBReaction: Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.HeterolyticCleavagePBReaction: Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.HeterolyticCleavageSBReaction: Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.HomolyticCleavageReaction: Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.HyperconjugationReaction: Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.PiBondingMovementReaction: Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.RadicalChargeSiteInitiationHReaction: Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.RadicalChargeSiteInitiationReaction: Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrAlphaReaction: Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrBetaReaction: Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrDeltaReaction: Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrGammaReaction: Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteInitiationHReaction: Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteInitiationReaction: Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrAlphaReaction: Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrBetaReaction: Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrDeltaReaction: Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrGammaReaction: Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.RearrangementAnionReaction: Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.RearrangementCationReaction: Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.RearrangementLonePairReaction: Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.RearrangementRadicalReaction: Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.SharingAnionReaction: Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.SharingChargeDBReaction: Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.SharingChargeSBReaction: Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.SharingLonePairReaction: Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.TautomerizationReaction: Initiate process.
initilize(Map) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D: Initialize the atomPlacer class.
initSingleAC() - Method in class org.openscience.cdk.structgen.maygen.Maygen: Setting the initial atom container of a molecular formula with a single heavy atom
inLower() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager: Test to see if the lower virtual pointer is in use.
INode - Interface in org.openscience.cdk.smsd.algorithm.vflib.interfaces: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
inOrder() - Method in class org.openscience.cdk.group.Partition: Check whether the cells are ordered such that for cells i and j, first(j) > first(i) and last(j) > last(i).
input - Variable in class org.openscience.cdk.inchi.InChIGenerator
input_stream - Variable in class org.openscience.cdk.iupac.parser.NomParserTokenManager
input_stream - Variable in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager
inputBuffer - Variable in class org.openscience.cdk.io.VASPReader
inputStream - Variable in class org.openscience.cdk.iupac.parser.SimpleCharStream
inputStream - Variable in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
inRange() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager: Check that the font pointer is in the range (0, numberOfFonts - 1).
inSameAromaticRing(IAtomContainer, IAtom, IAtom, IRingSet) - Static method in class org.openscience.cdk.atomtype.EStateAtomTypeMatcher
inSameCell(int, int) - Method in class org.openscience.cdk.group.Partition: Check that two elements are in the same cell of the partition.
INSATURATION - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if the number of double bonds equals the specified value.
insertCell(int, SortedSet<Integer>) - Method in class org.openscience.cdk.group.Partition: Insert a cell into the partition at the specified index.
instantiateDescriptors(List<String>) - Method in class org.openscience.cdk.qsar.DescriptorEngine
intAC(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Setting the initial atom container of a molecular formula
IntArrayCountFingerprint - Class in org.openscience.cdk.fingerprint
IntArrayCountFingerprint() - Constructor for class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
IntArrayCountFingerprint(Map<String, Integer>) - Constructor for class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
IntArrayCountFingerprint(Map<String, Integer>, boolean) - Constructor for class org.openscience.cdk.fingerprint.IntArrayCountFingerprint: Create an IntArrayCountFingerprint from a rawFingerprint and if behaveAsBitFingerprint make it only return 0 or 1 as count thus behaving like a bit finger print.
IntArrayFingerprint - Class in org.openscience.cdk.fingerprint
IntArrayFingerprint() - Constructor for class org.openscience.cdk.fingerprint.IntArrayFingerprint
IntArrayFingerprint(int[]) - Constructor for class org.openscience.cdk.fingerprint.IntArrayFingerprint
IntArrayFingerprint(Map<String, Integer>) - Constructor for class org.openscience.cdk.fingerprint.IntArrayFingerprint
IntArrayFingerprint(IBitFingerprint) - Constructor for class org.openscience.cdk.fingerprint.IntArrayFingerprint
IntegerArrayResult - Class in org.openscience.cdk.qsar.result
IntegerArrayResult() - Constructor for class org.openscience.cdk.qsar.result.IntegerArrayResult
IntegerArrayResult(int) - Constructor for class org.openscience.cdk.qsar.result.IntegerArrayResult
IntegerArrayResultType - Class in org.openscience.cdk.qsar.result: IDescriptorResult type for integers.
IntegerArrayResultType(int) - Constructor for class org.openscience.cdk.qsar.result.IntegerArrayResultType
IntegerDifference - Class in org.openscience.cdk.tools.diff.tree: IDifference between two Integer.
IntegerIOSetting - Class in org.openscience.cdk.io.setting: An class for a reader setting which must be of type String.
IntegerIOSetting(String, IOSetting.Importance, String, String) - Constructor for class org.openscience.cdk.io.setting.IntegerIOSetting
IntegerResult - Class in org.openscience.cdk.qsar.result: Object that provides access to the calculated descriptor value.
IntegerResult(int) - Constructor for class org.openscience.cdk.qsar.result.IntegerResult
IntegerResultType - Class in org.openscience.cdk.qsar.result: IDescriptorResult type for integer.
IntegerResultType() - Constructor for class org.openscience.cdk.qsar.result.IntegerResultType
interpretProjections(Projection...) - Method in class org.openscience.cdk.stereo.StereoElementFactory: Indicate that stereochemistry drawn as a certain projection should be interpreted.
intf() - Method in class org.openscience.cdk.DynamicFactory.ConstructorKey: Access the interface this key indexes.
Intractable - Exception in org.openscience.cdk.exception: Indicates a computation did not complete within some predefined bound.
Intractable(String) - Constructor for exception org.openscience.cdk.exception.Intractable: Create a new exception with the specified message.
intValue() - Method in class org.openscience.cdk.qsar.result.IntegerResult
inUpper() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager: Test to see if the upper virtual pointer is in use.
INVALID_LEXICAL_STATE - Static variable in error org.openscience.cdk.iupac.parser.TokenMgrError: Tried to change to an invalid lexical state.
INVALID_LEXICAL_STATE - Static variable in error org.openscience.cdk.smiles.smarts.parser.TokenMgrError: Tried to change to an invalid lexical state.
InvalidSmilesException - Exception in org.openscience.cdk.exception: Exception thrown when an error is occurred during SMILES parsing.
InvalidSmilesException(String) - Constructor for exception org.openscience.cdk.exception.InvalidSmilesException: Constructs a new exception with a custom message.
InvalidSmilesException(String, Exception) - Constructor for exception org.openscience.cdk.exception.InvalidSmilesException: Constructs a new exception with a custom message and a stacktrace.
INVARIANCE_PAIR - Static variable in class org.openscience.cdk.smiles.InvPair: The description used to set the invariance numbers in the atom's property
Invariant - Interface in org.openscience.cdk.group: Marker interface for invariants.
inverse() - Method in class org.openscience.cdk.graph.invariant.GIMatrix: Returns the transpose of this matrix.
InverseSymbolSetQueryAtom - Class in org.openscience.cdk.isomorphism.matchers: Deprecated.
InverseSymbolSetQueryAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom: Deprecated.

Constructor for the InverseSymbolSetQueryAtom object
invert() - Method in class org.openscience.cdk.group.Permutation: Invert the permutation, so that for all i : inv[p[i]] = i.
invert() - Method in enum org.openscience.cdk.interfaces.IDoubleBondStereochemistry.Conformation: Invert this conformation, inv(together) = opposite, inv(opposite) = together.
invert() - Method in enum org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo: Invert this conformation, inv(clockwise) = anti_clockwise, inv(anti_clockwise) = clockwise.
invertLine(int, int) - Method in class org.openscience.cdk.graph.invariant.GIMatrix: Returns the resulting matrix of an elementary linear operation that consists of inverting two lines.
invisibleCarbon(IAtom, IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator: Checks an atom to see if it is an 'invisible carbon' - that is, it is: a) a carbon atom and b) this carbon should not be shown.
invisibleHydrogen(IAtom, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator: Checks an atom to see if it is an 'invisible hydrogen' - that is, it is a) an (explicit) hydrogen, and b) explicit hydrogens are set to off.
InvPair - Class in org.openscience.cdk.smiles: This is used to hold the invariance numbers for the canonical labeling of IAtomContainers.
InvPair() - Constructor for class org.openscience.cdk.smiles.InvPair
InvPair(long, IAtom) - Constructor for class org.openscience.cdk.smiles.InvPair
invRange - Variable in class org.openscience.cdk.fingerprint.model.Bayesian
Iodine - org.openscience.cdk.config.Elements
IODINE - Static variable in enum org.openscience.cdk.config.Elements
IODO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
IonizationPotentialTool - Class in org.openscience.cdk.tools: Deprecated.
Results depend on the order of atoms in bonds, resolving this would require retraining the models which are not available.
IonizationPotentialTool() - Constructor for class org.openscience.cdk.tools.IonizationPotentialTool: Deprecated.
IOSetting - Class in org.openscience.cdk.io.setting: An interface for reader settings.
IOSetting(String, IOSetting.Importance, String, String) - Constructor for class org.openscience.cdk.io.setting.IOSetting: The default constructor that sets this field.
IOSetting.Importance - Enum in org.openscience.cdk.io.setting
IParameterReact - Interface in org.openscience.cdk.reaction.type.parameters: Interface for classes that generate parameters used in reactions.
IPAtomicHOSEDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic: This class returns the ionization potential of an atom containing lone pair electrons.
IPAtomicHOSEDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor: Constructor for the IPAtomicHOSEDescriptor object.
IPAtomicLearningDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic: Deprecated.
IPAtomicLearningDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor: Deprecated.

Constructor for the IPAtomicLearningDescriptor object.
IPBondLearningDescriptor - Class in org.openscience.cdk.qsar.descriptors.bond: Deprecated.
IPBondLearningDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor: Deprecated.

Constructor for the IPBondLearningDescriptor object
IPDBAtom - Interface in org.openscience.cdk.interfaces: A PDBAtom is a subclass of a Atom which is supposed to store additional informations about the Atom.
IPDBMonomer - Interface in org.openscience.cdk.interfaces: Represents the idea of an protein monomer as found in PDB files.
IPDBPolymer - Interface in org.openscience.cdk.interfaces: A PDBPolymer is a subclass of a BioPolymer which is supposed to store additional informations about the BioPolymer which are connected to BioPolymers.
IPDBStructure - Interface in org.openscience.cdk.interfaces: Represents the idea of an chemical structure.
IPMolecularLearningDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Deprecated.
IPMolecularLearningDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor: Deprecated.

Constructor for the IPMolecularLearningDescriptor object
IPolymer - Interface in org.openscience.cdk.interfaces: Subclass of Molecule to store Polymer specific attributes that a Polymer has.
IPseudoAtom - Interface in org.openscience.cdk.interfaces: Represents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc.
IQuery - Interface in org.openscience.cdk.smsd.algorithm.vflib.interfaces: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
IQueryAtom - Interface in org.openscience.cdk.isomorphism.matchers: Defines the ability to be matched against IAtom's.
IQueryAtomContainer - Interface in org.openscience.cdk.isomorphism.matchers: General concept of a IAtomContainer aimed at doing molecular subgraph queries using the UniversalIsomorphismTester.
IQueryBond - Interface in org.openscience.cdk.isomorphism.matchers: Defines the abililty to be matched against IBond's.
IQueryCompiler - Interface in org.openscience.cdk.smsd.algorithm.vflib.interfaces: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
Ir - Static variable in interface org.openscience.cdk.interfaces.IElement
IR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
IRandomAccessChemObjectReader<T> - Interface in org.openscience.cdk.io.random: Extension of ListIterator.
IRDFWeightFunction - Interface in org.openscience.cdk.geometry: Weight function used in the RDFCalculator.
IReaction - Interface in org.openscience.cdk.interfaces: Represents the idea of a chemical reaction.
IReaction.Direction - Enum in org.openscience.cdk.interfaces: Permissible reaction directions.
IReactionMechanism - Interface in org.openscience.cdk.reaction: Classes that implement this interface are reaction mechanisms.
IReactionProcess - Interface in org.openscience.cdk.reaction: Classes that implement this interface are Reactions types.
IReactionScheme - Interface in org.openscience.cdk.interfaces: Classes that implement this interface of a scheme.
IReactionSet - Interface in org.openscience.cdk.interfaces: A set of reactions, for example those taking part in a reaction.
IReaderListener - Interface in org.openscience.cdk.io.listener: Allows monitoring of progress of file reader activities.
IRenderer<T extends IChemObject> - Interface in org.openscience.cdk.renderer: Interface that all 2D renderers implement.
IRenderingElement - Interface in org.openscience.cdk.renderer.elements: Widget toolkit-independent, abstract definition of something to be drawn.
IRenderingVisitor - Interface in org.openscience.cdk.renderer.elements: An IRenderingVisitor is responsible of converting an abstract chemical drawing into a widget set specific drawing.
IResourceFormat - Interface in org.openscience.cdk.io.formats: This class is the interface that all ResourceFormat's should implement.
IRGroup - Interface in org.openscience.cdk.isomorphism.matchers: Represents a single substitute structure in an IRGroupList.
IRGroupList - Interface in org.openscience.cdk.isomorphism.matchers: Represents a list of Rgroup substitutes to be associated with some key in an IRGroupQuery.
IRGroupQuery - Interface in org.openscience.cdk.isomorphism.matchers: Interface definition for Rgroup query classes.
Iridium - org.openscience.cdk.config.Elements
IRIDIUM - Static variable in enum org.openscience.cdk.config.Elements
IRIDIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
IRing - Interface in org.openscience.cdk.interfaces: Class representing a ring structure in a molecule.
IRingSet - Interface in org.openscience.cdk.interfaces: Maintains a set of Ring objects.
Iron - org.openscience.cdk.config.Elements
IRON - Static variable in enum org.openscience.cdk.config.Elements
IRON - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
IRule - Interface in org.openscience.cdk.formula.rules: Interface which groups all method that validate a IMolecularFormula.
IS_ALIPHATIC - org.openscience.cdk.isomorphism.matchers.Expr.Type: Return true if IAtom.isAromatic() or IBond.isAromatic() is flase.
IS_ALIPHATIC_HETERO - org.openscience.cdk.isomorphism.matchers.Expr.Type: Return true if IElement.getAtomicNumber() is neither 6 (carbon) nor 1 (hydrogen) and the atom is aliphatic.
IS_AROMATIC - org.openscience.cdk.isomorphism.matchers.Expr.Type: Return true if IAtom.isAromatic() or IBond.isAromatic() is true.
IS_HETERO - org.openscience.cdk.isomorphism.matchers.Expr.Type: Return true if IElement.getAtomicNumber() is neither 6 (carbon) nor 1 (hydrogen).
IS_HYDROGENBOND_ACCEPTOR - Static variable in class org.openscience.cdk.CDKConstants: Sets to true if the atom is an hydrogen bond acceptor.
IS_HYDROGENBOND_DONOR - Static variable in class org.openscience.cdk.CDKConstants: Sets to true if the atom is an hydrogen bond donor.
IS_IN_CHAIN - org.openscience.cdk.isomorphism.matchers.Expr.Type: Return true if IAtom.isInRing() or IBond.isInRing() is false.
IS_IN_RING - org.openscience.cdk.isomorphism.matchers.Expr.Type: Return true if IAtom.isInRing() or IBond.isInRing() is true.
IS_TYPEABLE - Static variable in class org.openscience.cdk.CDKConstants: Flag is set if an atom could be typed.
ISALIPHATIC - Static variable in class org.openscience.cdk.CDKConstants: Flag that is set if a chemobject is part of an aliphatic chain.
isAntisymmetric() - Method in class org.openscience.cdk.graph.invariant.GIMatrix: Verifies if the matrix is antisymmetric, that is if the matrix is equal to the opposite of it's transpose.
isAromatic() - Method in class org.openscience.cdk.Atom: Access whether this atom has been marked as aromatic.
isAromatic() - Method in class org.openscience.cdk.AtomRef: Access whether this atom has been marked as aromatic.
isAromatic() - Method in class org.openscience.cdk.Bond: Access whether this bond has been marked as aromatic.
isAromatic() - Method in class org.openscience.cdk.BondRef: Access whether this bond has been marked as aromatic.
isAromatic() - Method in interface org.openscience.cdk.interfaces.IAtom: Access whether this atom has been marked as aromatic.
isAromatic() - Method in interface org.openscience.cdk.interfaces.IBond: Access whether this bond has been marked as aromatic.
isAromatic() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Access whether this atom has been marked as aromatic.
isAromatic() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Access whether this bond has been marked as aromatic.
isAromatic() - Method in class org.openscience.cdk.silent.Atom: Access whether this atom has been marked as aromatic.
isAromatic() - Method in class org.openscience.cdk.silent.Bond: Access whether this bond has been marked as aromatic.
isAromatic(IRing, IAtomContainer) - Static method in class org.openscience.cdk.aromaticity.AromaticityCalculator: Deprecated.

Tests the ring in the molecule for aromaticity.
ISAROMATIC - Static variable in class org.openscience.cdk.CDKConstants: Flag is set if chemobject is part of an aromatic system.
isAssignable(DynamicFactory.ConstructorKey) - Method in class org.openscience.cdk.DynamicFactory.ConstructorKey: Checks whether this key is assignable to the candidate.
isAtomMatch(String, String, String, String) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks: Deprecated.
isAtomMatch(AtomMatcher, AtomMatcher, IAtomContainer, IBond, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultMatcher: Deprecated.
isBondMatch(BondMatcher, IAtomContainer, IBond, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultMatcher: Deprecated.
isBondMatchFlag() - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultBondMatcher: Deprecated.
isBondMatchFlag() - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultMCSPlusAtomMatcher: Deprecated.
isBondMatchFlag() - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultRGraphAtomMatcher: Deprecated.
isBondMatchFlag() - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFAtomMatcher: Deprecated.
isBondMatchFlag() - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFBondMatcher: Deprecated.
isBondMatchFlag() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler: Deprecated.
isBondMatchFlag() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler: Deprecated.
isBondMatchFlag() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler: Deprecated.
isBoundary() - Method in class org.openscience.cdk.structgen.maygen.Maygen
isCachedAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.qsar.AbstractAtomicDescriptor: Returns true if the cached IDescriptorResult's are for the given IAtomContainer.
isCachedAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.qsar.AbstractBondDescriptor: Returns true if the cached IDescriptorResult's are for the given IAtomContainer.
isCanonical(IAtomContainer) - Method in interface org.openscience.cdk.group.AtomContainerDiscretePartitionRefiner: Checks if the atom container is canonical.
isCisTrans(IAtom, IAtom, IAtom, IAtom, IAtomContainer) - Static method in class org.openscience.cdk.geometry.BondTools: Says if two atoms are in cis or trans position around a double bond.
isClockwise() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom: Deprecated.
isColinear(Point3d, Point3d, Point3d) - Static method in class org.openscience.cdk.stereo.StereoTool: Checks the three supplied points to see if they fall on the same line.
ISCONJUGATED - Static variable in class org.openscience.cdk.CDKConstants: Flag is set if chemobject is part of a conjugated system.
isConnected(int, int) - Method in class org.openscience.cdk.signature.SignatureQuotientGraph
isConnected(IAtomContainer) - Static method in class org.openscience.cdk.graph.ConnectivityChecker: Check whether a set of atoms in an IAtomContainer is connected.
isConnectedTo(IBond) - Method in class org.openscience.cdk.Bond: Checks whether a bond is connected to another one.
isConnectedTo(IBond) - Method in class org.openscience.cdk.BondRef: Checks whether a bond is connected to another one.
isConnectedTo(IBond) - Method in class org.openscience.cdk.debug.DebugBond: Checks whether a bond is connected to another one.
isConnectedTo(IBond) - Method in interface org.openscience.cdk.interfaces.IBond: Checks whether a bond is connected to another one.
isConnectedTo(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Checks whether a query bond is connected to another one.
isConnectedTo(IBond) - Method in class org.openscience.cdk.silent.Bond: Checks whether a bond is connected to another one.
isCtabStandard() - Method in enum org.openscience.cdk.sgroup.SgroupType: Indicates if this SGroup type is support by standard CTAB (Molfile/SDfile) sgroups.
isCycle() - Method in class org.openscience.cdk.smsd.ring.PathEdge: Deprecated.
isDead() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IState: Deprecated.

Returns true if no match will come from this IState.
isDead() - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFState: Deprecated.

Returns true if no match will come from this IState.
isDebugEnabled() - Method in interface org.openscience.cdk.tools.ILoggingTool: Use this method for computational demanding debug info.
isDebugEnabled() - Method in class org.openscience.cdk.tools.SystemOutLoggingTool: Deprecated.

Use this method for computational demanding debug info.
isDiagonal() - Method in class org.openscience.cdk.graph.invariant.GIMatrix: Verifies whether or not the matrix is diagonal.
isDisconnected() - Method in class org.openscience.cdk.graph.SpanningTree: Is the molecule disconnected and has more then one component.
isDiscrete() - Method in class org.openscience.cdk.group.Partition: Checks that all the cells are singletons - that is, they only have one element.
isDiscreteCell(int) - Method in class org.openscience.cdk.group.Partition: Check to see if the cell at cellIndex is discrete - that is, it only has one element.
isElement(String) - Method in class org.openscience.cdk.config.IsotopeFactory: Checks whether the given element exists.
isEmpty() - Method in class org.openscience.cdk.AtomContainer: Indicates whether this container is empty.
isEmpty() - Method in class org.openscience.cdk.AtomContainerSet: Returns true if this IAtomContainerSet is empty.
isEmpty() - Method in class org.openscience.cdk.ChemModel: Returns true if this ChemModel is empty.
isEmpty() - Method in class org.openscience.cdk.ConformerContainer: Checks whether any conformers are stored or not.
isEmpty() - Method in class org.openscience.cdk.debug.DebugAtomContainer: Indicates whether this container is empty.
isEmpty() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Returns true if this IAtomContainerSet is empty.
isEmpty() - Method in class org.openscience.cdk.debug.DebugChemModel: Returns true if this ChemModel is empty.
isEmpty() - Method in class org.openscience.cdk.debug.DebugCrystal: Indicates whether this container is empty.
isEmpty() - Method in class org.openscience.cdk.debug.DebugReactionSet: Returns true if this IReactionSet is empty.
isEmpty() - Method in class org.openscience.cdk.debug.DebugSubstance: Returns true if this IAtomContainerSet is empty.
isEmpty() - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Indicates whether this container is empty.
isEmpty() - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet: Returns true if this IAtomContainerSet is empty.
isEmpty() - Method in interface org.openscience.cdk.interfaces.IChemModel: Returns true if this ChemModel is empty.
isEmpty() - Method in interface org.openscience.cdk.interfaces.IReactionSet: Returns true if this IReactionSet is empty.
isEmpty() - Method in interface org.openscience.cdk.interfaces.IRingSet: Returns true if this IRingSet has no atoms.
isEmpty() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Indicates whether this container is empty.
isEmpty() - Method in class org.openscience.cdk.ReactionSet: Returns true if this IReactionSet is empty.
isEmpty() - Method in class org.openscience.cdk.renderer.elements.Bounds: The bounds are empty and contain no elements.
isEmpty() - Method in class org.openscience.cdk.signature.Orbit: Checks to see if the orbit is empty.
isEmpty() - Method in class org.openscience.cdk.silent.AtomContainer: Indicates whether this container is empty.
isEmpty() - Method in class org.openscience.cdk.silent.AtomContainerSet: Returns true if this IAtomContainerSet is empty.
isEmpty() - Method in class org.openscience.cdk.silent.ChemModel: Returns true if this ChemModel is empty.
isEmpty() - Method in class org.openscience.cdk.silent.ReactionSet: Returns true if this IReactionSet is empty.
isEnabled(String) - Method in class org.openscience.cdk.depict.Abbreviations: Check whether an abbreviation is enabled.
ISequenceSubRule<ILigand> - Interface in org.openscience.cdk.geometry.cip.rules: Sequence sub rule used in the CIP method to decide which of the two ligands takes precedence [Cahn, R.S. et. al.. Angew. Chem. Int. Ed.. 1966. 5].
ISetting - Interface in org.openscience.cdk.interfaces: A simple setting that can be managed by the SettingManager.
isExpanded() - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Helper method to indicate that the method should be drawn fully, and not just the abbreviated form.
isExpanded() - Method in class org.openscience.cdk.FragmentAtom
isExpanded() - Method in interface org.openscience.cdk.interfaces.IFragmentAtom: Helper method to indicate that the method should be drawn fully, and not just the abbreviated form.
isExpanded() - Method in class org.openscience.cdk.silent.FragmentAtom
isFilled() - Method in interface org.openscience.cdk.renderer.selection.IChemObjectSelection: The opposite of a method like "isEmpty".
isFinished() - Method in interface org.openscience.cdk.group.PermutationGroup.Backtracker: Check to see if the backtracker is finished.
isFurtherMappingPossible(IAtomContainer, IAtomContainer, int, int, List<Integer>, List<Integer>, List<String>, List<String>, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks: Deprecated.
isGoal() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IState: Deprecated.

Returns true if all atoms in the query molecule have been mapped.
isGoal() - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFState: Deprecated.

Returns true if all atoms in the query molecule have been mapped.
isHigherOrder(IBond.Order, IBond.Order) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator: Returns true if the first bond has a higher bond order than the second bond.
isHydrogen(IAtom) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator: Determines if the atom is a hydrogen.
isIdentity() - Method in class org.openscience.cdk.group.Permutation: Check to see if this permutation is the identity permutation.
ISimpleChemObjectReader - Interface in org.openscience.cdk.io: This class is the interface that all IO readers should implement.
isIndexCreated() - Method in class org.openscience.cdk.io.random.RandomAccessReader
ISingleElectron - Interface in org.openscience.cdk.interfaces: A Single Electron is an orbital which is occupied by only one electron.
isInRing() - Method in class org.openscience.cdk.Atom: Access whether this atom has been flagged as in a ring.
isInRing() - Method in class org.openscience.cdk.AtomRef: Access whether this atom has been flagged as in a ring.
isInRing() - Method in class org.openscience.cdk.Bond: Access whether this bond has been flagged as in a ring.
isInRing() - Method in class org.openscience.cdk.BondRef: Access whether this bond has been flagged as in a ring.
isInRing() - Method in interface org.openscience.cdk.interfaces.IAtom: Access whether this atom has been flagged as in a ring.
isInRing() - Method in interface org.openscience.cdk.interfaces.IBond: Access whether this bond has been flagged as in a ring.
isInRing() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Access whether this atom has been flagged as in a ring.
isInRing() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Access whether this bond has been flagged as in a ring.
isInRing() - Method in class org.openscience.cdk.silent.Atom: Access whether this atom has been flagged as in a ring.
isInRing() - Method in class org.openscience.cdk.silent.Bond: Access whether this bond has been flagged as in a ring.
ISINRING - Static variable in class org.openscience.cdk.CDKConstants: Flag that is set when the chemobject is part of a ring.
isInterrupted() - Method in class org.openscience.cdk.smiles.DeduceBondSystemTool: Deprecated.

Returns if the next or running calculation should be interrupted.
isInterrupted() - Method in class org.openscience.cdk.smiles.FixBondOrdersTool: Deprecated.

Returns if the next or running calculation should be interrupted.
isInvertible() - Method in class org.openscience.cdk.graph.invariant.GIMatrix: Verifies if the matrix is invertible or not by asking for its determinant.
isIsomorph(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: Tests if g1 and g2 are isomorph.
isIsomorph(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS: Deprecated.

Tests if sourceGraph and targetGraph are isomorph.
isIsomorphic(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.IsomorphismTester: Checks whether a given molecule is isomorphic with the one that has been assigned to this IsomorphismTester at construction time.
isIsomorphic(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.IsomorphismTester: Checks whether a given molecule is isomorphic with the one that has been assigned to this IsomorphismTester at construction time.
isLeft(IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.geometry.BondTools: Says if an atom is on the left side of a another atom seen from a certain atom or not.
isLowerOrder(IBond.Order, IBond.Order) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator: Returns true if the first bond has a lower bond order than the second bond.
isMappingCheckFlag() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper: Deprecated.
isMatchBond() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph: Deprecated.
isMatchBonds() - Method in class org.openscience.cdk.smsd.Isomorphism: Deprecated.
isMatchFeasible(IAtomContainer, IBond, IAtomContainer, IBond, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks: Deprecated.
isMatchFeasible(Match) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IState: Deprecated.

Returns true if the given match will work with the current map, or false otherwise.
isMatchFeasible(Match) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFState: Deprecated.

Returns true if the given match will work with the current map, or false otherwise.
isMetal(int) - Static method in enum org.openscience.cdk.config.Elements: Utility method to determine if an atomic number is a metal.
isMetal(IAtom) - Static method in enum org.openscience.cdk.config.Elements: Utility method to determine if an atom is a metal.
isMultiThread() - Method in class org.openscience.cdk.structgen.maygen.Maygen
isNewMatrix() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregor: Deprecated.

Checks if its a new Matrix.
ISNOTINRING - Static variable in class org.openscience.cdk.CDKConstants: Flag that is set when the chemobject is part of a ring.
IsoAlkanes - Class in org.openscience.cdk.templates.saturatedhydrocarbons: This class contains methods for generating simple organic alkanes.
IsoAlkanes() - Constructor for class org.openscience.cdk.templates.saturatedhydrocarbons.IsoAlkanes
isOctahedral(IAtom, IAtom, IAtom, IAtom, IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.stereo.StereoTool: Checks these 7 atoms to see if they are at the points of an octahedron.
isOK(IAtomContainer) - Method in class org.openscience.cdk.smiles.DeduceBondSystemTool: Deprecated.

Determines if, according to the algorithms implemented in this class, the given AtomContainer has properly distributed double bonds.
isolated() - Method in interface org.openscience.cdk.ringsearch.CyclicVertexSearch: Construct the sets of vertices which belong to isolated cycles.
isolated() - Method in class org.openscience.cdk.ringsearch.RingSearch: Construct the sets of vertices which belong to isolated rings.
isolatedRingFragments() - Method in class org.openscience.cdk.ringsearch.RingSearch: Construct a list of IAtomContainers each of which only contains a single isolated ring.
isomeric() - Static method in class org.openscience.cdk.smiles.SmilesGenerator: Convenience method for creating an isomeric generator.
Isomeric - Static variable in class org.openscience.cdk.smiles.SmiFlavor: Output non-canonical SMILES with stereochemistry, atomic masses.
Isomorphism - Class in org.openscience.cdk.smsd: Deprecated.
A more recent version of SMSD is available at http://github.com/asad/smsd
Isomorphism(Algorithm, boolean) - Constructor for class org.openscience.cdk.smsd.Isomorphism: Deprecated.

This is the algorithm factory and entry port for all the MCS algorithm in the Isomorphism supported algorithm Algorithm types: 0: Default, 1: MCSPlus, 2: VFLibMCS, 3: CDKMCS, 4: SubStructure
IsomorphismTester - Class in org.openscience.cdk.isomorphism: A too simplistic implementation of an isomorphism test for chemical graphs.
IsomorphismTester() - Constructor for class org.openscience.cdk.isomorphism.IsomorphismTester: Constructor for the IsomorphismTester object
IsomorphismTester(IAtomContainer) - Constructor for class org.openscience.cdk.isomorphism.IsomorphismTester: Constructor for the IsomorphismTester object
isOnSm() - Method in class org.openscience.cdk.structgen.maygen.Maygen
isotope - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
Isotope - Class in org.openscience.cdk: Used to store and retrieve data of a particular isotope.
Isotope - Class in org.openscience.cdk.silent: Used to store and retrieve data of a particular isotope.
Isotope(int, String, double, double) - Constructor for class org.openscience.cdk.Isotope: Constructor for the Isotope object.
Isotope(int, String, double, double) - Constructor for class org.openscience.cdk.silent.Isotope: Constructor for the Isotope object.
Isotope(int, String, int, double, double) - Constructor for class org.openscience.cdk.Isotope: Constructor for the Isotope object.
Isotope(int, String, int, double, double) - Constructor for class org.openscience.cdk.silent.Isotope: Constructor for the Isotope object.
Isotope(String) - Constructor for class org.openscience.cdk.Isotope: Constructor for the Isotope object.
Isotope(String) - Constructor for class org.openscience.cdk.silent.Isotope: Constructor for the Isotope object.
Isotope(String, int) - Constructor for class org.openscience.cdk.Isotope: Constructor for the Isotope object.
Isotope(String, int) - Constructor for class org.openscience.cdk.silent.Isotope: Constructor for the Isotope object.
Isotope(IElement) - Constructor for class org.openscience.cdk.Isotope: Constructs an empty by copying the symbol, atomic number, flags, and identifier from the given IElement.
Isotope(IElement) - Constructor for class org.openscience.cdk.silent.Isotope: Constructs an empty by copying the symbol, atomic number, flags, and identifier from the given IElement.
ISOTOPE - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if the mass (IIsotope.getMassNumber()) of an atom equals the specified 'value'.
ISOTOPE - Static variable in class org.openscience.cdk.libio.jena.CDK
IsotopeContainer - Class in org.openscience.cdk.formula: This class defines a isotope container.
IsotopeContainer() - Constructor for class org.openscience.cdk.formula.IsotopeContainer: Constructor of the IsotopeContainer object.
IsotopeContainer(double, double) - Constructor for class org.openscience.cdk.formula.IsotopeContainer: Constructor of the IsotopeContainer object setting a mass and intensity value.
IsotopeContainer(IsotopeContainer) - Constructor for class org.openscience.cdk.formula.IsotopeContainer
IsotopeContainer(IMolecularFormula, double) - Constructor for class org.openscience.cdk.formula.IsotopeContainer: Constructor of the IsotopeContainer object setting a IMolecularFormula object and intensity value.
IsotopeDiff - Class in org.openscience.cdk.tools.diff: Compares two IIsotope classes.
IsotopeFactory - Class in org.openscience.cdk.config: Used to store and return data of a particular isotope.
IsotopeFactory() - Constructor for class org.openscience.cdk.config.IsotopeFactory
IsotopeHandler - Class in org.openscience.cdk.config.isotopes: Reads an isotope list in CML2 format.
IsotopeHandler(IChemObjectBuilder) - Constructor for class org.openscience.cdk.config.isotopes.IsotopeHandler: Constructs an IsotopeHandler used by the IsotopeReader.
IsotopePattern - Class in org.openscience.cdk.formula: This class defines the properties of a deisotoped pattern distribution.
IsotopePattern() - Constructor for class org.openscience.cdk.formula.IsotopePattern: Constructor of the IsotopePattern object.
IsotopePatternGenerator - Class in org.openscience.cdk.formula: Generates all Combinatorial chemical isotopes given a structure.
IsotopePatternGenerator() - Constructor for class org.openscience.cdk.formula.IsotopePatternGenerator: Constructor for the IsotopeGenerator.
IsotopePatternGenerator(double) - Constructor for class org.openscience.cdk.formula.IsotopePatternGenerator: Constructor for the IsotopeGenerator.
IsotopePatternManipulator - Class in org.openscience.cdk.formula: Class to manipulate IsotopePattern objects.
IsotopePatternManipulator() - Constructor for class org.openscience.cdk.formula.IsotopePatternManipulator
IsotopePatternRule - Class in org.openscience.cdk.formula.rules: This class validate if the Isotope Pattern from a given IMolecularFormula correspond with other to compare.
IsotopePatternRule() - Constructor for class org.openscience.cdk.formula.rules.IsotopePatternRule: Constructor for the IsotopePatternRule object.
IsotopePatternSimilarity - Class in org.openscience.cdk.formula: This class gives a score hit of similarity between two different isotope abundance pattern.
IsotopePatternSimilarity() - Constructor for class org.openscience.cdk.formula.IsotopePatternSimilarity: Constructor for the IsotopePatternSimilarity object.
IsotopeReader - Class in org.openscience.cdk.config.isotopes: Reader that instantiates an XML parser and customized handler to process the isotope information in the CML2 isotope data file.
IsotopeReader(InputStream, IChemObjectBuilder) - Constructor for class org.openscience.cdk.config.isotopes.IsotopeReader: Instantiates a new reader that parses the XML from the given input.
isotopes() - Method in class org.openscience.cdk.debug.DebugAdductFormula: Returns an Iterator for looping over all isotopes in this adduct formula.
isotopes() - Method in class org.openscience.cdk.debug.DebugMolecularFormula: Returns an Iterator for looping over all isotopes in this IMolecularFormula.
isotopes() - Method in class org.openscience.cdk.formula.AdductFormula: Returns an Iterator for looping over all isotopes in this adduct formula.
isotopes() - Method in class org.openscience.cdk.formula.MolecularFormula: Returns an Iterator for looping over all isotopes in this IMolecularFormula.
isotopes() - Method in class org.openscience.cdk.formula.MolecularFormulaRange: Returns an Iterator for looping over all isotopes in this MolecularFormulaExpand.
isotopes() - Method in interface org.openscience.cdk.interfaces.IAdductFormula: Returns an Iterator for looping over all isotopes in this adduct formula.
isotopes() - Method in interface org.openscience.cdk.interfaces.IMolecularFormula: Returns an Iterable for looping over all isotopes in this IMolecularFormula.
isotopes() - Method in class org.openscience.cdk.silent.AdductFormula: Returns an Iterator for looping over all isotopes in this adduct formula.
isotopes() - Method in class org.openscience.cdk.silent.MolecularFormula: Returns an Iterator for looping over all isotopes in this IMolecularFormula.
Isotopes - Class in org.openscience.cdk.config: List of isotopes.
isotopic() - Method in class org.openscience.cdk.hash.HashGeneratorMaker: Discriminate isotopes.
ISOTROPIC_SHIELDING - Static variable in class org.openscience.cdk.CDKConstants: The Isotropic Shielding, usually calculated by a quantum chemistry program like Gaussian.
isOverSaturated(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker: Checks if the current atom has exceeded its bond order sum value.
ISPLACED - Static variable in class org.openscience.cdk.CDKConstants: Flag that is set if the chemobject is placed (somewhere).
isPolar(IAtom) - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor.JPlogPCalculator
isPrecedingPathTo(int) - Method in class org.openscience.cdk.graph.ShortestPaths: Returns whether the first shortest path from the start to a given end vertex which only passed through vertices smaller then start.
isPreservingAromaticity() - Method in class org.openscience.cdk.smiles.SmilesParser: Deprecated.
IsProtonInAromaticSystemDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic: This descriptor returns 1 if the protons is directly bonded to an aromatic system, it returns 2 if the distance between aromatic system and proton is 2 bonds, and it return 0 for other positions.
IsProtonInAromaticSystemDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor: Constructor for the IsProtonInAromaticSystemDescriptor object
IsProtonInConjugatedPiSystemDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic: This class evaluates if a proton is joined to a conjugated system.
IsProtonInConjugatedPiSystemDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInConjugatedPiSystemDescriptor: Constructor for the IsProtonInConjugatedPiSystemDescriptor object
isReady() - Method in class org.openscience.cdk.io.MDLV3000Reader
isRecordEnd(String) - Method in class org.openscience.cdk.io.random.RandomAccessReader
isRecordEnd(String) - Method in class org.openscience.cdk.io.random.RandomAccessSDFReader
isRestH() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupList: Indicates that sites labeled with this Rgroup may only be substituted with a member of the Rgroup or with hydrogen.
isRestH() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
isReversalIsSmaller(int, int, boolean) - Method in class org.openscience.cdk.structgen.maygen.Maygen
isSameRing(IRingSet, IAtom, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator: Checks if atom1 and atom2 share membership in the same ring or ring system.
isSameRMap(CDKRMap, CDKRMap) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler: Deprecated.
isSaturated(IAtomContainer) - Method in class org.openscience.cdk.tools.AtomTypeAwareSaturationChecker
isSaturated(IAtomContainer) - Method in class org.openscience.cdk.tools.CDKValencyChecker
isSaturated(IAtomContainer) - Method in interface org.openscience.cdk.tools.IValencyChecker
isSaturated(IAtomContainer) - Method in class org.openscience.cdk.tools.LonePairElectronChecker: Determines of all atoms on the AtomContainer have the right number the lone pair electrons.
isSaturated(IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker: Determines of all atoms on the AtomContainer are saturated.
isSaturated(IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker: Determines of all atoms on the AtomContainer are saturated.
isSaturated(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.AtomTypeAwareSaturationChecker
isSaturated(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.CDKValencyChecker
isSaturated(IAtom, IAtomContainer) - Method in interface org.openscience.cdk.tools.IValencyChecker
isSaturated(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.LonePairElectronChecker: Checks if an Atom is saturated their lone pair electrons by comparing it with known AtomTypes.
isSaturated(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker: Checks whether an Atom is saturated by comparing it with known AtomTypes.
isSaturated(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker: Checks whether an Atom is saturated by comparing it with known AtomTypes.
isSaturated(IBond, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker: Returns whether a bond is saturated.
isSaturated(IBond, IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker: Returns whether a bond is saturated.
isSet() - Method in class org.openscience.cdk.io.setting.BooleanIOSetting
isSetElement() - Method in class org.openscience.cdk.structgen.maygen.Maygen
isSetParameter() - Method in interface org.openscience.cdk.reaction.type.parameters.IParameterReact: Get if this parameter needs to take account.
isSetParameter() - Method in class org.openscience.cdk.reaction.type.parameters.ParameterReact: Get if this parameter needs to take account.
isSquare() - Method in class org.openscience.cdk.graph.invariant.GIMatrix: Verifies if the matrix is square, that is if it has an equal number of lines and columns.
isSquarePlanar(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.BondTools: Says if an atom as a center of a square planar chirality.
isSquarePlanar(IAtom, IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.stereo.StereoTool: Checks these four atoms for square planarity.
isStereo(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.BondTools: Says if an atom as a center of any valid stereo configuration or not.
isStereocenter(int) - Method in class org.openscience.cdk.stereo.Stereocenters: Is the atom be a stereocenter (i.e.
isStereoMisMatch() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS: Deprecated.

Returns true if mols have different stereo chemistry else false if no stereo mismatch.
isStereoMisMatch() - Method in class org.openscience.cdk.smsd.Isomorphism: Deprecated.

Returns true if mols have different stereo chemistry else false if no stereo mismatch.
isSubgraph() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS: Deprecated.

Checks if query is a subgraph of the target.
isSubgraph() - Method in class org.openscience.cdk.smsd.Isomorphism: Deprecated.

Checks if query is a subgraph of the target.
isSubgraph(boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler: Deprecated.

Initialise the Subgraph search algorithm.
isSubgraph(boolean) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler: Deprecated.
isSubgraph(boolean) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler: Deprecated.
isSubgraph(boolean) - Method in class org.openscience.cdk.smsd.interfaces.AbstractSubGraph: Deprecated.

Initialise the Subgraph search algorithm.
isSubgraph(List<CDKRMap>, List<CDKRMap>) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler: Deprecated.
isSubgraph(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: Deprecated.
Use the Pattern APIs from the cdk-isomorphism module
isSubgraph(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS: Deprecated.

Tests if targetGraph atom subgraph of sourceGraph.
isSubset(BitSet, BitSet) - Static method in class org.openscience.cdk.fingerprint.FingerprinterTool: Checks whether all the positive bits in BitSet bs2 occur in BitSet bs1.
isSymmetric() - Method in class org.openscience.cdk.graph.invariant.GIMatrix: Verifies if the matrix is symmetric, that is if the matrix is equal to it's transpose.
IState - Interface in org.openscience.cdk.smsd.algorithm.vflib.interfaces: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
IStereoElement<F extends IChemObject,C extends IChemObject> - Interface in org.openscience.cdk.interfaces: Representation of stereochemical configuration.
isTetrahedral(IAtomContainer, IAtom, boolean) - Static method in class org.openscience.cdk.geometry.BondTools: Says if an atom as a center of a tetrahedral chirality.
isTheSame(IIsotope, IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormula: Compare to IIsotope.
isTheSame(IIsotope, IIsotope) - Method in class org.openscience.cdk.silent.MolecularFormula: Compare to IIsotope.
isTimeOut() - Static method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlus: Deprecated.
isTimeOut() - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS: Deprecated.
isTimeOut() - Static method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper: Deprecated.
isTimeOut() - Static method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper: Deprecated.
isTimeOut() - Method in class org.openscience.cdk.smsd.Isomorphism: Deprecated.
isTimeoutFlag() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler: Deprecated.

Returns true if a time out occurred else false
isTimeOutFlag() - Method in class org.openscience.cdk.smsd.global.TimeOut: Deprecated.

Return true if its a timeout else return false.
IStrand - Interface in org.openscience.cdk.interfaces: A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms.
isTriangularInferior() - Method in class org.openscience.cdk.graph.invariant.GIMatrix: Verifies if the matrix is triangular inferior or not.
isTriangularSuperior() - Method in class org.openscience.cdk.graph.invariant.GIMatrix: Verifies if the matrix is triangular superior or not.
isTrigonalBipyramidal(IAtom, IAtom, IAtom, IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.stereo.StereoTool: Checks these 6 atoms to see if they form a trigonal-bipyramidal shape.
isTrigonalBipyramidalOrOctahedral(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.BondTools: Says if an atom as a center of a trigonal-bipyramidal or actahedral chirality.
IStructureGenerationListener - Interface in org.openscience.cdk.structgen
isTsvoutput() - Method in class org.openscience.cdk.structgen.maygen.Maygen
ISubstance - Interface in org.openscience.cdk.interfaces: A chemical substance that consists of one or more chemical structures.
ISubstanceDescriptor - Interface in org.openscience.cdk.qsar.descriptors.substance: Classes that implement this interface are QSAR substance calculators.
isUniform() - Method in class org.openscience.cdk.DynamicFactory.ConstructorKey: Indicates whether this key has multiple parameters and they are of uniform type.
isUnsaturated(IBond, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker: Returns whether a bond is unsaturated.
isUnsaturated(IBond, IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker: Returns whether a bond is unsaturated.
isUnspecified() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom: Deprecated.
isValid(String) - Static method in class org.openscience.cdk.index.CASNumber: Checks whether the registry number is valid.
isValid(IMolecularFormula) - Method in class org.openscience.cdk.formula.MolecularFormulaChecker: Validate if a IMolecularFormula is valid.
isValidDoubleBondConfiguration(IAtomContainer, IBond) - Static method in class org.openscience.cdk.geometry.BondTools: Tells if a certain bond is center of a valid double bond configuration.
isValidOccurrenceSyntax(String) - Static method in class org.openscience.cdk.isomorphism.matchers.RGroupList: Validates the occurrence value.
isValidRgroupQueryLabel(String) - Static method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery: Validates a Pseudo atom's label to be valid RGroup query label (R1..R32).
isValidSum(IMolecularFormula) - Method in class org.openscience.cdk.formula.MolecularFormulaChecker: Validate if a IMolecularFormula is valid.
isVisited(IAtom) - Method in interface org.openscience.cdk.geometry.cip.ILigand: Returns a true if the atom has been visited before.
isVisited(IAtom) - Method in class org.openscience.cdk.geometry.cip.Ligand: Returns a true if the atom has been visited before.
isVisited(IAtom) - Method in class org.openscience.cdk.geometry.cip.VisitedAtoms: Returns true if the given atom already has been visited.
isXMLBased() - Method in class org.openscience.cdk.io.formats.ABINITFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.Aces2Format: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.ADFFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.AlchemyFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.BGFFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.BSFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
isXMLBased() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.CACheFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
isXMLBased() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.CIFFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.CMLFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.CRK2DFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.CRK3DFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.CrystClustFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.CTXFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.DaltonFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.DMol3Format: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.DOCK5Format: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.FingerprintFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.GamessFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.Gaussian03Format: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.Gaussian90Format: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.Gaussian92Format: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.Gaussian94Format: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.Gaussian95Format: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.Gaussian98Format: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.GROMOS96Format: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.HINFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.INChIFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in interface org.openscience.cdk.io.formats.IResourceFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.JaguarFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.JMEFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.MacroModelFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.MDLFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.MDLRXNV2000Format: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.MDLV2000Format: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.MDLV3000Format: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.MMODFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.Mol2Format: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.MOPAC7Format: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.MOPAC93Format: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.MOPAC97Format: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.MPQCFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.NWChemFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.PCModelFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.PDBFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.PDBMLFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.PMPFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.POVRayFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.PQSChemFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.QChemFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.RawCopyFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.SDFFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.ShelXFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.SMARTSFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.SMILESFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.SpartanFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.SVGFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.VASPFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.ViewmolFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.XEDFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.XYZFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.YasaraFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.ZindoFormat: Indicates if the format is an XML-based language.
isXMLBased() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat: Indicates if the format is an XML-based language.
ITALIC_DISPLAY_PREFIX - Static variable in class org.openscience.cdk.renderer.generators.standard.StandardGenerator: A special markup for annotation labels that hints the generator to renderer the annotation label in italic.
IteratingMDLConformerReader - Class in org.openscience.cdk.io.iterator: Iterate over conformers of a collection of molecules stored in SDF format.
IteratingMDLConformerReader(InputStream, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingMDLConformerReader
IteratingMDLConformerReader(Reader, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingMDLConformerReader
IteratingPCCompoundASNReader - Class in org.openscience.cdk.io.iterator: Iterating PubChem PCCompound ASN reader.
IteratingPCCompoundASNReader(InputStream, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingPCCompoundASNReader: Constructs a new IteratingPCCompoundASNReader that can read Molecule from a given InputStream and IChemObjectBuilder.
IteratingPCCompoundASNReader(Reader, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingPCCompoundASNReader: Constructs a new IteratingPCCompoundASNReader that can read Molecule from a given Reader.
IteratingPCCompoundXMLReader - Class in org.openscience.cdk.io.iterator: Iterating PubChem PCCompound ASN.1 XML reader.
IteratingPCCompoundXMLReader(InputStream, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader: Constructs a new IteratingPCCompoundXLReader that can read Molecule from a given InputStream and IChemObjectBuilder.
IteratingPCCompoundXMLReader(Reader, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader: Constructs a new IteratingPCCompoundXMLReader that can read Molecule from a given Reader and IChemObjectBuilder.
IteratingPCSubstancesXMLReader - Class in org.openscience.cdk.io.iterator: Iterating PubChem PC-Substances ASN.1 XML reader.
IteratingPCSubstancesXMLReader(InputStream, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader: Constructs a new IteratingPCSubstancesXMLReader that can read Molecule from a given InputStream and IChemObjectBuilder.
IteratingPCSubstancesXMLReader(Reader, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader: Constructs a new IteratingPCSubstancesXMLReader that can read Molecule from a given Reader and IChemObjectBuilder.
IteratingSDFReader - Class in org.openscience.cdk.io.iterator: Iterating MDL SDF reader.
IteratingSDFReader(InputStream, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingSDFReader: Constructs a new IteratingMDLReader that can read Molecule from a given InputStream.
IteratingSDFReader(InputStream, IChemObjectBuilder, boolean) - Constructor for class org.openscience.cdk.io.iterator.IteratingSDFReader: Constructs a new IteratingMDLReader that can read Molecule from a given a InputStream.
IteratingSDFReader(Reader, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingSDFReader: Constructs a new IteratingMDLReader that can read Molecule from a given Reader.
IteratingSDFReader(Reader, IChemObjectBuilder, boolean) - Constructor for class org.openscience.cdk.io.iterator.IteratingSDFReader: Constructs a new IteratingMDLReader that can read Molecule from a given a Reader.
IteratingSMILESReader - Class in org.openscience.cdk.io.iterator: Iterating SMILES file reader.
IteratingSMILESReader(InputStream, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingSMILESReader: Constructs a new IteratingSMILESReader that can read Molecule from a given InputStream and IChemObjectBuilder.
IteratingSMILESReader(Reader, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingSMILESReader: Constructs a new IteratingSMILESReader that can read Molecule from a given Reader.
iteration - Variable in class org.openscience.cdk.fingerprint.CircularFingerprinter.FP
iterator() - Method in class org.openscience.cdk.ConformerContainer: Gets an iterator over the conformers.
iterator() - Method in class org.openscience.cdk.debug.DebugAdductFormula: Returns an Iterator for looping over all IMolecularFormula in this adduct formula.
iterator() - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet: Returns an Iterator for looping over all IMolecularFormula in this MolecularFormulaSet.
iterator() - Method in class org.openscience.cdk.depict.Abbreviations: Iterate over loaded abbreviations.
iterator() - Method in class org.openscience.cdk.formula.AdductFormula: Returns an Iterator for looping over all IMolecularFormula in this adduct formula.
iterator() - Method in class org.openscience.cdk.formula.MolecularFormulaSet: Returns an Iterator for looping over all IMolecularFormula in this MolecularFormulaSet.
iterator() - Method in class org.openscience.cdk.isomorphism.Mappings
iterator() - Method in class org.openscience.cdk.renderer.elements.ElementGroup
iterator() - Method in class org.openscience.cdk.signature.Orbit
iterator() - Method in class org.openscience.cdk.silent.AdductFormula: Returns an Iterator for looping over all IMolecularFormula in this adduct formula.
iterator() - Method in class org.openscience.cdk.silent.MolecularFormulaSet: Returns an Iterator for looping over all IMolecularFormula in this MolecularFormulaSet.
ITetrahedralChirality - Interface in org.openscience.cdk.interfaces: Stereochemistry specification for quadrivalent atoms.
ITetrahedralChirality.Stereo - Enum in org.openscience.cdk.interfaces: Enumeration that defines the two possible chiralities for this stereochemistry type.
iupacRecommendations() - Static method in class org.openscience.cdk.renderer.SymbolVisibility: Displays a symbol based on the preferred representation from the IUPAC guidelines (GR-2.1.2) [Jonathan Brecher. Pure Appl. Chem. 2008. 80].
iupacRecommendationsWithoutTerminalCarbon() - Static method in class org.openscience.cdk.renderer.SymbolVisibility: Displays a symbol based on the acceptable representation from the IUPAC guidelines (GR-2.1.2) [Jonathan Brecher. Pure Appl. Chem. 2008. 80].
IValencyChecker - Interface in org.openscience.cdk.tools: A common interface for SaturationChecker and ValencyChecker.
IValidator - Interface in org.openscience.cdk.validate: Interface that Validators need to implement to be used in validation.
IVector - Class in org.openscience.cdk.math
IVector(int) - Constructor for class org.openscience.cdk.math.IVector: Constructs a vector with "size"-elements
IViewEventRelay - Interface in org.openscience.cdk.controller
IWriterListener - Interface in org.openscience.cdk.io.listener: Allows monitoring of progress of writing activities.

J

JaguarFormat - Class in org.openscience.cdk.io.formats: See here.
JaguarFormat() - Constructor for class org.openscience.cdk.io.formats.JaguarFormat
jcpAngles - Static variable in class org.openscience.cdk.layout.RingPlacer: Suggested ring start angles for JChempaint, different due to Y inversion of canvas.
jj_nt - Variable in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Next token.
jj_nt - Variable in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser: Next token.
jjFillToken() - Method in class org.openscience.cdk.iupac.parser.NomParserTokenManager
jjFillToken() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager
jjnewLexState - Static variable in class org.openscience.cdk.iupac.parser.NomParserTokenManager: Lex State array.
jjnewLexState - Static variable in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager: Lex State array.
jjstrLiteralImages - Static variable in class org.openscience.cdk.iupac.parser.NomParserTokenManager: Token literal values.
jjstrLiteralImages - Static variable in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager: Token literal values.
jjtAccept(SMARTSParserVisitor, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.Node: Deprecated.

Accept the visitor.
jjtAddChild(Node, int) - Method in interface org.openscience.cdk.smiles.smarts.parser.Node: Deprecated.

This method tells the node to add its argument to the node's list of children.
JJTALIPHATIC - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTANYATOM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTAROMATIC - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTATOM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTATOMICMASS - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTATOMICNUMBER - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTCHARGE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTCHIRALITY - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
jjtClose() - Method in interface org.openscience.cdk.smiles.smarts.parser.Node: Deprecated.

This method is called after all the child nodes have been added.
JJTELEMENT - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTEXPLICITATOM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTEXPLICITCONNECTIVITY - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTEXPLICITHIGHANDBOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTEXPLICITHIGHANDEXPRESSION - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
jjtGetChild(int) - Method in interface org.openscience.cdk.smiles.smarts.parser.Node: Deprecated.

This method returns a child node.
jjtGetNumChildren() - Method in interface org.openscience.cdk.smiles.smarts.parser.Node: Deprecated.

Return the number of children the node has.
jjtGetParent() - Method in interface org.openscience.cdk.smiles.smarts.parser.Node: Deprecated.
JJTGROUP - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTHYBRDIZATIONNUMBER - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTIMPLICITHCOUNT - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTIMPLICITHIGHANDBOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTIMPLICITHIGHANDEXPRESSION - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTLOWANDBOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTLOWANDEXPRESSION - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
jjtNodeName - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTNONCHHEAVYATOM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTNOTBOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTNOTEXPRESSION - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
jjtOpen() - Method in interface org.openscience.cdk.smiles.smarts.parser.Node: Deprecated.

This method is called after the node has been made the current node.
JJTORBOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTOREXPRESSION - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTPERIODICGROUPNUMBER - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTREACTION - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTRECURSIVESMARTSEXPRESSION - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
jjtree - Variable in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
jjtRemoveChild(int) - Method in interface org.openscience.cdk.smiles.smarts.parser.Node: Deprecated.

Removes a child from this node
JJTRINGCONNECTIVITY - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTRINGIDENTIFIER - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTRINGMEMBERSHIP - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
jjtSetParent(Node) - Method in interface org.openscience.cdk.smiles.smarts.parser.Node: Deprecated.

This pair of methods are used to inform the node of its parent.
JJTSIMPLEBOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTSMALLESTRINGSIZE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTSMARTS - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTSMARTSParserState - Class in org.openscience.cdk.smiles.smarts.parser
JJTSMARTSParserState() - Constructor for class org.openscience.cdk.smiles.smarts.parser.JJTSMARTSParserState
JJTSTART - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTTOTALCONNECTIVITY - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTTOTALHCOUNT - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTVALENCE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JJTVOID - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
JMEFormat - Class in org.openscience.cdk.io.formats
JMEFormat() - Constructor for class org.openscience.cdk.io.formats.JMEFormat
JMOLANIMATIONConvention - Class in org.openscience.cdk.io.cml
JMOLANIMATIONConvention(IChemFile) - Constructor for class org.openscience.cdk.io.cml.JMOLANIMATIONConvention
JMOLANIMATIONConvention(ICMLModule) - Constructor for class org.openscience.cdk.io.cml.JMOLANIMATIONConvention
JmolColors - Class in org.openscience.cdk.renderer.color: Default Jmol colors.
JmolColors() - Constructor for class org.openscience.cdk.renderer.color.JmolColors
JPG_FMT - Static variable in class org.openscience.cdk.depict.Depiction: Joint Photographic Experts Group (JPG) format key.
JPlogPCalculator() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor.JPlogPCalculator
JPlogPCalculator(Object[]) - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor.JPlogPCalculator: Initialises the required coefficients for the trained model from the paper.
JPlogPDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: A logP model donated by Lhasa Limited.
JPlogPDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor: Default constructor which will setup the required coefficients to enable a prediction
JPlogPDescriptor.JPlogPCalculator - Class in org.openscience.cdk.qsar.descriptors.molecular: The class that calculated the logP according to the JPlogP method described in: Journal of Cheminformatics 2018 10:61 https://doi.org/10.1186/s13321-018-0316-5 This is lower level access and should normally be obtained through the descriptor above.

K

K - Static variable in interface org.openscience.cdk.interfaces.IElement
K - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
KabschAlignment - Class in org.openscience.cdk.geometry.alignment: Aligns two structures to minimize the RMSD using the Kabsch algorithm.
KabschAlignment(IAtom[], IAtom[]) - Constructor for class org.openscience.cdk.geometry.alignment.KabschAlignment: Sets up variables for the alignment algorithm.
KabschAlignment(IAtom[], IAtom[], double[]) - Constructor for class org.openscience.cdk.geometry.alignment.KabschAlignment: Sets up variables for the alignment algorithm.
KabschAlignment(IAtomContainer, IAtomContainer) - Constructor for class org.openscience.cdk.geometry.alignment.KabschAlignment: Sets up variables for the alignment algorithm.
KabschAlignment(IAtomContainer, IAtomContainer, double[]) - Constructor for class org.openscience.cdk.geometry.alignment.KabschAlignment: Sets up variables for the alignment algorithm.
KappaShapeIndicesDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Kier and Hall kappa molecular shape indices compare the molecular graph with minimal and maximal molecular graphs; a description is given at: http://www.chemcomp.com/Journal_of_CCG/Features/descr.htm#KH : "they are intended to capture different aspects of molecular shape.
KappaShapeIndicesDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor: Constructor for the KappaShapeIndicesDescriptor object
KekuleStructure() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.KekuleStructure
kekulise(boolean) - Method in class org.openscience.cdk.smiles.SmilesParser: Indicated whether structures should be automatically kekulised if they are provided as aromatic.
kekuliseAromaticRings(IAtomContainer) - Method in class org.openscience.cdk.smiles.FixBondOrdersTool: Deprecated.

kekuliseAromaticRings - function to add double/single bond order information for molecules having rings containing all atoms marked SP2 or Planar3 hybridisation.
Kekulization - Class in org.openscience.cdk.aromaticity: Assign a Kekulé representation to the aromatic systems of a compound.
Kekulization() - Constructor for class org.openscience.cdk.aromaticity.Kekulization
kekulize(IAtomContainer) - Static method in class org.openscience.cdk.aromaticity.Kekulization: Assign a Kekulé representation to the aromatic systems of a compound.
KETO_ENOL - Static variable in class org.openscience.cdk.tautomers.InChITautomerGenerator: Generate InChI with -KET (keto-enol tautomers) option.
key(Class<?>, Class<?>...) - Static method in class org.openscience.cdk.DynamicFactory: Creates a constructor key for use in accessing constructors.
KierHallSmartsDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: A fragment count descriptor that uses e-state fragments.
KierHallSmartsDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor
kind - Variable in class org.openscience.cdk.iupac.parser.Token: An integer that describes the kind of this token.
kind - Variable in class org.openscience.cdk.smiles.smarts.parser.Token: An integer that describes the kind of this token.
KlekotaRothFingerprinter - Class in org.openscience.cdk.fingerprint: SMARTS based substructure fingerprint based on Chemical substructures that enrich for biological activity [Klekota, Justin and Roth, Frederick P.. Bioinformatics. 2008. 24].
KlekotaRothFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.KlekotaRothFingerprinter
Kr - Static variable in interface org.openscience.cdk.interfaces.IElement
KR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Krypton - org.openscience.cdk.config.Elements
KRYPTON - Static variable in enum org.openscience.cdk.config.Elements
kValues(int, Set<Integer>, int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Finding the connectivity partition, so the smallest index in the neighborhood.

L

L_AND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
L_BRACKET - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
L_PAREN - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
La - Static variable in interface org.openscience.cdk.interfaces.IElement
LA - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
label(IAtomContainer) - Static method in class org.openscience.cdk.geometry.cip.CIPTool: Convenience method for labelling all stereo elements.
label(IAtomContainer, int[][]) - Static method in class org.openscience.cdk.graph.invariant.Canon: Compute the canonical labels for the provided structure.
label(IAtomContainer, int[][], int) - Static method in class org.openscience.cdk.graph.invariant.Canon: Compute the canonical labels for the provided structure.
label(IAtomContainer, int[][], long[]) - Static method in class org.openscience.cdk.graph.invariant.Canon: Compute the canonical labels for the provided structure.
label(IAtomContainer, int[][], Comparator<IAtom>) - Static method in class org.openscience.cdk.graph.invariant.Canon: Compute the canonical labels for the provided structure.
LabelContainer - Class in org.openscience.cdk.smsd.helper: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
LabelContainer() - Constructor for class org.openscience.cdk.smsd.helper.LabelContainer: Deprecated.
labelReaction(IReaction, ICanonicalMoleculeLabeller) - Method in class org.openscience.cdk.smsd.labelling.AbstractReactionLabeller: Deprecated.
Lanthanum - org.openscience.cdk.config.Elements
LANTHANUM - Static variable in enum org.openscience.cdk.config.Elements
LANTHANUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
LARGE_FIRST - Static variable in class org.openscience.cdk.silent.RingSet: Flag to denote that the set is order with the largest ring first?
LARGE_FIRST - Static variable in class org.openscience.cdk.tools.manipulator.RingSizeComparator: Flag to denote that the set is order with the largest ring first
LARGEST_FIRST_COMPARATOR - Static variable in class org.openscience.cdk.layout.StructureDiagramGenerator
LargestChainDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Class that returns the number of atoms in the largest chain.
LargestChainDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor: Constructor for the LargestChain object.
LargestPiSystemDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Class that returns the number of atoms in the largest pi system.
LargestPiSystemDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor: Constructor for the LargestPiSystemDescriptor object.
last() - Method in interface org.openscience.cdk.io.random.IRandomAccessChemObjectReader
last() - Method in class org.openscience.cdk.io.random.RandomAccessReader
lastIndexOf(Object) - Method in class org.openscience.cdk.ConformerContainer: Returns the highest index at which the specific IAtomContainer appears in the list or -1 if is not found.
Lawrencium - org.openscience.cdk.config.Elements
LAWRENCIUM - Static variable in enum org.openscience.cdk.config.Elements
LAWRENCIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Lead - org.openscience.cdk.config.Elements
LEAD - Static variable in enum org.openscience.cdk.config.Elements
LEAD - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
left() - Method in class org.openscience.cdk.isomorphism.matchers.Expr: Access the left sub-expression of this atom expression being tested.
LEFT - Static variable in interface org.openscience.cdk.interfaces.IStereoElement
LEGACY_MODE - Static variable in class org.openscience.cdk.tools.HOSECodeGenerator: Ignored parent ordering be considered when sorting spheres (legacy mode) for compatibility with existing ML/AI models.
length() - Method in class org.openscience.cdk.io.cml.CMLModuleStack
length() - Method in class org.openscience.cdk.math.Vector: Return the length from this vector
length() - Method in class org.openscience.cdk.qsar.result.BooleanResultType
length() - Method in class org.openscience.cdk.qsar.result.DoubleArrayResult
length() - Method in class org.openscience.cdk.qsar.result.DoubleArrayResultType
length() - Method in class org.openscience.cdk.qsar.result.DoubleResult
length() - Method in class org.openscience.cdk.qsar.result.DoubleResultType
length() - Method in interface org.openscience.cdk.qsar.result.IDescriptorResult: Returns the length of this descriptor.
length() - Method in class org.openscience.cdk.qsar.result.IntegerArrayResult
length() - Method in class org.openscience.cdk.qsar.result.IntegerArrayResultType
length() - Method in class org.openscience.cdk.qsar.result.IntegerResult
length() - Method in class org.openscience.cdk.qsar.result.IntegerResultType
LengthOverBreadthDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Evaluates length over breadth descriptors.
LengthOverBreadthDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor: Constructor for the LengthOverBreadthDescriptor object.
level - Variable in class org.openscience.cdk.io.setting.IOSetting
LEXICAL_ERROR - Static variable in error org.openscience.cdk.iupac.parser.TokenMgrError: Lexical error occurred.
LEXICAL_ERROR - Static variable in error org.openscience.cdk.smiles.smarts.parser.TokenMgrError: Lexical error occurred.
LexicalErr(boolean, int, int, int, String, int) - Static method in error org.openscience.cdk.iupac.parser.TokenMgrError: Returns a detailed message for the Error when it is thrown by the token manager to indicate a lexical error.
LexicalErr(boolean, int, int, int, String, int) - Static method in error org.openscience.cdk.smiles.smarts.parser.TokenMgrError: Returns a detailed message for the Error when it is thrown by the token manager to indicate a lexical error.
lexStateNames - Static variable in class org.openscience.cdk.iupac.parser.NomParserTokenManager: Lexer state names.
lexStateNames - Static variable in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager: Lexer state names.
Li - Static variable in interface org.openscience.cdk.interfaces.IElement
LI - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Ligand - Class in org.openscience.cdk.geometry.cip: Concept of a ligand in CIP terms, reflecting a side chain of a central atom that can have precedence over another.
Ligand(IAtomContainer, VisitedAtoms, IAtom, IAtom) - Constructor for class org.openscience.cdk.geometry.cip.Ligand
limit(int) - Method in class org.openscience.cdk.isomorphism.Mappings: Limit the number of mappings - only this number of mappings will be generate.
limit(int, int, int[][], Permutation) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Looking for the upper limit where the original entry is smaller.
line - Variable in class org.openscience.cdk.iupac.parser.SimpleCharStream
line - Variable in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
LineElement - Class in org.openscience.cdk.renderer.elements: A line between two points.
LineElement(double, double, double, double, double, Color) - Constructor for class org.openscience.cdk.renderer.elements.LineElement: Make a line element.
LineElement.LineType - Enum in org.openscience.cdk.renderer.elements: The type of the line.
lineTo(Point2d) - Method in class org.openscience.cdk.renderer.elements.path.PathBuilder: Make a line in the path, from the last point to the given point.
LineTo - Class in org.openscience.cdk.renderer.elements.path: A line element in the path.
LineTo - org.openscience.cdk.renderer.elements.path.Type
LineTo(double[]) - Constructor for class org.openscience.cdk.renderer.elements.path.LineTo: Make a line path element.
LineTo(double, double) - Constructor for class org.openscience.cdk.renderer.elements.path.LineTo: Make a line path element.
LineTo(Point2d) - Constructor for class org.openscience.cdk.renderer.elements.path.LineTo: Make a line to this point.
LingoFingerprinter - Class in org.openscience.cdk.fingerprint: An implementation of the LINGO fingerprint [Vidal, D. et. al.. J. Chem. Inf. Model.. 2005. 45].
LingoFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.LingoFingerprinter: Initialize the fingerprinter with a default substring length of 4.
LingoFingerprinter(int) - Constructor for class org.openscience.cdk.fingerprint.LingoFingerprinter: Initialize the fingerprinter.
LingoSimilarity - Class in org.openscience.cdk.similarity: A class to evaluate the similarity between two LINGO's as described in [Vidal, D. et. al.. J. Chem. Inf. Model.. 2005. 45].
lInverse(int, int, int[][], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Calculating the sum of the entries in the ith row until the jth column.
listDictionaries() - Method in class org.openscience.cdk.dict.DictionaryDatabase: Returns true if the database contains the dictionary.
listDifferences(BitSet, BitSet) - Static method in class org.openscience.cdk.fingerprint.FingerprinterTool: This lists all bits set in bs2 and not in bs2 (other way round not considered) in a list and to logger.
listFormats() - Method in class org.openscience.cdk.depict.Depiction: List the available formats that can be rendered.
listIterator() - Method in class org.openscience.cdk.ConformerContainer
listIterator(int) - Method in class org.openscience.cdk.ConformerContainer
listNumbers(IAtomContainer, List<IAtom>) - Static method in class org.openscience.cdk.layout.AtomPlacer: Returns a string with the numbers of all atoms in a Vector relative to a given molecule.
listNumbers(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.layout.AtomPlacer: Returns a string with the numbers of all atoms in an AtomContainer relative to a given molecule.
listPlaced(IAtomContainer) - Method in class org.openscience.cdk.layout.AtomPlacer: Returns a string with the numbers of all placed atoms in an AtomContainer
Lithium - org.openscience.cdk.config.Elements
LITHIUM - Static variable in enum org.openscience.cdk.config.Elements
LITHIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
LITHO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Livermorium - org.openscience.cdk.config.Elements
LIVERMORIUM - Static variable in enum org.openscience.cdk.config.Elements
loadFromFile(String) - Method in class org.openscience.cdk.depict.Abbreviations: Load a set of abbreviations from a classpath resource or file in SMILES format.
loadIndex(File) - Method in class org.openscience.cdk.io.random.RandomAccessReader
loadMolecule(String) - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.
loadTemplates(IChemObjectBuilder) - Method in class org.openscience.cdk.layout.TemplateHandler: Loads all existing templates into memory.
logger - Static variable in class org.openscience.cdk.config.IsotopeFactory
logger - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
logger - Static variable in class org.openscience.cdk.io.iterator.event.EventCMLHandler
logger - Static variable in class org.openscience.cdk.io.random.RandomAccessReader
logger - Variable in class org.openscience.cdk.stereo.StereoElementFactory
logger - Static variable in class org.openscience.cdk.tools.SmilesValencyChecker
LoggingToolFactory - Class in org.openscience.cdk.tools: Factory used to instantiate a ILoggingTool.
LoggingToolFactory() - Constructor for class org.openscience.cdk.tools.LoggingToolFactory
LogicalOperatorAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
LogicalOperatorAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom: Deprecated.
LogicalOperatorBond - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
LogicalOperatorBond(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond: Deprecated.
LONE_PAIR_COUNT - Static variable in class org.openscience.cdk.CDKConstants: Used as property key for indicating the HOSE code for a certain atom type.
LonePair - Class in org.openscience.cdk: A LonePair is an orbital primarily located with one Atom, containing two electrons.
LonePair - Class in org.openscience.cdk.silent: A LonePair is an orbital primarily located with one Atom, containing two electrons.
LonePair() - Constructor for class org.openscience.cdk.LonePair: Constructs an unconnected lone pair.
LonePair() - Constructor for class org.openscience.cdk.silent.LonePair: Constructs an unconnected lone pair.
LonePair(IAtom) - Constructor for class org.openscience.cdk.LonePair: Constructs an lone pair on an Atom.
LonePair(IAtom) - Constructor for class org.openscience.cdk.silent.LonePair: Constructs an lone pair on an Atom.
lonePairCount - Variable in class org.openscience.cdk.AtomContainer: Number of lone pairs contained by this object.
lonePairCount - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Number of lone pairs contained by this object.
lonePairCount - Variable in class org.openscience.cdk.silent.AtomContainer: Number of lone pairs contained by this object.
LonePairDiff - Class in org.openscience.cdk.tools.diff: Compares two ILonePair classes.
LonePairElectronChecker - Class in org.openscience.cdk.tools: Provides methods for checking whether an atoms lone pair electrons are saturated with respect to a particular atom type.
LonePairElectronChecker() - Constructor for class org.openscience.cdk.tools.LonePairElectronChecker
LonePairGenerator - Class in org.openscience.cdk.renderer.generators: Generate the symbols for lone pairs.
LonePairGenerator() - Constructor for class org.openscience.cdk.renderer.generators.LonePairGenerator
lonePairs - Variable in class org.openscience.cdk.AtomContainer: Internal array of lone pairs.
lonePairs - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Internal array of lone pairs.
lonePairs - Variable in class org.openscience.cdk.silent.AtomContainer: Internal array of lone pairs.
lonePairs() - Method in class org.openscience.cdk.AtomContainer: Returns an Iterable for looping over all lone pairs in this container.
lonePairs() - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns an Iterable for looping over all lone pairs in this container.
lonePairs() - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns an Iterable for looping over all lone pairs in this container.
lonePairs() - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns an Iterable for looping over all lone pairs in this container.
lonePairs() - Method in class org.openscience.cdk.debug.DebugCrystal: Returns an Iterable for looping over all lone pairs in this container.
lonePairs() - Method in class org.openscience.cdk.debug.DebugMonomer: Returns an Iterable for looping over all lone pairs in this container.
lonePairs() - Method in class org.openscience.cdk.debug.DebugPolymer: Returns an Iterable for looping over all lone pairs in this container.
lonePairs() - Method in class org.openscience.cdk.debug.DebugRing: Returns an Iterable for looping over all lone pairs in this container.
lonePairs() - Method in class org.openscience.cdk.debug.DebugStrand: Returns an Iterable for looping over all lone pairs in this container.
lonePairs() - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Returns an Iterable for looping over all lone pairs in this container.
lonePairs() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns an Iterable for looping over all lone pairs in this container.
lonePairs() - Method in class org.openscience.cdk.silent.AtomContainer: Returns an Iterable for looping over all lone pairs in this container.
LongestAliphaticChainDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Counts the number of atoms in the longest aliphatic chain.
LongestAliphaticChainDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor: Constructor for the LongestAliphaticChainDescriptor object.
LOOP_DETECTED - Static variable in error org.openscience.cdk.iupac.parser.TokenMgrError: Detected (and bailed out of) an infinite loop in the token manager.
LOOP_DETECTED - Static variable in error org.openscience.cdk.smiles.smarts.parser.TokenMgrError: Detected (and bailed out of) an infinite loop in the token manager.
LOW - org.openscience.cdk.io.setting.IOSetting.Importance
LowAndBond() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
LowAndExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
lowerIndex(int, int, int[][], Permutation) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Looking for the maximum index where the entry is not zero.
lowThresh - Variable in class org.openscience.cdk.fingerprint.model.Bayesian
Lr - Static variable in interface org.openscience.cdk.interfaces.IElement
LR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
lsum(int, int, int[][][]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Summing ith rows entries starting from the jth column.
Lu - Static variable in interface org.openscience.cdk.interfaces.IElement
LU - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Lutetium - org.openscience.cdk.config.Elements
LUTETIUM - Static variable in enum org.openscience.cdk.config.Elements
LUTETIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Lv - Static variable in interface org.openscience.cdk.interfaces.IElement
lValue(int[], int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: To calculate the number of conjugacy classes, used in cycle transposition calculation.

M

MACCSFingerprinter - Class in org.openscience.cdk.fingerprint: This fingerprinter generates 166 bit MACCS keys.
MACCSFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.MACCSFingerprinter
MACCSFingerprinter(IChemObjectBuilder) - Constructor for class org.openscience.cdk.fingerprint.MACCSFingerprinter
MacroModelFormat - Class in org.openscience.cdk.io.formats
MacroModelFormat() - Constructor for class org.openscience.cdk.io.formats.MacroModelFormat
mag() - Method in class org.openscience.cdk.math.Quaternion
mag_sq() - Method in class org.openscience.cdk.math.Quaternion
Magnesium - org.openscience.cdk.config.Elements
MAGNESIUM - Static variable in enum org.openscience.cdk.config.Elements
MAGNESIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
main(String[]) - Static method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor
mainChainConstruct() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Main chains are compulsary and consist of an optional "cyclo", a length prefix and a posfix denoting functional groups.
mainChainPrefix() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Deal with the main chain's length.
mainChainSuffix() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Figure out the functional group by the main chain's suffix.
make123Triazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.

Returns 1,2,3-triazole without explicit hydrogens.
make123Triazole() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory: Returns 1,2,3-triazole without explicit hydrogens.
make124Triazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.

Returns 1,2,4-triazole without explicit hydrogens.
make124Triazole() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory: Returns 1,2,4-triazole without explicit hydrogens.
make4x3CondensedRings() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.
make4x3CondensedRings() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory
makeAdenine() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.
makeAdenine() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory
makeAlkane(int) - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.

Generate an Alkane (chain of carbons with no hydrogens) of a given length.
makeAlkane(int) - Static method in class org.openscience.cdk.templates.TestMoleculeFactory: Generate an Alkane (chain of carbons with no hydrogens) of a given length.
makeAlphaPinene() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.
makeAlphaPinene() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory
makeAnthracene() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory
makeAtomContainer(IAtom, List<IBond>, IAtom) - Static method in class org.openscience.cdk.fragment.FragmentUtils
makeAtomsMapOfBondsMap(List<RMap>, IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: This makes a map of matching atoms out of a map of matching bonds as produced by the get(Subgraph|Ismorphism)Map methods.
makeAtomsMapOfBondsMap(List<CDKRMap>, IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS: Deprecated.

This makes atom map of matching atoms out of atom map of matching bonds as produced by the get(Subgraph|Ismorphism)Map methods.
makeAtomsMapsOfBondsMaps(List<List<RMap>>, IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: This makes maps of matching atoms out of a maps of matching bonds as produced by the get(Subgraph|Ismorphism)Maps methods.
makeAtomsMapsOfBondsMaps(List<List<CDKRMap>>, IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS: Deprecated.

This makes maps of matching atoms out of atom maps of matching bonds as produced by the get(Subgraph|Ismorphism)Maps methods.
makeAzulene() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.

Returns azulene without explicit hydrogens.
makeAzulene() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory: Returns azulene without explicit hydrogens.
makeBenzene() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.
makeBenzene() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory
makeBicycloRings() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.
makeBicycloRings() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory
makeBiphenyl() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.

Returns biphenyl without explicit hydrogens.
makeBiphenyl() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory: Returns biphenyl without explicit hydrogens.
makeBitFingerprint(Map<String, Integer>) - Static method in class org.openscience.cdk.fingerprint.FingerprinterTool: Convert a mapping of features and their counts to a 1024-bit binary fingerprint.
makeBitFingerprint(Map<String, Integer>, int) - Static method in class org.openscience.cdk.fingerprint.FingerprinterTool: Convert a mapping of features and their counts to a binary fingerprint.
makeBitFingerprint(Map<String, Integer>, int, int) - Static method in class org.openscience.cdk.fingerprint.FingerprinterTool: Convert a mapping of features and their counts to a binary fingerprint.
makeBondMapOfAtomMap(IAtomContainer, IAtomContainer, Map<IAtom, IAtom>) - Static method in class org.openscience.cdk.smsd.Isomorphism: Deprecated.

Returns bond map between source and target molecules based on the atoms
makeBondMapsOfAtomMaps(IAtomContainer, IAtomContainer, List<Map<IAtom, IAtom>>) - Static method in class org.openscience.cdk.smsd.Isomorphism: Deprecated.

Returns bond maps between source and target molecules based on the atoms
makeBranchedAliphatic() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.
makeBranchedAliphatic() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory
makeBremserCompliant(String) - Method in class org.openscience.cdk.tools.HOSECodeGenerator
makeCanonicalSmileFromRingSystems(String, String) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor
makeCountFingerprint(Map<String, Integer>) - Static method in class org.openscience.cdk.fingerprint.FingerprinterTool: Wrap a mapping of features and their counts to a continuous (count based) fingerprint.
makeCyclobutadiene() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.

Returns cyclobutadiene without explicit hydrogens.
makeCyclobutadiene() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory: Returns cyclobutadiene without explicit hydrogens.
makeCyclobutane() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.

Returns cyclobutane without explicit hydrogens.
makeCyclobutane() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory: Returns cyclobutane without explicit hydrogens.
makeCyclohexane() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.

Returns cyclohexane without explicit hydrogens.
makeCyclohexane() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory: Returns cyclohexane without explicit hydrogens.
makeCyclohexene() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.

Returns cyclohexene without explicit hydrogens.
makeCyclohexene() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory: Returns cyclohexene without explicit hydrogens.
makeCyclopentane() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.

Returns cyclopentane without explicit hydrogens.
makeCyclopentane() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory: Returns cyclopentane without explicit hydrogens.
makeCyclophaneLike() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory: octacyclo[17.2.2.2¹,⁴.2⁴,⁷.2⁷,¹⁰.2¹⁰,¹³.2¹³,¹⁶.2¹⁶,¹⁹]pentatriacontane
makeDeepCopy(IAtomContainer) - Static method in class org.openscience.cdk.normalize.SMSDNormalizer: Deprecated.

Returns deep copy of the molecule
makeDeepCopy(IAtomContainer) - Static method in class org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator: Deprecated.

Retrurns deep copy of the molecule
makeDiamantane() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.
makeDiamantane() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory
makeEdge(int, int, String, String, String) - Method in class org.openscience.cdk.signature.MoleculeFromSignatureBuilder
makeEthylCyclohexane() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.
makeEthylCyclohexane() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory
makeEthylPropylPhenantren() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.
makeEthylPropylPhenantren() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory
makeFingerprintFromRingSystems(String, String, boolean, boolean) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor
makeFingerprintsFromSdf(boolean, boolean, Map<String, Integer>, BufferedReader, int) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor
makeFonts() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager: Make widget-specific fonts.
makeFonts() - Method in class org.openscience.cdk.renderer.font.AWTFontManager: Make widget-specific fonts.
makeFusedRings() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.
makeFusedRings() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory
makeGappedCyclophaneLike() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory: octacyclo[24.2.2.2²,⁵.2⁶,⁹.2¹⁰,¹³.2¹⁴,¹⁷.2¹⁸,²¹.2²²,²⁵]dotetracontane
makeGraph() - Method in class org.openscience.cdk.signature.MoleculeFromSignatureBuilder
makeImidazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.

Returns imidazole without explicit hydrogens.
makeImidazole() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory: Returns imidazole without explicit hydrogens.
makeIndex() - Method in class org.openscience.cdk.io.random.RandomAccessReader: The index file RandomAccessReader.getIndexFile(String) is loaded, if already exists, or created a new.
makeIndole() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.

Returns indole without explicit hydrogens.
makeIndole() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory: Returns indole without explicit hydrogens.
makeIsothiazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.

Returns isothiazole without explicit hydrogens.
makeIsothiazole() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory: Returns isothiazole without explicit hydrogens.
makeIsoxazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.

Returns Isoxazole without explicit hydrogens.
makeIsoxazole() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory: Returns Isoxazole without explicit hydrogens.
makeLabel(int) - Static method in class org.openscience.cdk.isomorphism.matchers.RGroup: Makes a label/title to be used for a substituent.
makeMethylDecaline() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.
makeMethylDecaline() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory
makeNaphthalene() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory: InChI=1/C10H8/c1-2-6-10-8-4-3-7-9(10)5-1/h1-8H
makeOxadiazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.

Returns oxadiazole without explicit hydrogens.
makeOxadiazole() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory: Returns oxadiazole without explicit hydrogens.
makeOxazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.

Returns Oxazole without explicit hydrogens.
makeOxazole() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory: Returns Oxazole without explicit hydrogens.
makePhenylAmine() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.
makePhenylAmine() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory
makePhenylEthylBenzene() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.
makePhenylEthylBenzene() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory
makePiperidine() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.
makePiperidine() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory
makePropylCycloPropane() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.
makePropylCycloPropane() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory
makePyrazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.

Returns pyrazole without explicit hydrogens.
makePyrazole() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory: Returns pyrazole without explicit hydrogens.
makePyridazine() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.

Returns pyridazine without explicit hydrogens.
makePyridazine() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory: Returns pyridazine without explicit hydrogens.
makePyridine() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.

Returns pyridine without explicit hydrogens.
makePyridine() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory: Returns pyridine without explicit hydrogens.
makePyridineOxide() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.

Returns pyridine oxide without explicit hydrogens.
makePyridineOxide() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory: Returns pyridine oxide without explicit hydrogens.
makePyrimidine() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.

Returns pyrimidine without explicit hydrogens.
makePyrimidine() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory: Returns pyrimidine without explicit hydrogens.
makePyrrole() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.

Returns pyrrole without explicit hydrogens.
makePyrrole() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory: Returns pyrrole without explicit hydrogens.
makePyrroleAnion() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.

Returns pyrrole anion without explicit hydrogens.
makePyrroleAnion() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory: Returns pyrrole anion without explicit hydrogens.
makeQuinone() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.
makeQuinone() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory
makeReferencesExplicit(IChemObject) - Static method in class org.openscience.cdk.dict.CDKDictionaryReferences
makeSingleRing() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.
makeSingleRing() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory
makeSpiroRings() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.
makeSpiroRings() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory
makeSteran() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.
makeSteran() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory
makeStereocenter(Point3d, IBond, Point3d, Point3d, Point3d[]) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D: set Atoms in respect to stereoinformation.
makeSymN(int) - Static method in class org.openscience.cdk.group.PermutationGroup: Make the symmetric group Sym(N) for N.
makeTetrahydropyran() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.
makeTetrahydropyran() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory
makeTetrazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.

Returns tetrazole without explicit hydrogens.
makeTetrazole() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory: Returns tetrazole without explicit hydrogens.
makeThiadiazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.

Returns thiadiazole without explicit hydrogens.
makeThiadiazole() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory: Returns thiadiazole without explicit hydrogens.
makeThiazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.

Returns thiazole without explicit hydrogens.
makeThiazole() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory: Returns thiazole without explicit hydrogens.
makeTriazine() - Static method in class org.openscience.cdk.templates.MoleculeFactory: Deprecated.

Returns triazine without explicit hydrogens.
makeTriazine() - Static method in class org.openscience.cdk.templates.TestMoleculeFactory: Returns triazine without explicit hydrogens.
makeUnion(int, int) - Method in class org.openscience.cdk.group.DisjointSetForest: Union these two elements - in other words, put them in the same set.
makeUpDownBonds(IAtomContainer) - Static method in class org.openscience.cdk.geometry.BondTools
makeVertex(String) - Method in class org.openscience.cdk.signature.MoleculeFromSignatureBuilder
Manganese - org.openscience.cdk.config.Elements
MANGANESE - Static variable in enum org.openscience.cdk.config.Elements
MANGANESE - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
MannholdLogPDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Prediction of logP based on the number of carbon and hetero atoms.
MannholdLogPDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor
map - Variable in class org.openscience.cdk.Reaction
map - Variable in class org.openscience.cdk.silent.Reaction
map(Function<int[], T>) - Method in class org.openscience.cdk.isomorphism.Mappings: Map the mappings to another type.
map(Map<IAtom, IAtom>, Map<IBond, IBond>) - Method in interface org.openscience.cdk.interfaces.IDoubleBondStereochemistry: Map the atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping.
map(Map<IAtom, IAtom>, Map<IBond, IBond>) - Method in interface org.openscience.cdk.interfaces.IStereoElement: Map the atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping.
map(Map<IAtom, IAtom>, Map<IBond, IBond>) - Method in interface org.openscience.cdk.interfaces.ITetrahedralChirality: Map the atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping.
map(Map<IAtom, IAtom>, Map<IBond, IBond>) - Method in class org.openscience.cdk.stereo.DoubleBondStereochemistry
map(Map<IAtom, IAtom>, Map<IBond, IBond>) - Method in class org.openscience.cdk.stereo.TetrahedralChirality
map(Map<IChemObject, IChemObject>) - Method in interface org.openscience.cdk.interfaces.IStereoElement: Update the stereo using the remapping of atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping.
map(Map<IChemObject, IChemObject>) - Method in class org.openscience.cdk.stereo.TetrahedralChirality
mapAtomsOfAlignedStructures(IAtomContainer, IAtomContainer, double, Map<Integer, Integer>) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Returns a Map with the AtomNumbers, the first number corresponds to the first (or the largest AtomContainer) atomcontainer.
mapAtomsOfAlignedStructures(IAtomContainer, IAtomContainer, double, Map<Integer, Integer>) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Returns a Map with the AtomNumbers, the first number corresponds to the first (or the largest AtomContainer) atomcontainer.
mapAtomsOfAlignedStructures(IAtomContainer, IAtomContainer, Map<Integer, Integer>) - Static method in class org.openscience.cdk.isomorphism.AtomMappingTools: Returns a Map with the AtomNumbers, the first number corresponds to the first (or the largest AtomContainer) atomContainer.
mapAtomType(String) - Method in class org.openscience.cdk.atomtype.mapper.AtomTypeMapper: Maps an atom type from one scheme to another, as specified in the input used when creating this AtomTypeMapper instance.
MAPPED - Static variable in class org.openscience.cdk.CDKConstants: Flag is set if a chemobject is mapped to another chemobject.
Mapping - Class in org.openscience.cdk: A Mapping is an relation between two ChemObjects in a non-chemical entity.
Mapping - Class in org.openscience.cdk.silent: A Mapping is an relation between two ChemObjects in a non-chemical entity.
Mapping(IChemObject, IChemObject) - Constructor for class org.openscience.cdk.Mapping: Constructs an unconnected lone pair.
Mapping(IChemObject, IChemObject) - Constructor for class org.openscience.cdk.silent.Mapping: Constructs an unconnected lone pair.
mappingCount - Variable in class org.openscience.cdk.Reaction
mappingCount - Variable in class org.openscience.cdk.silent.Reaction
MappingGenerator - Class in org.openscience.cdk.renderer.generators: IGenerator that will show how atoms map between the reactant and product side.
MappingGenerator() - Constructor for class org.openscience.cdk.renderer.generators.MappingGenerator
MappingGenerator.AtomAtomMappingLineColor - Class in org.openscience.cdk.renderer.generators: The width on screen of an atom-atom mapping line.
MappingGenerator.MappingLineWidth - Class in org.openscience.cdk.renderer.generators: The width on screen of an atom-atom mapping line.
MappingGenerator.ShowAtomAtomMapping - Class in org.openscience.cdk.renderer.generators: Boolean by which atom-atom mapping depiction can be temporarily disabled.
MappingLineWidth() - Constructor for class org.openscience.cdk.renderer.generators.MappingGenerator.MappingLineWidth
mappings() - Method in interface org.openscience.cdk.interfaces.IReaction: Returns the mappings between the reactant and the product side.
mappings() - Method in class org.openscience.cdk.Reaction: Returns the mappings between the reactant and the product side.
mappings() - Method in class org.openscience.cdk.silent.Reaction: Returns the mappings between the reactant and the product side.
Mappings - Class in org.openscience.cdk.isomorphism: A fluent interface for handling (sub)-graph mappings from a query to a target structure.
mapStrict(Map<IChemObject, IChemObject>) - Method in interface org.openscience.cdk.interfaces.IStereoElement: Update the stereo using the remapping of atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping.
mapTemplateExact(IAtomContainer) - Method in class org.openscience.cdk.layout.TemplateHandler: Checks if one of the loaded templates is isomorph to the given Molecule.
mapTemplates(IAtomContainer) - Method in class org.openscience.cdk.layout.TemplateHandler: Checks if one of the loaded templates is a substructure in the given Molecule.
mapTemplates(IAtomContainer, double) - Method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D: Deprecated.
Use TemplateHandler3D.mapTemplates(org.openscience.cdk.interfaces.IAtomContainer, int)
mapTemplates(IAtomContainer, int) - Method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D: Checks if one of the loaded templates is a substructure in the given Molecule.
Margin() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.Margin
markAromaticRings(IRing) - Static method in class org.openscience.cdk.tools.manipulator.RingManipulator: Marks the ring aromatic if all atoms and all bonds are aromatic.
markAromaticRings(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator: Iterates over the rings in the ring set, and marks the ring aromatic if all atoms and all bonds are aromatic.
MarkedElement - Class in org.openscience.cdk.renderer.elements: A marked element adds meta-data (id and tags) to a CDK rendering element (or group of elements).
MarkedOutput() - Constructor for class org.openscience.cdk.renderer.RendererModel.MarkedOutput
markNotPlaced(IAtomContainer) - Static method in class org.openscience.cdk.layout.AtomPlacer: Marks all the atoms in the given AtomContainer as not placed
markPlaced(IAtomContainer) - Static method in class org.openscience.cdk.layout.AtomPlacer: Marks all the atoms in the given AtomContainer as placed
markPlaced(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D: Mark all atoms in chain as placed.
markRingAtomsAndBonds(IAtomContainer) - Static method in class org.openscience.cdk.graph.Cycles: Find and mark all cyclic atoms and bonds in the provided molecule.
markRingAtomsAndBonds(IAtomContainer, int[][], GraphUtil.EdgeToBondMap) - Static method in class org.openscience.cdk.graph.Cycles: Find and mark all cyclic atoms and bonds in the provided molecule.
markup(IRenderingElement, String...) - Static method in class org.openscience.cdk.renderer.elements.MarkedElement: Markup a rendering element with the specified classes.
markupAtom(IRenderingElement, IAtom) - Static method in class org.openscience.cdk.renderer.elements.MarkedElement: Markup a atom with the class 'atom' and optionally the ids/classes from it's properties.
markupBond(IRenderingElement, IBond) - Static method in class org.openscience.cdk.renderer.elements.MarkedElement: Markup a bond with the class 'bond' and optionally the ids/classes from it's properties.
markupMol(IRenderingElement, IAtomContainer) - Static method in class org.openscience.cdk.renderer.elements.MarkedElement: Markup a molecule with the class 'mol' and optionally the ids/classes from it's properties.
markWithError(IChemObject) - Static method in class org.openscience.cdk.validate.ProblemMarker
markWithWarning(IChemObject) - Static method in class org.openscience.cdk.validate.ProblemMarker
MASS_ELECTRON - Static variable in class org.openscience.cdk.PhysicalConstants: Mass of an electron.
MASS_NUMBER - org.openscience.cdk.hash.BasicAtomEncoder: Encode the mass number of an atom, allowing distinction of isotopes.
MASS_PROTON - Static variable in class org.openscience.cdk.PhysicalConstants: Mass of a proton.
MassAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
MassAtom(int, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.MassAtom: Deprecated.

Creates a new instance
MassToFormulaTool - Class in org.openscience.cdk.formula: Deprecated.
Please use MolecularFormulaGenerator
MassToFormulaTool(IChemObjectBuilder) - Constructor for class org.openscience.cdk.formula.MassToFormulaTool: Deprecated.

Construct an instance of MassToFormulaTool.
match(int, int) - Method in class org.openscience.cdk.graph.Matching: Add the edge '{u,v}' to the matched edge set.
match(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.DfPattern: Find a matching of this pattern in the target.
match(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.Pattern: Find a matching of this pattern in the target.
match(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.Ullmann
match(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.VentoFoggia: Find a matching of this pattern in the target.
match(IAtomContainer) - Method in class org.openscience.cdk.smarts.SmartsPattern: Find a matching of this pattern in the target.
match(IAtomContainer) - Method in class org.openscience.cdk.smiles.smarts.SmartsPattern: Deprecated.

Find a matching of this pattern in the target.
Match - Class in org.openscience.cdk.smsd.algorithm.vflib.map: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
Match(INode, IAtom) - Constructor for class org.openscience.cdk.smsd.algorithm.vflib.map.Match: Deprecated.

Constructor
matchAll(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.DfPattern: Find all mappings of this pattern in the target.
matchAll(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.Pattern: Find all mappings of this pattern in the target.
matchAll(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.Ullmann
matchAll(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.VentoFoggia: Find all mappings of this pattern in the target.
matchAll(IAtomContainer) - Method in class org.openscience.cdk.smarts.SmartsPattern: Obtain the mappings of the query pattern against the target compound.
matchAll(IAtomContainer) - Method in class org.openscience.cdk.smiles.smarts.SmartsPattern: Deprecated.

Obtain the mappings of the query pattern against the target compound.
matchAll(IReaction) - Method in class org.openscience.cdk.isomorphism.Pattern: Find all mappings of this pattern in the target reaction.
matched() - Method in class org.openscience.cdk.io.formats.IChemFormatMatcher.MatchResult: Did the chem format match.
matched(int) - Method in class org.openscience.cdk.graph.Matching: Determine if a vertex has a match.
matches(int, String) - Method in class org.openscience.cdk.io.formats.ABINITFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.Aces2Format
matches(int, String) - Method in class org.openscience.cdk.io.formats.ADFFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.CACheFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.CDKOWLFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.CIFFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.CMLFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.CrystClustFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.CTXFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.DaltonFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.GamessFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.Gaussian03Format
matches(int, String) - Method in class org.openscience.cdk.io.formats.Gaussian90Format
matches(int, String) - Method in class org.openscience.cdk.io.formats.Gaussian92Format
matches(int, String) - Method in class org.openscience.cdk.io.formats.Gaussian94Format
matches(int, String) - Method in class org.openscience.cdk.io.formats.Gaussian95Format
matches(int, String) - Method in class org.openscience.cdk.io.formats.Gaussian98Format
matches(int, String) - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.HINFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.INChIFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.JaguarFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.MDLFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.MDLRXNFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format
matches(int, String) - Method in class org.openscience.cdk.io.formats.MDLV2000Format
matches(int, String) - Method in class org.openscience.cdk.io.formats.MDLV3000Format
matches(int, String) - Method in class org.openscience.cdk.io.formats.Mol2Format
matches(int, String) - Method in class org.openscience.cdk.io.formats.MOPAC2002Format
matches(int, String) - Method in class org.openscience.cdk.io.formats.MOPAC2007Format
matches(int, String) - Method in class org.openscience.cdk.io.formats.MOPAC2009Format
matches(int, String) - Method in class org.openscience.cdk.io.formats.MOPAC2012Format
matches(int, String) - Method in class org.openscience.cdk.io.formats.MOPAC7Format
matches(int, String) - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.MOPAC93Format
matches(int, String) - Method in class org.openscience.cdk.io.formats.MOPAC97Format
matches(int, String) - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.NWChemFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.PDBFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.PMPFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.PubChemASNFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.QChemFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.SDFFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.ShelXFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.SpartanFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.VASPFormat
matches(int, String) - Method in class org.openscience.cdk.io.formats.ZMatrixFormat
matches(List<String>) - Method in interface org.openscience.cdk.io.formats.IChemFormatMatcher: Method that checks whether the given lines are part of the format read by this reader.
matches(List<String>) - Method in class org.openscience.cdk.io.formats.MDLRXNV2000Format: Method that checks whether the given lines are part of the format read by this reader.
matches(List<String>) - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat: Method that checks whether the given lines are part of the format read by this reader.
matches(List<String>) - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat: Method that checks whether the given lines are part of the format read by this reader.
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.Expr: Test whether this expression matches an atom instance.
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom: Deprecated.

The matches implementation of the QueryAtom interface.
matches(IAtom) - Method in interface org.openscience.cdk.isomorphism.matchers.IQueryAtom: Returns true of the given atom matches this IQueryAtom.
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Returns true of the given atom matches this IQueryAtom.
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AliphaticAtom: Deprecated.
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AliphaticSymbolAtom: Deprecated.
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AnyAtom: Deprecated.
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AromaticAtom: Deprecated.
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AromaticSymbolAtom: Deprecated.
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AtomicNumberAtom: Deprecated.
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom: Deprecated.
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ExplicitConnectionAtom: Deprecated.

Returns true of the given atom matches this IQueryAtom.
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.FormalChargeAtom: Deprecated.
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.HybridizationNumberAtom: Deprecated.
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.HydrogenAtom: Deprecated.
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ImplicitHCountAtom: Deprecated.
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom: Deprecated.
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.MassAtom: Deprecated.
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.NonCHHeavyAtom: Deprecated.
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.PeriodicGroupNumberAtom: Deprecated.
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ReactionRoleQueryAtom: Deprecated.
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RecursiveSmartsAtom: Deprecated.
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RingIdentifierAtom: Deprecated.
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RingMembershipAtom: Deprecated.

Returns true of the given atom matches this IQueryAtom.
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.SmallestRingAtom: Deprecated.

Returns true of the given atom matches this IQueryAtom.
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom: Deprecated.
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.TotalConnectionAtom: Deprecated.

Returns true of the given atom matches this IQueryAtom.
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.TotalHCountAtom: Deprecated.

Check if the total hydrogen count of the atom is equal to the query.
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.TotalRingConnectionAtom: Deprecated.

Returns true of the given atom matches this IQueryAtom.
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.TotalValencyAtom: Deprecated.

Returns true of the given atom matches this IQueryAtom.
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolAndChargeQueryAtom: Deprecated.
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolChargeIDQueryAtom
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom: Deprecated.
matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom: Deprecated.

The matches implementation of the QueryAtom interface.
matches(IAtom) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryAtom: Checks whether this query atom matches a target atom.
matches(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.DfPattern: Determine if there is a mapping of this pattern in the target.
matches(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.Pattern: Determine if there is a mapping of this pattern in the target.
matches(IAtomContainer) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher: Performs the pharmacophore matching.
matches(IAtomContainer) - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool: Deprecated.

Perform a SMARTS match and check whether the query is present in the target molecule.
matches(IAtomContainer, boolean) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher: Performs the pharmacophore matching.
matches(IAtomContainer, boolean) - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool: Deprecated.

Perform a SMARTS match and check whether the query is present in the target molecule.
matches(IAtomContainer, IAtom) - Method in interface org.openscience.cdk.smsd.algorithm.matchers.AtomMatcher: Deprecated.
matches(IAtomContainer, IAtom) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultMCSPlusAtomMatcher: Deprecated.
matches(IAtomContainer, IAtom) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultRGraphAtomMatcher: Deprecated.
matches(IAtomContainer, IBond) - Method in interface org.openscience.cdk.smsd.algorithm.matchers.BondMatcher: Deprecated.
matches(IAtomContainer, IBond) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultBondMatcher: Deprecated.
matches(IAtom, int) - Method in class org.openscience.cdk.isomorphism.matchers.Expr
matches(IAtom, IAtom) - Method in class org.openscience.cdk.isomorphism.AtomMatcher: Are the semantics of atom1 compatible with atom2.
matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.CTFileQueryBond: Deprecated.
matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.Expr
matches(IBond) - Method in interface org.openscience.cdk.isomorphism.matchers.IQueryBond: Returns true of the given bond matches this IQueryBond.
matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.OrderQueryBond: Deprecated.
matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.OrderQueryBondOrderOnly: Deprecated.
matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Returns true of the given bond matches this IQueryBond.
matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AnyOrderQueryBond: Deprecated.
matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AromaticOrSingleQueryBond: Deprecated.
matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AromaticQueryBond: Deprecated.
matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond: Deprecated.
matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.OrderQueryBond: Deprecated.
matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RingBond: Deprecated.
matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.SMARTSBond: Deprecated.
matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.StereoBond: Deprecated.
matches(IBond) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryAngleBond: Checks whether the query angle constraint matches a target distance.
matches(IBond) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryBond: Checks whether the query distance constraint matches a target distance.
matches(IBond) - Method in class org.openscience.cdk.smsd.helper.BondEnergy: Deprecated.
matches(IBond, int) - Method in class org.openscience.cdk.isomorphism.matchers.Expr
matches(IBond, IBond) - Method in class org.openscience.cdk.isomorphism.BondMatcher: Determines if bond1 is compatible with bond2.
matches(IReaction) - Method in class org.openscience.cdk.isomorphism.Pattern: Determine if there is a mapping of this pattern in the target reaction.
matches(TargetProperties, IAtom) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFAtomMatcher: Deprecated.
matches(TargetProperties, IAtom) - Method in interface org.openscience.cdk.smsd.algorithm.matchers.VFAtomMatcher: Deprecated.
matches(TargetProperties, IBond) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFBondMatcher: Deprecated.
matches(TargetProperties, IBond) - Method in interface org.openscience.cdk.smsd.algorithm.matchers.VFBondMatcher: Deprecated.
matchesRoot(IAtom) - Method in class org.openscience.cdk.isomorphism.DfPattern: Test whether the pattern matches at the provided atom.
Matching - Class in org.openscience.cdk.graph: A matching is an independent edge set of a graph.
matchOccurence(int) - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupList: Matches the 'occurrence' condition with a provided maximum number of RGroup attachments.
matchOccurence(int) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList: Matches the 'occurrence' condition with a provided maximum number of RGroup attachments.
MatchResult(boolean, IChemFormat, int) - Constructor for class org.openscience.cdk.io.formats.IChemFormatMatcher.MatchResult
matrix - Variable in class org.openscience.cdk.math.Matrix: the content of this matrix
Matrix - Class in org.openscience.cdk.math: This class contains a matrix.
Matrix(double[][]) - Constructor for class org.openscience.cdk.math.Matrix: Creates a Matrix with content of an array.
Matrix(int, int) - Constructor for class org.openscience.cdk.math.Matrix: Creates a new Matrix.
MatrixNotInvertibleException - Exception in org.openscience.cdk.graph.invariant.exception
MatrixNotInvertibleException() - Constructor for exception org.openscience.cdk.graph.invariant.exception.MatrixNotInvertibleException
MAX_AXIS_ANGLE - Static variable in class org.openscience.cdk.stereo.StereoTool: The maximum angle in radians for two lines to be 'diaxial'.
MAX_FLAG_INDEX - Static variable in class org.openscience.cdk.CDKConstants: Maximum flags array index.
MAX_POINTER_INDEX - Static variable in class org.openscience.cdk.CDKConstants: Maximum pointers array index.
MaxDrawableAromaticRing() - Constructor for class org.openscience.cdk.renderer.generators.RingGenerator.MaxDrawableAromaticRing
maximalEntry(int, int, int, int, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Calculating the maximal entry for the indices.
maximalIndexWithNonZeroEntry(int[][], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: In case if the index' entry is zero, updating the index with next index with non-zero entry.
maximalMatrix(int[], int[][][]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Possible maximal edge multiplicity for the atom pair (i,j).
maxNextCharInd - Variable in class org.openscience.cdk.iupac.parser.SimpleCharStream
maxNextCharInd - Variable in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
maxX - Variable in class org.openscience.cdk.renderer.elements.Bounds: Maximum x/y coordinates.
maxY - Variable in class org.openscience.cdk.renderer.elements.Bounds: Maximum x/y coordinates.
Maygen - Class in org.openscience.cdk.structgen.maygen: The main class of the MAYGEN package.
Maygen(IChemObjectBuilder) - Constructor for class org.openscience.cdk.structgen.maygen.Maygen
Maygen.Consumer - Interface in org.openscience.cdk.structgen.maygen
Mc - Static variable in interface org.openscience.cdk.interfaces.IElement
mcb() - Static method in class org.openscience.cdk.graph.Cycles: Create a cycle finder which will compute the minimum cycle basis (MCB) of a molecule.
mcb(IAtomContainer) - Static method in class org.openscience.cdk.graph.Cycles: Find the minimum cycle basis (MCB) of a molecule.
McGregor - Class in org.openscience.cdk.smsd.algorithm.mcgregor: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
McGregor(IAtomContainer, IAtomContainer, List<List<Integer>>, boolean) - Constructor for class org.openscience.cdk.smsd.algorithm.mcgregor.McGregor: Deprecated.

Constructor for the McGregor algorithm.
McGregor(IQueryAtomContainer, IAtomContainer, List<List<Integer>>) - Constructor for class org.openscience.cdk.smsd.algorithm.mcgregor.McGregor: Deprecated.

Constructor for the McGregor algorithm.
McGregorChecks - Class in org.openscience.cdk.smsd.algorithm.mcgregor: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
McGregorChecks() - Constructor for class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks: Deprecated.
McgregorHelper - Class in org.openscience.cdk.smsd.algorithm.mcgregor: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
McgregorHelper(boolean, int, List<Integer>, int, int, List<Integer>, List<Integer>, List<String>, List<String>, int, int, List<Integer>, List<Integer>, List<String>, List<String>) - Constructor for class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper: Deprecated.

Stores the variables
MCSPlus - Class in org.openscience.cdk.smsd.algorithm.mcsplus: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
MCSPlus - org.openscience.cdk.smsd.interfaces.Algorithm: Deprecated.

MCS Plus algorithm.
MCSPlus() - Constructor for class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlus: Deprecated.

Default constructor added
MCSPlusHandler - Class in org.openscience.cdk.smsd.algorithm.mcsplus: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
MCSPlusHandler() - Constructor for class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler: Deprecated.

Constructor for the MCS Plus algorithm class
Md - Static variable in interface org.openscience.cdk.interfaces.IElement
MD - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
MDEC11 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
MDEC12 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
MDEC13 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
MDEC14 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
MDEC22 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
MDEC23 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
MDEC24 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
MDEC33 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
MDEC34 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
MDEC44 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
MDEDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Calculates the Molecular Distance Edge descriptor described in [Liu, S. et. al.. Journal of Chemical Information and Computer Sciences. 1998. 38].
MDEDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
MDEN11 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
MDEN12 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
MDEN13 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
MDEN22 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
MDEN23 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
MDEN33 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
MDEO11 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
MDEO12 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
MDEO22 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
MDLFormat - Class in org.openscience.cdk.io.formats: See here.
MDLFormat() - Constructor for class org.openscience.cdk.io.formats.MDLFormat
MDLMolConvention - Class in org.openscience.cdk.io.cml: Implementation of the MDLMol Covention for CML.
MDLMolConvention(IChemFile) - Constructor for class org.openscience.cdk.io.cml.MDLMolConvention
MDLMolConvention(ICMLModule) - Constructor for class org.openscience.cdk.io.cml.MDLMolConvention
MDLReader - Class in org.openscience.cdk.io: Deprecated.
This reader is only for molfiles without a version tag, typically the most common molfile now encountered is V2000 and the MDLV2000Reader should be used instead. The V2000 reader can actually read files missing the version tag when in relaxed mode.
MDLReader() - Constructor for class org.openscience.cdk.io.MDLReader: Deprecated.
MDLReader(InputStream) - Constructor for class org.openscience.cdk.io.MDLReader: Deprecated.

Constructs a new MDLReader that can read Molecule from a given InputStream.
MDLReader(InputStream, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLReader: Deprecated.
MDLReader(Reader) - Constructor for class org.openscience.cdk.io.MDLReader: Deprecated.

Constructs a new MDLReader that can read Molecule from a given Reader.
MDLReader(Reader, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLReader: Deprecated.
MDLRXNFormat - Class in org.openscience.cdk.io.formats: See here.
MDLRXNFormat() - Constructor for class org.openscience.cdk.io.formats.MDLRXNFormat
MDLRXNReader - Class in org.openscience.cdk.io: Deprecated.
Use V2000 or V3000
MDLRXNReader() - Constructor for class org.openscience.cdk.io.MDLRXNReader: Deprecated.
MDLRXNReader(InputStream) - Constructor for class org.openscience.cdk.io.MDLRXNReader: Deprecated.
MDLRXNReader(InputStream, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLRXNReader: Deprecated.
MDLRXNReader(Reader) - Constructor for class org.openscience.cdk.io.MDLRXNReader: Deprecated.

Constructs a new MDLReader that can read Molecule from a given Reader.
MDLRXNReader(Reader, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLRXNReader: Deprecated.
MDLRXNV2000Format - Class in org.openscience.cdk.io.formats: See here.
MDLRXNV2000Format() - Constructor for class org.openscience.cdk.io.formats.MDLRXNV2000Format
MDLRXNV2000Reader - Class in org.openscience.cdk.io: Reads a molecule from an MDL RXN file [Dalby, A. et. al.. Journal of Chemical Information and Computer Sciences. 1992. 32].
MDLRXNV2000Reader() - Constructor for class org.openscience.cdk.io.MDLRXNV2000Reader
MDLRXNV2000Reader(InputStream) - Constructor for class org.openscience.cdk.io.MDLRXNV2000Reader
MDLRXNV2000Reader(InputStream, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLRXNV2000Reader
MDLRXNV2000Reader(Reader) - Constructor for class org.openscience.cdk.io.MDLRXNV2000Reader: Constructs a new MDLReader that can read Molecule from a given Reader.
MDLRXNV2000Reader(Reader, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLRXNV2000Reader
MDLRXNV3000Format - Class in org.openscience.cdk.io.formats: See here.
MDLRXNV3000Format() - Constructor for class org.openscience.cdk.io.formats.MDLRXNV3000Format
MDLRXNV3000Reader - Class in org.openscience.cdk.io: Class that implements the new MDL mol format introduced in August 2002.
MDLRXNV3000Reader() - Constructor for class org.openscience.cdk.io.MDLRXNV3000Reader
MDLRXNV3000Reader(InputStream) - Constructor for class org.openscience.cdk.io.MDLRXNV3000Reader
MDLRXNV3000Reader(InputStream, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLRXNV3000Reader
MDLRXNV3000Reader(Reader) - Constructor for class org.openscience.cdk.io.MDLRXNV3000Reader
MDLRXNV3000Reader(Reader, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLRXNV3000Reader
MDLRXNWriter - Class in org.openscience.cdk.io: Writes a reaction to a MDL rxn or SDF file.
MDLRXNWriter() - Constructor for class org.openscience.cdk.io.MDLRXNWriter
MDLRXNWriter(OutputStream) - Constructor for class org.openscience.cdk.io.MDLRXNWriter: Constructs a new MDLWriter that can write an array of Molecules to a given OutputStream.
MDLRXNWriter(Writer) - Constructor for class org.openscience.cdk.io.MDLRXNWriter: Constructs a new MDLWriter that can write an array of Molecules to a Writer.
MDLV2000Format - Class in org.openscience.cdk.io.formats
MDLV2000Format() - Constructor for class org.openscience.cdk.io.formats.MDLV2000Format
MDLV2000Reader - Class in org.openscience.cdk.io: Reads content from MDL molfiles and SD files.
MDLV2000Reader() - Constructor for class org.openscience.cdk.io.MDLV2000Reader
MDLV2000Reader(InputStream) - Constructor for class org.openscience.cdk.io.MDLV2000Reader: Constructs a new MDLReader that can read Molecule from a given InputStream.
MDLV2000Reader(InputStream, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLV2000Reader
MDLV2000Reader(Reader) - Constructor for class org.openscience.cdk.io.MDLV2000Reader: Constructs a new MDLReader that can read Molecule from a given Reader.
MDLV2000Reader(Reader, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLV2000Reader
MDLV2000Writer - Class in org.openscience.cdk.io: Writes MDL molfiles, which contains a single molecule (see [Dalby, A. et. al.. Journal of Chemical Information and Computer Sciences. 1992. 32]).
MDLV2000Writer() - Constructor for class org.openscience.cdk.io.MDLV2000Writer
MDLV2000Writer(OutputStream) - Constructor for class org.openscience.cdk.io.MDLV2000Writer: Constructs a new MDLWriter that can write an IAtomContainer to a given OutputStream.
MDLV2000Writer(Writer) - Constructor for class org.openscience.cdk.io.MDLV2000Writer: Constructs a new MDLWriter that can write an IAtomContainer to the MDL molfile format.
MDLV2000Writer.SPIN_MULTIPLICITY - Enum in org.openscience.cdk.io: Enumeration of all valid radical values.
MDLV3000Format - Class in org.openscience.cdk.io.formats
MDLV3000Format() - Constructor for class org.openscience.cdk.io.formats.MDLV3000Format
MDLV3000Reader - Class in org.openscience.cdk.io: Class that implements the MDL mol V3000 format.
MDLV3000Reader() - Constructor for class org.openscience.cdk.io.MDLV3000Reader
MDLV3000Reader(InputStream) - Constructor for class org.openscience.cdk.io.MDLV3000Reader
MDLV3000Reader(InputStream, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLV3000Reader
MDLV3000Reader(Reader) - Constructor for class org.openscience.cdk.io.MDLV3000Reader
MDLV3000Reader(Reader, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLV3000Reader
MDLV3000Writer - Class in org.openscience.cdk.io: Ctab V3000 format output.
MDLV3000Writer() - Constructor for class org.openscience.cdk.io.MDLV3000Writer: Default empty constructor.
MDLV3000Writer(OutputStream) - Constructor for class org.openscience.cdk.io.MDLV3000Writer: Create a new V3000 writer, output to the provided JDK output stream.
MDLV3000Writer(Writer) - Constructor for class org.openscience.cdk.io.MDLV3000Writer: Create a new V3000 writer, output to the provided JDK writer.
MDMolecule - Class in org.openscience.cdk.libio.md
MDMolecule() - Constructor for class org.openscience.cdk.libio.md.MDMolecule
MDMolecule(IAtomContainer) - Constructor for class org.openscience.cdk.libio.md.MDMolecule
MDMoleculeConvention - Class in org.openscience.cdk.io.cml: Implements a Convention for parsing an MDMolecule from CML.
MDMoleculeConvention(IChemFile) - Constructor for class org.openscience.cdk.io.cml.MDMoleculeConvention
MDMoleculeConvention(ICMLModule) - Constructor for class org.openscience.cdk.io.cml.MDMoleculeConvention
MDMoleculeCustomizer - Class in org.openscience.cdk.libio.cml: Customize persistence of MDMolecule by adding support for residues and charge groups.
MDMoleculeCustomizer() - Constructor for class org.openscience.cdk.libio.cml.MDMoleculeCustomizer
mechanism - Variable in class org.openscience.cdk.reaction.ReactionEngine
MECURY - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
MEDIUM - org.openscience.cdk.io.setting.IOSetting.Importance
MEITMERIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Meitnerium - org.openscience.cdk.config.Elements
MEITNERIUM - Static variable in enum org.openscience.cdk.config.Elements
Mendelevium - org.openscience.cdk.config.Elements
MENDELEVIUM - Static variable in enum org.openscience.cdk.config.Elements
MENDELEVIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Mercury - org.openscience.cdk.config.Elements
MERCURY - Static variable in enum org.openscience.cdk.config.Elements
merge(ICountFingerprint) - Method in interface org.openscience.cdk.fingerprint.ICountFingerprint: Merge all from fp into the current fingerprint.
merge(ICountFingerprint) - Method in class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
METH - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
method1(ICountFingerprint, ICountFingerprint) - Static method in class org.openscience.cdk.similarity.Tanimoto: Calculates Tanimoto distance for two count fingerprints using method 1.
method2(ICountFingerprint, ICountFingerprint) - Static method in class org.openscience.cdk.similarity.Tanimoto: Calculates Tanimoto distance for two count fingerprints using method 2 [J.A. Grant, J.A. Haigh, B.T. Pickup, A. Nicholls and R.A. Sayle. J. Chem. Inf. Model.. 2006. 46].
Mg - Static variable in interface org.openscience.cdk.interfaces.IElement
MG - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
MIN_COLINEAR_NORMAL - Static variable in class org.openscience.cdk.stereo.StereoTool: The maximum tolerance for the normal calculated during colinearity.
minComponentIndex(Set<Integer>, int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Getting the minimum component index.
MinimalPathIterator - Class in org.openscience.cdk.graph: Deprecated.
use ShortestPaths
MinimalPathIterator(SimpleGraph, Object, Object) - Constructor for class org.openscience.cdk.graph.MinimalPathIterator: Deprecated.

Creates a minimal path iterator for the specified undirected graph.
MinimumCycleBasis - Class in org.openscience.cdk.graph: Compute the minimum cycle basis (MCB) of a graph.
MinimumCycleBasis(int[][]) - Constructor for class org.openscience.cdk.graph.MinimumCycleBasis: Generate the minimum cycle basis for a graph.
MINUS - org.openscience.cdk.stereo.StereoTool.TetrahedralSign
Minus1000 - org.openscience.cdk.formula.rules.MMElementRule.RangeMass: IMolecularFormula from a metabolite with a mass lower than 1000 Da.
Minus2000 - org.openscience.cdk.formula.rules.MMElementRule.RangeMass: IMolecularFormula from a metabolite with a mass lower than 2000 Da.
Minus3000 - org.openscience.cdk.formula.rules.MMElementRule.RangeMass: IMolecularFormula from a metabolite with a mass lower than 3000 Da.
Minus500 - org.openscience.cdk.formula.rules.MMElementRule.RangeMass: IMolecularFormula from a metabolite with a mass lower than 500 Da.
minX - Variable in class org.openscience.cdk.renderer.elements.Bounds: Minimum x/y coordinates.
minY - Variable in class org.openscience.cdk.renderer.elements.Bounds: Minimum x/y coordinates.
MM_TO_POINT - Static variable in class org.openscience.cdk.depict.Depiction: For converting MM coordinates to PS Point (1/72 inch)
MM2AtomTypeMatcher - Class in org.openscience.cdk.atomtype: Deprecated.
Incomplete and error prone - use at your own risk.
MM2AtomTypeMatcher() - Constructor for class org.openscience.cdk.atomtype.MM2AtomTypeMatcher: Deprecated.

Constructor for the MMFF94AtomTypeMatcher object.
MM2BasedAtomTypePattern - Class in org.openscience.cdk.modeling.builder3d: Class stores hose code patterns to identify mm2 force field atom types.
MM2BasedParameterSetReader - Class in org.openscience.cdk.modeling.builder3d: AtomType list configurator that uses the ParameterSet originally defined in mm2.prm from tinker.
MM2BasedParameterSetReader() - Constructor for class org.openscience.cdk.modeling.builder3d.MM2BasedParameterSetReader: Constructor for the MM2BasedParameterSetReader object.
MMElementRule - Class in org.openscience.cdk.formula.rules: This class validate if the occurrence of the IElements in the IMolecularFormula, for metabolites, are into a maximal limit according paper: .
MMElementRule() - Constructor for class org.openscience.cdk.formula.rules.MMElementRule: Constructor for the MMElementRule object.
MMElementRule.Database - Enum in org.openscience.cdk.formula.rules: A enumeration of the possible databases according the rules.
MMElementRule.RangeMass - Enum in org.openscience.cdk.formula.rules: A enumeration of the possible mass range according the rules.
Mmff - Class in org.openscience.cdk.forcefield.mmff: Facade to access Merck Molecular Force Field (MMFF) functions.
Mmff() - Constructor for class org.openscience.cdk.forcefield.mmff.Mmff
MMFF_94_CHARGE - Static variable in class org.openscience.cdk.charges.MMFF94PartialCharges
MMFF94AtomTypeMatcher - Class in org.openscience.cdk.atomtype: Deprecated.
use the newer Mmff.assignAtomTypes()
MMFF94AtomTypeMatcher() - Constructor for class org.openscience.cdk.atomtype.MMFF94AtomTypeMatcher: Deprecated.

Constructor for the MMFF94AtomTypeMatcher object.
MMFF94BasedAtomTypePattern - Class in org.openscience.cdk.modeling.builder3d: Deprecated.
Mmff is faster more robust and fully validated
MMFF94BasedParameterSetReader - Class in org.openscience.cdk.modeling.builder3d: AtomType list configurator that uses the ParameterSet originally defined in mmff94.prm from moe.
MMFF94BasedParameterSetReader() - Constructor for class org.openscience.cdk.modeling.builder3d.MMFF94BasedParameterSetReader: Constructor for the MM2BasedParameterSetReader object
MMFF94ParametersCall - Class in org.openscience.cdk.modeling.builder3d: Set the right atoms order to get the parameters.
MMFF94ParametersCall() - Constructor for class org.openscience.cdk.modeling.builder3d.MMFF94ParametersCall
MMFF94PartialCharges - Class in org.openscience.cdk.charges: The calculation of the MMFF94 partial charges.
MMFF94PartialCharges() - Constructor for class org.openscience.cdk.charges.MMFF94PartialCharges: Constructor for the MMFF94PartialCharges object
MMODFormat - Class in org.openscience.cdk.io.formats: See here.
MMODFormat() - Constructor for class org.openscience.cdk.io.formats.MMODFormat
Mn - Static variable in interface org.openscience.cdk.interfaces.IElement
MN - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Mo - Static variable in interface org.openscience.cdk.interfaces.IElement
MO - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
mode - Variable in class org.openscience.cdk.io.DefaultChemObjectReader
mode - Variable in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader
mode - Variable in class org.openscience.cdk.io.random.DefaultRandomAccessChemObjectReader
MODE_EXACT - Static variable in class org.openscience.cdk.smarts.SmartsFragmentExtractor: Sets the mode of the extractor to produce exact SMARTS.
MODE_JCOMPOUNDMAPPER - Static variable in class org.openscience.cdk.smarts.SmartsFragmentExtractor: Sets the mode of the extractor to produce SMARTS similar to JCompoundMapper.
model - Variable in class org.openscience.cdk.depict.Depiction
model2Molecule(Model, IChemObjectBuilder) - Static method in class org.openscience.cdk.libio.jena.Convertor: Converts a Model into an IAtomContainer using the given IChemObjectBuilder.
ModelBuilder3D - Class in org.openscience.cdk.modeling.builder3d: The main class to generate the 3D coordinates of a molecule ModelBuilder3D.
modelCenter - Variable in class org.openscience.cdk.renderer.AbstractRenderer: The center point of the model (IAtomContainer, IAtomContainerSet, etc).
modify(T) - Method in interface org.openscience.cdk.DynamicFactory.CreationModifier
Mol2Format - Class in org.openscience.cdk.io.formats: See here.
Mol2Format() - Constructor for class org.openscience.cdk.io.formats.Mol2Format
Mol2Reader - Class in org.openscience.cdk.io: Reads a molecule from an Mol2 file, such as written by Sybyl.
Mol2Reader() - Constructor for class org.openscience.cdk.io.Mol2Reader
Mol2Reader(InputStream) - Constructor for class org.openscience.cdk.io.Mol2Reader
Mol2Reader(Reader) - Constructor for class org.openscience.cdk.io.Mol2Reader: Constructs a new MDLReader that can read Molecule from a given Reader.
Mol2Writer - Class in org.openscience.cdk.io: An output Writer that writes molecular data into the Tripos Mol2 format.
Mol2Writer() - Constructor for class org.openscience.cdk.io.Mol2Writer
Mol2Writer(OutputStream) - Constructor for class org.openscience.cdk.io.Mol2Writer
Mol2Writer(Writer) - Constructor for class org.openscience.cdk.io.Mol2Writer: Constructs a new Mol2 writer.
molecular() - Method in class org.openscience.cdk.hash.HashGeneratorMaker: Given the current configuration create an MoleculeHashGenerator.
MolecularFormula - Class in org.openscience.cdk.formula: Class defining a molecular formula object.
MolecularFormula - Class in org.openscience.cdk.silent: Class defining a molecular formula object.
MolecularFormula() - Constructor for class org.openscience.cdk.formula.MolecularFormula: Constructs an empty MolecularFormula.
MolecularFormula() - Constructor for class org.openscience.cdk.silent.MolecularFormula: Constructs an empty MolecularFormula.
MolecularFormulaChecker - Class in org.openscience.cdk.formula: Validate a molecular formula given in IMolecularformula object.
MolecularFormulaChecker(List<IRule>) - Constructor for class org.openscience.cdk.formula.MolecularFormulaChecker: Construct an instance of MolecularFormulaChecker.
MolecularFormulaGenerator - Class in org.openscience.cdk.formula: This class generates molecular formulas within given mass range and elemental composition.
MolecularFormulaGenerator(IChemObjectBuilder, double, double, MolecularFormulaRange) - Constructor for class org.openscience.cdk.formula.MolecularFormulaGenerator: Initiate the MolecularFormulaGenerator.
MolecularFormulaManipulator - Class in org.openscience.cdk.tools.manipulator: Class with convenience methods that provide methods to manipulate IMolecularFormula's.
MolecularFormulaManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
MolecularFormulaRange - Class in org.openscience.cdk.formula: Class defining a expanded molecular formula object.
MolecularFormulaRange() - Constructor for class org.openscience.cdk.formula.MolecularFormulaRange: Constructs an empty MolecularFormulaExpand.
MolecularFormulaRangeManipulator - Class in org.openscience.cdk.tools.manipulator: Class with convenience methods that provide methods to manipulate MolecularFormulaRange's.
MolecularFormulaRangeManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.MolecularFormulaRangeManipulator
molecularFormulas() - Method in class org.openscience.cdk.debug.DebugAdductFormula: Returns an Iterable for looping over all IMolecularFormula in this adduct formula.
molecularFormulas() - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet: Returns an Iterable for looping over all IMolecularFormula in this MolecularFormulaSet.
molecularFormulas() - Method in class org.openscience.cdk.formula.AdductFormula: Returns an Iterable for looping over all IMolecularFormula in this adduct formula.
molecularFormulas() - Method in class org.openscience.cdk.formula.MolecularFormulaSet: Returns an Iterable for looping over all IMolecularFormula in this MolecularFormulaSet.
molecularFormulas() - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet: Returns the array of IMolecularFormula of this chemObject.
molecularFormulas() - Method in class org.openscience.cdk.silent.AdductFormula: Returns an Iterable for looping over all IMolecularFormula in this adduct formula.
molecularFormulas() - Method in class org.openscience.cdk.silent.MolecularFormulaSet: Returns an Iterable for looping over all IMolecularFormula in this MolecularFormulaSet.
MolecularFormulaSet - Class in org.openscience.cdk.formula: Class defining an set object of MolecularFormulas.
MolecularFormulaSet - Class in org.openscience.cdk.silent: Class defining an set object of MolecularFormulas.
MolecularFormulaSet() - Constructor for class org.openscience.cdk.formula.MolecularFormulaSet: Constructs an empty MolecularFormulaSet.
MolecularFormulaSet() - Constructor for class org.openscience.cdk.silent.MolecularFormulaSet: Constructs an empty MolecularFormulaSet.
MolecularFormulaSet(IMolecularFormula) - Constructor for class org.openscience.cdk.formula.MolecularFormulaSet: Constructs a MolecularFormulaSet with a copy MolecularFormulaSet of another MolecularFormulaSet (A shallow copy, i.e., with the same objects as in the original MolecularFormulaSet).
MolecularFormulaSet(IMolecularFormula) - Constructor for class org.openscience.cdk.silent.MolecularFormulaSet: Constructs a MolecularFormulaSet with a copy MolecularFormulaSet of another MolecularFormulaSet (A shallow copy, i.e., with the same objects as in the original MolecularFormulaSet).
MolecularFormulaSetManipulator - Class in org.openscience.cdk.tools.manipulator: Class with convenience methods that provide methods to manipulate MolecularFormulaSet's.
MolecularFormulaSetManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.MolecularFormulaSetManipulator
molecule - Variable in class org.openscience.cdk.inchi.InChIToStructure
MOLECULE - Static variable in class org.openscience.cdk.libio.jena.CDK
molecule2Model(IAtomContainer) - Static method in class org.openscience.cdk.libio.jena.Convertor: Converts a IAtomContainer into a Model representation using the CDK OWL.
MoleculeBuilder - Class in org.openscience.cdk.iupac.parser: Takes in parsed Tokens from NomParser and contains rules to convert those tokens to a Molecule.
MoleculeBuilder() - Constructor for class org.openscience.cdk.iupac.parser.MoleculeBuilder: Instantiates a builder using the DefaultChemObjectBuilder.
MoleculeBuilder(IChemObjectBuilder) - Constructor for class org.openscience.cdk.iupac.parser.MoleculeBuilder
moleculeCustomProperty - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
MoleculeFactory - Class in org.openscience.cdk.templates: Deprecated.
Old CDK class primarily for testing, for CDK Tests please use TestMoleculeFactory in cdk-data (testjar).
MoleculeFactory() - Constructor for class org.openscience.cdk.templates.MoleculeFactory: Deprecated.
MoleculeFeaturesTool - Class in org.openscience.cdk.tools.features: Utility that helps determine which data features are present.
MoleculeFeaturesTool() - Constructor for class org.openscience.cdk.tools.features.MoleculeFeaturesTool
MoleculeFromSignatureBuilder - Class in org.openscience.cdk.signature: Builds a molecule from a signature.
MoleculeFromSignatureBuilder(IChemObjectBuilder) - Constructor for class org.openscience.cdk.signature.MoleculeFromSignatureBuilder: Uses the chem object builder for making molecules.
MoleculeGraphs - Class in org.openscience.cdk.graph: Deprecated.
MoleculeHashGenerator - Interface in org.openscience.cdk.hash: A hash function which generates a single 64-bit hash code for a molecule.
MoleculeSanityCheck - Class in org.openscience.cdk.smsd.tools: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
MoleculeSanityCheck() - Constructor for class org.openscience.cdk.smsd.tools.MoleculeSanityCheck: Deprecated.
MoleculeSetManipulator - Class in org.openscience.cdk.tools.manipulator
MoleculeSetManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
MoleculeSetRenderer - Class in org.openscience.cdk.renderer: A general renderer for IChemModels, IReactions, and IAtomContainers.
MoleculeSetRenderer(List<IGenerator<IAtomContainer>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.MoleculeSetRenderer: A renderer that generates diagrams using the specified generators and manages fonts with the supplied font manager.
MoleculeSetRenderer(RendererModel, List<IGenerator<IAtomContainer>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.MoleculeSetRenderer
MoleculeSignature - Class in org.openscience.cdk.signature: A molecule signature is a way to produce AtomSignatures and to get the canonical [Faulon, J. L., Collins, M. J., and Carr, R. D.. Journal of Chemical Information and Computer Sciences. 2004. 44] signature string for a molecule.
MoleculeSignature(IAtomContainer) - Constructor for class org.openscience.cdk.signature.MoleculeSignature: Creates a signature that represents this molecule.
MoleculeSignature(IAtomContainer, int) - Constructor for class org.openscience.cdk.signature.MoleculeSignature: Creates a signature with a maximum height of height for molecule molecule.
MoleculeSignatureLabellingAdaptor - Class in org.openscience.cdk.smsd.labelling: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
MoleculeSignatureLabellingAdaptor() - Constructor for class org.openscience.cdk.smsd.labelling.MoleculeSignatureLabellingAdaptor: Deprecated.
MolHandler - Class in org.openscience.cdk.smsd.tools: Deprecated.
A more recent version of SMSD is available at http://github.com/asad/smsd
MolHandler(String, boolean, boolean) - Constructor for class org.openscience.cdk.smsd.tools.MolHandler: Deprecated.

Creates a new instance of MolHandler
MolHandler(IAtomContainer, boolean, boolean) - Constructor for class org.openscience.cdk.smsd.tools.MolHandler: Deprecated.

Creates a new instance of MolHandler
MolWeight - Static variable in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: For use with AtomContainerManipulator.getMass(IAtomContainer).
MolWeight - Static variable in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: For use with MolecularFormulaManipulator.getMass(IMolecularFormula).
MolWeightIgnoreSpecified - Static variable in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: For use with AtomContainerManipulator.getMass(IAtomContainer).
MolWeightIgnoreSpecified - Static variable in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: For use with MolecularFormulaManipulator.getMass(IMolecularFormula).
Molybdenum - org.openscience.cdk.config.Elements
MOLYBDENUM - Static variable in enum org.openscience.cdk.config.Elements
MOLYBDENUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
MomentOfInertiaDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: A descriptor that calculates the moment of inertia and radius of gyration.
MomentOfInertiaDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor
MonoIsotopic - Static variable in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: For use with AtomContainerManipulator.getMass(IAtomContainer).
MonoIsotopic - Static variable in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: For use with MolecularFormulaManipulator.getMass(IMolecularFormula).
Monomer - Class in org.openscience.cdk: A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.
Monomer - Class in org.openscience.cdk.silent: A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.
Monomer() - Constructor for class org.openscience.cdk.Monomer: Constructs a new Monomer.
Monomer() - Constructor for class org.openscience.cdk.silent.Monomer: Constructs a new Monomer.
Monovalent - org.openscience.cdk.io.MDLV2000Writer.SPIN_MULTIPLICITY
MOPAC2002Format - Class in org.openscience.cdk.io.formats
MOPAC2002Format() - Constructor for class org.openscience.cdk.io.formats.MOPAC2002Format
MOPAC2007Format - Class in org.openscience.cdk.io.formats
MOPAC2007Format() - Constructor for class org.openscience.cdk.io.formats.MOPAC2007Format
MOPAC2009Format - Class in org.openscience.cdk.io.formats
MOPAC2009Format() - Constructor for class org.openscience.cdk.io.formats.MOPAC2009Format
MOPAC2012Format - Class in org.openscience.cdk.io.formats
MOPAC2012Format() - Constructor for class org.openscience.cdk.io.formats.MOPAC2012Format
MOPAC7Format - Class in org.openscience.cdk.io.formats
MOPAC7Format() - Constructor for class org.openscience.cdk.io.formats.MOPAC7Format
MOPAC7InputFormat - Class in org.openscience.cdk.io.formats
MOPAC7InputFormat() - Constructor for class org.openscience.cdk.io.formats.MOPAC7InputFormat
Mopac7Reader - Class in org.openscience.cdk.io: Reads MOPAC output, extracts several electronic parameters and assigns them as a molecule properties.
Mopac7Reader() - Constructor for class org.openscience.cdk.io.Mopac7Reader: Constructs a new Mopac7reader that can read a molecule.
Mopac7Reader(InputStream) - Constructor for class org.openscience.cdk.io.Mopac7Reader: Constructs a new Mopac7reader that can read a molecule from a given InputStream.
Mopac7Reader(Reader) - Constructor for class org.openscience.cdk.io.Mopac7Reader: Constructs a new Mopac7reader that can read a molecule from a given Reader.
Mopac7Writer - Class in org.openscience.cdk.io.program: Prepares input file for running MOPAC.
Mopac7Writer() - Constructor for class org.openscience.cdk.io.program.Mopac7Writer: Creates a writer to serialize a molecule as Mopac7 input.
Mopac7Writer(OutputStream) - Constructor for class org.openscience.cdk.io.program.Mopac7Writer: Creates a writer to serialize a molecule as Mopac7 input.
Mopac7Writer(Writer) - Constructor for class org.openscience.cdk.io.program.Mopac7Writer: Creates a writer to serialize a molecule as Mopac7 input.
MOPAC93Format - Class in org.openscience.cdk.io.formats
MOPAC93Format() - Constructor for class org.openscience.cdk.io.formats.MOPAC93Format
MOPAC97Format - Class in org.openscience.cdk.io.formats
MOPAC97Format() - Constructor for class org.openscience.cdk.io.formats.MOPAC97Format
MorganNumbersTools - Class in org.openscience.cdk.graph.invariant: Compute the extended connectivity values (Morgan Numbers) [Morgan, H.L.. J.Chem.Doc.. 1965. 5].
MorganNumbersTools() - Constructor for class org.openscience.cdk.graph.invariant.MorganNumbersTools
Moscovium - org.openscience.cdk.config.Elements
MoSSOutputFormat - Class in org.openscience.cdk.io.formats
MoSSOutputFormat() - Constructor for class org.openscience.cdk.io.formats.MoSSOutputFormat
MoSSOutputReader - Class in org.openscience.cdk.io: Reader for MoSS output files [Unknown BibTeXML type: BOR2002] which present the results of a substructure mining study.
MoSSOutputReader() - Constructor for class org.openscience.cdk.io.MoSSOutputReader: Create a reader for MoSS output files from an empty string.
MoSSOutputReader(InputStream) - Constructor for class org.openscience.cdk.io.MoSSOutputReader: Create a reader for MoSS output files from an InputStream.
MoSSOutputReader(Reader) - Constructor for class org.openscience.cdk.io.MoSSOutputReader: Create a reader for MoSS output files from a Reader.
MostAbundant - Static variable in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: For use with AtomContainerManipulator.getMass(IAtomContainer).
MostAbundant - Static variable in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: For use with MolecularFormulaManipulator.getMass(IMolecularFormula).
mouseClicked(MouseEvent) - Method in class org.openscience.cdk.controller.SwingMouseEventRelay
mouseClickedDouble(int, int) - Method in interface org.openscience.cdk.controller.IMouseEventRelay: Event to signal that a mouse button has been double clicked.
mouseClickedDown(int, int) - Method in interface org.openscience.cdk.controller.IMouseEventRelay: Event to signal that the left mouse button has been pushed but not released yet.
mouseClickedDownRight(int, int) - Method in interface org.openscience.cdk.controller.IMouseEventRelay: Event to signal that the right mouse button has been pushed but not released yet.
mouseClickedUp(int, int) - Method in interface org.openscience.cdk.controller.IMouseEventRelay: Event to signal that the left mouse button has been released.
mouseClickedUpRight(int, int) - Method in interface org.openscience.cdk.controller.IMouseEventRelay: Event to signal that the right mouse button has been released.
mouseDrag(int, int, int, int) - Method in interface org.openscience.cdk.controller.IMouseEventRelay: Event to signal that a mouse has been dragged from one point to a next.
mouseDragged(MouseEvent) - Method in class org.openscience.cdk.controller.SwingMouseEventRelay
mouseEnter(int, int) - Method in interface org.openscience.cdk.controller.IMouseEventRelay
mouseEntered(MouseEvent) - Method in class org.openscience.cdk.controller.SwingMouseEventRelay
mouseExit(int, int) - Method in interface org.openscience.cdk.controller.IMouseEventRelay
mouseExited(MouseEvent) - Method in class org.openscience.cdk.controller.SwingMouseEventRelay
mouseMove(int, int) - Method in interface org.openscience.cdk.controller.IMouseEventRelay: Event to signal that a mouse has been moved to the new coordinates.
mouseMoved(MouseEvent) - Method in class org.openscience.cdk.controller.SwingMouseEventRelay
mousePressed(MouseEvent) - Method in class org.openscience.cdk.controller.SwingMouseEventRelay
mouseReleased(MouseEvent) - Method in class org.openscience.cdk.controller.SwingMouseEventRelay
mouseWheelMovedBackward(int) - Method in interface org.openscience.cdk.controller.IMouseEventRelay: Event to signal that the mouse wheel has been rotated a certain amount backward.
mouseWheelMovedForward(int) - Method in interface org.openscience.cdk.controller.IMouseEventRelay: Event to signal that the mouse wheel has been rotated a certain amount forward.
moveTo(Point2d) - Method in class org.openscience.cdk.renderer.elements.path.PathBuilder: Make a move in the path, without drawing anything.
MoveTo - Class in org.openscience.cdk.renderer.elements.path: A MoveTo path element moves the drawing 'pen' without making any lines or curves and is commonly used to start a path or make gaps in the path.
MoveTo - org.openscience.cdk.renderer.elements.path.Type
MoveTo(double[]) - Constructor for class org.openscience.cdk.renderer.elements.path.MoveTo: Make a move to path element.
MoveTo(double, double) - Constructor for class org.openscience.cdk.renderer.elements.path.MoveTo: Make a move to path element.
MoveTo(Point2d) - Constructor for class org.openscience.cdk.renderer.elements.path.MoveTo: Make a move to path element.
MPQCFormat - Class in org.openscience.cdk.io.formats: See here.
MPQCFormat() - Constructor for class org.openscience.cdk.io.formats.MPQCFormat
Mt - Static variable in interface org.openscience.cdk.interfaces.IElement
mul(double) - Method in class org.openscience.cdk.math.IVector: Multiplication from a vectors with an double
mul(double) - Method in class org.openscience.cdk.math.Matrix: Multiplies a scalar with this Matrix.
mul(double) - Method in class org.openscience.cdk.math.Quaternion
mul(double) - Method in class org.openscience.cdk.math.Vector: Multiplikation from a vectors with an double
mul(double, IVector) - Method in class org.openscience.cdk.math.IVector: Multiplication from a vectors with an double
mul(Complex) - Method in class org.openscience.cdk.math.Complex: Multiply this value with a complex value
mul(Complex) - Method in class org.openscience.cdk.math.IMatrix: Multiplikation from a scalar and a matrix
mul(Complex, IMatrix) - Method in class org.openscience.cdk.math.IMatrix: Multiplikation from a scalar and a matrix
mul(IMatrix) - Method in class org.openscience.cdk.math.IMatrix: Multiplikation from two matrices
mul(IMatrix, IMatrix) - Method in class org.openscience.cdk.math.IMatrix: Multiplikation from two matrices
mul(IVector) - Method in class org.openscience.cdk.math.IMatrix: Multiplikation from a vector and a matrix
mul(IVector, IVector) - Method in class org.openscience.cdk.math.IMatrix: Multiplikation from a vector and a matrix
mul(Matrix) - Method in class org.openscience.cdk.math.Matrix: Multiplies this Matrix with another one.
mul(Quaternion) - Method in class org.openscience.cdk.math.Quaternion
mul(Vector) - Method in class org.openscience.cdk.math.Matrix: Multiplies a Vector with this Matrix.
multipliers - Variable in class org.openscience.cdk.AtomContainerSet: Defines the number of instances of a certain molecule in the set.
multipliers - Variable in class org.openscience.cdk.silent.AtomContainerSet: Defines the number of instances of a certain molecule in the set.
multiply(double) - Method in class org.openscience.cdk.graph.invariant.GIMatrix: Returns the result of the scalar multiplication of the matrix, that is the multiplication of every of its elements by a given number.
multiply(GIMatrix) - Method in class org.openscience.cdk.graph.invariant.GIMatrix: Returns the result of the matrix multiplication of this matrix by another one.
multiply(Permutation) - Method in class org.openscience.cdk.group.Permutation: Multiply this permutation by another such that for all i, this[i] = this[other[i]].
multiplyLine(int, double) - Method in class org.openscience.cdk.graph.invariant.GIMatrix: Returns the resulting matrix of an elementary linear operation that consists of multiplying a single line of the matrix by a constant.
MurckoFragmenter - Class in org.openscience.cdk.fragment: An implementation of the Murcko fragmenation method [Bemis, G.W. and Murcko, M.A. . Journal of Medicinal Chemistry. 1996. 39].
MurckoFragmenter() - Constructor for class org.openscience.cdk.fragment.MurckoFragmenter: Instantiate Murcko fragmenter.
MurckoFragmenter(boolean, int) - Constructor for class org.openscience.cdk.fragment.MurckoFragmenter: Instantiate Murcko fragmenter.
MurckoFragmenter(boolean, int, MoleculeHashGenerator) - Constructor for class org.openscience.cdk.fragment.MurckoFragmenter: Instantiate Murcko fragmenter.
mutate(IAtomContainer) - Method in class org.openscience.cdk.structgen.RandomGenerator: Randomly chooses four atoms and alters the bonding pattern between them according to rules described in "Faulon, JCICS 1996, 36, 731".

N

n - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
n() - Method in class org.openscience.cdk.DynamicFactory.ConstructorKey: Access the number of parameters in the constructor.
N - org.openscience.cdk.renderer.elements.TextGroupElement.Position
N - Static variable in interface org.openscience.cdk.interfaces.IElement: Nitrogen atomic number
N - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
N_CONNECTED_ATOMS - org.openscience.cdk.hash.BasicAtomEncoder: Encode the number of explicitly connected atoms (degree).
Na - Static variable in interface org.openscience.cdk.interfaces.IElement
NA - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
name - Variable in class org.openscience.cdk.io.setting.IOSetting
NAMES - Static variable in class org.openscience.cdk.CDKConstants: A List of names.
NAT_ABUN_COMP - Static variable in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
NAT_ABUN_COMP - Static variable in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
naturalAbundance - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Natural abundance of this isotope.
naturalAbundance - Variable in class org.openscience.cdk.Isotope: Natural abundance of this isotope.
naturalAbundance - Variable in class org.openscience.cdk.silent.Isotope: Natural abundance of this isotope.
Nb - Static variable in interface org.openscience.cdk.interfaces.IElement
NB - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
nComponents() - Method in class org.openscience.cdk.graph.ConnectedComponents
Nd - Static variable in interface org.openscience.cdk.interfaces.IElement
ND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Ne - Static variable in interface org.openscience.cdk.interfaces.IElement
NE - org.openscience.cdk.renderer.elements.TextGroupElement.Position
NE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
negate() - Method in class org.openscience.cdk.isomorphism.matchers.Expr: Negate the expression, the expression will not return true only if the condition is not met.
negate() - Method in class org.openscience.cdk.math.Quaternion
negate() - Method in class org.openscience.cdk.math.Vector: Negates this vector
NeighborList - Class in org.openscience.cdk.geometry.surface: Creates a list of atoms neighboring each atom in the molecule.
NeighborList(IAtom[], double) - Constructor for class org.openscience.cdk.geometry.surface.NeighborList
neighbors() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.NodeBuilder: Deprecated.

Returns neighbors.
neighbors() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.INode: Deprecated.

Returns neighbors.
neighboursInBlock(Set<Integer>, int) - Method in interface org.openscience.cdk.group.Refinable: Given a block (or cell) of a partition, determine the invariant that represents the intersection between the block and the neighbours of vertexIndex supplied.
Neodymium - org.openscience.cdk.config.Elements
NEODYMIUM - Static variable in enum org.openscience.cdk.config.Elements
NEODYMIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Neon - org.openscience.cdk.config.Elements
NEON - Static variable in enum org.openscience.cdk.config.Elements
Neptunium - org.openscience.cdk.config.Elements
NEPTUNIUM - Static variable in enum org.openscience.cdk.config.Elements
NEPTUNIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
net.sf.jniinchi - package net.sf.jniinchi
newAtom() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder: Create a new atom using the default constructor.
newAtom() - Method in class org.openscience.cdk.DefaultChemObjectBuilder: Create a new atom using the default constructor.
newAtom() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder: Create a new atom using the default constructor.
newAtom() - Method in class org.openscience.cdk.silent.SilentChemObjectBuilder: Create a new atom using the default constructor.
newAtomContainer() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder: Create a new atom container using the default constructor.
newAtomContainer() - Method in class org.openscience.cdk.DefaultChemObjectBuilder: Create a new atom container using the default constructor.
newAtomContainer() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder: Create a new atom container using the default constructor.
newAtomContainer() - Method in class org.openscience.cdk.silent.SilentChemObjectBuilder: Create a new atom container using the default constructor.
newAtomData() - Method in class org.openscience.cdk.io.cml.CMLCoreModule: Clean all data about read atoms.
newBond() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder: Create a new bond using the default constructor.
newBond() - Method in class org.openscience.cdk.DefaultChemObjectBuilder: Create a new bond using the default constructor.
newBond() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder: Create a new bond using the default constructor.
newBond() - Method in class org.openscience.cdk.silent.SilentChemObjectBuilder: Create a new bond using the default constructor.
newBondData() - Method in class org.openscience.cdk.io.cml.CMLCoreModule: Clean all data about read bonds.
newChemModel(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator: Create a new ChemModel containing an IAtomContainer.
newCrystalData() - Method in class org.openscience.cdk.io.cml.CMLCoreModule: Clean all data about read bonds.
newFormulaData() - Method in class org.openscience.cdk.io.cml.CMLCoreModule: Clean all data about read formulas.
newInstance(Class<T>, Object...) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder: Creates a new instance of an ICDKObject, using the constructor defined by the given parameters.
newInstance(Class<T>, Object...) - Method in class org.openscience.cdk.DefaultChemObjectBuilder: Creates a new instance of an ICDKObject, using the constructor defined by the given parameters.
newInstance(Class<T>, Object...) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder: Creates a new instance of an ICDKObject, using the constructor defined by the given parameters.
newInstance(Class<T>, Object...) - Method in class org.openscience.cdk.silent.SilentChemObjectBuilder: Creates a new instance of an ICDKObject, using the constructor defined by the given parameters.
newMolecule() - Method in class org.openscience.cdk.io.cml.CMLCoreModule: Clean all data about parsed data.
newMoleculeData() - Method in class org.openscience.cdk.io.cml.CMLCoreModule: Clean all data about the molecule itself.
NEWPS - net.sf.jniinchi.INCHI_OPTION
newReaction() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder: Create a new reaction using the default constructor.
newReaction() - Method in class org.openscience.cdk.DefaultChemObjectBuilder: Create a new reaction using the default constructor.
newReaction() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder: Create a new reaction using the default constructor.
newReaction() - Method in class org.openscience.cdk.silent.SilentChemObjectBuilder: Create a new reaction using the default constructor.
newSaturate(IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker: Saturates a molecule by setting appropriate bond orders.
newSaturate(IBond[], IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker: Saturates a set of Bonds in an AtomContainer.
newSaturate(IBond, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker: Saturate atom by adjusting its bond orders.
newSequence() - Method in class org.openscience.cdk.io.cml.PDBConvention
newToken(int) - Static method in class org.openscience.cdk.iupac.parser.Token
newToken(int) - Static method in class org.openscience.cdk.smiles.smarts.parser.Token
newToken(int, String) - Static method in class org.openscience.cdk.iupac.parser.Token: Returns a new Token object, by default.
newToken(int, String) - Static method in class org.openscience.cdk.smiles.smarts.parser.Token: Returns a new Token object, by default.
next - Variable in class org.openscience.cdk.iupac.parser.Token: A reference to the next regular (non-special) token from the input stream.
next - Variable in class org.openscience.cdk.smiles.smarts.parser.Token: A reference to the next regular (non-special) token from the input stream.
next() - Method in class org.openscience.cdk.graph.AtomContainerPermutor
next() - Method in class org.openscience.cdk.graph.MinimalPathIterator: Deprecated.
next() - Method in class org.openscience.cdk.io.iterator.IteratingMDLConformerReader
next() - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundASNReader
next() - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader
next() - Method in class org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader
next() - Method in class org.openscience.cdk.io.iterator.IteratingSDFReader: Returns the next IAtomContainer.
next() - Method in class org.openscience.cdk.io.iterator.IteratingSMILESReader: Get the next molecule from the stream.
next() - Method in class org.openscience.cdk.io.random.RandomAccessReader
next() - Method in class org.openscience.cdk.smsd.labelling.AtomContainerAtomPermutor: Deprecated.
nextCandidate() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IState: Deprecated.

Returns the next candidate match.
nextCandidate() - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFState: Deprecated.

Returns the next candidate match.
nextCount(int, int, int, int[], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Counting the occurrence of a value in a degree.
nextCount(int, int, int, List<String>, int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen
nextElement() - Method in class org.openscience.cdk.formula.rules.RDBERule.Combinations
nextIndex() - Method in class org.openscience.cdk.io.random.RandomAccessReader
nextState(Match) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IState: Deprecated.

Returns a state in which the atoms in match have been added to the current mapping.
nextState(Match) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFState: Deprecated.

Returns a state in which the atoms in match have been added to the current mapping.
nextStep(IAtomContainer, String[], int[][], int[], int[], int[], int[][], boolean[], int[], boolean[], int[], List<ArrayList<Permutation>>, int[], int[], int[], int[], int[], int[][][], int[][][], int[][][], int[][], int[][], boolean[], boolean[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Calling foward or backward function in a nextstep function.
nextToAromatic(IAtom) - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor.JPlogPCalculator
nextVASPToken(boolean) - Method in class org.openscience.cdk.io.VASPReader: Find the next token of an VASP file.
nextVASPTokenFollowing(String) - Method in class org.openscience.cdk.io.VASPReader: Find the next token of a VASP file beginning with the *next* line.
Nh - Static variable in interface org.openscience.cdk.interfaces.IElement
Ni - Static variable in interface org.openscience.cdk.interfaces.IElement
NI - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Nickel - org.openscience.cdk.config.Elements
NICKEL - Static variable in enum org.openscience.cdk.config.Elements
NICKEL - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Nihonium - org.openscience.cdk.config.Elements
Niobium - org.openscience.cdk.config.Elements
NIOBIUM - Static variable in enum org.openscience.cdk.config.Elements
NIOBIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
NITRILE - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
NITRO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Nitrogen - org.openscience.cdk.config.Elements
NITROGEN - Static variable in enum org.openscience.cdk.config.Elements
NitrogenRule - Class in org.openscience.cdk.formula.rules: This class validate if the rule of nitrogen is kept.
NitrogenRule() - Constructor for class org.openscience.cdk.formula.rules.NitrogenRule: Constructor for the NitrogenRule object.
NMRSHIFT_CARBON - Static variable in class org.openscience.cdk.CDKConstants: Carbon NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.
NMRSHIFT_DEUTERIUM - Static variable in class org.openscience.cdk.CDKConstants: Deuterium NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.
NMRSHIFT_FLUORINE - Static variable in class org.openscience.cdk.CDKConstants: Fluorine NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.
NMRSHIFT_HYDROGEN - Static variable in class org.openscience.cdk.CDKConstants: Hydrogen NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.
NMRSHIFT_NITROGEN - Static variable in class org.openscience.cdk.CDKConstants: Nitrogen NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.
NMRSHIFT_PHOSPORUS - Static variable in class org.openscience.cdk.CDKConstants: Phosphorus NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.
NMRSHIFT_SULFUR - Static variable in class org.openscience.cdk.CDKConstants: Sulfur NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.
NMRSIGNAL_INTENSITY - Static variable in class org.openscience.cdk.CDKConstants: NMR signal intensity constant for use as a key in the IChemObject.physicalProperties hashtable.
NMRSIGNAL_MULTIPLICITY - Static variable in class org.openscience.cdk.CDKConstants: NMR signal multiplicity constant for use as a key in the IChemObject.physicalProperties hashtable.
NMRSPECTYPE_1D - Static variable in class org.openscience.cdk.CDKConstants: NMR spectrum type constant for use as key for an arbitrary 1-dimensional NMR experiment.
NMRSPECTYPE_1D_DEPT135 - Static variable in class org.openscience.cdk.CDKConstants: NMR spectrum type constant for use as key for a 1-dimensional DEPT135 NMR experiment.
NMRSPECTYPE_1D_DEPT90 - Static variable in class org.openscience.cdk.CDKConstants: NMR spectrum type constant for use as key for a 1-dimensional DEPT90 NMR experiment.
NMRSPECTYPE_2D_HHCOSY - Static variable in class org.openscience.cdk.CDKConstants: NMR spectrum type constant for use as key for a 2-dimensional H,H-COSY NMR experiment.
NMRSPECTYPE_2D_HMBC - Static variable in class org.openscience.cdk.CDKConstants: NMR spectrum type constant for use as key for a 2-dimensional HMBC NMR experiment.
NMRSPECTYPE_2D_HSQC - Static variable in class org.openscience.cdk.CDKConstants: NMR spectrum type constant for use as key for a 2-dimensional HSQC NMR experiment.
NMRSPECTYPE_2D_INADEQUATE - Static variable in class org.openscience.cdk.CDKConstants: NMR spectrum type constant for use as key for a 2-dimensional INADEQUATE NMR experiment.
No - Static variable in interface org.openscience.cdk.interfaces.IElement
NO - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
NO_ATOMS - Static variable in class org.openscience.cdk.templates.AminoAcids
NO_BONDS - Static variable in class org.openscience.cdk.templates.AminoAcids
NO_GO - org.openscience.cdk.interfaces.IReaction.Direction: Reaction is a no-go, Often denoted by a cross or hash arrow.
NO_MATCH - Static variable in interface org.openscience.cdk.io.formats.IChemFormatMatcher: Convenience method for indicating a format did not match.
NoADP - net.sf.jniinchi.INCHI_OPTION
Nobelium - org.openscience.cdk.config.Elements
NOBELIUM - Static variable in enum org.openscience.cdk.config.Elements
NOBELIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Node - Interface in org.openscience.cdk.smiles.smarts.parser: Deprecated.
nodeArity() - Method in class org.openscience.cdk.smiles.smarts.parser.JJTSMARTSParserState
NodeBuilder - Class in org.openscience.cdk.smsd.algorithm.vflib.builder: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
NodeBuilder(VFAtomMatcher) - Constructor for class org.openscience.cdk.smsd.algorithm.vflib.builder.NodeBuilder: Deprecated.

Construct a node for a query atom
nodeCreated() - Method in class org.openscience.cdk.smiles.smarts.parser.JJTSMARTSParserState
nodes() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder: Deprecated.

Returns nodes of the query.
nodes() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQuery: Deprecated.

Returns nodes of the query.
NoHydrogenElement() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
NomParser - Class in org.openscience.cdk.iupac.parser: Deprecated.
The OPSIN (http://opsin.ch.cam.ac.uk/) tool offers a more comprehensive alternative to this parsers functionality.
NomParser(InputStream) - Constructor for class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Constructor with InputStream.
NomParser(InputStream, String) - Constructor for class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Constructor with InputStream and supplied encoding
NomParser(Reader) - Constructor for class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Constructor.
NomParser(NomParserTokenManager) - Constructor for class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Constructor with generated Token Manager.
NomParserConstants - Interface in org.openscience.cdk.iupac.parser: Token literal values and constants.
NomParserTokenManager - Class in org.openscience.cdk.iupac.parser: Token Manager.
NomParserTokenManager(SimpleCharStream) - Constructor for class org.openscience.cdk.iupac.parser.NomParserTokenManager: Constructor.
NomParserTokenManager(SimpleCharStream, int) - Constructor for class org.openscience.cdk.iupac.parser.NomParserTokenManager: Constructor.
Non - org.openscience.cdk.stereo.Stereocenters.Stereocenter: Non stereo-centre.
NON - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
NonCHHeavyAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
NonCHHeavyAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.NonCHHeavyAtom: Deprecated.

Creates a new instance
NonCHHeavyAtom() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
None - org.openscience.cdk.io.MDLV2000Writer.SPIN_MULTIPLICITY
None - org.openscience.cdk.ReactionRole
None - org.openscience.cdk.renderer.generators.standard.StandardGenerator.HighlightStyle: Ignore highlight hints.
None - org.openscience.cdk.ringsearch.AllRingsFinder.Threshold: Run without any threshold, possibly until the end of time itself.
None - org.openscience.cdk.stereo.Stereocenters.Type: A non-stereogenic atom.
NONE - org.openscience.cdk.geometry.cip.CIPTool.CIP_CHIRALITY
NONE - org.openscience.cdk.geometry.GeometryTools.CoordinateCoverage: Deprecated.

No atoms have coordinates.
NONE - org.openscience.cdk.geometry.GeometryUtil.CoordinateCoverage: No atoms have coordinates.
NONE - org.openscience.cdk.interfaces.IBond.Stereo: A bond for which there is no stereochemistry.
NONE - org.openscience.cdk.isomorphism.matchers.Expr.Type: Undefined expression type.
NONE - Static variable in class org.openscience.cdk.tools.DataFeatures: Indicated that no feature are defined.
nonHNeighbours(IAtom) - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor.JPlogPCalculator
NOOP_CONSUMER - Static variable in class org.openscience.cdk.structgen.maygen.Maygen
NORMAL - org.openscience.cdk.renderer.font.IFontManager.FontStyle: Regular font style.
NORMAL - Static variable in class org.openscience.cdk.renderer.GraphRendererModel: Paints the function normal
normalize() - Method in class org.openscience.cdk.math.Quaternion
normalize() - Method in class org.openscience.cdk.math.Vector: Normalize this vector
normalize() - Method in class org.openscience.cdk.stereo.Octahedral: Normalize the configuration to the lowest order (1).
normalize() - Method in class org.openscience.cdk.stereo.SquarePlanar: Normalize the configuration to the lowest configuration order (1) - U-shaped.
normalize() - Method in class org.openscience.cdk.stereo.TrigonalBipyramidal: Normalize the configuration to the lowest configuration order (1) - the axis goes from the first to last carrier, the three middle carriers are anti-clockwise looking from the first carrier.
normalize(Point3d) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Normalizes a point.
normalize(Point3d) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Normalizes a point.
normalize(IsotopePattern) - Static method in class org.openscience.cdk.formula.IsotopePatternManipulator: Return the isotope pattern normalized to the highest abundance.
normalize(IAtomContainer, Document) - Static method in class org.openscience.cdk.normalize.Normalizer: Deprecated.

The method takes an XML files like the following:
<replace-set>
<replace>O=N=O</replace>
<replacement>[O-][N+]=O</replacement>
</replace-set>
All parts in ac which are the same as replace will be changed according to replacement.
normalize(Matrix) - Method in class org.openscience.cdk.math.Matrix: Normalizes the vectors of this matrix.
normalizeFormula(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen
Normalizer - Class in org.openscience.cdk.normalize: Deprecated.
The functionality provided by with class is better suited to SMIRKS
Normalizer() - Constructor for class org.openscience.cdk.normalize.Normalizer: Deprecated.
NoSuchAtomException - Exception in org.openscience.cdk.exception: Exception that is thrown when an Atom is requested or required that does not exist in the relevant environment.
NoSuchAtomException(String) - Constructor for exception org.openscience.cdk.exception.NoSuchAtomException: Constructs a new NoSuchAtomException with the given message.
NoSuchAtomTypeException - Exception in org.openscience.cdk.exception: Exception that may be thrown when an atom type is looked up or perceived but no such atom type was found.
NoSuchAtomTypeException(String) - Constructor for exception org.openscience.cdk.exception.NoSuchAtomTypeException: Constructs a new NoSuchAtomTypeException.
NoSuchBondException - Exception in org.openscience.cdk.exception: Exception that is thrown when a Bond is requested or required that does not exist in the relevant environment.
NoSuchBondException(String) - Constructor for exception org.openscience.cdk.exception.NoSuchBondException: Constructs a new NoSuchBondException with the given message.
not(IQueryAtom) - Static method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom: Deprecated.

Negate the provided expression.
NOT - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if the subexpression is not true.
NOT - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
NotBond() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
NotExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
notify(String, String, int, int) - Method in class org.openscience.cdk.io.cml.CMLCoreModule
notifyChanged() - Method in class org.openscience.cdk.ChemObject: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged() - Method in class org.openscience.cdk.debug.DebugAminoAcid: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged() - Method in class org.openscience.cdk.debug.DebugAtom: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged() - Method in class org.openscience.cdk.debug.DebugAtomContainer: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged() - Method in class org.openscience.cdk.debug.DebugAtomType: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged() - Method in class org.openscience.cdk.debug.DebugBioPolymer: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged() - Method in class org.openscience.cdk.debug.DebugBond: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged() - Method in class org.openscience.cdk.debug.DebugChemFile: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged() - Method in class org.openscience.cdk.debug.DebugChemModel: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged() - Method in class org.openscience.cdk.debug.DebugChemObject: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged() - Method in class org.openscience.cdk.debug.DebugChemSequence: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged() - Method in class org.openscience.cdk.debug.DebugCrystal: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged() - Method in class org.openscience.cdk.debug.DebugElectronContainer: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged() - Method in class org.openscience.cdk.debug.DebugElement: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged() - Method in class org.openscience.cdk.debug.DebugFragmentAtom: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged() - Method in class org.openscience.cdk.debug.DebugIsotope: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged() - Method in class org.openscience.cdk.debug.DebugLonePair: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged() - Method in class org.openscience.cdk.debug.DebugMapping: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged() - Method in class org.openscience.cdk.debug.DebugMonomer: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged() - Method in class org.openscience.cdk.debug.DebugPolymer: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged() - Method in class org.openscience.cdk.debug.DebugPseudoAtom: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged() - Method in class org.openscience.cdk.debug.DebugReaction: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged() - Method in class org.openscience.cdk.debug.DebugReactionScheme: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged() - Method in class org.openscience.cdk.debug.DebugReactionSet: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged() - Method in class org.openscience.cdk.debug.DebugRing: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged() - Method in class org.openscience.cdk.debug.DebugSingleElectron: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged() - Method in class org.openscience.cdk.debug.DebugStrand: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged() - Method in class org.openscience.cdk.debug.DebugSubstance: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged() - Method in interface org.openscience.cdk.interfaces.IChemObject: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged() - Method in class org.openscience.cdk.silent.ChemObject: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.ChemObject: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugAminoAcid: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugAtom: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugAtomContainer: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugAtomType: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugBioPolymer: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugBond: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugChemFile: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugChemModel: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugChemObject: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugChemSequence: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugCrystal: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugElectronContainer: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugElement: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugIsotope: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugLonePair: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugMapping: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugMonomer: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugPolymer: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugPseudoAtom: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugReaction: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugReactionScheme: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugReactionSet: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugRing: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugSingleElectron: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugStrand: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugSubstance: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged(IChemObjectChangeEvent) - Method in interface org.openscience.cdk.interfaces.IChemObject: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.ChemObject: This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
notionalToCartesian(double, double, double, double, double, double) - Static method in class org.openscience.cdk.geometry.CrystalGeometryTools: Calculates Cartesian vectors for unit cell axes from axes lengths and angles between axes.
Np - Static variable in interface org.openscience.cdk.interfaces.IElement
NP - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
nPathsTo(int) - Method in class org.openscience.cdk.graph.ShortestPaths: Access the number of possible paths to the end vertex.
nPathsTo(IAtom) - Method in class org.openscience.cdk.graph.ShortestPaths: Access the number of possible paths to the end atom.
NS_CML - Static variable in class org.openscience.cdk.libio.cml.Convertor
NULLVECTOR - Static variable in class org.openscience.cdk.math.Vector: Null vector in 3 dimensional space
numAtoms - Variable in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
number() - Method in enum org.openscience.cdk.config.Elements: The atomic number of the element.
numberOfCycles() - Method in class org.openscience.cdk.graph.Cycles: How many cycles are stored.
numberOfElements() - Method in class org.openscience.cdk.group.Partition: Calculate the size of the partition as the sum of the sizes of the cells.
numberOfUnplacedHeavyAtoms(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D: Gets numberOfUnplacedHeavyAtoms (no Flag ISPLACED, no Hydrogens)
numCycles() - Method in interface org.openscience.cdk.ringsearch.CyclicVertexSearch: Returns the number of cycles (circuit rank, frère jacques number, num SSSR).
numeric() - Method in enum org.openscience.cdk.interfaces.IBond.Order: Access a numeric value for the number of bonded electron pairs.
NumericalSurface - Class in org.openscience.cdk.geometry.surface: A class representing the solvent accessible surface area surface of a molecule.
NumericalSurface(IAtomContainer) - Constructor for class org.openscience.cdk.geometry.surface.NumericalSurface: Constructor to initialize the surface calculation with default values.
NumericalSurface(IAtomContainer, double, int) - Constructor for class org.openscience.cdk.geometry.surface.NumericalSurface: Constructor to initialize the surface calculation with user specified values.
numOfPopulatedbins() - Method in interface org.openscience.cdk.fingerprint.ICountFingerprint: Returns the number of bins that are populated.
numOfPopulatedbins() - Method in class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
numRings() - Method in class org.openscience.cdk.ringsearch.RingSearch: Access the number of rings found (aka.
nValues(int, int, int[][]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Finding the neighbors of a given index.
NW - org.openscience.cdk.renderer.elements.TextGroupElement.Position
NWChemFormat - Class in org.openscience.cdk.io.formats: See here.
NWChemFormat() - Constructor for class org.openscience.cdk.io.formats.NWChemFormat

O

o - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
O - Static variable in interface org.openscience.cdk.interfaces.IElement: Oxygen atomic number
O - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
OATE - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
OBJECT_UNIQUE_POLICY - Static variable in class org.openscience.cdk.tools.IDCreator: New ID generation policy - to generate IDs unique only in a molecule
OC - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Octahedral (OC-6)
occupancies - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
OCT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Octahedral - Class in org.openscience.cdk.stereo: Represents an octahedral configuration of an atom six neighbors.
Octahedral - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Octahedral (OC-6)
Octahedral(IAtom, IAtom[], int) - Constructor for class org.openscience.cdk.stereo.Octahedral: Create a new octahedral configuration.
OCTAHEDRAL - org.openscience.cdk.stereo.StereoTool.StereoClass
of(IAtomContainer) - Static method in class org.openscience.cdk.stereo.Stereocenters: Determine the stereocenter atoms in the provided container based on connectivity.
ofClass(Class<T>) - Method in class org.openscience.cdk.DynamicFactory: Construct an implementation using the default constructor.
ofClass(Class<T>, Object...) - Method in class org.openscience.cdk.DynamicFactory: Construct an implementation using a constructor whose parameters match that of the provided objects.
OFF - Static variable in interface org.openscience.cdk.tools.ILoggingTool: Logging is OFF
Offset() - Constructor for class org.openscience.cdk.renderer.generators.AtomNumberGenerator.Offset
ofNumber(int) - Static method in enum org.openscience.cdk.config.Elements: Obtain the element with the specified atomic number.
ofString(String) - Static method in enum org.openscience.cdk.config.Elements: Obtain the element with the specified symbol or name.
ofType(IBond, int) - Static method in class org.openscience.cdk.isomorphism.matchers.CTFileQueryBond: Deprecated.

Create a CTFileQueryBond of the specified type (from the MDL spec).
ofValue(int) - Static method in enum org.openscience.cdk.io.MDLV2000Writer.SPIN_MULTIPLICITY: Create a SPIN_MULTIPLICITY instance for the specified value.
Og - Static variable in interface org.openscience.cdk.interfaces.IElement
Oganesson - org.openscience.cdk.config.Elements
OICACID - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
ok() - Method in class org.openscience.cdk.smarts.SmartsResult: Was the SMARTS parsed ok.
OKAY - net.sf.jniinchi.INCHI_RET
OL - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
OmitMajorIsotopes() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.OmitMajorIsotopes
ONE - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
ONE_FIVE_SHIFT - Static variable in class org.openscience.cdk.tautomers.InChITautomerGenerator: Generate InChI with -15T (1,5-shift tautomers) option.
oneAttachLocation() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Only one attach location specified, should be followed by a dash.
OneElectronJob - Class in org.openscience.cdk.math.qm: Calculates the orbitals and orbital energies of electron systems without electron electron interactions
OneElectronJob(Orbitals) - Constructor for class org.openscience.cdk.math.qm.OneElectronJob: Constructs a one electron job
openNodeScope(Node) - Method in class org.openscience.cdk.smiles.smarts.parser.JJTSMARTSParserState
OPPOSITE - org.openscience.cdk.interfaces.IDoubleBondStereochemistry.Conformation
OPPOSITE - Static variable in interface org.openscience.cdk.interfaces.IStereoElement
OptAlwaysV3000 - Static variable in class org.openscience.cdk.io.SDFWriter
OptForceWriteAs2DCoordinates - Static variable in class org.openscience.cdk.io.MDLV2000Writer
OptionIOSetting - Class in org.openscience.cdk.io.setting: An class for a reader setting which must be found in the list of possible settings.
OptionIOSetting(String, IOSetting.Importance, String, List<String>, String) - Constructor for class org.openscience.cdk.io.setting.OptionIOSetting: OptionIOSetting is IOSetting for which the value must be in the list of possible options.
options - Variable in class org.openscience.cdk.inchi.InChIGenerator
options - Variable in class org.openscience.cdk.inchi.InChIToStructure
OptProgramName - Static variable in class org.openscience.cdk.io.MDLV2000Writer
OptTruncateLongData - Static variable in class org.openscience.cdk.io.SDFWriter
OptWriteAgents - Static variable in class org.openscience.cdk.io.MDLRXNWriter
OptWriteAromaticBondTypes - Static variable in class org.openscience.cdk.io.MDLV2000Writer
OptWriteData - Static variable in class org.openscience.cdk.io.SDFWriter
OptWriteDefaultProperties - Static variable in class org.openscience.cdk.io.MDLV2000Writer
OptWriteMajorIsotopes - Static variable in class org.openscience.cdk.io.MDLV2000Writer
OptWriteQueryFormatValencies - Static variable in class org.openscience.cdk.io.MDLV2000Writer
or(IBitFingerprint) - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
or(IBitFingerprint) - Method in interface org.openscience.cdk.fingerprint.IBitFingerprint: Performs a logical OR of the bits in this target bit set with the bits in the argument fingerprint.
or(IBitFingerprint) - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
or(IntArrayFingerprint) - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
or(CycleFinder, CycleFinder) - Static method in class org.openscience.cdk.graph.Cycles: Use an auxiliary cycle finder if the primary method was intractable.
or(Expr) - Method in class org.openscience.cdk.isomorphism.matchers.Expr: Utility, combine this expression with another, using disjunction.
or(IQueryAtom, IQueryAtom) - Static method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom: Deprecated.

Disjunction the provided expressions.
OR - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if both either subexpressions are true.
OR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Orbit - Class in org.openscience.cdk.signature: A list of atom indices, and the label of the orbit.
Orbit(String, int) - Constructor for class org.openscience.cdk.signature.Orbit
orbital() - Method in class org.openscience.cdk.hash.HashGeneratorMaker: Discriminate atomic orbitals.
ORBITAL_HYBRIDIZATION - org.openscience.cdk.hash.BasicAtomEncoder: Encode the orbital hybridization of an atom.
Orbitals - Class in org.openscience.cdk.math.qm: This class represents a set of orbitals
Orbitals(IBasis) - Constructor for class org.openscience.cdk.math.qm.Orbitals: Constructs orbitals with a specified base set
Orbitals(IBasis, Matrix) - Constructor for class org.openscience.cdk.math.qm.Orbitals: Constructs orbitals with a specified base set and a coefficient matrix
OrBond() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
order - Variable in class org.openscience.cdk.Bond: The bond order of this bond.
order - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
order - Variable in class org.openscience.cdk.isomorphism.matchers.QueryBond: The bond order of this query bond.
order - Variable in class org.openscience.cdk.silent.Bond: The bond order of this bond.
order() - Method in class org.openscience.cdk.group.Partition: Sort the cells in increasing order.
order() - Method in class org.openscience.cdk.group.PermutationGroup: Calculates the size of the group.
order(ILigand[]) - Static method in class org.openscience.cdk.geometry.cip.CIPTool: Reorders the ILigand objects in the array according to the CIP rules.
ORDER - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if the bond order IBond.getOrder() equals the specified value and the bond, aromaticity is not check.
order2Resource(IBond.Order) - Static method in class org.openscience.cdk.libio.jena.Convertor: Create the Resource matching the given IBond.Order.
orderDegreeSymbols(int[], String[], int, int, int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Ordering degrees, hydrogens and symbols in ascending order
OrderQueryBond - Class in org.openscience.cdk.isomorphism.matchers: Deprecated.
OrderQueryBond - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
OrderQueryBond(IBond.Order, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.OrderQueryBond: Deprecated.

Creates a new instance
OrderQueryBond(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.OrderQueryBond: Deprecated.
OrderQueryBond(IQueryAtom, IQueryAtom, IBond.Order, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.OrderQueryBond: Deprecated.
OrderQueryBondOrderOnly - Class in org.openscience.cdk.isomorphism.matchers: Deprecated.
Use new QueryBond(beg, end, ORDER, bord)
OrderQueryBondOrderOnly(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.OrderQueryBondOrderOnly: Deprecated.
OrderQueryBondOrderOnly(IQueryAtom, IQueryAtom, IBond.Order, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.OrderQueryBondOrderOnly: Deprecated.
OrExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
org.openscience.cdk - package org.openscience.cdk
org.openscience.cdk.aromaticity - package org.openscience.cdk.aromaticity
org.openscience.cdk.atomtype - package org.openscience.cdk.atomtype
org.openscience.cdk.atomtype.mapper - package org.openscience.cdk.atomtype.mapper
org.openscience.cdk.charges - package org.openscience.cdk.charges
org.openscience.cdk.config - package org.openscience.cdk.config
org.openscience.cdk.config.atomtypes - package org.openscience.cdk.config.atomtypes
org.openscience.cdk.config.fragments - package org.openscience.cdk.config.fragments
org.openscience.cdk.config.isotopes - package org.openscience.cdk.config.isotopes
org.openscience.cdk.controller - package org.openscience.cdk.controller
org.openscience.cdk.debug - package org.openscience.cdk.debug
org.openscience.cdk.depict - package org.openscience.cdk.depict
org.openscience.cdk.dict - package org.openscience.cdk.dict
org.openscience.cdk.event - package org.openscience.cdk.event
org.openscience.cdk.exception - package org.openscience.cdk.exception
org.openscience.cdk.fingerprint - package org.openscience.cdk.fingerprint
org.openscience.cdk.fingerprint.model - package org.openscience.cdk.fingerprint.model
org.openscience.cdk.forcefield.mmff - package org.openscience.cdk.forcefield.mmff
org.openscience.cdk.formula - package org.openscience.cdk.formula
org.openscience.cdk.formula.rules - package org.openscience.cdk.formula.rules
org.openscience.cdk.fragment - package org.openscience.cdk.fragment
org.openscience.cdk.geometry - package org.openscience.cdk.geometry
org.openscience.cdk.geometry.alignment - package org.openscience.cdk.geometry.alignment
org.openscience.cdk.geometry.cip - package org.openscience.cdk.geometry.cip
org.openscience.cdk.geometry.cip.rules - package org.openscience.cdk.geometry.cip.rules
org.openscience.cdk.geometry.surface - package org.openscience.cdk.geometry.surface
org.openscience.cdk.geometry.volume - package org.openscience.cdk.geometry.volume
org.openscience.cdk.graph - package org.openscience.cdk.graph
org.openscience.cdk.graph.invariant - package org.openscience.cdk.graph.invariant
org.openscience.cdk.graph.invariant.exception - package org.openscience.cdk.graph.invariant.exception
org.openscience.cdk.graph.matrix - package org.openscience.cdk.graph.matrix
org.openscience.cdk.graph.rebond - package org.openscience.cdk.graph.rebond
org.openscience.cdk.group - package org.openscience.cdk.group
org.openscience.cdk.hash - package org.openscience.cdk.hash
org.openscience.cdk.hash.stereo - package org.openscience.cdk.hash.stereo
org.openscience.cdk.inchi - package org.openscience.cdk.inchi
org.openscience.cdk.index - package org.openscience.cdk.index
org.openscience.cdk.interfaces - package org.openscience.cdk.interfaces
org.openscience.cdk.io - package org.openscience.cdk.io
org.openscience.cdk.io.cml - package org.openscience.cdk.io.cml
org.openscience.cdk.io.formats - package org.openscience.cdk.io.formats
org.openscience.cdk.io.inchi - package org.openscience.cdk.io.inchi
org.openscience.cdk.io.iterator - package org.openscience.cdk.io.iterator
org.openscience.cdk.io.iterator.event - package org.openscience.cdk.io.iterator.event
org.openscience.cdk.io.listener - package org.openscience.cdk.io.listener
org.openscience.cdk.io.program - package org.openscience.cdk.io.program
org.openscience.cdk.io.pubchemxml - package org.openscience.cdk.io.pubchemxml
org.openscience.cdk.io.random - package org.openscience.cdk.io.random
org.openscience.cdk.io.rdf - package org.openscience.cdk.io.rdf
org.openscience.cdk.io.setting - package org.openscience.cdk.io.setting
org.openscience.cdk.isomorphism - package org.openscience.cdk.isomorphism
org.openscience.cdk.isomorphism.matchers - package org.openscience.cdk.isomorphism.matchers
org.openscience.cdk.isomorphism.matchers.smarts - package org.openscience.cdk.isomorphism.matchers.smarts
org.openscience.cdk.isomorphism.mcss - package org.openscience.cdk.isomorphism.mcss
org.openscience.cdk.iupac.parser - package org.openscience.cdk.iupac.parser
org.openscience.cdk.layout - package org.openscience.cdk.layout
org.openscience.cdk.libio.cml - package org.openscience.cdk.libio.cml
org.openscience.cdk.libio.jena - package org.openscience.cdk.libio.jena
org.openscience.cdk.libio.md - package org.openscience.cdk.libio.md
org.openscience.cdk.math - package org.openscience.cdk.math
org.openscience.cdk.math.qm - package org.openscience.cdk.math.qm
org.openscience.cdk.modeling.builder3d - package org.openscience.cdk.modeling.builder3d
org.openscience.cdk.normalize - package org.openscience.cdk.normalize
org.openscience.cdk.pharmacophore - package org.openscience.cdk.pharmacophore
org.openscience.cdk.protein - package org.openscience.cdk.protein
org.openscience.cdk.protein.data - package org.openscience.cdk.protein.data
org.openscience.cdk.qsar - package org.openscience.cdk.qsar
org.openscience.cdk.qsar.descriptors.atomic - package org.openscience.cdk.qsar.descriptors.atomic
org.openscience.cdk.qsar.descriptors.atompair - package org.openscience.cdk.qsar.descriptors.atompair
org.openscience.cdk.qsar.descriptors.bond - package org.openscience.cdk.qsar.descriptors.bond
org.openscience.cdk.qsar.descriptors.molecular - package org.openscience.cdk.qsar.descriptors.molecular
org.openscience.cdk.qsar.descriptors.protein - package org.openscience.cdk.qsar.descriptors.protein
org.openscience.cdk.qsar.descriptors.substance - package org.openscience.cdk.qsar.descriptors.substance
org.openscience.cdk.qsar.result - package org.openscience.cdk.qsar.result
org.openscience.cdk.reaction - package org.openscience.cdk.reaction
org.openscience.cdk.reaction.mechanism - package org.openscience.cdk.reaction.mechanism
org.openscience.cdk.reaction.type - package org.openscience.cdk.reaction.type
org.openscience.cdk.reaction.type.parameters - package org.openscience.cdk.reaction.type.parameters
org.openscience.cdk.renderer - package org.openscience.cdk.renderer
org.openscience.cdk.renderer.color - package org.openscience.cdk.renderer.color
org.openscience.cdk.renderer.elements - package org.openscience.cdk.renderer.elements
org.openscience.cdk.renderer.elements.path - package org.openscience.cdk.renderer.elements.path
org.openscience.cdk.renderer.font - package org.openscience.cdk.renderer.font
org.openscience.cdk.renderer.generators - package org.openscience.cdk.renderer.generators
org.openscience.cdk.renderer.generators.parameter - package org.openscience.cdk.renderer.generators.parameter
org.openscience.cdk.renderer.generators.standard - package org.openscience.cdk.renderer.generators.standard
org.openscience.cdk.renderer.selection - package org.openscience.cdk.renderer.selection
org.openscience.cdk.renderer.visitor - package org.openscience.cdk.renderer.visitor
org.openscience.cdk.ringsearch - package org.openscience.cdk.ringsearch
org.openscience.cdk.ringsearch.cyclebasis - package org.openscience.cdk.ringsearch.cyclebasis
org.openscience.cdk.sgroup - package org.openscience.cdk.sgroup
org.openscience.cdk.signature - package org.openscience.cdk.signature
org.openscience.cdk.silent - package org.openscience.cdk.silent
org.openscience.cdk.similarity - package org.openscience.cdk.similarity
org.openscience.cdk.smarts - package org.openscience.cdk.smarts
org.openscience.cdk.smiles - package org.openscience.cdk.smiles
org.openscience.cdk.smiles.smarts - package org.openscience.cdk.smiles.smarts
org.openscience.cdk.smiles.smarts.parser - package org.openscience.cdk.smiles.smarts.parser
org.openscience.cdk.smsd - package org.openscience.cdk.smsd
org.openscience.cdk.smsd.algorithm.matchers - package org.openscience.cdk.smsd.algorithm.matchers
org.openscience.cdk.smsd.algorithm.mcgregor - package org.openscience.cdk.smsd.algorithm.mcgregor
org.openscience.cdk.smsd.algorithm.mcsplus - package org.openscience.cdk.smsd.algorithm.mcsplus
org.openscience.cdk.smsd.algorithm.rgraph - package org.openscience.cdk.smsd.algorithm.rgraph
org.openscience.cdk.smsd.algorithm.single - package org.openscience.cdk.smsd.algorithm.single
org.openscience.cdk.smsd.algorithm.vflib - package org.openscience.cdk.smsd.algorithm.vflib
org.openscience.cdk.smsd.algorithm.vflib.builder - package org.openscience.cdk.smsd.algorithm.vflib.builder
org.openscience.cdk.smsd.algorithm.vflib.interfaces - package org.openscience.cdk.smsd.algorithm.vflib.interfaces
org.openscience.cdk.smsd.algorithm.vflib.map - package org.openscience.cdk.smsd.algorithm.vflib.map
org.openscience.cdk.smsd.algorithm.vflib.query - package org.openscience.cdk.smsd.algorithm.vflib.query
org.openscience.cdk.smsd.filters - package org.openscience.cdk.smsd.filters
org.openscience.cdk.smsd.global - package org.openscience.cdk.smsd.global
org.openscience.cdk.smsd.helper - package org.openscience.cdk.smsd.helper
org.openscience.cdk.smsd.interfaces - package org.openscience.cdk.smsd.interfaces
org.openscience.cdk.smsd.labelling - package org.openscience.cdk.smsd.labelling
org.openscience.cdk.smsd.ring - package org.openscience.cdk.smsd.ring
org.openscience.cdk.smsd.tools - package org.openscience.cdk.smsd.tools
org.openscience.cdk.stereo - package org.openscience.cdk.stereo
org.openscience.cdk.structgen - package org.openscience.cdk.structgen
org.openscience.cdk.structgen.maygen - package org.openscience.cdk.structgen.maygen
org.openscience.cdk.structgen.stochastic - package org.openscience.cdk.structgen.stochastic
org.openscience.cdk.structgen.stochastic.operator - package org.openscience.cdk.structgen.stochastic.operator
org.openscience.cdk.tautomers - package org.openscience.cdk.tautomers
org.openscience.cdk.templates - package org.openscience.cdk.templates
org.openscience.cdk.templates.saturatedhydrocarbons - package org.openscience.cdk.templates.saturatedhydrocarbons
org.openscience.cdk.tools - package org.openscience.cdk.tools
org.openscience.cdk.tools.diff - package org.openscience.cdk.tools.diff
org.openscience.cdk.tools.diff.tree - package org.openscience.cdk.tools.diff.tree
org.openscience.cdk.tools.features - package org.openscience.cdk.tools.features
org.openscience.cdk.tools.manipulator - package org.openscience.cdk.tools.manipulator
org.openscience.cdk.tools.periodictable - package org.openscience.cdk.tools.periodictable
org.openscience.cdk.validate - package org.openscience.cdk.validate
orthonormalize(Matrix) - Method in class org.openscience.cdk.math.Matrix: Orthonormalize the vectors of this matrix by Gram-Schmidt.
ORTHOPAIR - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor
Os - Static variable in interface org.openscience.cdk.interfaces.IElement
OS - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Osmium - org.openscience.cdk.config.Elements
OSMIUM - Static variable in enum org.openscience.cdk.config.Elements
OSMIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
other(int) - Method in class org.openscience.cdk.graph.Matching: Access the vertex matched with 'v'.
OuterGlow - org.openscience.cdk.renderer.generators.standard.StandardGenerator.HighlightStyle: An outer glow is placed in the background behind the depiction.
OuterGlowWhiteEdge - org.openscience.cdk.renderer.generators.standard.StandardGenerator.HighlightStyle: Same as outer glow but puts a white edge around element symbols.
OuterGlowWidth() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.OuterGlowWidth
outline(double) - Method in class org.openscience.cdk.renderer.elements.GeneralPath: Outline the general path with the specified stroke size.
outlineOf(Shape, double, Color) - Static method in class org.openscience.cdk.renderer.elements.GeneralPath: Create an outline path of the specified Java 2D Shape and color.
output - Variable in class org.openscience.cdk.inchi.InChIGenerator
output - Variable in class org.openscience.cdk.inchi.InChIToStructure
OutputSDF - net.sf.jniinchi.INCHI_OPTION
OVAL - org.openscience.cdk.renderer.generators.BasicAtomGenerator.Shape
OvalElement - Class in org.openscience.cdk.renderer.elements: An oval element (should) have both a width and a height.
OvalElement(double, double, double, boolean, Color) - Constructor for class org.openscience.cdk.renderer.elements.OvalElement
OvalElement(double, double, double, double, boolean, Color) - Constructor for class org.openscience.cdk.renderer.elements.OvalElement: Make an oval with a particular fill and color.
OvalElement(double, double, double, Color) - Constructor for class org.openscience.cdk.renderer.elements.OvalElement: Make an oval with the supplied radius.
OvalElement(double, double, Color) - Constructor for class org.openscience.cdk.renderer.elements.OvalElement: Make an oval with a default radius of 10.
OVERAREA - Static variable in class org.openscience.cdk.renderer.GraphRendererModel: Paints the area over the function
OverlapPair(IChemObject, IChemObject) - Constructor for class org.openscience.cdk.layout.OverlapResolver.OverlapPair: Deprecated.

Constructor for the OverlapPair object.
OverlapResolver - Class in org.openscience.cdk.layout: Deprecated.
does not resolve overlaps correctly
OverlapResolver() - Constructor for class org.openscience.cdk.layout.OverlapResolver: Deprecated.
OverlapResolver.OverlapPair - Class in org.openscience.cdk.layout: Deprecated.

A little helper class to store pairs of overlapping atoms.
OWLAtomTypeHandler - Class in org.openscience.cdk.config.atomtypes: SAX Handler for the OWLAtomTypeReader.
OWLAtomTypeHandler(IChemObjectBuilder) - Constructor for class org.openscience.cdk.config.atomtypes.OWLAtomTypeHandler: Constructs a new AtomTypeHandler and will create IAtomType implementations using the given IChemObjectBuilder.
OWLAtomTypeMappingHandler - Class in org.openscience.cdk.config.atomtypes: SAX Handler for the OWLAtomTypeMappingReader.
OWLAtomTypeMappingHandler() - Constructor for class org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingHandler: Constructs a new OWLAtomTypeMappingHandler.
OWLAtomTypeMappingReader - Class in org.openscience.cdk.config.atomtypes: XML Reader for the OWLBasedAtomTypeConfigurator.
OWLAtomTypeMappingReader(Reader) - Constructor for class org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingReader: Instantiates the XML based AtomTypeReader.
OWLAtomTypeReader - Class in org.openscience.cdk.config.atomtypes: XML Reader for the OWLBasedAtomTypeConfigurator.
OWLAtomTypeReader(Reader) - Constructor for class org.openscience.cdk.config.atomtypes.OWLAtomTypeReader: Instantiates the XML based AtomTypeReader.
OWLBasedAtomTypeConfigurator - Class in org.openscience.cdk.config: AtomType resource that reads the atom type configuration from an OWL file.
OWLBasedAtomTypeConfigurator() - Constructor for class org.openscience.cdk.config.OWLBasedAtomTypeConfigurator
OWLFile - Class in org.openscience.cdk.dict: Dictionary with entries build from an OWL file.
OWLFile() - Constructor for class org.openscience.cdk.dict.OWLFile
OWLReact - Class in org.openscience.cdk.dict: Dictionary with entries build from an OWL React.
OWLReact() - Constructor for class org.openscience.cdk.dict.OWLReact: Constructor of the OWLReact object.
OXO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Oxygen - org.openscience.cdk.config.Elements
OXYGEN - Static variable in enum org.openscience.cdk.config.Elements
OxygenAtomCountDescriptor - Class in org.openscience.cdk.qsar.descriptors.substance: Descriptor that returns the number of oxygens in the chemical formula.
OxygenAtomCountDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.substance.OxygenAtomCountDescriptor
OYLCHLORIDE - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.

P

p - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
P - Static variable in interface org.openscience.cdk.interfaces.IElement
P - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
P_AMINO_SULPHONIC_ACID - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor
Pa - Static variable in interface org.openscience.cdk.interfaces.IElement
PA - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Padding() - Constructor for class org.openscience.cdk.renderer.RendererModel.Padding
paint(IAtomContainer, IDrawVisitor) - Method in class org.openscience.cdk.renderer.AtomContainerRenderer: Paint an IChemObject.
paint(IAtomContainer, IDrawVisitor, Rectangle2D, boolean) - Method in class org.openscience.cdk.renderer.AtomContainerRenderer: Paint a molecule (an IAtomContainer).
paint(IAtomContainerSet, IDrawVisitor) - Method in class org.openscience.cdk.renderer.MoleculeSetRenderer: Paint an IChemObject.
paint(IAtomContainerSet, IDrawVisitor, Rectangle2D, boolean) - Method in class org.openscience.cdk.renderer.MoleculeSetRenderer: Paint a set of molecules.
paint(IChemModel, IDrawVisitor) - Method in class org.openscience.cdk.renderer.ChemModelRenderer: Paint an IChemModel using the IDrawVisitor at a scale determined by the bond length in RendererModel.
paint(IChemModel, IDrawVisitor, Rectangle2D, boolean) - Method in class org.openscience.cdk.renderer.ChemModelRenderer: Paint a ChemModel.
paint(IReaction, IDrawVisitor) - Method in class org.openscience.cdk.renderer.ReactionRenderer: Paint an IChemObject.
paint(IReaction, IDrawVisitor, Rectangle2D, boolean) - Method in class org.openscience.cdk.renderer.ReactionRenderer: Paint a reaction.
paint(IReactionSet, IDrawVisitor) - Method in class org.openscience.cdk.renderer.ReactionSetRenderer: Paint an IChemObject.
paint(IReactionSet, IDrawVisitor, Rectangle2D, boolean) - Method in class org.openscience.cdk.renderer.ReactionSetRenderer: Paint a set of reactions.
paint(IDrawVisitor, IRenderingElement) - Method in class org.openscience.cdk.renderer.AbstractRenderer: The target method for paintChemModel, paintReaction, and paintMolecule.
paint(T, IDrawVisitor) - Method in interface org.openscience.cdk.renderer.IRenderer: Paint an IChemObject.
paint(T, IDrawVisitor, Rectangle2D, boolean) - Method in interface org.openscience.cdk.renderer.IRenderer: Paint the chem object within the specified bounds.
Palladium - org.openscience.cdk.config.Elements
PALLADIUM - Static variable in enum org.openscience.cdk.config.Elements
PALLADIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Para - org.openscience.cdk.stereo.Stereocenters.Stereocenter: Atom resembles a stereo-centre (para).
ParameterReact - Class in org.openscience.cdk.reaction.type.parameters: Class which defines the allowed parameters of a reaction.
ParameterReact() - Constructor for class org.openscience.cdk.reaction.type.parameters.ParameterReact
paramsMap - Variable in class org.openscience.cdk.reaction.ReactionEngine
paramsMap2 - Variable in class org.openscience.cdk.reaction.ReactionEngine
parityARef1 - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
parityARef2 - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
parityARef3 - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
parityARef4 - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
parityAtomsGiven - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
parityGiven - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
parse(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser: This method parses a Smarts String and returns an instance of QueryAtomContainer
parse(BitSet, BitSet, boolean, boolean) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Parsing of the RGraph.
parse(BitSet, BitSet, boolean, boolean, TimeManager) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph: Deprecated.

Parsing of the CDKRGraph.
parse(IAtomContainer, String) - Static method in class org.openscience.cdk.smarts.Smarts: Parse the provided SMARTS string appending query atom/bonds to the provided molecule.
parse(IAtomContainer, String, int) - Static method in class org.openscience.cdk.smarts.Smarts: Parse the provided SMARTS string appending query atom/bonds to the provided molecule.
parseAtomCharges(XMLStreamReader, IAtomContainer) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
parseAtomElements(XMLStreamReader, IAtomContainer) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
parseAuxInfo(String, long[]) - Static method in class org.openscience.cdk.graph.invariant.InChINumbersTools: Parse the atom numbering from the auxinfo.
parseCompoundsBlock(XMLStreamReader) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
parseCtabKey(String) - Static method in enum org.openscience.cdk.sgroup.SgroupType
ParseException - Exception in org.openscience.cdk.iupac.parser: This exception is thrown when parse errors are encountered.
ParseException - Exception in org.openscience.cdk.smiles.smarts.parser: This exception is thrown when parse errors are encountered.
ParseException() - Constructor for exception org.openscience.cdk.iupac.parser.ParseException: The following constructors are for use by you for whatever purpose you can think of.
ParseException() - Constructor for exception org.openscience.cdk.smiles.smarts.parser.ParseException: The following constructors are for use by you for whatever purpose you can think of.
ParseException(String) - Constructor for exception org.openscience.cdk.iupac.parser.ParseException: Constructor with message.
ParseException(String) - Constructor for exception org.openscience.cdk.smiles.smarts.parser.ParseException: Constructor with message.
ParseException(Token, int[][], String[]) - Constructor for exception org.openscience.cdk.iupac.parser.ParseException: This constructor is used by the method "generateParseException" in the generated parser.
ParseException(Token, int[][], String[]) - Constructor for exception org.openscience.cdk.smiles.smarts.parser.ParseException: This constructor is used by the method "generateParseException" in the generated parser.
parseMolecule(XMLStreamReader, IChemObjectBuilder) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
parserAtomBlock(XMLStreamReader, IAtomContainer) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
parserBondBlock(XMLStreamReader, IAtomContainer) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
parserCompoundInfoData(XMLStreamReader, IAtomContainer) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
parserCoordBlock(XMLStreamReader, IAtomContainer) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
parseReactionSetSmiles(String) - Method in class org.openscience.cdk.smiles.SmilesParser: Parse a SMILES that describes a set of reactions representing multiple synthesis steps or a metabolic pathway.
parseReactionSmiles(String) - Method in class org.openscience.cdk.smiles.SmilesParser: Parse a reaction SMILES.
parseSmiles(String) - Method in class org.openscience.cdk.smiles.SmilesParser: Parses a SMILES string and returns a structure (IAtomContainer).
parseSubstance(XMLStreamReader) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
parseToResult(IAtomContainer, String) - Static method in class org.openscience.cdk.smarts.Smarts: Parse the provided SMARTS string appending query atom/bonds to the provided molecule.
parseToResult(IAtomContainer, String, int) - Static method in class org.openscience.cdk.smarts.Smarts: Parse the provided SMARTS string appending query atom/bonds to the provided molecule.
PART_OF_RING_OF_SIZE - Static variable in class org.openscience.cdk.CDKConstants: Used as property key for indicating the ring size of a certain atom type.
PARTIAL - org.openscience.cdk.geometry.GeometryTools.CoordinateCoverage: Deprecated.

At least one atom has coordinates but not all.
PARTIAL - org.openscience.cdk.geometry.GeometryUtil.CoordinateCoverage: At least one atom has coordinates but not all.
PartialAtomicChargeColors - Class in org.openscience.cdk.renderer.color: Class defining the color which with atoms are colored.
PartialAtomicChargeColors() - Constructor for class org.openscience.cdk.renderer.color.PartialAtomicChargeColors
partialCharges - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
partialCharges(IAtomContainer) - Method in class org.openscience.cdk.forcefield.mmff.Mmff: Assign the partial charges, all existing charges are cleared.
PartialFilledStructureMerger - Class in org.openscience.cdk.structgen.stochastic: Randomly generates a single, connected, correctly bonded structure from a number of fragments.
PartialFilledStructureMerger() - Constructor for class org.openscience.cdk.structgen.stochastic.PartialFilledStructureMerger: Constructor for the PartialFilledStructureMerger object.
PartialPiChargeDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic: The calculation of pi partial charges in pi-bonded systems of an heavy atom was made by Saller-Gasteiger.
PartialPiChargeDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor: Constructor for the PartialPiChargeDescriptor object
PartialSigmaChargeDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic: The calculation of sigma partial charges in sigma-bonded systems of an heavy atom was made by Marsilli-Gasteiger.
PartialSigmaChargeDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor: Constructor for the PartialSigmaChargeDescriptor object
PartialTChargeMMFF94Descriptor - Class in org.openscience.cdk.qsar.descriptors.atomic: The calculation of total partial charges of an heavy atom is based on MMFF94 model.
PartialTChargeMMFF94Descriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor: Constructor for the PartialTChargeMMFF94Descriptor object
PartialTChargePEOEDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic: The calculation of total partial charges of an heavy atom is based on Partial Equalization of Electronegativity method (PEOE-PEPE) from Gasteiger.
PartialTChargePEOEDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor: Constructor for the PartialTChargePEOEDescriptor object
Partition - Class in org.openscience.cdk.group: A partition of a set of integers, such as the discrete partition {{1}, {2}, {3}, {4}} or the unit partition {{1, 2, 3, 4}} or an intermediate like {{1, 2}, {3, 4}}.
Partition() - Constructor for class org.openscience.cdk.group.Partition: Creates a new, empty partition with no cells.
Partition(int[][]) - Constructor for class org.openscience.cdk.group.Partition: Constructor to make a partition from an array of int arrays.
Partition(Partition) - Constructor for class org.openscience.cdk.group.Partition: Copy constructor to make one partition from another.
partitionCriteria(int[], int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Partitioning criteria
partitionIntoMolecules(IAtomContainer) - Static method in class org.openscience.cdk.graph.ConnectivityChecker: Partitions the atoms in an AtomContainer into covalently connected components.
partitionIntoMolecules(IAtomContainer, int[]) - Static method in class org.openscience.cdk.graph.ConnectivityChecker: Split a molecule based on the provided component array.
partitionNonRingPartners(IAtom, IRing, IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.layout.RingPlacer: Partition the bonding partners of a given atom into ring atoms and non-ring atoms
partitionPartners(IAtom, IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.layout.AtomPlacer: Partition the bonding partners of a given atom into placed (coordinates assinged) and not placed.
PartitionRefinement - Class in org.openscience.cdk.group: Factory for partition refiners.
PartitionRefinement() - Constructor for class org.openscience.cdk.group.PartitionRefinement
PartitionRefinement.AtomRefinerBuilder - Class in org.openscience.cdk.group
PartitionRefinement.BondRefinerBuilder - Class in org.openscience.cdk.group
partitionRings(IRingSet) - Static method in class org.openscience.cdk.ringsearch.RingPartitioner: Partitions a RingSet into RingSets of connected rings.
PartitionRingsFromComplexRing(String) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor
PathBuilder - Class in org.openscience.cdk.renderer.elements.path: Builder class for paths.
PathBuilder() - Constructor for class org.openscience.cdk.renderer.elements.path.PathBuilder: Make a new path builder with a default color of black.
PathBuilder(Color) - Constructor for class org.openscience.cdk.renderer.elements.path.PathBuilder: Make a path builder that will make a path with a particular color.
PathEdge - Class in org.openscience.cdk.smsd.ring: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK and a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
PathEdge(List<IAtom>) - Constructor for class org.openscience.cdk.smsd.ring.PathEdge: Deprecated.
PathElement - Class in org.openscience.cdk.renderer.elements.path: A path element.
PathElement - Class in org.openscience.cdk.renderer.elements: A path composed of points.
PathElement(List<Point2d>, Color) - Constructor for class org.openscience.cdk.renderer.elements.PathElement: Make a path from the list of points.
PathElement(Type) - Constructor for class org.openscience.cdk.renderer.elements.path.PathElement: Create a path element.
PathGraph - Class in org.openscience.cdk.smsd.ring: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK and a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
PathGraph(IAtomContainer) - Constructor for class org.openscience.cdk.smsd.ring.PathGraph: Deprecated.
paths() - Method in class org.openscience.cdk.fingerprint.ShortestPathWalker: Access a set of all shortest paths.
paths() - Method in class org.openscience.cdk.graph.AllCycles: The paths describing all simple cycles in the given graph.
paths() - Method in class org.openscience.cdk.graph.Cycles
paths() - Method in class org.openscience.cdk.graph.EssentialCycles: The paths for each essential cycle.
paths() - Method in class org.openscience.cdk.graph.MinimumCycleBasis: The paths of all cycles in the minimum cycle basis.
paths() - Method in class org.openscience.cdk.graph.RelevantCycles: Reconstruct the paths of all relevant cycles.
paths() - Method in class org.openscience.cdk.graph.TripletShortCycles: Access the vertex paths for all cycles of the basis.
pathsTo(int) - Method in class org.openscience.cdk.graph.ShortestPaths: Reconstruct all shortest paths to the provided end vertex.
pathsTo(IAtom) - Method in class org.openscience.cdk.graph.ShortestPaths: Reconstruct all shortest paths to the provided end vertex.
pathTo(int) - Method in class org.openscience.cdk.graph.ShortestPaths: Reconstruct a shortest path to the provided end vertex.
pathTo(IAtom) - Method in class org.openscience.cdk.graph.ShortestPaths: Reconstruct a shortest path to the provided end atom.
PathTools - Class in org.openscience.cdk.graph: Tools class with methods for handling molecular graphs.
PathTools() - Constructor for class org.openscience.cdk.graph.PathTools
Pattern - Class in org.openscience.cdk.isomorphism: A structural pattern for finding an exact matching in a target compound.
Pattern() - Constructor for class org.openscience.cdk.isomorphism.Pattern
Pb - Static variable in interface org.openscience.cdk.interfaces.IElement
PB - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
pBlockMetals() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.
PBPY - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Pentagonal Bipyramidal (PBPY-7)
PCCompoundASNReader - Class in org.openscience.cdk.io: Reads an object from ASN formated input for PubChem Compound entries.
PCCompoundASNReader() - Constructor for class org.openscience.cdk.io.PCCompoundASNReader
PCCompoundASNReader(InputStream) - Constructor for class org.openscience.cdk.io.PCCompoundASNReader
PCCompoundASNReader(Reader) - Constructor for class org.openscience.cdk.io.PCCompoundASNReader: Construct a new reader from a Reader type object.
PCCompoundXMLReader - Class in org.openscience.cdk.io: Reads an object from ASN.1 XML formated input for PubChem Compound entries.
PCCompoundXMLReader() - Constructor for class org.openscience.cdk.io.PCCompoundXMLReader
PCCompoundXMLReader(InputStream) - Constructor for class org.openscience.cdk.io.PCCompoundXMLReader
PCCompoundXMLReader(Reader) - Constructor for class org.openscience.cdk.io.PCCompoundXMLReader: Construct a new reader from a Reader type object.
PCModelFormat - Class in org.openscience.cdk.io.formats: See here.
PCModelFormat() - Constructor for class org.openscience.cdk.io.formats.PCModelFormat
PCSubstanceXMLReader - Class in org.openscience.cdk.io: Reads an object from ASN formated input for PubChem Compound entries.
PCSubstanceXMLReader() - Constructor for class org.openscience.cdk.io.PCSubstanceXMLReader
PCSubstanceXMLReader(InputStream) - Constructor for class org.openscience.cdk.io.PCSubstanceXMLReader
PCSubstanceXMLReader(Reader) - Constructor for class org.openscience.cdk.io.PCSubstanceXMLReader: Construct a new reader from a Reader type object.
Pd - Static variable in interface org.openscience.cdk.interfaces.IElement
PD - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
PDBAtom - Class in org.openscience.cdk.protein.data: Represents the idea of an atom as used in PDB files.
PDBAtom - Class in org.openscience.cdk.silent: Represents the idea of an atom as used in PDB files.
PDBAtom(String) - Constructor for class org.openscience.cdk.protein.data.PDBAtom: Constructs an IPDBAtom from a String containing an element symbol.
PDBAtom(String) - Constructor for class org.openscience.cdk.silent.PDBAtom: Constructs an IPDBAtom from a String containing an element symbol.
PDBAtom(String, Point3d) - Constructor for class org.openscience.cdk.protein.data.PDBAtom: Constructs an IPDBAtom from an Element and a Point3d.
PDBAtom(String, Point3d) - Constructor for class org.openscience.cdk.silent.PDBAtom: Constructs an IPDBAtom from an Element and a Point3d.
PDBAtom(IElement) - Constructor for class org.openscience.cdk.protein.data.PDBAtom: Constructs an IPDBAtom from a Element.
PDBAtom(IElement) - Constructor for class org.openscience.cdk.silent.PDBAtom: Constructs an IPDBAtom from a Element.
PDBAtomCustomizer - Class in org.openscience.cdk.libio.cml: ICMLCustomizer for the libio-cml Convertor to be able to export details for IPDBAtom's.
PDBAtomCustomizer() - Constructor for class org.openscience.cdk.libio.cml.PDBAtomCustomizer
PDBConvention - Class in org.openscience.cdk.io.cml: Implements the PDB convention used by PDB2CML.
PDBConvention(IChemFile) - Constructor for class org.openscience.cdk.io.cml.PDBConvention
PDBConvention(ICMLModule) - Constructor for class org.openscience.cdk.io.cml.PDBConvention
PDBFormat - Class in org.openscience.cdk.io.formats: See here.
PDBFormat() - Constructor for class org.openscience.cdk.io.formats.PDBFormat
PDBMLFormat - Class in org.openscience.cdk.io.formats: XML version of the PDB format.
PDBMLFormat() - Constructor for class org.openscience.cdk.io.formats.PDBMLFormat
PDBMonomer - Class in org.openscience.cdk.protein.data: Represents the idea of an monomer as used in PDB files.
PDBMonomer - Class in org.openscience.cdk.silent: Represents the idea of an monomer as used in PDB files.
PDBMonomer() - Constructor for class org.openscience.cdk.protein.data.PDBMonomer
PDBMonomer() - Constructor for class org.openscience.cdk.silent.PDBMonomer
PDBPolymer - Class in org.openscience.cdk.protein.data: An entry in the PDB database.
PDBPolymer - Class in org.openscience.cdk.silent: An entry in the PDB database.
PDBPolymer() - Constructor for class org.openscience.cdk.protein.data.PDBPolymer: Constructs a new Polymer to store the IMonomers.
PDBPolymer() - Constructor for class org.openscience.cdk.silent.PDBPolymer: Constructs a new Polymer to store the IMonomers.
PDBReader - Class in org.openscience.cdk.io: Reads the contents of a PDBFile.
PDBReader() - Constructor for class org.openscience.cdk.io.PDBReader
PDBReader(InputStream) - Constructor for class org.openscience.cdk.io.PDBReader: Constructs a new PDBReader that can read Molecules from a given InputStream.
PDBReader(Reader) - Constructor for class org.openscience.cdk.io.PDBReader: Constructs a new PDBReader that can read Molecules from a given Reader.
PDBStrand - Class in org.openscience.cdk.protein.data: An entry in the PDB database.
PDBStrand() - Constructor for class org.openscience.cdk.protein.data.PDBStrand: Constructs a new Polymer to store the Monomers.
PDBStructure - Class in org.openscience.cdk.protein.data: Holder for secundary protein structure elements.
PDBStructure - Class in org.openscience.cdk.silent: Holder for secundary protein structure elements.
PDBStructure() - Constructor for class org.openscience.cdk.protein.data.PDBStructure
PDBStructure() - Constructor for class org.openscience.cdk.silent.PDBStructure
PDBWriter - Class in org.openscience.cdk.io: Saves small molecules in a rudimentary PDB format.
PDBWriter() - Constructor for class org.openscience.cdk.io.PDBWriter
PDBWriter(OutputStream) - Constructor for class org.openscience.cdk.io.PDBWriter
PDBWriter(Writer) - Constructor for class org.openscience.cdk.io.PDBWriter: Creates a PDB writer.
PDF_FMT - Static variable in class org.openscience.cdk.depict.Depiction: Portable Document Format (PDF) format key.
peekNode() - Method in class org.openscience.cdk.smiles.smarts.parser.JJTSMARTSParserState
PENT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
PentagonalBipyramidal - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Pentagonal Bipyramidal (PBPY-7)
perceiveAtomTypesAndConfigureAtoms(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator: Convenience method to perceive atom types for all IAtoms of all components of the provided IReaction.
perceiveAtomTypesAndConfigureUnsetProperties(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator: Convenience method to perceive atom types for all IAtoms of all components of the provided IReaction.
percieveAtomTypesAndConfigureAtoms(IAtomContainer) - Static method in class org.openscience.cdk.normalize.SMSDNormalizer: Deprecated.

Convenience method to perceive atom types for all IAtoms in the IAtomContainer, using the CDKAtomTypeMatcher.
percieveAtomTypesAndConfigureAtoms(IAtomContainer) - Static method in class org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator: Deprecated.

Convenience method to perceive atom types for all IAtoms in the IAtomContainer, using the CDKAtomTypeMatcher.
percieveAtomTypesAndConfigureAtoms(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Convenience method to perceive atom types for all IAtoms in the IAtomContainer, using the CDKAtomTypeMatcher.
percieveAtomTypesAndConfigureUnsetProperties(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Convenience method to perceive atom types for all IAtoms in the IAtomContainer, using the CDKAtomTypeMatcher.
perfect(int[][], BitSet) - Method in class org.openscience.cdk.graph.Matching: Attempt to augment the matching such that it is perfect over the subset of vertices in the provided graph.
period() - Method in enum org.openscience.cdk.config.Elements: Return the period in the periodic table this element belongs to.
PERIODIC_GROUP - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if the periodic table group of this atom is equal to the specified value.
PeriodicGroupNumber() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
PeriodicGroupNumberAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
PeriodicGroupNumberAtom(int, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.PeriodicGroupNumberAtom: Deprecated.

Creates a new instance
periodicTable - Variable in class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor
PeriodicTable - Class in org.openscience.cdk.tools.periodictable: Represents elements of the Periodic Table.
PeriodicTable() - Constructor for class org.openscience.cdk.tools.periodictable.PeriodicTable
PeriodicTablePositionDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic: This class returns the period in the periodic table of an atom belonging to an atom container Parameters for this descriptor: Name Default Description no parameters
PeriodicTablePositionDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor: Constructor for the PeriodicTablePositionDescriptor object
peripherals() - Method in class org.openscience.cdk.stereo.ExtendedTetrahedral: The neighbouring peripherals atoms, these are attached to the terminal atoms in the cumulated system.
Permutation - Class in org.openscience.cdk.group: A permutation with some associated methods to multiply, invert, and convert to cycle strings.
Permutation(int) - Constructor for class org.openscience.cdk.group.Permutation: Constructs an identity permutation with size elements.
Permutation(int...) - Constructor for class org.openscience.cdk.group.Permutation: Make a permutation from a set of values such that p[i] = x for the value x at position i.
Permutation(Permutation) - Constructor for class org.openscience.cdk.group.Permutation: Construct a permutation from another one by cloning the values.
PermutationGroup - Class in org.openscience.cdk.group: A permutation group with a Schreier-Sims representation.
PermutationGroup(int) - Constructor for class org.openscience.cdk.group.PermutationGroup: Make a group with just a single identity permutation of size n.
PermutationGroup(int, List<Permutation>) - Constructor for class org.openscience.cdk.group.PermutationGroup: Creates a group from a set of generators.
PermutationGroup(Permutation) - Constructor for class org.openscience.cdk.group.PermutationGroup: Creates the initial group, with the base base.
PermutationGroup.Backtracker - Interface in org.openscience.cdk.group: An interface for use with the apply method, which runs through all the permutations in this group.
permute(int[], IAtomContainer) - Static method in class org.openscience.cdk.smsd.labelling.AtomContainerAtomPermutor: Deprecated.
permuteArray(int[], int, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Permuting two entries of an Integer array.
Permutor - Class in org.openscience.cdk.graph: General permutation generator, that uses orderly generation by ranking and unranking.
Permutor - Class in org.openscience.cdk.smsd.labelling: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
Permutor(int) - Constructor for class org.openscience.cdk.graph.Permutor: Create a permutor that will generate permutations of numbers up to size.
Permutor(int) - Constructor for class org.openscience.cdk.smsd.labelling.Permutor: Deprecated.

Create a permutor that will generate permutations of numbers up to size.
perturbed() - Method in class org.openscience.cdk.hash.HashGeneratorMaker: Discriminate atoms experiencing uniform environments.
PetitjeanNumberDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: According to the Petitjean definition, the eccentricity of a vertex corresponds to the distance from that vertex to the most remote vertex in the graph.
PetitjeanNumberDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor: Constructor for the PetitjeanNumberDescriptor object
PetitjeanShapeIndexDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Evaluates the Petitjean shape indices, These original Petitjean number was described by Petitjean ([ Petitjean, M. . Journal of Chemical Information and Computer Science. 1992. 32]) and considered the molecular graph.
PetitjeanShapeIndexDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor
PharmacophoreAngleBond - Class in org.openscience.cdk.pharmacophore: Represents an angle relationship between three pharmacophore groups.
PharmacophoreAngleBond(PharmacophoreAtom, PharmacophoreAtom, PharmacophoreAtom) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreAngleBond: Create a pharmacophore distance constraint.
PharmacophoreAtom - Class in org.openscience.cdk.pharmacophore: A representation of a pharmacophore group.
PharmacophoreAtom(String, String, Point3d) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreAtom: Create a pharmacophore group.
PharmacophoreAtom(PharmacophoreAtom) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreAtom: Create a pharmacophore group.
PharmacophoreBond - Class in org.openscience.cdk.pharmacophore: Represents a distance relationship between two pharmacophore groups.
PharmacophoreBond(PharmacophoreAtom, PharmacophoreAtom) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreBond: Create a pharmacophore distance constraint.
PharmacophoreMatcher - Class in org.openscience.cdk.pharmacophore: Identifies atoms whose 3D arrangement matches a specified pharmacophore query.
PharmacophoreMatcher() - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreMatcher: An empty constructor.
PharmacophoreMatcher(PharmacophoreQuery) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreMatcher: Initialize the matcher with a query.
PharmacophoreQuery - Class in org.openscience.cdk.pharmacophore: Represents a colleciton of pharmacophore groups and constraints.
PharmacophoreQuery() - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreQuery
PharmacophoreQueryAngleBond - Class in org.openscience.cdk.pharmacophore: Represents a pharmacophore query angle constraint.
PharmacophoreQueryAngleBond() - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreQueryAngleBond
PharmacophoreQueryAngleBond(PharmacophoreQueryAtom, PharmacophoreQueryAtom, PharmacophoreQueryAtom, double) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreQueryAngleBond: Create a query angle constraint between three query groups.
PharmacophoreQueryAngleBond(PharmacophoreQueryAtom, PharmacophoreQueryAtom, PharmacophoreQueryAtom, double, double) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreQueryAngleBond: Create a query angle constraint between three query groups.
PharmacophoreQueryAtom - Class in org.openscience.cdk.pharmacophore: Represents a query pharmacophore group.
PharmacophoreQueryAtom(String, String) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreQueryAtom: Creat a new query pharmacophore group
PharmacophoreQueryBond - Class in org.openscience.cdk.pharmacophore: Represents a pharmacophore query distance constraint.
PharmacophoreQueryBond() - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreQueryBond
PharmacophoreQueryBond(PharmacophoreQueryAtom, PharmacophoreQueryAtom, double) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreQueryBond: Create a query distance constraint between two query groups.
PharmacophoreQueryBond(PharmacophoreQueryAtom, PharmacophoreQueryAtom, double, double) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreQueryBond: Create a query distance constraint between two query groups.
PharmacophoreUtils - Class in org.openscience.cdk.pharmacophore: Provides some utility methods for pharmacophore handling.
PharmacophoreUtils() - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreUtils
PHENYL - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Phosphorus - org.openscience.cdk.config.Elements
PHOSPHORUS - Static variable in enum org.openscience.cdk.config.Elements
PhysicalConstants - Class in org.openscience.cdk: An class providing predefined properties of physical constants.
PhysicalConstants() - Constructor for class org.openscience.cdk.PhysicalConstants
PI_BOND_COUNT - Static variable in class org.openscience.cdk.CDKConstants: Used as property key for indicating the HOSE code for a certain atom type.
PiBondingMovementReaction - Class in org.openscience.cdk.reaction.type: IReactionProcess which tries to reproduce the delocalization of electrons which are unsaturated bonds from conjugated rings.
PiBondingMovementReaction() - Constructor for class org.openscience.cdk.reaction.type.PiBondingMovementReaction: Constructor of the PiBondingMovementReaction object
piBonds() - Static method in class org.openscience.cdk.aromaticity.ElectronDonation: A very simple aromaticity model which only allows atoms adjacent to cyclic pi bonds.
pickBFgraph() - Method in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
pickDFgraph() - Method in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
PiContactDetectionDescriptor - Class in org.openscience.cdk.qsar.descriptors.atompair: This class checks if two atoms have pi-contact (this is true when there is one and the same conjugated pi-system which contains both atoms, or directly linked neighbours of the atoms).
PiContactDetectionDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor: Constructor for the PiContactDetectionDescriptor object.
PiElectronegativity - Class in org.openscience.cdk.charges: Calculation of the electronegativity of orbitals of a molecule by the method Gasteiger based on electronegativity is given by X = a + bq + c(q*q).
PiElectronegativity() - Constructor for class org.openscience.cdk.charges.PiElectronegativity: Constructor for the PiElectronegativity object.
PiElectronegativity(int, int) - Constructor for class org.openscience.cdk.charges.PiElectronegativity: Constructor for the Electronegativity object.
PiElectronegativityDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic: Pi electronegativity is given by X = a + bq + c(q*q) Parameters for this descriptor: Name Default Description maxIterations 0 Number of maximum iterations
PiElectronegativityDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor: Constructor for the PiElectronegativityDescriptor object
placeAliphaticHeavyChain(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D: Method assigns 3D coordinates to the heavy atoms in an aliphatic chain.
placeFusedRing(IRing, IAtomContainer, Vector2d, double) - Method in class org.openscience.cdk.layout.RingPlacer: Generated coordinates for a given ring, which is fused to another ring.
placeHydrogens2D(IAtomContainer, double) - Method in class org.openscience.cdk.layout.HydrogenPlacer: Place all hydrogens connected to atoms which have already been laid out.
placeHydrogens2D(IAtomContainer, IAtom) - Method in class org.openscience.cdk.layout.HydrogenPlacer: Place hydrogens connected to the given atom using the average bond length in the container.
placeHydrogens2D(IAtomContainer, IAtom, double) - Method in class org.openscience.cdk.layout.HydrogenPlacer: Place hydrogens connected to the provided atom atom using the specified bondLength.
placeLinearChain(IAtomContainer, Vector2d, double) - Method in class org.openscience.cdk.layout.AtomPlacer: Places the atoms in a linear chain.
placeRing(IRing, Point2d, double) - Method in class org.openscience.cdk.layout.RingPlacer: Place ring with default start angles, using RingPlacer.defaultAngles.
placeRing(IRing, Point2d, double, Map<Integer, Double>) - Method in class org.openscience.cdk.layout.RingPlacer: Place ring with user provided angles.
placeRing(IRing, IAtomContainer, Point2d, Vector2d, double) - Method in class org.openscience.cdk.layout.RingPlacer: Generated coordinates for a given ring.
placeRingSubstituents(IRingSet, double) - Method in class org.openscience.cdk.layout.RingPlacer: Positions the aliphatic substituents of a ring system
placeSpiroRing(IRing, IAtomContainer, Point2d, Vector2d, double) - Method in class org.openscience.cdk.layout.RingPlacer: Generated coordinates for a given ring, which is connected to a spiro ring.
PLANAR3 - org.openscience.cdk.interfaces.IAtomType.Hybridization
PLANE_TOLERANCE - Static variable in class org.openscience.cdk.stereo.StereoTool
Platinum - org.openscience.cdk.config.Elements
PLATINUM - Static variable in enum org.openscience.cdk.config.Elements
PLATINUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
PLUS - org.openscience.cdk.stereo.StereoTool.TetrahedralSign
PLUS - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
PLUTOMNIUM - Static variable in enum org.openscience.cdk.config.Elements: Deprecated.
Plutonium - org.openscience.cdk.config.Elements
PLUTONIUM - Static variable in enum org.openscience.cdk.config.Elements
PLUTONIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Pm - Static variable in interface org.openscience.cdk.interfaces.IElement
PM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
PMPConvention - Class in org.openscience.cdk.io.cml: Implementation of the PMPMol Covention for CML.
PMPConvention(IChemFile) - Constructor for class org.openscience.cdk.io.cml.PMPConvention
PMPConvention(ICMLModule) - Constructor for class org.openscience.cdk.io.cml.PMPConvention
PMPFormat - Class in org.openscience.cdk.io.formats
PMPFormat() - Constructor for class org.openscience.cdk.io.formats.PMPFormat
PMPReader - Class in org.openscience.cdk.io: Reads an frames from a PMP formated input.
PMPReader() - Constructor for class org.openscience.cdk.io.PMPReader
PMPReader(InputStream) - Constructor for class org.openscience.cdk.io.PMPReader
PMPReader(Reader) - Constructor for class org.openscience.cdk.io.PMPReader
PNG_FMT - Static variable in class org.openscience.cdk.depict.Depiction: Portable Network Graphics (PNG) format key.
Po - Static variable in interface org.openscience.cdk.interfaces.IElement
PO - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Point - Class in org.openscience.cdk.graph.rebond
Point(double, double, double) - Constructor for class org.openscience.cdk.graph.rebond.Point
point2d - Variable in class org.openscience.cdk.Atom: A 2D point specifying the location of this atom in a 2D coordinate space.
point2d - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom: A 2D point specifying the location of this atom in a 2D coordinate space.
point2d - Variable in class org.openscience.cdk.silent.Atom: A 2D point specifying the location of this atom in a 2D coordinate space.
Point2dDifference - Class in org.openscience.cdk.tools.diff.tree: Difference between two boolean[]'s.
point3d - Variable in class org.openscience.cdk.Atom: A 3 point specifying the location of this atom in a 3D coordinate space.
point3d - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom: A 3 point specifying the location of this atom in a 3D coordinate space.
point3d - Variable in class org.openscience.cdk.silent.Atom: A 3 point specifying the location of this atom in a 3D coordinate space.
Point3dDifference - Class in org.openscience.cdk.tools.diff.tree: Difference between two boolean[]'s.
points - Variable in class org.openscience.cdk.renderer.elements.PathElement: The points that make up the path.
points() - Method in class org.openscience.cdk.renderer.elements.path.Close: Get the points in the path.
points() - Method in class org.openscience.cdk.renderer.elements.path.CubicTo: Get the points in the path.
points() - Method in class org.openscience.cdk.renderer.elements.path.LineTo: Get the points in the path.
points() - Method in class org.openscience.cdk.renderer.elements.path.MoveTo: Get the points in the path.
points() - Method in class org.openscience.cdk.renderer.elements.path.PathElement: Deprecated.
points() - Method in class org.openscience.cdk.renderer.elements.path.QuadTo: Get the points in the path.
points(double[]) - Method in class org.openscience.cdk.renderer.elements.path.Close: Load the provided array with the specified coordinates of this path element.
points(double[]) - Method in class org.openscience.cdk.renderer.elements.path.CubicTo: Load the provided array with the specified coordinates of this path element.
points(double[]) - Method in class org.openscience.cdk.renderer.elements.path.LineTo: Load the provided array with the specified coordinates of this path element.
points(double[]) - Method in class org.openscience.cdk.renderer.elements.path.MoveTo: Load the provided array with the specified coordinates of this path element.
points(double[]) - Method in class org.openscience.cdk.renderer.elements.path.PathElement: Load the provided array with the specified coordinates of this path element.
points(double[]) - Method in class org.openscience.cdk.renderer.elements.path.QuadTo: Load the provided array with the specified coordinates of this path element.
polarAtomComparator(Point2d) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Sort the atoms using polar/radial coords around a central point in 2D.
polarAtomComparator(IAtom) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Sort the atoms using polar/radial coords around a central atom in 2D.
polarBondComparator(IAtom) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Sort the bonds using polar/radial coords around a central atom in 2D.
Polarizability - Class in org.openscience.cdk.charges: Calculation of the polarizability of a molecule by the method of Kang and Jhon and Gasteiger based on [Kang, Y.K. and Jhon, M.S.. Theoretica Chimica Acta. 1982. 61] and [Gasteiger, J. and Hutchings, M.G.. J. Amer. Chem. Soc.. 1984. 106] Limitations in parameterization of atoms: H, Csp3, Csp2, Csp2arom, Csp3, Nsp3, Nsp2, Nsp3, P, Osp3 and Osp2.
Polarizability() - Constructor for class org.openscience.cdk.charges.Polarizability: Constructor for the Polarizability object.
Polonium - org.openscience.cdk.config.Elements
POLONIUM - Static variable in enum org.openscience.cdk.config.Elements
POLONIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Polymer - Class in org.openscience.cdk: Subclass of Molecule to store Polymer specific attributes that a Polymer has.
Polymer - Class in org.openscience.cdk.silent: Subclass of Molecule to store Polymer specific attributes that a Polymer has.
Polymer() - Constructor for class org.openscience.cdk.Polymer: Constructs a new Polymer to store the Monomers.
Polymer() - Constructor for class org.openscience.cdk.silent.Polymer: Constructs a new Polymer to store the Monomers.
pop() - Method in class org.openscience.cdk.io.cml.CMLModuleStack: Retrieves and deletes to last added entry.
pop() - Method in class org.openscience.cdk.ringsearch.Queue: Deprecated.

Returns an Object from the queue
popNode() - Method in class org.openscience.cdk.smiles.smarts.parser.JJTSMARTSParserState
populatePolygonCorners(List<IAtom>, Point2d, double, double, double) - Method in class org.openscience.cdk.layout.AtomPlacer: Populates the corners of a polygon with atoms.
position - Variable in class org.openscience.cdk.renderer.elements.TextGroupElement.Child: The position of the child relative to the parent.
POSITION_FORMAT - Variable in class org.openscience.cdk.io.PDBWriter
possibleAtomTypes(IAtomContainer, IAtom) - Method in interface org.openscience.cdk.atomtype.IAtomTypeGuesser: Method that returns an iterator with a suitable list of atom types given the provided atom.
possibleAtomTypes(IAtomContainer, IAtom) - Method in class org.openscience.cdk.atomtype.StructGenAtomTypeGuesser: Finds the AtomType matching the Atom's element symbol, formal charge and hybridization state.
PostFilter - Class in org.openscience.cdk.smsd.filters: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
PostFilter() - Constructor for class org.openscience.cdk.smsd.filters.PostFilter: Deprecated.
Potassium - org.openscience.cdk.config.Elements
POTASSIUM - Static variable in enum org.openscience.cdk.config.Elements
POTASSIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Potential - org.openscience.cdk.stereo.Stereocenters.Stereocenter: Atom is a potential stereo-centre
POVRayFormat - Class in org.openscience.cdk.io.formats: See here.
POVRayFormat() - Constructor for class org.openscience.cdk.io.formats.POVRayFormat
PQSChemFormat - Class in org.openscience.cdk.io.formats: See here.
PQSChemFormat() - Constructor for class org.openscience.cdk.io.formats.PQSChemFormat
Pr - Static variable in interface org.openscience.cdk.interfaces.IElement
PR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Praseodymium - org.openscience.cdk.config.Elements
PRASEODYMIUM - Static variable in enum org.openscience.cdk.config.Elements
PRASEODYMIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
predecessor(int[], int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Calculation of the former index pair in a matrix.
predict(String) - Method in class org.openscience.cdk.tools.BremserOneSphereHOSECodePredictor
predict(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.model.Bayesian: For a given molecule, determines its fingerprints and uses them to calculate a Bayesian prediction.
predictFull(String) - Method in class org.openscience.cdk.tools.BremserOneSphereHOSECodePredictor
predictIP(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.tools.IonizationPotentialTool: Deprecated.

Method which is predict the Ionization Potential from given atom.
predictIP(IAtomContainer, IBond) - Static method in class org.openscience.cdk.tools.IonizationPotentialTool: Deprecated.

Method which is predict the Ionization Potential from given atom.
prefixConstruct() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Allows 1 or more prefixes
prefixFunctionalGroups() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.
prefixType() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.
prepare(IAtomContainer) - Static method in class org.openscience.cdk.smarts.SmartsPattern
prepare(IAtomContainer, boolean) - Static method in class org.openscience.cdk.isomorphism.matchers.smarts.SmartsMatchers: Deprecated.

Do not use - temporary method until the SMARTS packages are cleaned up.
prepareNode(IAtomContainer) - Method in class org.openscience.cdk.graph.invariant.EquivalentClassPartitioner: Prepare the node identifier.
prevCharIsCR - Variable in class org.openscience.cdk.iupac.parser.SimpleCharStream
prevCharIsCR - Variable in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
prevCharIsLF - Variable in class org.openscience.cdk.iupac.parser.SimpleCharStream
prevCharIsLF - Variable in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
previous() - Method in class org.openscience.cdk.io.random.RandomAccessReader
previousIndex() - Method in class org.openscience.cdk.io.random.RandomAccessReader
Primes - Class in org.openscience.cdk.math: Deprecated.
Primes() - Constructor for class org.openscience.cdk.math.Primes: Deprecated.
PrimitiveAtomExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
printIncidenceMatrix() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis: Deprecated.
printInt2D(int[][]) - Static method in class org.openscience.cdk.tools.SwissArmyKnife: Deprecated.

Returns a string representation of a 2D int matrix for printing or listing to the console.
printPaths() - Method in class org.openscience.cdk.smsd.ring.PathGraph: Deprecated.
PRIORITY - Static variable in class org.openscience.cdk.layout.AtomPlacer
prioritySubstituents() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Things which have sub chains branching off them but the molecule has no main chain.
prioritySubstituentsFunGroups() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Things which have sub chains branching off them and the molecule does have a main chain.
ProblemMarker - Class in org.openscience.cdk.validate: Tool to mark IChemObject's as having a problem.
ProblemMarker() - Constructor for class org.openscience.cdk.validate.ProblemMarker
process() - Method in class org.openscience.cdk.io.iterator.event.EventCMLReader: Starts the reading of the CML file.
process(int, int, List<Integer>, List<Integer>, List<Integer>, List<Integer>, int) - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.QueryProcessor: Deprecated.
process(int, List<Integer>, int, List<Integer>, List<String>, List<Integer>, int, List<Integer>, List<String>) - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.TargetProcessor: Deprecated.
process(IAtomContainer) - Method in class org.openscience.cdk.qsar.DescriptorEngine: Calculates all available (or only those specified) descriptors for a molecule.
process(IAtomContainer, List<Integer>, int, List<Integer>, List<String>, List<Integer>, int) - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.TargetProcessor: Deprecated.
process(IAtomContainer, IAtomContainer, List<Integer>, List<Integer>, int) - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.QueryProcessor: Deprecated.
process(IQueryAtomContainer, IAtomContainer, List<Integer>, List<Integer>, int) - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.QueryProcessor: Deprecated.
processConnections(String, IAtomContainer, int) - Method in class org.openscience.cdk.io.inchi.INChIContentProcessorTool: Deprecated.

Processes the content from the connections field of the INChI.
processContent() - Method in class org.openscience.cdk.io.random.RandomAccessReader: The reader is already set to read the record buffer.
processContent() - Method in class org.openscience.cdk.io.random.RandomAccessSDFReader
processFormula(String, long) - Method in class org.openscience.cdk.structgen.maygen.Maygen
processFormula(IAtomContainer, String) - Method in class org.openscience.cdk.io.inchi.INChIContentProcessorTool: Deprecated.

Processes the content from the formula field of the INChI.
processIOSettingQuestion(IOSetting) - Method in interface org.openscience.cdk.io.listener.IChemObjectIOListener: Prompted when the IO filter needs information to process the file.
processIOSettingQuestion(IOSetting) - Method in class org.openscience.cdk.io.listener.PropertiesListener: Processes the IOSettings by listing the question, giving the options and asking the user to provide their choice.
processIOSettingQuestion(IOSetting) - Method in class org.openscience.cdk.io.listener.SwingGUIListener: Processes the IOSettings by listing the question, giving the options and asking the user to provide their choice.
processIOSettingQuestion(IOSetting) - Method in class org.openscience.cdk.io.listener.TextGUIListener: Processes the IOSettings by listing the question, giving the options and asking the user to provide their choice.
processRun(String, long) - Method in class org.openscience.cdk.structgen.maygen.Maygen
Product - org.openscience.cdk.ReactionRole
products - Variable in class org.openscience.cdk.Reaction
products - Variable in class org.openscience.cdk.silent.Reaction
ProductsBoxGenerator - Class in org.openscience.cdk.renderer.generators: Generate the symbols for radicals.
ProductsBoxGenerator() - Constructor for class org.openscience.cdk.renderer.generators.ProductsBoxGenerator
project(List<RMap>, IAtomContainer, int) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: Projects a list of RMap on a molecule.
project(List<CDKRMap>, IAtomContainer, int) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS: Deprecated.

Projects atom list of CDKRMap on atom molecule.
project2D(IAtomContainer) - Static method in class org.openscience.cdk.geometry.Projector
project2D(IAtomContainer, HashMap<IAtom, Point2d>) - Static method in class org.openscience.cdk.geometry.Projector
projectG1(BitSet) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Projects a RGraph bitset on the source graph G1.
projectG1(BitSet) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph: Deprecated.

Projects a CDKRGraph bitset on the source graph G1.
projectG2(BitSet) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Projects a RGraph bitset on the source graph G2.
projectG2(BitSet) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph: Deprecated.

Projects a CDKRGraph bitset on the source graph G2.
Projection - Enum in org.openscience.cdk.stereo: Stereochemistry projection types.
projections - Variable in class org.openscience.cdk.stereo.StereoElementFactory
projectList(List<List<RMap>>, IAtomContainer, int) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: Projects a list of RMapsList on a molecule.
projectList(List<List<CDKRMap>>, IAtomContainer, int) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS: Deprecated.

Projects atom list of RMapsList on atom molecule.
Projector - Class in org.openscience.cdk.geometry: Tool to make projections from 3D to 2D.
Projector() - Constructor for class org.openscience.cdk.geometry.Projector
Promethium - org.openscience.cdk.config.Elements
PROMETHIUM - Static variable in enum org.openscience.cdk.config.Elements
PROMETHIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
PROP - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
PropertiesListener - Class in org.openscience.cdk.io.listener: Answers the questions by looking up the values in a Properties object.
PropertiesListener(Properties) - Constructor for class org.openscience.cdk.io.listener.PropertiesListener
proposeStructure() - Method in class org.openscience.cdk.structgen.RandomGenerator: Proposes a structure which can be accepted or rejected by an external entity.
Protactinium - org.openscience.cdk.config.Elements
PROTACTINIUM - Static variable in enum org.openscience.cdk.config.Elements
PROTACTINIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
ProteinBuilderTool - Class in org.openscience.cdk.tools: Class that facilitates building protein structures.
ProteinBuilderTool() - Constructor for class org.openscience.cdk.tools.ProteinBuilderTool
proteinGridToPmesh(String) - Method in class org.openscience.cdk.protein.ProteinPocketFinder: Method writes the protein grid points to pmesh format.
ProteinPocketFinder - Class in org.openscience.cdk.protein: The detection of pocket and cavities in a bioPolymer is done similar to the program LIGSITE [Hendlich, M. et. al.. Journal of Molecular Graphics and Modelling. 1997. 15].
ProteinPocketFinder(String, boolean) - Constructor for class org.openscience.cdk.protein.ProteinPocketFinder
ProteinPocketFinder(String, double[][][]) - Constructor for class org.openscience.cdk.protein.ProteinPocketFinder
ProteinPocketFinder(String, double, boolean) - Constructor for class org.openscience.cdk.protein.ProteinPocketFinder
ProteinPocketFinder(IBioPolymer, double[][][]) - Constructor for class org.openscience.cdk.protein.ProteinPocketFinder
ProtonAffinityHOSEDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic: This class returns the proton affinity of an atom containing.
ProtonAffinityHOSEDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor: Constructor for the ProtonAffinityDescriptor object.
ProtonTotalPartialChargeDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic: The calculation of partial charges of an heavy atom and its protons is based on Gasteiger Marsili (PEOE).
ProtonTotalPartialChargeDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor: Constructor for the ProtonTotalPartialChargeDescriptor object
PS_FMT - Static variable in class org.openscience.cdk.depict.Depiction: PostScript (PS) format key.
PseudoAtom - Class in org.openscience.cdk: Represents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc.
PseudoAtom - Class in org.openscience.cdk.silent: Represents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc.
PseudoAtom() - Constructor for class org.openscience.cdk.PseudoAtom: Constructs an empty PseudoAtom.
PseudoAtom() - Constructor for class org.openscience.cdk.silent.PseudoAtom: Constructs an empty PseudoAtom.
PseudoAtom(String) - Constructor for class org.openscience.cdk.PseudoAtom: Constructs an Atom from a String containing an element symbol.
PseudoAtom(String) - Constructor for class org.openscience.cdk.silent.PseudoAtom: Constructs an Atom from a String containing an element symbol.
PseudoAtom(String, Point2d) - Constructor for class org.openscience.cdk.PseudoAtom: Constructs an Atom from an Element and a Point2d.
PseudoAtom(String, Point2d) - Constructor for class org.openscience.cdk.silent.PseudoAtom: Constructs an Atom from an Element and a Point2d.
PseudoAtom(String, Point3d) - Constructor for class org.openscience.cdk.PseudoAtom: Constructs an Atom from an Element and a Point3d.
PseudoAtom(String, Point3d) - Constructor for class org.openscience.cdk.silent.PseudoAtom: Constructs an Atom from an Element and a Point3d.
PseudoAtom(IElement) - Constructor for class org.openscience.cdk.PseudoAtom: Constructs an PseudoAtom from a IAtom.
PseudoAtom(IElement) - Constructor for class org.openscience.cdk.silent.PseudoAtom: Constructs an PseudoAtom from a IAtom.
PSEUDOATOM - Static variable in class org.openscience.cdk.libio.jena.CDK
PseudoFontStyle() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.PseudoFontStyle
pspGridToPmesh(String) - Method in class org.openscience.cdk.protein.ProteinPocketFinder: Method writes the PSP points (≥minPSPocket) to pmesh format.
Pt - Static variable in interface org.openscience.cdk.interfaces.IElement
PT - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Pu - Static variable in interface org.openscience.cdk.interfaces.IElement
PU - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
PubChem_95 - org.openscience.cdk.ringsearch.AllRingsFinder.Threshold: Based on PubChem Compound (Dec '12), perception will complete for 99.95% of ring systems.
PubChem_96 - org.openscience.cdk.ringsearch.AllRingsFinder.Threshold: Based on PubChem Compound (Dec '12), perception will complete for 99.96% of ring systems.
PubChem_97 - org.openscience.cdk.ringsearch.AllRingsFinder.Threshold: Based on PubChem Compound (Dec '12), perception will complete for 99.97% of ring systems.
PubChem_98 - org.openscience.cdk.ringsearch.AllRingsFinder.Threshold: Based on PubChem Compound (Dec '12), perception will complete for 99.98% of ring systems.
PubChem_99 - org.openscience.cdk.ringsearch.AllRingsFinder.Threshold: Based on PubChem Compound (Dec '12), perception will complete for 99.99% of ring systems.
PubChem_991 - org.openscience.cdk.ringsearch.AllRingsFinder.Threshold: Based on PubChem Compound (Dec '12), perception will complete for 99.991% of ring systems.
PubChem_992 - org.openscience.cdk.ringsearch.AllRingsFinder.Threshold: Based on PubChem Compound (Dec '12), perception will complete for 99.992% of ring systems.
PubChem_993 - org.openscience.cdk.ringsearch.AllRingsFinder.Threshold: Based on PubChem Compound (Dec '12), perception will complete for 99.993% of ring systems.
PubChem_994 - org.openscience.cdk.ringsearch.AllRingsFinder.Threshold: Based on PubChem Compound (Dec '12), perception will complete for 99.994% of ring systems.
PubChemASNFormat - Class in org.openscience.cdk.io.formats
PubChemASNFormat() - Constructor for class org.openscience.cdk.io.formats.PubChemASNFormat
PubChemCompoundsXMLFormat - Class in org.openscience.cdk.io.formats
PubChemCompoundsXMLFormat() - Constructor for class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
PubChemCompoundXMLFormat - Class in org.openscience.cdk.io.formats
PubChemCompoundXMLFormat() - Constructor for class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
PubchemFingerprinter - Class in org.openscience.cdk.fingerprint: Generates a Pubchem fingerprint for a molecule.
PubchemFingerprinter(IChemObjectBuilder) - Constructor for class org.openscience.cdk.fingerprint.PubchemFingerprinter
PubchemFingerprinter(IChemObjectBuilder, boolean) - Constructor for class org.openscience.cdk.fingerprint.PubchemFingerprinter
PubChemFormat - Class in org.openscience.cdk.io.formats: See here.
PubChemFormat() - Constructor for class org.openscience.cdk.io.formats.PubChemFormat
PubChemSubstancesASNFormat - Class in org.openscience.cdk.io.formats
PubChemSubstancesASNFormat() - Constructor for class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
PubChemSubstancesXMLFormat - Class in org.openscience.cdk.io.formats
PubChemSubstancesXMLFormat() - Constructor for class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
PubChemSubstanceXMLFormat - Class in org.openscience.cdk.io.formats
PubChemSubstanceXMLFormat() - Constructor for class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
PubChemXMLHelper - Class in org.openscience.cdk.io.pubchemxml: Helper class to parse PubChem XML documents.
PubChemXMLHelper(IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
push(Object) - Method in class org.openscience.cdk.ringsearch.Queue: Deprecated.

Places an Object into the queue
push(ICMLModule) - Method in class org.openscience.cdk.io.cml.CMLModuleStack: Adds an entry to the stack.
pushNode(Node) - Method in class org.openscience.cdk.smiles.smarts.parser.JJTSMARTSParserState
putInOrder(String[], IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
putValue(SgroupKey, Object) - Method in class org.openscience.cdk.sgroup.Sgroup: Store an attribute for the Sgroup.
PYRIDINE_RING - Static variable in class org.openscience.cdk.tools.AtomTypeTools
PYRIMIDINE_RING - Static variable in class org.openscience.cdk.tools.AtomTypeTools
PYROLE_RING - Static variable in class org.openscience.cdk.tools.AtomTypeTools

Q

Q_MARK - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
QChemFormat - Class in org.openscience.cdk.io.formats: See here.
QChemFormat() - Constructor for class org.openscience.cdk.io.formats.QChemFormat
QSARConvention - Class in org.openscience.cdk.io.cml: This is an implementation for the CDK convention.
QSARConvention(IChemFile) - Constructor for class org.openscience.cdk.io.cml.QSARConvention
QSARConvention(ICMLModule) - Constructor for class org.openscience.cdk.io.cml.QSARConvention
QSARCustomizer - Class in org.openscience.cdk.libio.cml: Customizer for the libio-cml Convertor to be able to export details for QSAR descriptors calculated for Molecules.
QSARCustomizer() - Constructor for class org.openscience.cdk.libio.cml.QSARCustomizer
QUADRUPLE - org.openscience.cdk.interfaces.IBond.Order
QUADRUPLE - org.openscience.cdk.renderer.elements.LineElement.LineType
QUADRUPLEBOND - Static variable in class org.openscience.cdk.libio.jena.CDK
quadTo(Point2d, Point2d) - Method in class org.openscience.cdk.renderer.elements.path.PathBuilder: Make a quadratic curve in the path, with one control point.
QuadTo - Class in org.openscience.cdk.renderer.elements.path: Make a quadratic curve in the path.
QuadTo - org.openscience.cdk.renderer.elements.path.Type
QuadTo(double[]) - Constructor for class org.openscience.cdk.renderer.elements.path.QuadTo: Make a quad curve path element.
QuadTo(double, double, double, double) - Constructor for class org.openscience.cdk.renderer.elements.path.QuadTo: Make a quad curve path element.
QuadTo(Point2d, Point2d) - Constructor for class org.openscience.cdk.renderer.elements.path.QuadTo: Make a quad curve.
Quaternion - Class in org.openscience.cdk.math: This class handles quaternions.
Quaternion() - Constructor for class org.openscience.cdk.math.Quaternion
Quaternion(double, double, double) - Constructor for class org.openscience.cdk.math.Quaternion: Generate a quaternion from spherical coordinates and a rotation angle
Quaternion(double, double, double, double) - Constructor for class org.openscience.cdk.math.Quaternion
Quaternion(Vector, double) - Constructor for class org.openscience.cdk.math.Quaternion: Generate a quaternion from a rotation axis and an angle
QueryAtom - Class in org.openscience.cdk.isomorphism.matchers
QueryAtom(String, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryAtom
QueryAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryAtom
QueryAtom(Expr) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryAtom: Create a new query atom with the given an expression.
QueryAtom(Expr.Type) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryAtom: Create a new query atom with the given an predicate expression type.
QueryAtom(Expr.Type, int) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryAtom: Create a new query atom with the given an value expression type.
QueryAtomContainer - Class in org.openscience.cdk.isomorphism.matchers
QueryAtomContainer(int, int, int, int, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Constructs an empty AtomContainer that will contain a certain number of atoms and electronContainers.
QueryAtomContainer(IAtomContainer, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Constructs an AtomContainer with a copy of the atoms and electronContainers of another AtomContainer (A shallow copy, i.e., with the same objects as in the original AtomContainer).
QueryAtomContainer(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Constructs an empty AtomContainer.
QueryAtomContainerCreator - Class in org.openscience.cdk.isomorphism.matchers: Utilities for creating queries from 'real' molecules.
QueryAtomContainerCreator() - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
QueryBond - Class in org.openscience.cdk.isomorphism.matchers: Implements the concept of a "query bond" between two or more atoms.
QueryBond(IAtom[], IBond.Order, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryBond: Constructs a multi-center query bond, with a specified order and no stereo information.
QueryBond(IAtom[], IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryBond: Constructs a multi-center query bond, with undefined order and no stereo information.
QueryBond(IAtom, IAtom, IBond.Order, IBond.Stereo, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryBond: Constructs a query bond with a given order and stereo orientation from an array of atoms.
QueryBond(IAtom, IAtom, IBond.Order, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryBond: Constructs a query bond with a given order.
QueryBond(IAtom, IAtom, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryBond: Constructs a query bond with a single query bond order..
QueryBond(IAtom, IAtom, Expr) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryBond: Constructs an query bond from an expression.
QueryBond(IAtom, IAtom, Expr.Type) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryBond: Constructs an query bond from an expression type.
QueryBond(IAtom, IAtom, Expr.Type, int) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryBond: Constructs an query bond from an expression type and value.
QueryBond(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryBond: Constructs an empty query bond.
QueryChemObject - Class in org.openscience.cdk.isomorphism.matchers
QueryChemObject(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryChemObject
QueryCompiler - Class in org.openscience.cdk.smsd.algorithm.vflib.query: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
QueryCompiler(IAtomContainer, boolean) - Constructor for class org.openscience.cdk.smsd.algorithm.vflib.query.QueryCompiler: Deprecated.

Construct query object from the molecule
QueryCompiler(IQueryAtomContainer) - Constructor for class org.openscience.cdk.smsd.algorithm.vflib.query.QueryCompiler: Deprecated.

Construct query object from the molecule
QueryProcessor - Class in org.openscience.cdk.smsd.algorithm.mcgregor: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
QueryProcessor(List<String>, List<String>, String[], int, int, List<Integer>, List<String>, int, List<Integer>, List<String>) - Constructor for class org.openscience.cdk.smsd.algorithm.mcgregor.QueryProcessor: Deprecated.

Query molecule
question - Variable in class org.openscience.cdk.io.setting.IOSetting
Queue - Class in org.openscience.cdk.ringsearch: Deprecated.
internal implemenation detail from SSSRFinder, do not use
Queue() - Constructor for class org.openscience.cdk.ringsearch.Queue: Deprecated.

Constructs an empty Queue
QUINTUPLE - org.openscience.cdk.interfaces.IBond.Order

R

r - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
R - org.openscience.cdk.geometry.cip.CIPTool.CIP_CHIRALITY
R - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
R_BOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
R_BRACKET - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
R_PAREN - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Ra - Static variable in interface org.openscience.cdk.interfaces.IElement
RA - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
RAD_30 - Static variable in class org.openscience.cdk.layout.RingPlacer
radical() - Method in class org.openscience.cdk.hash.HashGeneratorMaker: Discriminate free radicals.
RadicalChargeSiteInitiationHReaction - Class in org.openscience.cdk.reaction.type: IReactionProcess which participate mass spectrum process.
RadicalChargeSiteInitiationHReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalChargeSiteInitiationHReaction: Constructor of the RadicalChargeSiteInitiationHReaction object
RadicalChargeSiteInitiationReaction - Class in org.openscience.cdk.reaction.type: IReactionProcess which participate mass spectrum process.
RadicalChargeSiteInitiationReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalChargeSiteInitiationReaction: Constructor of the RadicalChargeSiteInitiationReaction object
RadicalGenerator - Class in org.openscience.cdk.renderer.generators: Generate the symbols for radicals.
RadicalGenerator() - Constructor for class org.openscience.cdk.renderer.generators.RadicalGenerator
RadicalSiteHrAlphaReaction - Class in org.openscience.cdk.reaction.type: This reaction could be represented as [A*]-(C)_2-C3[H] => A([H])-(C_2)-[C3*].
RadicalSiteHrAlphaReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalSiteHrAlphaReaction: Constructor of the RadicalSiteHrAlphaReaction object
RadicalSiteHrBetaReaction - Class in org.openscience.cdk.reaction.type: This reaction could be represented as [A*]-(C)_3-C4[H] => A([H])-(C_3)-[C4*].
RadicalSiteHrBetaReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalSiteHrBetaReaction: Constructor of the RadicalSiteHrBetaReaction object
RadicalSiteHrDeltaReaction - Class in org.openscience.cdk.reaction.type: This reaction could be represented as [A*]-(C)_4-C5[H] => A([H])-(C_4)-[C5*].
RadicalSiteHrDeltaReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalSiteHrDeltaReaction: Constructor of the RadicalSiteHrDeltaReaction object
RadicalSiteHrGammaReaction - Class in org.openscience.cdk.reaction.type: This reaction could be represented as [A*]-C1-C2-C3[H] => A([H])-C1-C2-[C3*].
RadicalSiteHrGammaReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalSiteHrGammaReaction: Constructor of the RadicalSiteHrGammaReaction object
RadicalSiteInitiationHReaction - Class in org.openscience.cdk.reaction.type: IReactionProcess which participate mass spectrum process.
RadicalSiteInitiationHReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalSiteInitiationHReaction: Constructor of the RadicalSiteInitiationHReaction object
RadicalSiteInitiationReaction - Class in org.openscience.cdk.reaction.type: IReactionProcess which participate mass spectrum process.
RadicalSiteInitiationReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalSiteInitiationReaction: Constructor of the RadicalSiteInitiationReaction object
RadicalSiteIonizationMechanism - Class in org.openscience.cdk.reaction.mechanism: This mechanism extracts an atom because of the stabilization of a radical.
RadicalSiteIonizationMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.RadicalSiteIonizationMechanism
RadicalSiteRearrangementMechanism - Class in org.openscience.cdk.reaction.mechanism: This mechanism displaces an Atom or substructure (R) from one position to an other.
RadicalSiteRearrangementMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.RadicalSiteRearrangementMechanism
RadicalSiteRrAlphaReaction - Class in org.openscience.cdk.reaction.type: This reaction could be represented as [A*]-(C)_2-C3[R] => A([RH])-(C_2)-[C3*].
RadicalSiteRrAlphaReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalSiteRrAlphaReaction: Constructor of the RadicalSiteRrAlphaReaction object
RadicalSiteRrBetaReaction - Class in org.openscience.cdk.reaction.type: This reaction could be represented as [A*]-(C)_3-C4[R] => A([R])-(C_3)-[C4*].
RadicalSiteRrBetaReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalSiteRrBetaReaction: Constructor of the RadicalSiteRrBetaReaction object
RadicalSiteRrDeltaReaction - Class in org.openscience.cdk.reaction.type: This reaction could be represented as [A*]-(C)_5-C6[R] => A([R])-(C_5)-[C6*].
RadicalSiteRrDeltaReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalSiteRrDeltaReaction: Constructor of the RadicalSiteRrDeltaReaction object
RadicalSiteRrGammaReaction - Class in org.openscience.cdk.reaction.type: This reaction could be represented as [A*]-(C)_4-C5[R] => A([R])-(C_4)-[C5*].
RadicalSiteRrGammaReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalSiteRrGammaReaction: Constructor of the RadicalSiteRrGammaReaction object
Radium - org.openscience.cdk.config.Elements
RADIUM - Static variable in enum org.openscience.cdk.config.Elements
RADIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
radius - Variable in class org.openscience.cdk.renderer.elements.OvalElement: The radius of the oval.
Radon - org.openscience.cdk.config.Elements
RADON - Static variable in enum org.openscience.cdk.config.Elements
raFile - Variable in class org.openscience.cdk.io.random.RandomAccessReader
RandomAccessReader - Class in org.openscience.cdk.io.random: Random access to text files of compounds.
RandomAccessReader(File, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.random.RandomAccessReader: Reads the file and builds an index file, if the index file doesn't already exist.
RandomAccessReader(File, IChemObjectBuilder, IReaderListener) - Constructor for class org.openscience.cdk.io.random.RandomAccessReader: Reads the file and builds an index file, if the index file doesn't already exist.
RandomAccessSDFReader - Class in org.openscience.cdk.io.random: Random access of SDF file.
RandomAccessSDFReader(File, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.random.RandomAccessSDFReader
RandomAccessSDFReader(File, IChemObjectBuilder, IReaderListener) - Constructor for class org.openscience.cdk.io.random.RandomAccessSDFReader
randomBit() - Static method in class org.openscience.cdk.math.RandomNumbersTool: Generates a random bit: either 0 or 1.
randomBoolean() - Static method in class org.openscience.cdk.math.RandomNumbersTool: Generates a random boolean.
randomDouble() - Static method in class org.openscience.cdk.math.RandomNumbersTool: Generates a random double between 0 and 1.
randomDouble(double, double) - Static method in class org.openscience.cdk.math.RandomNumbersTool: Generates a random double between the specified values.
randomFloat() - Static method in class org.openscience.cdk.math.RandomNumbersTool: Generates a random float between 0 and 1.
randomFloat(float, float) - Static method in class org.openscience.cdk.math.RandomNumbersTool: Generates a random float between the specified values.
RandomGenerator - Class in org.openscience.cdk.structgen: RandomGenerator is a generator of constitutional isomers.
RandomGenerator(IAtomContainer) - Constructor for class org.openscience.cdk.structgen.RandomGenerator: Constructs a RandomGenerator with a given starting structure.
randomInt() - Static method in class org.openscience.cdk.math.RandomNumbersTool: Generates a random integer between 0 and 1.
randomInt(int, int) - Static method in class org.openscience.cdk.math.RandomNumbersTool: Generates a random integer between the specified values.
randomLong() - Static method in class org.openscience.cdk.math.RandomNumbersTool: Generates a random long between 0 and 1.
randomLong(long, long) - Static method in class org.openscience.cdk.math.RandomNumbersTool: Generates a random long between the specified values.
randomNext() - Method in class org.openscience.cdk.graph.AtomContainerPermutor: Get a new container, but randomly skip forwards in the list of possible permutations to generate it.
RandomNumbersTool - Class in org.openscience.cdk.math: Class supplying useful methods to generate random numbers.
RandomNumbersTool() - Constructor for class org.openscience.cdk.math.RandomNumbersTool
range - Variable in class org.openscience.cdk.fingerprint.model.Bayesian
RasmolColors - Class in org.openscience.cdk.renderer.color: Atom coloring following RasMol/Chime Color scheme http://www.umass.edu/microbio/rasmol/rascolor.htm.
RasmolColors() - Constructor for class org.openscience.cdk.renderer.color.RasmolColors
RawCopyFormat - Class in org.openscience.cdk.io.formats: See here.
RawCopyFormat() - Constructor for class org.openscience.cdk.io.formats.RawCopyFormat
Rb - Static variable in interface org.openscience.cdk.interfaces.IElement
RB - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
RDBERule - Class in org.openscience.cdk.formula.rules: Ring Double Bond Equivalents (RDBE) or Double Bond Equivalents (DBE) are calculated from valence values of elements contained in a formula and should tell the number of bonds - or rings.
RDBERule() - Constructor for class org.openscience.cdk.formula.rules.RDBERule: Constructor for the RDBE object.
RDBERule.Combinations - Class in org.openscience.cdk.formula.rules
RDFCalculator - Class in org.openscience.cdk.geometry: Calculator of radial distribution functions.
RDFCalculator(double, double, double, double) - Constructor for class org.openscience.cdk.geometry.RDFCalculator: Constructs a RDF calculator that calculates a unweighted, digitized RDF function.
RDFCalculator(double, double, double, double, IRDFWeightFunction) - Constructor for class org.openscience.cdk.geometry.RDFCalculator: Constructs a RDF calculator that calculates a digitized RDF function.
rdFields - Variable in class org.openscience.cdk.io.MDLRXNWriter
RDFProtonDescriptor_G3R - Class in org.openscience.cdk.qsar.descriptors.atomic: This class calculates G3R proton descriptors used in neural networks for H1 NMR shift [Aires-de-Sousa, J. et. al.. J. Chem. Inf. Mod.. 2002. 74].
RDFProtonDescriptor_G3R() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R: Constructor for the RDFProtonDescriptor object
RDFProtonDescriptor_GDR - Class in org.openscience.cdk.qsar.descriptors.atomic: This class calculates GDR proton descriptors used in neural networks for H1 NMR shift [Aires-de-Sousa, J. et. al.. J. Chem. Inf. Mod.. 2002. 74].
RDFProtonDescriptor_GDR() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR: Constructor for the RDFProtonDescriptor object
RDFProtonDescriptor_GHR - Class in org.openscience.cdk.qsar.descriptors.atomic: This class calculates GHR proton descriptors used in neural networks for H1 NMR shift [Aires-de-Sousa, J. et. al.. J. Chem. Inf. Mod.. 2002. 74].
RDFProtonDescriptor_GHR() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR: Constructor for the RDFProtonDescriptor object
RDFProtonDescriptor_GHR_topol - Class in org.openscience.cdk.qsar.descriptors.atomic: This class calculates GHR topological proton descriptors used in neural networks for H1 NMR shift [Aires-de-Sousa, J. et. al.. J. Chem. Inf. Mod.. 2002. 74].
RDFProtonDescriptor_GHR_topol() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol: Constructor for the RDFProtonDescriptor object
RDFProtonDescriptor_GSR - Class in org.openscience.cdk.qsar.descriptors.atomic: This class calculates GDR proton descriptors used in neural networks for H1 NMR shift [Aires-de-Sousa, J. et. al.. J. Chem. Inf. Mod.. 2002. 74].
RDFProtonDescriptor_GSR() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR: Constructor for the RDFProtonDescriptor object
Re - Static variable in interface org.openscience.cdk.interfaces.IElement
RE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Reactant - org.openscience.cdk.ReactionRole
reactants - Variable in class org.openscience.cdk.Reaction
reactants - Variable in class org.openscience.cdk.silent.Reaction
ReactantsBoxGenerator - Class in org.openscience.cdk.renderer.generators: Generate the symbols for radicals.
ReactantsBoxGenerator() - Constructor for class org.openscience.cdk.renderer.generators.ReactantsBoxGenerator
Reaction - Class in org.openscience.cdk: Represents the idea of a chemical reaction.
Reaction - Class in org.openscience.cdk.silent: Represents the idea of a chemical reaction.
Reaction() - Constructor for class org.openscience.cdk.Reaction: Constructs an empty, forward reaction.
Reaction() - Constructor for class org.openscience.cdk.silent.Reaction: Constructs an empty, forward reaction.
REACTION_ARROW - Static variable in class org.openscience.cdk.CDKConstants: Arrow display type
REACTION_CONDITIONS - Static variable in class org.openscience.cdk.CDKConstants: Property for reaction objects where the conditions of reactions can be placed.
REACTION_GROUP - Static variable in class org.openscience.cdk.CDKConstants: Property used for reactions when converted to/from molecules.
REACTION_ROLE - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if an atom has the specified reaction role.
REACTION_ROLE - Static variable in class org.openscience.cdk.CDKConstants: Property used for reactions when converted to/from molecules.
ReactionArrowGenerator - Class in org.openscience.cdk.renderer.generators: Generate the arrow for a reaction.
ReactionArrowGenerator() - Constructor for class org.openscience.cdk.renderer.generators.ReactionArrowGenerator
ReactionBoxGenerator - Class in org.openscience.cdk.renderer.generators: Generate the symbols for radicals.
ReactionBoxGenerator() - Constructor for class org.openscience.cdk.renderer.generators.ReactionBoxGenerator
ReactionChain - Class in org.openscience.cdk.reaction: Classes that extends the definition of reaction to a chain reaction.
ReactionChain() - Constructor for class org.openscience.cdk.reaction.ReactionChain
ReactionEngine - Class in org.openscience.cdk.reaction: The base class for all chemical reactions objects in this cdk.
ReactionEngine() - Constructor for class org.openscience.cdk.reaction.ReactionEngine: Constructor of the ReactionEngine object.
ReactionExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
ReactionManipulator - Class in org.openscience.cdk.tools.manipulator: Provides a variety of methods to manipulate and convert from/to IReaction.
ReactionManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.ReactionManipulator
ReactionPlusGenerator - Class in org.openscience.cdk.renderer.generators: Generate the arrow for a reaction.
ReactionPlusGenerator() - Constructor for class org.openscience.cdk.renderer.generators.ReactionPlusGenerator
ReactionRenderer - Class in org.openscience.cdk.renderer: A general renderer for IChemModels, IReactions, and IAtomContainers.
ReactionRenderer(List<IGenerator<IAtomContainer>>, List<IGenerator<IReaction>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.ReactionRenderer: A renderer that draws IReactions with the passed IGenerator for both IAtomContainer and IReaction content.
ReactionRenderer(List<IGenerator<IAtomContainer>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.ReactionRenderer: A renderer that generates diagrams using the specified generators and manages fonts with the supplied font manager.
ReactionRenderer(RendererModel, List<IGenerator<IAtomContainer>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.ReactionRenderer
ReactionRole - Enum in org.openscience.cdk
ReactionRoleQueryAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
ReactionRoleQueryAtom(IChemObjectBuilder, int) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.ReactionRoleQueryAtom: Deprecated.
reactions() - Method in class org.openscience.cdk.debug.DebugReactionSet: Get an iterator for this reaction set.
reactions() - Method in interface org.openscience.cdk.interfaces.IReactionSet: Returns the Iterable over Reactions of this container.
reactions() - Method in class org.openscience.cdk.ReactionSet: Get an iterator for this reaction set.
reactions() - Method in class org.openscience.cdk.silent.ReactionSet: Get an iterator for this reaction set.
ReactionSceneGenerator - Class in org.openscience.cdk.renderer.generators: Generator for general reaction scene components.
ReactionSceneGenerator() - Constructor for class org.openscience.cdk.renderer.generators.ReactionSceneGenerator
ReactionSceneGenerator.ArrowHeadWidth - Class in org.openscience.cdk.renderer.generators: Double which indicates how wide the arrow head is in screen pixels.
ReactionSceneGenerator.ShowReactionBoxes - Class in org.openscience.cdk.renderer.generators: Boolean that indicates if boxes are drawn around the reaction.
ReactionScheme - Class in org.openscience.cdk: Classes that extends the definition of reaction to a scheme.
ReactionScheme - Class in org.openscience.cdk.silent: Classes that extends the definition of reaction to a scheme.
ReactionScheme() - Constructor for class org.openscience.cdk.ReactionScheme: Constructs an empty ReactionScheme.
ReactionScheme() - Constructor for class org.openscience.cdk.silent.ReactionScheme: Constructs an empty ReactionScheme.
ReactionSchemeManipulator - Class in org.openscience.cdk.tools.manipulator
ReactionSchemeManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator
reactionSchemes() - Method in class org.openscience.cdk.debug.DebugReactionScheme: Returns an Iterable for looping over all IMolecularScheme in this ReactionScheme.
reactionSchemes() - Method in interface org.openscience.cdk.interfaces.IReactionScheme: Returns an Iterable for looping over all IMolecularScheme in this ReactionScheme.
reactionSchemes() - Method in class org.openscience.cdk.ReactionScheme: Returns an Iterable for looping over all IMolecularScheme in this ReactionScheme.
reactionSchemes() - Method in class org.openscience.cdk.silent.ReactionScheme: Returns an Iterable for looping over all IMolecularScheme in this ReactionScheme.
ReactionSet - Class in org.openscience.cdk: A set of reactions, for example those taking part in a reaction.
ReactionSet - Class in org.openscience.cdk.silent: A set of reactions, for example those taking part in a reaction.
ReactionSet() - Constructor for class org.openscience.cdk.ReactionSet: Constructs an empty ReactionSet.
ReactionSet() - Constructor for class org.openscience.cdk.silent.ReactionSet: Constructs an empty ReactionSet.
ReactionSetManipulator - Class in org.openscience.cdk.tools.manipulator
ReactionSetManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
ReactionSetRenderer - Class in org.openscience.cdk.renderer: A general renderer for IChemModels, IReactions, and IAtomContainers.
ReactionSetRenderer(List<IGenerator<IAtomContainer>>, List<IGenerator<IReaction>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.ReactionSetRenderer: A renderer that generates diagrams using the specified generators for IAtomContainers and IReactionSets and manages fonts with the supplied font manager.
ReactionSetRenderer(List<IGenerator<IAtomContainer>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.ReactionSetRenderer: A renderer that generates diagrams using the specified generators and manages fonts with the supplied font manager.
ReactionSetRenderer(RendererModel, List<IGenerator<IAtomContainer>>, List<IGenerator<IReaction>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.ReactionSetRenderer
ReactionSetRenderer(RendererModel, List<IGenerator<IAtomContainer>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.ReactionSetRenderer
ReactionSpecification - Class in org.openscience.cdk.reaction: Class that is used to distribute reactions specifications.
ReactionSpecification(String, String, String, String) - Constructor for class org.openscience.cdk.reaction.ReactionSpecification: Container for specifying the type of reaction.
REACTIVE_CENTER - Static variable in class org.openscience.cdk.CDKConstants: Flag is set if a chemobject has reactive center.
read(T) - Method in class org.openscience.cdk.io.CIFReader: Read a ChemFile from input.
read(T) - Method in class org.openscience.cdk.io.CMLReader: Read a IChemObject from input.
read(T) - Method in class org.openscience.cdk.io.CrystClustReader
read(T) - Method in class org.openscience.cdk.io.CTXReader
read(T) - Method in class org.openscience.cdk.io.GamessReader
read(T) - Method in class org.openscience.cdk.io.Gaussian03Reader
read(T) - Method in class org.openscience.cdk.io.Gaussian98Reader
read(T) - Method in class org.openscience.cdk.io.GhemicalMMReader
read(T) - Method in class org.openscience.cdk.io.HINReader: Reads the content from a HIN input.
read(T) - Method in class org.openscience.cdk.io.INChIPlainTextReader: Reads a IChemObject of type object from input.
read(T) - Method in class org.openscience.cdk.io.INChIReader: Reads a IChemObject of type object from input.
read(T) - Method in interface org.openscience.cdk.io.ISimpleChemObjectReader: Reads an IChemObject of type "object" from input.
read(T) - Method in class org.openscience.cdk.io.MDLReader: Deprecated.

Takes an object which subclasses IChemObject, e.g.
read(T) - Method in class org.openscience.cdk.io.MDLRXNReader: Deprecated.

Takes an object which subclasses IChemObject, e.g.Molecule, and will read this (from file, database, internet etc).
read(T) - Method in class org.openscience.cdk.io.MDLRXNV2000Reader: Takes an object which subclasses IChemObject, e.g.Molecule, and will read this (from file, database, internet etc).
read(T) - Method in class org.openscience.cdk.io.MDLRXNV3000Reader
read(T) - Method in class org.openscience.cdk.io.MDLV2000Reader: Takes an object which subclasses IChemObject, e.g.
read(T) - Method in class org.openscience.cdk.io.MDLV3000Reader
read(T) - Method in class org.openscience.cdk.io.Mol2Reader
read(T) - Method in class org.openscience.cdk.io.Mopac7Reader
read(T) - Method in class org.openscience.cdk.io.MoSSOutputReader: Read a IAtomContainerSet from the input source.
read(T) - Method in class org.openscience.cdk.io.PCCompoundASNReader
read(T) - Method in class org.openscience.cdk.io.PCCompoundXMLReader
read(T) - Method in class org.openscience.cdk.io.PCSubstanceXMLReader
read(T) - Method in class org.openscience.cdk.io.PDBReader: Takes an object which subclasses IChemObject, e.g.
read(T) - Method in class org.openscience.cdk.io.PMPReader: reads the content from a PMP input.
read(T) - Method in class org.openscience.cdk.io.rdf.CDKOWLReader: Reads an IChemObject of type "object" from input.
read(T) - Method in class org.openscience.cdk.io.RGroupQueryReader: Check input IChemObject and proceed to parse.
read(T) - Method in class org.openscience.cdk.io.ShelXReader: Read a ChemFile from input.
read(T) - Method in class org.openscience.cdk.io.SMILESReader: Reads the content from a XYZ input.
read(T) - Method in class org.openscience.cdk.io.VASPReader
read(T) - Method in class org.openscience.cdk.io.XYZReader: reads the content from a XYZ input.
read(T) - Method in class org.openscience.cdk.io.ZMatrixReader: Returns a IChemObject of type object bye reading from the input.
readAtomBlock(MDLV3000Reader.ReadState) - Method in class org.openscience.cdk.io.MDLV3000Reader: Reads the atoms, coordinates and charges.
readAtomTypeMappings() - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingReader: Reads the atom type mappings from the data file.
readAtomTypes(IChemObjectBuilder) - Method in class org.openscience.cdk.config.atomtypes.AtomTypeReader: Reads the atom types from the data file.
readAtomTypes(IChemObjectBuilder) - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeReader: Reads the atom types from the data file.
readAtomTypes(IChemObjectBuilder) - Method in class org.openscience.cdk.config.CDKBasedAtomTypeConfigurator: Reads the atom types from the CDK based atom type list.
readAtomTypes(IChemObjectBuilder) - Method in interface org.openscience.cdk.config.IAtomTypeConfigurator: Reads a set of configured AtomType's into a List.
readAtomTypes(IChemObjectBuilder) - Method in class org.openscience.cdk.config.OWLBasedAtomTypeConfigurator: Reads the atom types from the OWL based atom type list.
readAtomTypes(IChemObjectBuilder) - Method in class org.openscience.cdk.config.TXTBasedAtomTypeConfigurator: Reads a text based configuration file.
readBondBlock(MDLV3000Reader.ReadState) - Method in class org.openscience.cdk.io.MDLV3000Reader: Reads the bond atoms, order and stereo configuration.
readChar() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream: Read a character.
readChar() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Read a character.
readConnectionTable(IChemObjectBuilder) - Method in class org.openscience.cdk.io.MDLV3000Reader
readContent(int) - Method in class org.openscience.cdk.io.random.RandomAccessReader: Reads the record text content into a String.
readDictionary(Reader, String) - Method in class org.openscience.cdk.dict.DictionaryDatabase: Reads a custom dictionary into the database.
ReaderEvent - Class in org.openscience.cdk.io: Signals that something has happened in a file reader.
ReaderEvent(Object) - Constructor for class org.openscience.cdk.io.ReaderEvent: Creates a reader event.
ReaderFactory - Class in org.openscience.cdk.io: A factory for creating ChemObjectReaders.
ReaderFactory() - Constructor for class org.openscience.cdk.io.ReaderFactory: Constructs a ReaderFactory which tries to detect the format in the first 65536 chars.
ReaderFactory(int) - Constructor for class org.openscience.cdk.io.ReaderFactory: Constructs a ReaderFactory which tries to detect the format in the first given number of chars.
readHeader(MDLV3000Reader.ReadState) - Method in class org.openscience.cdk.io.MDLV3000Reader
readIsotopes() - Method in class org.openscience.cdk.config.isotopes.IsotopeReader: Triggers the XML parsing of the data file and returns the read Isotopes.
readLine() - Method in class org.openscience.cdk.io.MDLV3000Reader
readMolecule(IChemObjectBuilder) - Method in class org.openscience.cdk.io.MDLV3000Reader
ReadNCISdfFileAsTemplate(String) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor
readParameterSets(IChemObjectBuilder) - Method in class org.openscience.cdk.modeling.builder3d.MM2BasedParameterSetReader: The main method which parses through the force field configuration file
readParameterSets(IChemObjectBuilder) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94BasedParameterSetReader: The main method which parses through the force field configuration file
readPharmacophoreDefinitions(InputStream) - Static method in class org.openscience.cdk.pharmacophore.PharmacophoreUtils: Read in a set of pharmacophore definitions to create pharmacophore queries.
readPharmacophoreDefinitions(String) - Static method in class org.openscience.cdk.pharmacophore.PharmacophoreUtils: Read in a set of pharmacophore definitions to create pharmacophore queries.
readRecord(int) - Method in interface org.openscience.cdk.io.random.IRandomAccessChemObjectReader
readRecord(int) - Method in class org.openscience.cdk.io.random.RandomAccessReader: Returns the object at given record No.
readSGroup(MDLV3000Reader.ReadState) - Method in class org.openscience.cdk.io.MDLV3000Reader: Reads labels.
real - Variable in class org.openscience.cdk.math.Complex: The real part of this value
realmatrix - Variable in class org.openscience.cdk.math.IMatrix: the real part of the content
realvector - Variable in class org.openscience.cdk.math.IVector: The real part of this vector
RearrangementAnionReaction - Class in org.openscience.cdk.reaction.type: IReactionProcess which participate in movement resonance.
RearrangementAnionReaction() - Constructor for class org.openscience.cdk.reaction.type.RearrangementAnionReaction: Constructor of the RearrangementAnionReaction object
RearrangementCationReaction - Class in org.openscience.cdk.reaction.type: IReactionProcess which participate in movement resonance.
RearrangementCationReaction() - Constructor for class org.openscience.cdk.reaction.type.RearrangementCationReaction: Constructor of the RearrangementCharge2Reaction object
RearrangementChargeMechanism - Class in org.openscience.cdk.reaction.mechanism: This mechanism displaces the charge(radical, charge + or charge -) because of a double bond which is associated.
RearrangementChargeMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.RearrangementChargeMechanism
RearrangementLonePairReaction - Class in org.openscience.cdk.reaction.type: IReactionProcess which participate in movement resonance.
RearrangementLonePairReaction() - Constructor for class org.openscience.cdk.reaction.type.RearrangementLonePairReaction: Constructor of the RearrangementLonePairReaction object
RearrangementRadicalReaction - Class in org.openscience.cdk.reaction.type: IReactionProcess which participate in movement resonance.
RearrangementRadicalReaction() - Constructor for class org.openscience.cdk.reaction.type.RearrangementRadicalReaction: Constructor of the RearrangementRadicalReaction object
rebond(IAtomContainer) - Method in class org.openscience.cdk.graph.rebond.RebondTool: Rebonding using a Binary Space Partition Tree.
RebondTool - Class in org.openscience.cdk.graph.rebond: Provides tools to rebond a molecule from 3D coordinates only.
RebondTool(double, double, double) - Constructor for class org.openscience.cdk.graph.rebond.RebondTool
RecMet - net.sf.jniinchi.INCHI_OPTION
recolor(Color) - Method in class org.openscience.cdk.renderer.elements.GeneralPath: Recolor the path with the specified color.
records - Variable in class org.openscience.cdk.io.random.RandomAccessReader
RectangleElement - Class in org.openscience.cdk.renderer.elements: A rectangle, with width and height.
RectangleElement(double, double, double, double, boolean, Color) - Constructor for class org.openscience.cdk.renderer.elements.RectangleElement: Make a rectangle centered on (x, y).
RectangleElement(double, double, double, double, Color) - Constructor for class org.openscience.cdk.renderer.elements.RectangleElement: Make a rectangle from two opposite corners (x1, y1) and (x2, y2).
RECURSIVE - org.openscience.cdk.isomorphism.matchers.Expr.Type: Recursive query.
RecursiveSmartsAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
RecursiveSmartsAtom(IQueryAtomContainer) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.RecursiveSmartsAtom: Deprecated.

Creates a new instance
RecursiveSmartsExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
Refinable - Interface in org.openscience.cdk.group: Implementors are graph-like objects that are refinable by the equitable and discrete partition refiners.
refine(IAtomContainer) - Method in interface org.openscience.cdk.group.AtomContainerDiscretePartitionRefiner: Refine an atom container, which has the side effect of calculating the automorphism group.
refine(IAtomContainer, Partition) - Method in interface org.openscience.cdk.group.AtomContainerDiscretePartitionRefiner: Refine an atom partition based on the connectivity in the atom container.
refinedPartitioning(int[], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Refining the input partition based on the row entries.
reflect(Collection<IAtom>, Point2d, Point2d) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Reflect a collection of atoms in the line formed by the two specified points (beg,end).
reflect(Collection<IAtom>, IBond) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Reflect a collection of atoms in the line formed by the specified bond.
register(Class<? extends T>) - Method in class org.openscience.cdk.DynamicFactory: Registers a class with the factory.
register(Class<S>, Class<T>, DynamicFactory.CreationModifier<T>) - Method in class org.openscience.cdk.DynamicFactory: Explicitly register a concrete class with a provided interface and a given modifier.
register(Class<S>, Constructor<T>) - Method in class org.openscience.cdk.DynamicFactory: Register a specific constructor with an explicit interface.
register(Class<S>, Constructor<T>, DynamicFactory.CreationModifier<T>) - Method in class org.openscience.cdk.DynamicFactory: Register a specific constructor with a creation modifier to an explicit interface.
register(Class<T>, Class<? extends T>) - Method in class org.openscience.cdk.DynamicFactory: Explicitly register a concrete class with a provided interface.
register(DynamicFactory.ConstructorKey, DynamicFactory.Creator<T>) - Method in class org.openscience.cdk.DynamicFactory: Register a constructor key with a defined DynamicFactory.Creator.
registerConvention(String, ICMLModule) - Method in class org.openscience.cdk.io.cml.CMLHandler
registerConvention(String, ICMLModule) - Method in class org.openscience.cdk.io.CMLReader
registerCustomizer(ICMLCustomizer) - Method in class org.openscience.cdk.io.CMLWriter
registerCustomizer(ICMLCustomizer) - Method in class org.openscience.cdk.libio.cml.Convertor
registerFontSizeMapping(double, int) - Method in class org.openscience.cdk.renderer.font.AbstractFontManager: For a particular zoom level, register a font point-size so that this size of font will be used when the zoom is at this level.
registerFormat(IChemFormatMatcher) - Method in class org.openscience.cdk.io.FormatFactory: Registers a format for detection.
registerFormat(IChemFormatMatcher) - Method in class org.openscience.cdk.io.ReaderFactory: Registers a format for detection.
registerParameters(IGenerator<? extends IChemObject>) - Method in class org.openscience.cdk.renderer.RendererModel: Registers rendering parameters from IGenerators with this model.
registerWriter(Class<?>) - Method in class org.openscience.cdk.io.WriterFactory
ReInit(InputStream) - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Reinitialise.
ReInit(InputStream) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream: Reinitialise.
ReInit(InputStream) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Reinitialise.
ReInit(InputStream) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser: Reinitialise.
ReInit(InputStream, int, int) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream: Reinitialise.
ReInit(InputStream, int, int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Reinitialise.
ReInit(InputStream, int, int, int) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream: Reinitialise.
ReInit(InputStream, int, int, int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Reinitialise.
ReInit(InputStream, String) - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Reinitialise.
ReInit(InputStream, String) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream: Reinitialise.
ReInit(InputStream, String) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Reinitialise.
ReInit(InputStream, String) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser: Reinitialise.
ReInit(InputStream, String, int, int) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream: Reinitialise.
ReInit(InputStream, String, int, int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Reinitialise.
ReInit(InputStream, String, int, int, int) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream: Reinitialise.
ReInit(InputStream, String, int, int, int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Reinitialise.
ReInit(Reader) - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Reinitialise.
ReInit(Reader) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream: Reinitialise.
ReInit(Reader) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Reinitialise.
ReInit(Reader) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser: Reinitialise.
ReInit(Reader, int, int) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream: Reinitialise.
ReInit(Reader, int, int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Reinitialise.
ReInit(Reader, int, int, int) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream: Reinitialise.
ReInit(Reader, int, int, int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Reinitialise.
ReInit(NomParserTokenManager) - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Reinitialise.
ReInit(SimpleCharStream) - Method in class org.openscience.cdk.iupac.parser.NomParserTokenManager: Reinitialise parser.
ReInit(SimpleCharStream, int) - Method in class org.openscience.cdk.iupac.parser.NomParserTokenManager: Reinitialise parser.
ReInit(SimpleCharStream) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager: Reinitialise parser.
ReInit(SimpleCharStream, int) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager: Reinitialise parser.
ReInit(SMARTSParserTokenManager) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser: Reinitialise.
relatedChemObjects() - Method in class org.openscience.cdk.debug.DebugMapping: Returns an Iterable to the two IChemObjects.
relatedChemObjects() - Method in interface org.openscience.cdk.interfaces.IMapping: Returns an Iterable to the two IChemObjects.
relatedChemObjects() - Method in class org.openscience.cdk.Mapping: Returns an Iterable to the two IChemObjects.
relatedChemObjects() - Method in class org.openscience.cdk.silent.Mapping: Returns an Iterable to the two IChemObjects.
RELAXED - org.openscience.cdk.io.IChemObjectReader.Mode: Only fail on serious format problems
relevant() - Static method in class org.openscience.cdk.graph.Cycles: Create a cycle finder which will compute the relevant cycle basis (RC) of a molecule.
relevant(IAtomContainer) - Static method in class org.openscience.cdk.graph.Cycles: Find the relevant cycles of a molecule.
RELEVANT_RINGS - Static variable in class org.openscience.cdk.CDKConstants: The relevant rings computed for this molecule.
relevantCycles() - Method in class org.openscience.cdk.ringsearch.cyclebasis.CycleBasis: Deprecated.

Returns the essential cycles of this cycle basis.
relevantCycles() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis: Deprecated.
RelevantCycles - Class in org.openscience.cdk.graph: Compute the relevant cycles (C_R) of a graph.
RelevantCycles(int[][]) - Constructor for class org.openscience.cdk.graph.RelevantCycles: Generate the relevant cycle basis for a graph.
REMARK - Static variable in class org.openscience.cdk.CDKConstants: A remark for a IChemObject.
remove() - Method in class org.openscience.cdk.graph.AtomContainerPermutor
remove() - Method in class org.openscience.cdk.graph.MinimalPathIterator: Deprecated.
remove() - Method in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader: File IO generally does not support removing of entries.
remove() - Method in class org.openscience.cdk.io.iterator.event.DefaultEventChemObjectReader: File IO generally does not support removing of entries.
remove() - Method in class org.openscience.cdk.io.iterator.IteratingMDLConformerReader
remove() - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundASNReader
remove() - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader
remove() - Method in class org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader
remove() - Method in class org.openscience.cdk.io.iterator.IteratingSDFReader
remove() - Method in class org.openscience.cdk.io.iterator.IteratingSMILESReader
remove() - Method in class org.openscience.cdk.io.random.RandomAccessSDFReader
remove() - Method in class org.openscience.cdk.smsd.labelling.AtomContainerAtomPermutor: Deprecated.
remove(int) - Method in class org.openscience.cdk.ConformerContainer: Removes the conformer at the specified position.
remove(int) - Method in class org.openscience.cdk.signature.Orbit: Removes an atom index from the orbit.
remove(Object) - Method in class org.openscience.cdk.ConformerContainer: Remove the specified conformer.
remove(IAtom) - Method in class org.openscience.cdk.smsd.ring.PathGraph: Deprecated.
remove(IAtomContainer) - Method in class org.openscience.cdk.AtomContainer: Removes all atoms and electronContainers of a given atomcontainer from this container.
remove(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Removes all atoms and electronContainers of a given atomcontainer from this container.
remove(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Removes all atoms and electronContainers of a given atomcontainer from this container.
remove(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Removes all atoms and electronContainers of a given atomcontainer from this container.
remove(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugCrystal: Removes all atoms and electronContainers of a given atomcontainer from this container.
remove(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugMonomer: Removes all atoms and electronContainers of a given atomcontainer from this container.
remove(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugPolymer: Removes all atoms and electronContainers of a given atomcontainer from this container.
remove(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugRing: Removes all atoms and electronContainers of a given atomcontainer from this container.
remove(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugStrand: Removes all atoms and electronContainers of a given atomcontainer from this container.
remove(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Removes all atoms and electronContainers of a given atomcontainer from this container.
remove(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Removes all atoms and electronContainers of a given atomcontainer from this container.
remove(IAtomContainer) - Method in class org.openscience.cdk.silent.AtomContainer: Removes all atoms and electronContainers of a given atomcontainer from this container.
remove(IMolecularFormulaSet, MolecularFormulaRange) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaSetManipulator: Remove all those IMolecularFormula which are not fit theirs IElement occurrence into a limits.
remove(IMolecularFormulaSet, IMolecularFormula, IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaSetManipulator: Remove all those IMolecularFormula which are not fit theirs IElement occurrence into a limits.
removeAcidicOxygen(IAminoAcid) - Static method in class org.openscience.cdk.tools.manipulator.AminoAcidManipulator: Removes the singly bonded oxygen from the acid group of the AminoAcid.
removeAll(Collection<?>) - Method in class org.openscience.cdk.ConformerContainer
removeAllAtomContainers() - Method in class org.openscience.cdk.AtomContainerSet: Removes all AtomContainer from this container.
removeAllAtomContainers() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Removes all AtomContainer from this container.
removeAllAtomContainers() - Method in class org.openscience.cdk.debug.DebugSubstance: Removes all AtomContainer from this container.
removeAllAtomContainers() - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet: Removes all AtomContainer from this container.
removeAllAtomContainers() - Method in class org.openscience.cdk.silent.AtomContainerSet: Removes all AtomContainer from this container.
removeAllBonds() - Method in class org.openscience.cdk.AtomContainer: Removes all Bonds from this container.
removeAllBonds() - Method in class org.openscience.cdk.debug.DebugAminoAcid: Removes all Bonds from this container.
removeAllBonds() - Method in class org.openscience.cdk.debug.DebugAtomContainer: Removes all Bonds from this container.
removeAllBonds() - Method in class org.openscience.cdk.debug.DebugBioPolymer: Removes all Bonds from this container.
removeAllBonds() - Method in class org.openscience.cdk.debug.DebugCrystal: Removes all Bonds from this container.
removeAllBonds() - Method in class org.openscience.cdk.debug.DebugMonomer: Removes all Bonds from this container.
removeAllBonds() - Method in class org.openscience.cdk.debug.DebugPolymer: Removes all Bonds from this container.
removeAllBonds() - Method in class org.openscience.cdk.debug.DebugRing: Removes all Bonds from this container.
removeAllBonds() - Method in class org.openscience.cdk.debug.DebugStrand: Removes all Bonds from this container.
removeAllBonds() - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Removes all Bonds from this container.
removeAllBonds() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Removes all Bonds from this container.
removeAllBonds() - Method in class org.openscience.cdk.silent.AtomContainer: Removes all Bonds from this container.
removeAllElectronContainers() - Method in class org.openscience.cdk.AtomContainer: Removes electronContainers from this container.
removeAllElectronContainers() - Method in class org.openscience.cdk.debug.DebugAminoAcid: Removes electronContainers from this container.
removeAllElectronContainers() - Method in class org.openscience.cdk.debug.DebugAtomContainer: Removes electronContainers from this container.
removeAllElectronContainers() - Method in class org.openscience.cdk.debug.DebugBioPolymer: Removes electronContainers from this container.
removeAllElectronContainers() - Method in class org.openscience.cdk.debug.DebugCrystal: Removes electronContainers from this container.
removeAllElectronContainers() - Method in class org.openscience.cdk.debug.DebugMonomer: Removes electronContainers from this container.
removeAllElectronContainers() - Method in class org.openscience.cdk.debug.DebugPolymer: Removes electronContainers from this container.
removeAllElectronContainers() - Method in class org.openscience.cdk.debug.DebugRing: Removes electronContainers from this container.
removeAllElectronContainers() - Method in class org.openscience.cdk.debug.DebugStrand: Removes electronContainers from this container.
removeAllElectronContainers() - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Removes electronContainers from this container.
removeAllElectronContainers() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Removes electronContainers from this container.
removeAllElectronContainers() - Method in class org.openscience.cdk.silent.AtomContainer: Removes electronContainers from this container.
removeAllElements() - Method in class org.openscience.cdk.AtomContainer: Removes all atoms, bonds and stereo elements from this container.
removeAllElements() - Method in class org.openscience.cdk.debug.DebugAminoAcid: Removes all atoms, bonds and stereo elements from this container.
removeAllElements() - Method in class org.openscience.cdk.debug.DebugAtomContainer: Removes all atoms, bonds and stereo elements from this container.
removeAllElements() - Method in class org.openscience.cdk.debug.DebugBioPolymer: Removes all atoms, bonds and stereo elements from this container.
removeAllElements() - Method in class org.openscience.cdk.debug.DebugCrystal: Removes all atoms, bonds and stereo elements from this container.
removeAllElements() - Method in class org.openscience.cdk.debug.DebugMonomer: Removes all atoms, bonds and stereo elements from this container.
removeAllElements() - Method in class org.openscience.cdk.debug.DebugPolymer: Removes all atoms, bonds and stereo elements from this container.
removeAllElements() - Method in class org.openscience.cdk.debug.DebugRing: Removes all atoms, bonds and stereo elements from this container.
removeAllElements() - Method in class org.openscience.cdk.debug.DebugStrand: Removes all atoms, bonds and stereo elements from this container.
removeAllElements() - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Removes all atoms, bonds and stereo elements from this container.
removeAllElements() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Removes all atoms and bond from this container.
removeAllElements() - Method in class org.openscience.cdk.silent.AtomContainer: Removes all atoms, bonds and stereo elements from this container.
removeAllIsotopes() - Method in class org.openscience.cdk.debug.DebugMolecularFormula: Removes all isotopes of this molecular formula.
removeAllIsotopes() - Method in class org.openscience.cdk.formula.MolecularFormula: Removes all isotopes of this molecular formula.
removeAllIsotopes() - Method in class org.openscience.cdk.formula.MolecularFormulaRange: Removes all isotopes of this molecular formula.
removeAllIsotopes() - Method in interface org.openscience.cdk.interfaces.IMolecularFormula: Removes all isotopes of this molecular formula.
removeAllIsotopes() - Method in class org.openscience.cdk.silent.MolecularFormula: Removes all isotopes of this molecular formula.
removeAllMolecularFormulas() - Method in class org.openscience.cdk.debug.DebugAdductFormula: Removes all IMolecularFormula from this chemObject.
removeAllMolecularFormulas() - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet: Removes all IMolecularFormula from this chemObject.
removeAllMolecularFormulas() - Method in class org.openscience.cdk.formula.AdductFormula: Removes all IMolecularFormula from this chemObject.
removeAllMolecularFormulas() - Method in class org.openscience.cdk.formula.MolecularFormulaSet: Removes all IMolecularFormula from this chemObject.
removeAllMolecularFormulas() - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet: Removes all IMolecularFormula of this IMolecularFormulaSet.
removeAllMolecularFormulas() - Method in class org.openscience.cdk.silent.AdductFormula: Removes all IMolecularFormula from this chemObject.
removeAllMolecularFormulas() - Method in class org.openscience.cdk.silent.MolecularFormulaSet: Removes all IMolecularFormula from this chemObject.
removeAllReactions() - Method in class org.openscience.cdk.debug.DebugReactionSet: Removes all Reactions from this container.
removeAllReactions() - Method in interface org.openscience.cdk.interfaces.IReactionSet: Removes all reactions from this set.
removeAllReactions() - Method in class org.openscience.cdk.ReactionSet: Removes all Reactions from this container.
removeAllReactions() - Method in class org.openscience.cdk.silent.ReactionSet: Removes all Reactions from this container.
removeAllReactionSchemes() - Method in class org.openscience.cdk.debug.DebugReactionScheme: Removes all IReactionScheme from this chemObject.
removeAllReactionSchemes() - Method in interface org.openscience.cdk.interfaces.IReactionScheme: Removes all IReactionScheme from this chemObject.
removeAllReactionSchemes() - Method in class org.openscience.cdk.ReactionScheme: Removes all IReactionScheme from this chemObject.
removeAllReactionSchemes() - Method in class org.openscience.cdk.silent.ReactionScheme: Removes all IReactionScheme from this chemObject.
removeAromaticityFlagsFromHoseCode(String) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
removeAtom(int) - Method in class org.openscience.cdk.AtomContainer: Safely remove an atom from the container.
removeAtom(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Safely remove an atom from the container.
removeAtom(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Safely remove an atom from the container.
removeAtom(int) - Method in class org.openscience.cdk.silent.AtomContainer: Safely remove an atom from the container.
removeAtom(IAtom) - Method in class org.openscience.cdk.AtomContainer: Safely remove an atom from the container.
removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Safely remove an atom from the container.
removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Safely remove an atom from the container.
removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Safely remove an atom from the container.
removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal: Safely remove an atom from the container.
removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer: Safely remove an atom from the container.
removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer: Safely remove an atom from the container.
removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugRing: Safely remove an atom from the container.
removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand: Safely remove an atom from the container.
removeAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Safely remove an atom from the container.
removeAtom(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Removes the given atom and all connected electronContainers from the AtomContainer.
removeAtom(IAtom) - Method in class org.openscience.cdk.sgroup.Sgroup: Remove an atom from this Sgroup.
removeAtom(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer: Safely remove an atom from the container.
removeAtomAndConnectedElectronContainers(IAtom) - Method in class org.openscience.cdk.AtomContainer: Deprecated.
removeAtomAndConnectedElectronContainers(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Deprecated.
Method has be renamed IAtomContainer.removeAtom(IAtom).
removeAtomAndConnectedElectronContainers(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Deprecated.
removeAtomAndConnectedElectronContainers(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer: Deprecated.
removeAtomAndConnectedElectronContainers(IAtomContainerSet, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
removeAtomAndConnectedElectronContainers(IAtomContainerSet, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
removeAtomAndConnectedElectronContainers(IChemModel, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator: Remove an Atom and the connected ElectronContainers from all AtomContainers inside an IChemModel.
removeAtomAndConnectedElectronContainers(IReaction, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator: Removes the provided atom and its connected electron containers from the reaction.
removeAtomAndConnectedElectronContainers(IReactionSet, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
removeAtomContainer(int) - Method in class org.openscience.cdk.AtomContainerSet: Removes an AtomContainer from this container.
removeAtomContainer(int) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Removes an AtomContainer from this container.
removeAtomContainer(int) - Method in class org.openscience.cdk.debug.DebugSubstance: Removes an AtomContainer from this container.
removeAtomContainer(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet: Removes an AtomContainer from this container.
removeAtomContainer(int) - Method in class org.openscience.cdk.silent.AtomContainerSet: Removes an AtomContainer from this container.
removeAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.AtomContainerSet: Removes an AtomContainer from this container.
removeAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Removes an AtomContainer from this container.
removeAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugSubstance: Removes an AtomContainer from this container.
removeAtomContainer(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet: Removes an AtomContainer from this container.
removeAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.silent.AtomContainerSet: Removes an AtomContainer from this container.
removeAtomOnly(int) - Method in class org.openscience.cdk.AtomContainer: Unsafely remove atom at index.
removeAtomOnly(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Unsafely remove atom at index.
removeAtomOnly(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Unsafely remove atom at index.
removeAtomOnly(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Unsafely remove atom at index.
removeAtomOnly(int) - Method in class org.openscience.cdk.debug.DebugCrystal: Unsafely remove atom at index.
removeAtomOnly(int) - Method in class org.openscience.cdk.debug.DebugMonomer: Unsafely remove atom at index.
removeAtomOnly(int) - Method in class org.openscience.cdk.debug.DebugPolymer: Unsafely remove atom at index.
removeAtomOnly(int) - Method in class org.openscience.cdk.debug.DebugRing: Unsafely remove atom at index.
removeAtomOnly(int) - Method in class org.openscience.cdk.debug.DebugStrand: Unsafely remove atom at index.
removeAtomOnly(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Unsafely remove atom at index.
removeAtomOnly(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Removes the atom at the given position from the AtomContainer.
removeAtomOnly(int) - Method in class org.openscience.cdk.silent.AtomContainer: Unsafely remove atom at index.
removeAtomOnly(IAtom) - Method in class org.openscience.cdk.AtomContainer: Unsafely remove atom.
removeAtomOnly(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Unsafely remove atom.
removeAtomOnly(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Unsafely remove atom.
removeAtomOnly(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Unsafely remove atom.
removeAtomOnly(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal: Unsafely remove atom.
removeAtomOnly(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer: Unsafely remove atom.
removeAtomOnly(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer: Unsafely remove atom.
removeAtomOnly(IAtom) - Method in class org.openscience.cdk.debug.DebugRing: Unsafely remove atom.
removeAtomOnly(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand: Unsafely remove atom.
removeAtomOnly(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Unsafely remove atom.
removeAtomOnly(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Removes the given atom from the AtomContainer.
removeAtomOnly(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer: Unsafely remove atom.
removeAtomVectors() - Method in class org.openscience.cdk.Vibration: Removes all atom vectors from this vibration.
removeBond(int) - Method in class org.openscience.cdk.AtomContainer: Removes the bond at the given position from the AtomContainer.
removeBond(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Removes the bond at the given position from the AtomContainer.
removeBond(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Removes the bond at the given position from the AtomContainer.
removeBond(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Removes the bond at the given position from the AtomContainer.
removeBond(int) - Method in class org.openscience.cdk.debug.DebugCrystal: Removes the bond at the given position from the AtomContainer.
removeBond(int) - Method in class org.openscience.cdk.debug.DebugMonomer: Removes the bond at the given position from the AtomContainer.
removeBond(int) - Method in class org.openscience.cdk.debug.DebugPolymer: Removes the bond at the given position from the AtomContainer.
removeBond(int) - Method in class org.openscience.cdk.debug.DebugRing: Removes the bond at the given position from the AtomContainer.
removeBond(int) - Method in class org.openscience.cdk.debug.DebugStrand: Removes the bond at the given position from the AtomContainer.
removeBond(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Removes the bond at the given position from the AtomContainer.
removeBond(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Removes the bond at the given position from the AtomContainer.
removeBond(int) - Method in class org.openscience.cdk.silent.AtomContainer: Removes the bond at the given position from the AtomContainer.
removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.AtomContainer: Removes the bond that connects the two given atoms.
removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Removes the bond that connects the two given atoms.
removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Removes the bond that connects the two given atoms.
removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Removes the bond that connects the two given atoms.
removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal: Removes the bond that connects the two given atoms.
removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer: Removes the bond that connects the two given atoms.
removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer: Removes the bond that connects the two given atoms.
removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugRing: Removes the bond that connects the two given atoms.
removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugStrand: Removes the bond that connects the two given atoms.
removeBond(IAtom, IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Removes the bond that connects the two given atoms.
removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Removes the bond that connects the two given atoms.
removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.silent.AtomContainer: Removes the bond that connects the two given atoms.
removeBond(IBond) - Method in class org.openscience.cdk.AtomContainer: Removes the bond from this container.
removeBond(IBond) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Removes the bond from this container.
removeBond(IBond) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Removes the bond from this container.
removeBond(IBond) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Removes the bond from this container.
removeBond(IBond) - Method in class org.openscience.cdk.debug.DebugCrystal: Removes the bond from this container.
removeBond(IBond) - Method in class org.openscience.cdk.debug.DebugMonomer: Removes the bond from this container.
removeBond(IBond) - Method in class org.openscience.cdk.debug.DebugPolymer: Removes the bond from this container.
removeBond(IBond) - Method in class org.openscience.cdk.debug.DebugRing: Removes the bond from this container.
removeBond(IBond) - Method in class org.openscience.cdk.debug.DebugStrand: Removes the bond from this container.
removeBond(IBond) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Removes the bond from this container.
removeBond(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Removes the bond from this container.
removeBond(IBond) - Method in class org.openscience.cdk.sgroup.Sgroup: Remove a bond from this Sgroup.
removeBond(IBond) - Method in class org.openscience.cdk.silent.AtomContainer: Removes the bond from this container.
removeCDKChangeListener(ICDKChangeListener) - Method in class org.openscience.cdk.renderer.RendererModel: Removes a change listener from the list of listeners.
removeCell(int) - Method in class org.openscience.cdk.group.Partition: Removes the cell at the specified index.
removeChemModel(int) - Method in class org.openscience.cdk.ChemSequence: Remove a ChemModel from this ChemSequence.
removeChemModel(int) - Method in class org.openscience.cdk.debug.DebugChemSequence: Remove a ChemModel from this ChemSequence.
removeChemModel(int) - Method in interface org.openscience.cdk.interfaces.IChemSequence: Remove a ChemModel from this ChemSequence.
removeChemModel(int) - Method in class org.openscience.cdk.silent.ChemSequence: Remove a ChemModel from this ChemSequence.
removeChemObjectIOListener(IChemObjectIOListener) - Method in class org.openscience.cdk.io.ChemObjectIO: Removes a IChemObjectIOListener from this IChemObjectIO.
removeChemObjectIOListener(IChemObjectIOListener) - Method in interface org.openscience.cdk.io.IChemObjectIO: Removes a IChemObjectIOListener from this IChemObjectIO.
removeChemObjectIOListener(IChemObjectIOListener) - Method in class org.openscience.cdk.io.random.DefaultRandomAccessChemObjectReader
removeChemObjectIOListener(IChemObjectIOListener) - Method in class org.openscience.cdk.io.random.RandomAccessReader
removeChemSequence(int) - Method in class org.openscience.cdk.ChemFile: Removes a ChemSequence from this container.
removeChemSequence(int) - Method in class org.openscience.cdk.debug.DebugChemFile: Removes a ChemSequence from this container.
removeChemSequence(int) - Method in interface org.openscience.cdk.interfaces.IChemFile: Removes the IChemSequence at the given position from this container.
removeChemSequence(int) - Method in class org.openscience.cdk.silent.ChemFile: Removes a ChemSequence from this container.
removeElectronContainer(int) - Method in class org.openscience.cdk.AtomContainer: Removes the bond at the given position from this container.
removeElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Removes the bond at the given position from this container.
removeElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Removes the bond at the given position from this container.
removeElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Removes the bond at the given position from this container.
removeElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugCrystal: Removes the bond at the given position from this container.
removeElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugMonomer: Removes the bond at the given position from this container.
removeElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugPolymer: Removes the bond at the given position from this container.
removeElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugRing: Removes the bond at the given position from this container.
removeElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugStrand: Removes the bond at the given position from this container.
removeElectronContainer(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Removes the bond at the given position from this container.
removeElectronContainer(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Removes the bond at the given position from this container.
removeElectronContainer(int) - Method in class org.openscience.cdk.silent.AtomContainer: Removes the bond at the given position from this container.
removeElectronContainer(IAtomContainerSet, IElectronContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
removeElectronContainer(IAtomContainerSet, IElectronContainer) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
removeElectronContainer(IChemModel, IElectronContainer) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator: Remove an ElectronContainer from all AtomContainers inside an IChemModel.
removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.AtomContainer: Removes this ElectronContainer from this container.
removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Removes this ElectronContainer from this container.
removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Removes this ElectronContainer from this container.
removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Removes this ElectronContainer from this container.
removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugCrystal: Removes this ElectronContainer from this container.
removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugMonomer: Removes this ElectronContainer from this container.
removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugPolymer: Removes this ElectronContainer from this container.
removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugRing: Removes this ElectronContainer from this container.
removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugStrand: Removes this ElectronContainer from this container.
removeElectronContainer(IElectronContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Removes this ElectronContainer from this container.
removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Removes this ElectronContainer from this container.
removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.silent.AtomContainer: Removes this ElectronContainer from this container.
removeElectronContainer(IReaction, IElectronContainer) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator: Removes the provided electrons from the reaction.
removeElectronContainer(IReactionSet, IElectronContainer) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
removeElement(IMolecularFormula, IElement) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Removes all isotopes from a given element in the MolecularFormula.
removeHydrogens(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Create an copy of the org structure with explicit hydrogens removed.
removeHydrogensAndPreserveAtomID(IAtomContainer) - Static method in class org.openscience.cdk.normalize.SMSDNormalizer: Deprecated.

Returns IAtomContainer without Hydrogen.
removeHydrogensExceptSingleAndPreserveAtomID(IAtomContainer) - Static method in class org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator: Deprecated.

Returns IAtomContainer without Hydrogen.
removeHydrogensPreserveMultiplyBonded(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Deprecated.
AtomContainerManipulator.suppressHydrogens(org.openscience.cdk.interfaces.IAtomContainer) will now not removed bridging hydrogens by default
removeIsotope(IIsotope) - Method in class org.openscience.cdk.debug.DebugMolecularFormula: Removes the given isotope from the MolecularFormula.
removeIsotope(IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormula: Removes the given isotope from the MolecularFormula.
removeIsotope(IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormulaRange: Removes the given isotope from the MolecularFormulaExpand.
removeIsotope(IIsotope) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula: Removes the given isotope from the MolecularFormula.
removeIsotope(IIsotope) - Method in class org.openscience.cdk.silent.MolecularFormula: Removes the given isotope from the MolecularFormula.
removeListener(IChemObjectListener) - Method in class org.openscience.cdk.ChemObject: Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAtom: Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAtomType: Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugBond: Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugChemFile: Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugChemModel: Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugChemObject: Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugChemSequence: Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugCrystal: Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugElectronContainer: Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugElement: Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugIsotope: Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugLonePair: Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugMapping: Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugMonomer: Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugPolymer: Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugReaction: Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugReactionScheme: Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugReactionSet: Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugRing: Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugSingleElectron: Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugStrand: Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugSubstance: Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
removeListener(IChemObjectListener) - Method in interface org.openscience.cdk.interfaces.IChemObject: Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
removeListener(IChemObjectListener) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject: Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
removeListener(IChemObjectListener) - Method in class org.openscience.cdk.silent.ChemObject: Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
removeLonePair(int) - Method in class org.openscience.cdk.AtomContainer: Removes the lone pair at the given position from the AtomContainer.
removeLonePair(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Removes the lone pair at the given position from the AtomContainer.
removeLonePair(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Removes the lone pair at the given position from the AtomContainer.
removeLonePair(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Removes the lone pair at the given position from the AtomContainer.
removeLonePair(int) - Method in class org.openscience.cdk.debug.DebugCrystal: Removes the lone pair at the given position from the AtomContainer.
removeLonePair(int) - Method in class org.openscience.cdk.debug.DebugMonomer: Removes the lone pair at the given position from the AtomContainer.
removeLonePair(int) - Method in class org.openscience.cdk.debug.DebugPolymer: Removes the lone pair at the given position from the AtomContainer.
removeLonePair(int) - Method in class org.openscience.cdk.debug.DebugRing: Removes the lone pair at the given position from the AtomContainer.
removeLonePair(int) - Method in class org.openscience.cdk.debug.DebugStrand: Removes the lone pair at the given position from the AtomContainer.
removeLonePair(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Removes the lone pair at the given position from the AtomContainer.
removeLonePair(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Removes the lone pair at the given position from the AtomContainer.
removeLonePair(int) - Method in class org.openscience.cdk.silent.AtomContainer: Removes the lone pair at the given position from the AtomContainer.
removeLonePair(ILonePair) - Method in class org.openscience.cdk.AtomContainer: Removes the lone pair from the AtomContainer.
removeLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Removes the lone pair from the AtomContainer.
removeLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Removes the lone pair from the AtomContainer.
removeLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Removes the lone pair from the AtomContainer.
removeLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugCrystal: Removes the lone pair from the AtomContainer.
removeLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugMonomer: Removes the lone pair from the AtomContainer.
removeLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugPolymer: Removes the lone pair from the AtomContainer.
removeLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugRing: Removes the lone pair from the AtomContainer.
removeLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugStrand: Removes the lone pair from the AtomContainer.
removeLonePair(ILonePair) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Removes the lone pair from the AtomContainer.
removeLonePair(ILonePair) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Removes the lone pair from the AtomContainer.
removeLonePair(ILonePair) - Method in class org.openscience.cdk.silent.AtomContainer: Removes the lone pair from the AtomContainer.
removeLoopBonds(IAtomContainer, int) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor
removeMapping(int) - Method in interface org.openscience.cdk.interfaces.IReaction: Removes a mapping between the reactant and product side to this Reaction.
removeMapping(int) - Method in class org.openscience.cdk.Reaction: Removes a mapping between the reactant and product side to this Reaction.
removeMapping(int) - Method in class org.openscience.cdk.silent.Reaction: Removes a mapping between the reactant and product side to this Reaction.
removeMolecularFormula(int) - Method in class org.openscience.cdk.debug.DebugAdductFormula: Removes an MolecularFormula from this chemObject.
removeMolecularFormula(int) - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet: Removes an MolecularFormula from this chemObject.
removeMolecularFormula(int) - Method in class org.openscience.cdk.formula.AdductFormula: Removes an MolecularFormula from this chemObject.
removeMolecularFormula(int) - Method in class org.openscience.cdk.formula.MolecularFormulaSet: Removes an MolecularFormula from this chemObject.
removeMolecularFormula(int) - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet: Removes the IMolecularFormula at the given position from the IMolecularFormulaSet.
removeMolecularFormula(int) - Method in class org.openscience.cdk.silent.AdductFormula: Removes an MolecularFormula from this chemObject.
removeMolecularFormula(int) - Method in class org.openscience.cdk.silent.MolecularFormulaSet: Removes an MolecularFormula from this chemObject.
removeMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugAdductFormula: Removes an IMolecularFormula from this chemObject.
removeMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet: Removes an IMolecularFormula from this chemObject.
removeMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.formula.AdductFormula: Removes an IMolecularFormula from this chemObject.
removeMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.formula.MolecularFormulaSet: Removes an IMolecularFormula from this chemObject.
removeMolecularFormula(IMolecularFormula) - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet: Removes the given IMolecularFormula from the IMolecularFormulaSet.
removeMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.silent.AdductFormula: Removes an IMolecularFormula from this chemObject.
removeMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.silent.MolecularFormulaSet: Removes an IMolecularFormula from this chemObject.
removeMolecule(IAtomContainer) - Method in class org.openscience.cdk.layout.TemplateHandler
removeMonomer(String) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Removes a particular monomer, specified by its name.
removeMonomer(String) - Method in class org.openscience.cdk.debug.DebugPolymer: Removes a particular monomer, specified by its name.
removeMonomer(String) - Method in class org.openscience.cdk.debug.DebugStrand: Removes a particular monomer, specified by its name.
removeMonomer(String) - Method in interface org.openscience.cdk.interfaces.IPolymer: Removes a particular monomer, specified by its name.
removeMonomer(String) - Method in interface org.openscience.cdk.interfaces.IStrand: Removes a particular monomer, specified by its name.
removeMonomer(String) - Method in class org.openscience.cdk.Polymer: Removes a particular monomer, specified by its name.
removeMonomer(String) - Method in class org.openscience.cdk.silent.Polymer: Removes a particular monomer, specified by its name.
removeMonomer(String) - Method in class org.openscience.cdk.silent.Strand: Removes a particular monomer, specified by its name.
removeMonomer(String) - Method in class org.openscience.cdk.Strand: Removes a particular monomer, specified by its name.
removeNonChiralHydrogens(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Produces an AtomContainer without explicit non stereo-relevant Hs but with H count from one with Hs.
removeParents(Collection<Sgroup>) - Method in class org.openscience.cdk.sgroup.Sgroup: Remove the specified parent associations from this Sgroup.
removeProperty(Object) - Method in class org.openscience.cdk.ChemObject: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugAtom: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugAtomType: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugBond: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugChemFile: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugChemModel: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugChemObject: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugChemSequence: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugCrystal: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugElectronContainer: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugElement: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugIsotope: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugLonePair: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugMapping: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugMolecularFormula: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugMonomer: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugPolymer: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugReaction: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugReactionScheme: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugReactionSet: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugRing: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugSingleElectron: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugStrand: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugSubstance: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.formula.MolecularFormula: Removes a property for a IChemObject.
removeProperty(Object) - Method in interface org.openscience.cdk.interfaces.IChemObject: Removes a property for a IChemObject.
removeProperty(Object) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.silent.ChemObject: Removes a property for a IChemObject.
removeProperty(Object) - Method in class org.openscience.cdk.silent.MolecularFormula: Removes a property for a IChemObject.
removeReaction(int) - Method in interface org.openscience.cdk.interfaces.IReactionSet: Remove a reaction from this set.
removeReaction(int) - Method in class org.openscience.cdk.ReactionSet: Remove a reaction from this set.
removeReaction(int) - Method in class org.openscience.cdk.silent.ReactionSet: Remove a reaction from this set.
removeReaction(IReaction) - Method in class org.openscience.cdk.debug.DebugReactionSet: Removes all instances of a reaction from this IReactionSet.
removeReaction(IReaction) - Method in interface org.openscience.cdk.interfaces.IReactionSet: Removes all instances of a reaction from this IReactionSet.
removeReaction(IReaction) - Method in class org.openscience.cdk.ReactionSet
removeReaction(IReaction) - Method in class org.openscience.cdk.silent.ReactionSet
removeReactionScheme(IReactionScheme) - Method in interface org.openscience.cdk.interfaces.IReactionScheme: Removes an IReactionScheme from this chemObject.
removeReactionScheme(IReactionScheme) - Method in class org.openscience.cdk.ReactionScheme: Removes an IReactionScheme from this chemObject.
removeReactionScheme(IReactionScheme) - Method in class org.openscience.cdk.silent.ReactionScheme: Removes an IReactionScheme from this chemObject.
removeRecurringMappings(List<Integer>) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks: Deprecated.
removeRedundantArcs(int, int, List<Integer>, McgregorHelper) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks: Deprecated.

The function is called in function partsearch.
removeRedundantMappingsForSingleAtomCase(List<CDKRMap>) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler: Deprecated.
removeSingleElectron(int) - Method in class org.openscience.cdk.AtomContainer: Removes the single electron at the given position from the AtomContainer.
removeSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Removes the single electron at the given position from the AtomContainer.
removeSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Removes the single electron at the given position from the AtomContainer.
removeSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Removes the single electron at the given position from the AtomContainer.
removeSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugCrystal: Removes the single electron at the given position from the AtomContainer.
removeSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugMonomer: Removes the single electron at the given position from the AtomContainer.
removeSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugPolymer: Removes the single electron at the given position from the AtomContainer.
removeSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugRing: Removes the single electron at the given position from the AtomContainer.
removeSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugStrand: Removes the single electron at the given position from the AtomContainer.
removeSingleElectron(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Removes the single electron at the given position from the AtomContainer.
removeSingleElectron(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Removes the single electron at the given position from the AtomContainer.
removeSingleElectron(int) - Method in class org.openscience.cdk.silent.AtomContainer: Removes the single electron at the given position from the AtomContainer.
removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.AtomContainer: Removes the single electron from the AtomContainer.
removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Removes the single electron from the AtomContainer.
removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Removes the single electron from the AtomContainer.
removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Removes the single electron from the AtomContainer.
removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugCrystal: Removes the single electron from the AtomContainer.
removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugMonomer: Removes the single electron from the AtomContainer.
removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugPolymer: Removes the single electron from the AtomContainer.
removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugRing: Removes the single electron from the AtomContainer.
removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugStrand: Removes the single electron from the AtomContainer.
removeSingleElectron(ISingleElectron) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Removes the single electron from the AtomContainer.
removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Removes the single electron from the AtomContainer.
removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.silent.AtomContainer: Removes the single electron from the AtomContainer.
removeStrand(String) - Method in class org.openscience.cdk.BioPolymer: Removes a particular strand, specified by its name.
removeStrand(String) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Removes a particular strand, specified by its name.
removeStrand(String) - Method in interface org.openscience.cdk.interfaces.IBioPolymer: Removes a particular strand, specified by its name.
removeStrand(String) - Method in class org.openscience.cdk.silent.BioPolymer: Removes a particular strand, specified by its name.
removeSubGraph(List<List<CDKRMap>>) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler: Deprecated.
removeSymbol(String) - Method in class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom: Deprecated.

Remove a symbol from this QueryAtom
removeSymbol(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom: Deprecated.

Remove a symbol from this QueryAtom
removeTreeStructure(BinaryTree) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks: Deprecated.
removeValidator(IValidator) - Method in class org.openscience.cdk.validate.ValidatorEngine
RemovingSEofBMechanism - Class in org.openscience.cdk.reaction.mechanism: This mechanism extracts a single electron from a bonding orbital which located in an bond.
RemovingSEofBMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.RemovingSEofBMechanism
RemovingSEofNBMechanism - Class in org.openscience.cdk.reaction.mechanism: This mechanism extracts a single electron from a non-bonding orbital which located in a ILonePair container.
RemovingSEofNBMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.RemovingSEofNBMechanism
rendererModel - Variable in class org.openscience.cdk.renderer.AbstractRenderer: The renderer model is final as it is not intended to be replaced.
RendererModel - Class in org.openscience.cdk.renderer: Model for IRenderer that contains settings for drawing objects.
RendererModel() - Constructor for class org.openscience.cdk.renderer.RendererModel: Construct a renderer model with no parameters.
RendererModel.ColorHash - Class in org.openscience.cdk.renderer: The color hash is used to color substructures.
RendererModel.ExternalHighlightColor - Class in org.openscience.cdk.renderer: The color used to highlight external selections.
RendererModel.MarkedOutput - Class in org.openscience.cdk.renderer: If format supports it (e.g.
RendererModel.Padding - Class in org.openscience.cdk.renderer: Padding between molecules in a grid or row.
RendererModel.SelectionColor - Class in org.openscience.cdk.renderer: Color of a selection.
RendererModel.TitleColor - Class in org.openscience.cdk.renderer: Color of title text.
RendererModel.TitleFontScale - Class in org.openscience.cdk.renderer: Size of title font relative compared to atom symbols
reOrder(int[], int[], String[], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Re-order all the global variables based on the refined new partitioning.
repaint(IDrawVisitor) - Method in class org.openscience.cdk.renderer.AbstractRenderer: Repaint using the cached diagram.
repaint(IDrawVisitor) - Method in class org.openscience.cdk.renderer.ChemModelRenderer: Repaint using the cached diagram.
replaceAtomByAtom(IAtomContainer, IAtom, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Substitute one atom in a container for another adjusting bonds, single electrons, lone pairs, and stereochemistry as required.
replaceAtomContainer(int, IAtomContainer) - Method in class org.openscience.cdk.AtomContainerSet: Replace the AtomContainer at a specific position (array has to be large enough).
replaceAtomContainer(int, IAtomContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Replace the AtomContainer at a specific position (array has to be large enough).
replaceAtomContainer(int, IAtomContainer) - Method in class org.openscience.cdk.debug.DebugSubstance: Replace the AtomContainer at a specific position (array has to be large enough).
replaceAtomContainer(int, IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet: Replace the AtomContainer at a specific position (array has to be large enough).
replaceAtomContainer(int, IAtomContainer) - Method in class org.openscience.cdk.silent.AtomContainerSet: Replace the AtomContainer at a specific position (array has to be large enough).
reportErrors - Variable in class org.openscience.cdk.io.cml.CMLErrorHandler
repVal - Variable in class org.openscience.cdk.io.VASPReader
REQUIRE_EXPLICIT_HYDROGENS - Static variable in class org.openscience.cdk.atomtype.CDKAtomTypeMatcher
REQUIRE_NOTHING - Static variable in class org.openscience.cdk.atomtype.CDKAtomTypeMatcher
rescaleBondLength(IAtom, IAtom, Point3d) - Static method in class org.openscience.cdk.geometry.AtomTools: Rescales Point2 so that length 1-2 is sum of covalent radii.
rescaleBondLength(IAtom, IAtom, Point3d) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D: Rescales Point2 so that length 1-2 is sum of covalent radii.
reset() - Method in interface org.openscience.cdk.hash.stereo.StereoEncoder: Reset the stereo-encoders, any currently perceived configurations will be re-activated.
reset() - Method in class org.openscience.cdk.renderer.AtomContainerRenderer: Reset the draw center and model center, and set the zoom to 100%.
reset() - Method in class org.openscience.cdk.smiles.smarts.parser.JJTSMARTSParserState
reset() - Method in class org.openscience.cdk.tools.FormatStringBuffer: Reset this FormatStringBuffer with the format string given in the constructor or last call to reset(String).
reset(String) - Method in class org.openscience.cdk.tools.FormatStringBuffer: Reset this FormatStringBuffer.
resetCEdgesSize() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph: Deprecated.
resetDEdgesSize() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph: Deprecated.
resetFlags(IAtomContainer) - Static method in class org.openscience.cdk.graph.PathTools
resetFlags(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor
resetTimeOut() - Method in class org.openscience.cdk.smsd.Isomorphism: Deprecated.
resetVirtualCounts() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager: Reset the virtual counts.
reshape(int) - Method in class org.openscience.cdk.math.IVector: Resize this vector
reshape(int, int) - Method in class org.openscience.cdk.math.IMatrix: Resize the matrix
Residue - Class in org.openscience.cdk.libio.md: A residue is a named, numbered collection of atoms in an MDMolecule.
Residue() - Constructor for class org.openscience.cdk.libio.md.Residue: Empty constructor
Residue(IAtomContainer, int, MDMolecule) - Constructor for class org.openscience.cdk.libio.md.Residue: Constructor to create a Residue based on an AC, a number, and a MDMolecule.
RESIDUE_FORMAT - Variable in class org.openscience.cdk.io.PDBWriter
RESIDUE_NAME - Static variable in class org.openscience.cdk.templates.AminoAcids
RESIDUE_NAME_SHORT - Static variable in class org.openscience.cdk.templates.AminoAcids
resize(long[][], int) - Method in class org.openscience.cdk.io.random.RandomAccessReader
resolveEntity(String, String) - Method in class org.openscience.cdk.io.cml.CMLResolver: Resolves SYSTEM and PUBLIC identifiers for CML DTDs.
resolveEntity(String, String, String, String) - Method in class org.openscience.cdk.io.cml.CMLResolver: Not implemented, but uses resolveEntity(String publicId, String systemId) instead.
resolveOverlap(IAtomContainer, IRingSet) - Method in class org.openscience.cdk.layout.OverlapResolver: Deprecated.

Main method to be called to resolve overlap situations.
RESONANCE - org.openscience.cdk.interfaces.IReaction.Direction: Reaction shows interconversion between resonance forms.
resource2Order(Resource) - Static method in class org.openscience.cdk.libio.jena.Convertor: Converts a Resource object into the matching IBond.Order.
REST_H - Static variable in class org.openscience.cdk.CDKConstants: A property to indicate RestH being true or false.
retainAll(Collection<?>) - Method in class org.openscience.cdk.ConformerContainer
RETRO_SYNTHETIC - org.openscience.cdk.interfaces.IReaction.Direction: Indicate the precursors for a given molecule, note this will make swap where reactant/products appear.
returnChemFile() - Method in class org.openscience.cdk.io.cml.CMLCoreModule
returnChemFile() - Method in interface org.openscience.cdk.io.cml.ICMLModule
reverse(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator: Returns a new IReaction which is the reverse of the given reaction.
reverseComparison(int, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: The function to compare a node labelling array when the number of left consecutive entries is equal to the right consecutive entries.
Rf - Static variable in interface org.openscience.cdk.interfaces.IElement
Rg - Static variable in interface org.openscience.cdk.interfaces.IElement
RGraph - Class in org.openscience.cdk.isomorphism.mcss: This class implements the Resolution Graph (RGraph).
RGraph() - Constructor for class org.openscience.cdk.isomorphism.mcss.RGraph: Constructor for the RGraph object and creates an empty RGraph.
RGroup - Class in org.openscience.cdk.isomorphism.matchers: Represents a single substitute structure in an RGroupList.
RGroup() - Constructor for class org.openscience.cdk.isomorphism.matchers.RGroup
RGroupList - Class in org.openscience.cdk.isomorphism.matchers: Represents a list of Rgroup substitutes to be associated with some RGroupQuery.
RGroupList(int) - Constructor for class org.openscience.cdk.isomorphism.matchers.RGroupList: Default constructor.
RGroupList(int, boolean, String, int) - Constructor for class org.openscience.cdk.isomorphism.matchers.RGroupList: Constructor with attributes given.
RGroupQuery - Class in org.openscience.cdk.isomorphism.matchers: Represents information contained in a Symyx RGfile (R-group query file).
It contains a root structure (the scaffold if you like), a map with R-group definitions (each of which can contain multiple substitutes) and a map with attachment points.
RGroupQuery(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.RGroupQuery
RGroupQueryFormat - Class in org.openscience.cdk.io.formats: Format for Symyx RGfiles (Rgroup query files).
RGroupQueryFormat() - Constructor for class org.openscience.cdk.io.formats.RGroupQueryFormat
RGroupQueryReader - Class in org.openscience.cdk.io: A reader for Symyx' Rgroup files (RGFiles).
RGroupQueryReader() - Constructor for class org.openscience.cdk.io.RGroupQueryReader: Default constructor, input not set.
RGroupQueryReader(InputStream) - Constructor for class org.openscience.cdk.io.RGroupQueryReader: Constructs a new RgroupQueryReader that can read RgroupAtomContainerSet from a given InputStream.
RGroupQueryReader(Reader) - Constructor for class org.openscience.cdk.io.RGroupQueryReader: Constructs a new RgroupQueryReader that can read RgroupAtomContainerSet from a given Reader.
RGroupQueryWriter - Class in org.openscience.cdk.io: A writer for Symyx' Rgroup files (RGFiles).
An RGfile describes a single molecular query with Rgroups.
RGroupQueryWriter() - Constructor for class org.openscience.cdk.io.RGroupQueryWriter: Zero argument constructor.
RGroupQueryWriter(Writer) - Constructor for class org.openscience.cdk.io.RGroupQueryWriter: Constructs a new writer that can write an IRGroupQuery to the Symx RGFile format.
Rh - Static variable in interface org.openscience.cdk.interfaces.IElement
RH - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Rhenium - org.openscience.cdk.config.Elements
RHENIUM - Static variable in enum org.openscience.cdk.config.Elements
RHENIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Rhodium - org.openscience.cdk.config.Elements
RHODIUM - Static variable in enum org.openscience.cdk.config.Elements
RHODIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
right() - Method in class org.openscience.cdk.isomorphism.matchers.Expr: Access the right sub-expression of this atom expression being tested.
RIGHT - Static variable in interface org.openscience.cdk.interfaces.IStereoElement
Ring - Class in org.openscience.cdk: Class representing a ring structure in a molecule.
Ring - Class in org.openscience.cdk.silent: Class representing a ring structure in a molecule.
Ring() - Constructor for class org.openscience.cdk.Ring: Constructs an empty ring.
Ring() - Constructor for class org.openscience.cdk.silent.Ring: Constructs an empty ring.
Ring(int) - Constructor for class org.openscience.cdk.Ring: Constructs an empty ring that will have a certain size.
Ring(int) - Constructor for class org.openscience.cdk.silent.Ring: Constructs an empty ring that will have a certain size.
Ring(int, String) - Constructor for class org.openscience.cdk.Ring: Constructs a ring that will have a certain number of atoms of the given elements.
Ring(int, String) - Constructor for class org.openscience.cdk.silent.Ring: Constructs a ring that will have a certain number of atoms of the given elements.
Ring(IAtomContainer) - Constructor for class org.openscience.cdk.Ring: Constructs a ring from the atoms in an IAtomContainer object.
Ring(IAtomContainer) - Constructor for class org.openscience.cdk.silent.Ring: Constructs a ring from the atoms in an IAtomContainer object.
RING_BOND_COUNT - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if the ring bond count of an atom equals the specified 'value'.
RING_CONNECTIONS - Static variable in class org.openscience.cdk.CDKConstants: This property indicates how many ring bonds are connected to the given atom.
RING_COUNT - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if the number of rings this atom belongs to matches the specified 'value'.
RING_SIZE - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if the this atom belongs to a ring equal to the specified 'value'
RING_SIZES - Static variable in class org.openscience.cdk.CDKConstants: This property will contain an ArrayList of Integers.
RING_SMALLEST - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if the smallest ring this atom belongs to equals the specified 'value'
ringAlreadyInSet(IRing, IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator: Checks - and returns 'true' - if a certain ring is already stored in the ringset.
RingBond - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
RingBond(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.RingBond: Deprecated.

Creates a new instance
RingConnectivity() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
RingElement - Class in org.openscience.cdk.renderer.elements: A ring is just a circle - in other words, an oval whose width and height are the same.
RingElement(double, double, double, Color) - Constructor for class org.openscience.cdk.renderer.elements.RingElement: Make a ring element centered on (x, y) with radius and color given.
RingFilter - Class in org.openscience.cdk.smsd.ring: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK and a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
RingFilter(AtomMatcher, RingFinder) - Constructor for class org.openscience.cdk.smsd.ring.RingFilter: Deprecated.
RingFinder - Interface in org.openscience.cdk.smsd.ring: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
ringFragments() - Method in class org.openscience.cdk.ringsearch.RingSearch: Extract the cyclic atom and bond fragments of the container.
RingGenerator - Class in org.openscience.cdk.renderer.generators: Generates just the aromatic indicators for rings : circles, or light-gray inner bonds, depending on the value of CDKStyleAromaticity.
RingGenerator() - Constructor for class org.openscience.cdk.renderer.generators.RingGenerator: Make a generator for ring elements.
RingGenerator.CDKStyleAromaticity - Class in org.openscience.cdk.renderer.generators: Depicts aromaticity of rings in the original CDK style.
RingGenerator.MaxDrawableAromaticRing - Class in org.openscience.cdk.renderer.generators: The maximum ring size for which an aromatic ring should be drawn.
RingGenerator.RingProportion - Class in org.openscience.cdk.renderer.generators: The proportion of a ring bounds to use to draw the ring.
RingGenerator.ShowAromaticity - Class in org.openscience.cdk.renderer.generators: Determines whether rings should be drawn with a circle if they are aromatic.
RingIdentifier() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
RingIdentifierAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
RingIdentifierAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.RingIdentifierAtom: Deprecated.
RingManipulator - Class in org.openscience.cdk.tools.manipulator
RingManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.RingManipulator
RingMembership() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
RingMembershipAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
RingMembershipAtom(int, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.RingMembershipAtom: Deprecated.

Ring membership query atom.
RingPartitioner - Class in org.openscience.cdk.ringsearch: Partitions a RingSet into RingSets of connected rings.
RingPartitioner() - Constructor for class org.openscience.cdk.ringsearch.RingPartitioner
RingPlacer - Class in org.openscience.cdk.layout: Class providing methods for generating coordinates for ring atoms.
RingPlacer() - Constructor for class org.openscience.cdk.layout.RingPlacer: The empty constructor.
RingProportion() - Constructor for class org.openscience.cdk.renderer.generators.RingGenerator.RingProportion
RingSearch - Class in org.openscience.cdk.ringsearch: Efficiently search for atoms that are members of a ring.
RingSearch(IAtomContainer) - Constructor for class org.openscience.cdk.ringsearch.RingSearch: Create a new RingSearch for the specified container.
RingSearch(IAtomContainer, int[][]) - Constructor for class org.openscience.cdk.ringsearch.RingSearch: Create a new RingSearch for the specified container and graph.
RingSearch(IAtomContainer, CyclicVertexSearch) - Constructor for class org.openscience.cdk.ringsearch.RingSearch: Create a new RingSearch for the specified container using the provided search.
ringSet - Variable in class org.openscience.cdk.ChemModel: A RingSet.
ringSet - Variable in class org.openscience.cdk.renderer.generators.BasicBondGenerator: Necessary for calculating inner-ring bond elements.
ringSet - Variable in class org.openscience.cdk.silent.ChemModel: A RingSet.
RingSet - Class in org.openscience.cdk: Maintains a set of Ring objects.
RingSet - Class in org.openscience.cdk.silent: Maintains a set of Ring objects.
RingSet() - Constructor for class org.openscience.cdk.RingSet: The constructor.
RingSet() - Constructor for class org.openscience.cdk.silent.RingSet: The constructor.
RingSetManipulator - Class in org.openscience.cdk.tools.manipulator
RingSetManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.RingSetManipulator
RingSizeComparator - Class in org.openscience.cdk.tools.manipulator
RingSizeComparator(int) - Constructor for class org.openscience.cdk.tools.manipulator.RingSizeComparator: Constructs a new comparator to sort rings by size.
RMap - Class in org.openscience.cdk.isomorphism.mcss: An RMap implements the association between an edge (bond) in G1 and an edge (bond) in G2, G1 and G2 being the compared graphs in a RGraph context.
RMap(int, int) - Constructor for class org.openscience.cdk.isomorphism.mcss.RMap: Constructor for the RMap.
Rn - Static variable in interface org.openscience.cdk.interfaces.IElement
RN - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
RNode - Class in org.openscience.cdk.isomorphism.mcss: Node of the resolution graph (RGraph) An RNode represents an association between two edges of the source graphs G1 and G2 that are compared.
RNode(int, int) - Constructor for class org.openscience.cdk.isomorphism.mcss.RNode: Constructor for the RNode object.
rocAUC - Variable in class org.openscience.cdk.fingerprint.model.Bayesian
rocType - Variable in class org.openscience.cdk.fingerprint.model.Bayesian
rocX - Variable in class org.openscience.cdk.fingerprint.model.Bayesian
rocY - Variable in class org.openscience.cdk.fingerprint.model.Bayesian
Roentgenium - org.openscience.cdk.config.Elements
ROENTGENIUM - Static variable in enum org.openscience.cdk.config.Elements
ROLE_AGENT - Static variable in class org.openscience.cdk.isomorphism.matchers.smarts.ReactionRoleQueryAtom: Deprecated.
ROLE_ANY - Static variable in class org.openscience.cdk.isomorphism.matchers.smarts.ReactionRoleQueryAtom: Deprecated.
ROLE_PRODUCT - Static variable in class org.openscience.cdk.isomorphism.matchers.smarts.ReactionRoleQueryAtom: Deprecated.
ROLE_REACTANT - Static variable in class org.openscience.cdk.isomorphism.matchers.smarts.ReactionRoleQueryAtom: Deprecated.
RoleAgent - Static variable in class org.openscience.cdk.isomorphism.matchers.smarts.ReactionRoleQueryAtom: Deprecated.
RoleProduct - Static variable in class org.openscience.cdk.isomorphism.matchers.smarts.ReactionRoleQueryAtom: Deprecated.
RoleReactant - Static variable in class org.openscience.cdk.isomorphism.matchers.smarts.ReactionRoleQueryAtom: Deprecated.
root() - Method in class org.openscience.cdk.renderer.elements.Bounds: Access the root rendering element, it contains all elements added to the bounds so far.
ROOT_LABEL - Static variable in class org.openscience.cdk.isomorphism.matchers.RGroup: Standard label/title to be used for the root atom container.
rootNode() - Method in class org.openscience.cdk.smiles.smarts.parser.JJTSMARTSParserState
RotatableBondsCountDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: The number of rotatable bonds is given by the SMARTS specified by Daylight on SMARTS tutorial
RotatableBondsCountDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor: Constructor for the RotatableBondsCountDescriptor object
rotate(Vector3d, Vector3d, double) - Static method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D: Rotates a vector around an axis.
rotate(IAtomContainer, Point2d, double) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Rotates a molecule around a given center by a given angle.
rotate(IAtomContainer, Point2d, double) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Rotates a molecule around a given center by a given angle.
rotate(IAtom, Point3d, Point3d, double) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Rotates a 3D point about a specified line segment by a specified angle.
rotate(IAtom, Point3d, Point3d, double) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Rotates a 3D point about a specified line segment by a specified angle.
rotateAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.geometry.alignment.KabschAlignment: Rotates the IAtomContainer coordinates by the rotation matrix.
row2compare(int, int[][], Permutation) - Method in class org.openscience.cdk.structgen.maygen.Maygen: For a row given by index, detecting the other row to compare in the block.
rowCanonicalTest(int, int[], int[][], int[], int[], int[], int[][], int[], List<ArrayList<Permutation>>, int[], int[][], boolean[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Canonical test for a row in the tested block.
rowDescendingTest(int, int[][], int[], int[], boolean[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: The row descending test is the part of canonical test function.
rows - Variable in class org.openscience.cdk.math.IMatrix: the count of rows of the matrix
rows - Variable in class org.openscience.cdk.math.Matrix: the number of rows of this matrix
RssWriter - Class in org.openscience.cdk.io: Generates an RSS feed.
RssWriter() - Constructor for class org.openscience.cdk.io.RssWriter
Ru - Static variable in interface org.openscience.cdk.interfaces.IElement
RU - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Rubidium - org.openscience.cdk.config.Elements
RUBIDIUM - Static variable in enum org.openscience.cdk.config.Elements
RUBIDIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
RuleOfFiveDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: This Class contains a method that returns the number failures of the Lipinski's Rule Of 5.
RuleOfFiveDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor: Constructor for the RuleOfFiveDescriptor object.
run() - Method in class org.openscience.cdk.structgen.maygen.Maygen: Main function to initialize the global variables and calling the generate function.
runDistributeSymbols(int, int, int, int, int, boolean, int, int, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen
runDistributeSymbolsCheckNodeLabels(int, int, int, int, int, int, boolean) - Method in class org.openscience.cdk.structgen.maygen.Maygen
Ruthenium - org.openscience.cdk.config.Elements
RUTHENIUM - Static variable in enum org.openscience.cdk.config.Elements
RUTHENIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Rutherfordium - org.openscience.cdk.config.Elements
RUTHERFORDIUM - Static variable in enum org.openscience.cdk.config.Elements
RUTHERFORDIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.

S

s - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
S - org.openscience.cdk.geometry.cip.CIPTool.CIP_CHIRALITY
S - org.openscience.cdk.interfaces.IAtomType.Hybridization
S - org.openscience.cdk.renderer.elements.TextGroupElement.Position
S - Static variable in interface org.openscience.cdk.interfaces.IElement
S - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
S_BOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
SAbs - net.sf.jniinchi.INCHI_OPTION
SALICYLIC_ACID_PTRN - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor
Samarium - org.openscience.cdk.config.Elements
SAMARIUM - Static variable in enum org.openscience.cdk.config.Elements
sample(IAtomContainer) - Static method in class org.openscience.cdk.structgen.VicinitySampler: Choose any possible quadruple of the set of atoms in ac and establish all of the possible bonding schemes according to Faulon's equations.
SANARIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
SAsXYZ - net.sf.jniinchi.INCHI_OPTION
saturate(IAtomContainer) - Method in class org.openscience.cdk.tools.AtomTypeAwareSaturationChecker
saturate(IAtomContainer) - Method in interface org.openscience.cdk.tools.IDeduceBondOrderTool
saturate(IAtomContainer) - Method in class org.openscience.cdk.tools.LonePairElectronChecker: Saturates a molecule by setting appropriate number lone pair electrons.
saturate(IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker: The method is known to fail for certain compounds.
saturate(IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker: Saturates a molecule by setting appropriate bond orders.
saturate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.LonePairElectronChecker: Saturates an IAtom by adding the appropriate number lone pairs.
saturate(IBond[], IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker: Saturates a set of Bonds in an AtomContainer.
saturateByIncreasingBondOrder(IBond, IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker: Tries to saturate a bond by increasing its bond orders by 1.0.
saturateRingSystems(IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker
SaturationChecker - Class in org.openscience.cdk.tools: Provides methods for checking whether an atoms valences are saturated with respect to a particular atom type.
SaturationChecker() - Constructor for class org.openscience.cdk.tools.SaturationChecker
saveIndex(File) - Method in class org.openscience.cdk.io.random.RandomAccessReader
Sb - Static variable in interface org.openscience.cdk.interfaces.IElement
SB - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Sc - Static variable in interface org.openscience.cdk.interfaces.IElement
SC - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
scaffold(IAtomContainer) - Static method in class org.openscience.cdk.fragment.MurckoFragmenter: Computes the Murcko Scaffold for the provided molecule in linear time.
Scale() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.Scale
scaleMolecule(IAtomContainer, double) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Multiplies all the coordinates of the atoms of the given molecule with the scalefactor.
scaleMolecule(IAtomContainer, double) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Multiplies all the coordinates of the atoms of the given molecule with the scalefactor.
scaleMolecule(IAtomContainer, double[], double) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Scales a molecule such that it fills a given percentage of a given dimension.
scaleMolecule(IAtomContainer, Dimension, double) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Scales a molecule such that it fills a given percentage of a given dimension.
scalePredictor(double) - Method in class org.openscience.cdk.fingerprint.model.Bayesian: Converts a raw Bayesian prediction and transforms it into a probability-like range, i.e.
Scandium - org.openscience.cdk.config.Elements
SCANDIUM - Static variable in enum org.openscience.cdk.config.Elements
SCANDIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
SDFFormat - Class in org.openscience.cdk.io.formats: See here.
SDFFormat() - Constructor for class org.openscience.cdk.io.formats.SDFFormat
SDFWriter - Class in org.openscience.cdk.io: Writes MDL SD files ([Dalby, A. et. al.. Journal of Chemical Information and Computer Sciences. 1992. 32]).
SDFWriter() - Constructor for class org.openscience.cdk.io.SDFWriter
SDFWriter(BufferedWriter) - Constructor for class org.openscience.cdk.io.SDFWriter: Create an SDfile writer that will output directly to the provided buffered writer.
SDFWriter(OutputStream) - Constructor for class org.openscience.cdk.io.SDFWriter: Create an SDfile writer, the provided output stream is wrapped in a UTF-8 buffered writer.
SDFWriter(OutputStream, Set<String>) - Constructor for class org.openscience.cdk.io.SDFWriter: Constructs a new SdfWriter that can write to a given OutputStream.
SDFWriter(Writer) - Constructor for class org.openscience.cdk.io.SDFWriter: Create an SDfile writer, the provided writer is buffered if it's not an instance of BufferedWriter.
SDFWriter(Writer, Set<String>) - Constructor for class org.openscience.cdk.io.SDFWriter: Constructs a new SDFWriter that writes to the given Writer.
SDFWriter(Set<String>) - Constructor for class org.openscience.cdk.io.SDFWriter: Writes SD-File to a String including the given properties
se - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Se - Static variable in interface org.openscience.cdk.interfaces.IElement
SE - org.openscience.cdk.renderer.elements.TextGroupElement.Position
SE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Seaborgium - org.openscience.cdk.config.Elements
SEABORGIUM - Static variable in enum org.openscience.cdk.config.Elements
SEABORGIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
search(IAtomContainer, IAtomContainer, BitSet, BitSet, boolean, boolean) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: General RGraph parsing method (usually not used directly) This method is the entry point for the recursive search adapted to the atom container input.
search(IAtomContainer, IAtomContainer, BitSet, BitSet, boolean, boolean, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS: Deprecated.

General Rgraph parsing method (usually not used directly) This method is the entry point for the recursive search adapted to the atom container input.
searchCorrespondingAtom(int, int, int, List<Integer>) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks: Deprecated.
searchMCS(boolean) - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler: Deprecated.

Initialise the MCS search algorithm.
searchMCS(boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler: Deprecated.

Initialise the MCS search algorithm.
searchMCS(boolean) - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler: Deprecated.

Initialise the MCS search algorithm.
searchMCS(boolean) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler: Deprecated.

Initialise the MCS search algorithm.
searchMCS(boolean) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCSAlgorithm: Deprecated.

Initialise the MCS search algorithm.
secondPointX - Variable in class org.openscience.cdk.renderer.elements.LineElement: The x-coordinate of the second point.
secondPointY - Variable in class org.openscience.cdk.renderer.elements.LineElement: The y-coordinate of the second point.
select(IChemModel) - Method in class org.openscience.cdk.renderer.selection.AbstractSelection: Perform a selection by some method.
select(IChemModel) - Method in interface org.openscience.cdk.renderer.selection.IChemObjectSelection: Perform a selection by some method.
SelectionColor() - Constructor for class org.openscience.cdk.renderer.RendererModel.SelectionColor
SelectionVisibility - Class in org.openscience.cdk.renderer.generators.standard: Extended existing symbol visibility options to account for selection of atoms in the standard generator.
Selenium - org.openscience.cdk.config.Elements
SELENIUM - Static variable in enum org.openscience.cdk.config.Elements
SELENIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
SERIAL_FORMAT - Variable in class org.openscience.cdk.io.PDBWriter
serialise() - Method in class org.openscience.cdk.fingerprint.model.Bayesian: Converts the current model into a serialised string representation.
set(int) - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
set(int) - Method in interface org.openscience.cdk.fingerprint.IBitFingerprint: Sets the bit at the specified index to true.
set(int) - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
set(int, boolean) - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
set(int, boolean) - Method in interface org.openscience.cdk.fingerprint.IBitFingerprint: Sets the bit at the specified index to the specified value.
set(int, boolean) - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
set(int, int) - Method in class org.openscience.cdk.group.Permutation: Set the value at the specified index.
set(int, IAtomContainer) - Method in class org.openscience.cdk.ConformerContainer
set(Class<T>, U) - Method in class org.openscience.cdk.renderer.RendererModel: Sets the IGeneratorParameter for the active IRenderer.
set(List<Map<Integer, Integer>>) - Method in class org.openscience.cdk.smsd.helper.FinalMappings: Deprecated.

Sets mapping list
set(List<Map<Integer, Integer>>) - Method in interface org.openscience.cdk.smsd.interfaces.IFinalMapping: Deprecated.

Sets mapping list
set(IChemObject) - Method in class org.openscience.cdk.io.random.RandomAccessReader
set(Expr) - Method in class org.openscience.cdk.isomorphism.matchers.Expr: Set this expression to another (shallow copy).
set(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler: Deprecated.

Initialise the query and target molecule.
set(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler: Deprecated.

Initialise the query and target molecule.
set(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler: Deprecated.

Initialise the query and target molecule.
set(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler: Deprecated.

Initialise the query and target molecule.
set(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler: Deprecated.

Initialise the query and target molecule.
set(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler: Deprecated.

Initialise the query and target molecule.
set(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler: Deprecated.

Initialise the query and target molecule.
set(IQueryAtomContainer, IAtomContainer) - Method in interface org.openscience.cdk.smsd.interfaces.IMCSBase: Deprecated.

Initialise the query and target molecule.
set(MolHandler, MolHandler) - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler: Deprecated.

Initialise the query and target molecule.
set(MolHandler, MolHandler) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler: Deprecated.

Initialise the query and target molecule.
set(MolHandler, MolHandler) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler: Deprecated.

Initialise the query and target molecule.
set(MolHandler, MolHandler) - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler: Deprecated.

Initialise the query and target molecule.
set(MolHandler, MolHandler) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler: Deprecated.

Initialise the query and target molecule.
set(MolHandler, MolHandler) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler: Deprecated.

Initialise the query and target molecule.
set(MolHandler, MolHandler) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler: Deprecated.

Initialise the query and target molecule.
set(MolHandler, MolHandler) - Method in interface org.openscience.cdk.smsd.interfaces.IMCSBase: Deprecated.

Initialise the query and target molecule.
SET_UNIQUE_POLICY - Static variable in class org.openscience.cdk.tools.IDCreator: Old ID generation policy - to generate IDs unique over the entire set
setA(Vector3d) - Method in class org.openscience.cdk.Crystal: Sets the A unit cell axes in Cartesian coordinates in a Euclidean space.
setA(Vector3d) - Method in class org.openscience.cdk.debug.DebugCrystal: Sets the A unit cell axes in Cartesian coordinates in a Euclidean space.
setA(Vector3d) - Method in interface org.openscience.cdk.interfaces.ICrystal: Sets the A unit cell axes in carthesian coordinates in a eucledian space.
setA(Vector3d) - Method in class org.openscience.cdk.silent.Crystal: Sets the A unit cell axes in Cartesian coordinates in a Euclidean space.
setAbout(String) - Method in class org.openscience.cdk.io.RssWriter
setAlignMappedReaction(boolean) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator: Set whether reaction reactants should be allignned to their product.
setAllMap(boolean) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Sets the 'finAllMap' option.
setAllMap(boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph: Deprecated.

Sets the 'finAllMap' option.
setAllStructure(boolean) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Sets the 'AllStructres' option.
setAllStructure(boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph: Deprecated.

Sets the 'AllStructres' option.
setAltLoc(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom: set the Alternate location indicator of this atom.
setAltLoc(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom: set the Alternate location indicator of this atom.
setAltLoc(String) - Method in class org.openscience.cdk.protein.data.PDBAtom: set the Alternate location indicator of this atom.
setAltLoc(String) - Method in class org.openscience.cdk.silent.PDBAtom: set the Alternate location indicator of this atom.
setAlwaysV3000(boolean) - Method in class org.openscience.cdk.io.SDFWriter
setArcs(IAtomContainer, IAtomContainer, int, int, List<Integer>, List<Integer>, List<String>, List<String>, List<Integer>, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks: Deprecated.
setAromaticity(Aromaticity) - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool: Deprecated.

Set the aromaticity perception to use.
setArrayValue(double[][]) - Method in class org.openscience.cdk.graph.invariant.GIMatrix: Resets the value of the matrix to the given array of double numbers.
setAsPermutation(int) - Method in class org.openscience.cdk.group.Partition: Fill the elements of a permutation from the first element of each cell, up to the point upTo.
setAtom(int, IAtom) - Method in class org.openscience.cdk.AtomContainer: Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().
setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().
setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().
setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().
setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal: Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().
setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer: Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().
setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer: Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().
setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugRing: Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().
setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugStrand: Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().
setAtom(int, IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().
setAtom(int, IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().
setAtom(int, IAtom) - Method in class org.openscience.cdk.silent.AtomContainer: Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().
setAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugLonePair: Sets the associated Atom.
setAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugSingleElectron: Sets the associated Atom.
setAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.ILonePair: Sets the associated Atom.
setAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.ISingleElectron: Sets the associated Atom.
setAtom(IAtom) - Method in class org.openscience.cdk.LonePair: Sets the associated Atom.
setAtom(IAtom) - Method in class org.openscience.cdk.silent.LonePair: Sets the associated Atom.
setAtom(IAtom) - Method in class org.openscience.cdk.silent.SingleElectron: Sets the associated Atom.
setAtom(IAtom) - Method in class org.openscience.cdk.SingleElectron: Sets the associated Atom.
setAtom(IAtom) - Method in class org.openscience.cdk.smiles.InvPair
setAtom(IAtom, int) - Method in class org.openscience.cdk.Bond: Sets an Atom in this bond.
setAtom(IAtom, int) - Method in class org.openscience.cdk.BondRef: Sets an Atom in this bond.
setAtom(IAtom, int) - Method in class org.openscience.cdk.debug.DebugBond: Sets an Atom in this bond.
setAtom(IAtom, int) - Method in interface org.openscience.cdk.interfaces.IBond: Sets an Atom in this bond.
setAtom(IAtom, int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Sets an atom in this query bond.
setAtom(IAtom, int) - Method in class org.openscience.cdk.silent.Bond: Sets an Atom in this bond.
setAtom(IQueryAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RingIdentifierAtom: Deprecated.
setAtomAt(IAtom, int) - Method in class org.openscience.cdk.Association: Sets an Atom in this Association.
setAtomAt(IAtom, int) - Method in class org.openscience.cdk.isomorphism.matchers.OrderQueryBond: Deprecated.
setAtomAt(IAtom, int) - Method in class org.openscience.cdk.isomorphism.matchers.OrderQueryBondOrderOnly: Deprecated.
setAtomCheckRadius(double) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
setAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.structgen.SingleStructureRandomGenerator: Sets the AtomContainer attribute of the SingleStructureRandomGenerator object.
setAtomicNumber(Integer) - Method in class org.openscience.cdk.AtomRef: Sets the atomic number of this element.
setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugAtom: Sets the atomic number of this element.
setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugAtomType: Sets the atomic number of this element.
setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugElement: Sets the atomic number of this element.
setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Sets the atomic number of this element.
setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugIsotope: Sets the atomic number of this element.
setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Sets the atomic number of this element.
setAtomicNumber(Integer) - Method in class org.openscience.cdk.Element: Sets the atomic number of this element.
setAtomicNumber(Integer) - Method in interface org.openscience.cdk.interfaces.IElement: Sets the atomic number of this element.
setAtomicNumber(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Sets the atomic number of this element.
setAtomicNumber(Integer) - Method in class org.openscience.cdk.silent.Element: Sets the atomic number of this element.
setAtomPlacer(AtomPlacer) - Method in class org.openscience.cdk.layout.RingPlacer
setAtomProperties(IAtomContainer, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Sets a property on all Atoms in the given container.
setAtomProperties(IAtomContainerSet, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
setAtomProperties(IAtomContainerSet, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
setAtomProperties(IChemModel, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator: Sets the AtomProperties of all Atoms inside an IChemModel.
setAtomProperties(IReaction, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
setAtomProperties(IReactionSet, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
setAtoms(IAtom[]) - Method in class org.openscience.cdk.Association: Sets the array of atoms making up this Association.
setAtoms(IAtom[]) - Method in class org.openscience.cdk.AtomContainer: Sets the array of atoms of this AtomContainer.
setAtoms(IAtom[]) - Method in class org.openscience.cdk.Bond: Sets the array of atoms making up this bond.
setAtoms(IAtom[]) - Method in class org.openscience.cdk.BondRef: Sets the array of atoms making up this bond.
setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Sets the array of atoms of this AtomContainer.
setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Sets the array of atoms of this AtomContainer.
setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Sets the array of atoms of this AtomContainer.
setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugBond: Sets the array of atoms making up this bond.
setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugCrystal: Sets the array of atoms of this AtomContainer.
setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugMonomer: Sets the array of atoms of this AtomContainer.
setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugPolymer: Sets the array of atoms of this AtomContainer.
setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugRing: Sets the array of atoms of this AtomContainer.
setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugStrand: Sets the array of atoms of this AtomContainer.
setAtoms(IAtom[]) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Sets the array of atoms of this AtomContainer.
setAtoms(IAtom[]) - Method in interface org.openscience.cdk.interfaces.IBond: Sets the array of atoms making up this bond.
setAtoms(IAtom[]) - Method in class org.openscience.cdk.isomorphism.matchers.OrderQueryBond: Deprecated.
setAtoms(IAtom[]) - Method in class org.openscience.cdk.isomorphism.matchers.OrderQueryBondOrderOnly: Deprecated.
setAtoms(IAtom[]) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Sets the array of atoms of this AtomContainer.
setAtoms(IAtom[]) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Sets the array of atoms making up this query bond.
setAtoms(IAtom[]) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond: Deprecated.
setAtoms(IAtom[]) - Method in class org.openscience.cdk.silent.AtomContainer: Sets the array of atoms of this AtomContainer.
setAtoms(IAtom[]) - Method in class org.openscience.cdk.silent.Bond: Sets the array of atoms making up this bond.
setAtomTypeName(String) - Method in class org.openscience.cdk.AtomRef: Sets the if attribute of the AtomType object.
setAtomTypeName(String) - Method in class org.openscience.cdk.AtomType: Sets the if attribute of the AtomType object.
setAtomTypeName(String) - Method in class org.openscience.cdk.debug.DebugAtom: Sets the if attribute of the AtomType object.
setAtomTypeName(String) - Method in class org.openscience.cdk.debug.DebugAtomType: Sets the if attribute of the AtomType object.
setAtomTypeName(String) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Sets the if attribute of the AtomType object.
setAtomTypeName(String) - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Sets the if attribute of the AtomType object.
setAtomTypeName(String) - Method in interface org.openscience.cdk.interfaces.IAtomType: Sets the if attribute of the AtomType object.
setAtomTypeName(String) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Sets the if attribute of the AtomType object.
setAtomTypeName(String) - Method in class org.openscience.cdk.silent.AtomType: Sets the if attribute of the AtomType object.
setAtomTypes(List<IAtomType>) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator: Sets the atomTypes attribute of the ForceFieldConfigurator object
setAttachPointNum(int) - Method in interface org.openscience.cdk.interfaces.IPseudoAtom: Set the attachment point number.
setAttachPointNum(int) - Method in class org.openscience.cdk.PseudoAtom: Set the attachment point number.
setAttachPointNum(int) - Method in class org.openscience.cdk.silent.PseudoAtom: Set the attachment point number.
setB(Vector3d) - Method in class org.openscience.cdk.Crystal: Sets the B unit cell axes in Cartesian coordinates.
setB(Vector3d) - Method in class org.openscience.cdk.debug.DebugCrystal: Sets the B unit cell axes in Cartesian coordinates.
setB(Vector3d) - Method in interface org.openscience.cdk.interfaces.ICrystal: Sets the B unit cell axes in carthesian coordinates.
setB(Vector3d) - Method in class org.openscience.cdk.silent.Crystal: Sets the B unit cell axes in Cartesian coordinates.
setBasis(int[], int[], int[], double[], Vector[], IAtom[]) - Method in class org.openscience.cdk.math.qm.GaussiansBasis: Set up basis with gauss funktions f(x,y,z) = (x-rx)^nx * (y-ry)^ny * (z-rz)^nz * exp(-alpha*(r-ri)^2).
setBehaveAsBitFingerprint(boolean) - Method in interface org.openscience.cdk.fingerprint.ICountFingerprint: Changes behaviour, if true is given the count fingerprint will behave as a bit fingerprint and return 0 or 1 for counts.
setBehaveAsBitFingerprint(boolean) - Method in class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
setBiggest(int, int[][], Permutation, int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Checks whether there is a permutation making the row bigger in descending order.
setBondInSensitiveTimeOut(double) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS: Deprecated.

set timeout in mins (default 1.00 min) for bond insensitive searches
setBondInSensitiveTimeOut(double) - Method in class org.openscience.cdk.smsd.Isomorphism: Deprecated.

set timeout in mins (default 1.00 min) for bond insensitive searches
setBondLength(double) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator: Deprecated.
use GeometryUtil.scaleMolecule(IAtomContainer, double)
setBondMatchFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultBondMatcher: Deprecated.
setBondMatchFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultMCSPlusAtomMatcher: Deprecated.
setBondMatchFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultRGraphAtomMatcher: Deprecated.
setBondMatchFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFAtomMatcher: Deprecated.
setBondMatchFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFBondMatcher: Deprecated.
setBondMatchFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler: Deprecated.
setBondMatchFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler: Deprecated.
setBondMatchFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler: Deprecated.
setBondOrderSum(Double) - Method in class org.openscience.cdk.AtomRef: Sets the the exact bond order sum attribute of the AtomType object.
setBondOrderSum(Double) - Method in class org.openscience.cdk.AtomType: Sets the the exact bond order sum attribute of the AtomType object.
setBondOrderSum(Double) - Method in class org.openscience.cdk.debug.DebugAtom: Sets the the exact bond order sum attribute of the AtomType object.
setBondOrderSum(Double) - Method in class org.openscience.cdk.debug.DebugAtomType: Sets the the exact bond order sum attribute of the AtomType object.
setBondOrderSum(Double) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Sets the the exact bond order sum attribute of the AtomType object.
setBondOrderSum(Double) - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Sets the the exact bond order sum attribute of the AtomType object.
setBondOrderSum(Double) - Method in interface org.openscience.cdk.interfaces.IAtomType: Sets the the exact bond order sum attribute of the AtomType object.
setBondOrderSum(Double) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Sets the the exact bond order sum attribute of the AtomType object.
setBondOrderSum(Double) - Method in class org.openscience.cdk.silent.AtomType: Sets the the exact bond order sum attribute of the AtomType object.
setBonds(IBond[]) - Method in class org.openscience.cdk.AtomContainer: Sets the array of bonds of this AtomContainer.
setBonds(IBond[]) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Sets the array of bonds of this AtomContainer.
setBonds(IBond[]) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Sets the array of bonds of this AtomContainer.
setBonds(IBond[]) - Method in class org.openscience.cdk.silent.AtomContainer: Sets the array of bonds of this AtomContainer.
setBondSensitiveTimeOut(double) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS: Deprecated.

set timeout in mins (default 0.10 min) for bond sensitive searches
setBondSensitiveTimeOut(double) - Method in class org.openscience.cdk.smsd.Isomorphism: Deprecated.

set timeout in mins (default 0.10 min) for bond sensitive searches
setBoundary(boolean) - Method in class org.openscience.cdk.structgen.maygen.Maygen
setBuilder(IChemObjectBuilder) - Method in class org.openscience.cdk.stereo.DoubleBondStereochemistry
setBuilder(IChemObjectBuilder) - Method in class org.openscience.cdk.stereo.TetrahedralChirality
setC(Vector3d) - Method in class org.openscience.cdk.Crystal: Sets the C unit cell axes in Cartesian coordinates.
setC(Vector3d) - Method in class org.openscience.cdk.debug.DebugCrystal: Sets the C unit cell axes in Cartesian coordinates.
setC(Vector3d) - Method in interface org.openscience.cdk.interfaces.ICrystal: Sets the C unit cell axes in carthesian coordinates.
setC(Vector3d) - Method in class org.openscience.cdk.silent.Crystal: Sets the C unit cell axes in Cartesian coordinates.
setChainID(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom: set the Chain identifier of this atom.
setChainID(String) - Method in class org.openscience.cdk.debug.DebugPDBMonomer: Sets the Chain ID of this monomer.
setChainID(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom: set the Chain identifier of this atom.
setChainID(String) - Method in interface org.openscience.cdk.interfaces.IPDBMonomer: Sets the Chain ID of this monomer.
setChainID(String) - Method in class org.openscience.cdk.protein.data.PDBAtom: set the Chain identifier of this atom.
setChainID(String) - Method in class org.openscience.cdk.protein.data.PDBMonomer
setChainID(String) - Method in class org.openscience.cdk.silent.PDBAtom: set the Chain identifier of this atom.
setChainID(String) - Method in class org.openscience.cdk.silent.PDBMonomer
setCharge(double) - Method in class org.openscience.cdk.formula.IsotopePattern: Set the charge in this pattern.
setCharge(Double) - Method in class org.openscience.cdk.Atom: Sets the partial charge of this atom.
setCharge(Double) - Method in class org.openscience.cdk.AtomRef: Sets the partial charge of this atom.
setCharge(Double) - Method in class org.openscience.cdk.debug.DebugAtom: Sets the partial charge of this atom.
setCharge(Double) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Sets the partial charge of this atom.
setCharge(Double) - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Sets the partial charge of this atom.
setCharge(Double) - Method in interface org.openscience.cdk.interfaces.IAtom: Sets the partial charge of this atom.
setCharge(Double) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Sets the partial charge of this atom.
setCharge(Double) - Method in class org.openscience.cdk.silent.Atom: Sets the partial charge of this atom.
setCharge(Integer) - Method in class org.openscience.cdk.debug.DebugAdductFormula: No use this method.
setCharge(Integer) - Method in class org.openscience.cdk.debug.DebugMolecularFormula: Sets the charge of this IMolecularFormula, since there is no atom associated with the charge the number of a given isotope is not modified.
setCharge(Integer) - Method in class org.openscience.cdk.formula.AdductFormula: Deprecated.
setCharge(Integer) - Method in class org.openscience.cdk.formula.MolecularFormula: Sets the charge of this IMolecularFormula, since there is no atom associated with the charge the number of a given isotope is not modified.
setCharge(Integer) - Method in interface org.openscience.cdk.interfaces.IAdductFormula: Sets the partial charge of this adduct formula.
setCharge(Integer) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula: Sets the charge of this IMolecularFormula, since there is no atom associated with the charge the number of a given isotope is not modified.
setCharge(Integer) - Method in class org.openscience.cdk.silent.AdductFormula: Deprecated.
setCharge(Integer) - Method in class org.openscience.cdk.silent.MolecularFormula: Sets the charge of this IMolecularFormula, since there is no atom associated with the charge the number of a given isotope is not modified.
setChargeGroups(List<ChargeGroup>) - Method in class org.openscience.cdk.libio.md.MDMolecule
setCharges(IAtomContainer) - Method in class org.openscience.cdk.charges.AtomTypeCharges: Sets initial charges for atom types.
setChemFilters(boolean, boolean, boolean) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS: Deprecated.

initialize query and target molecules.
setChemFilters(boolean, boolean, boolean) - Method in class org.openscience.cdk.smsd.Isomorphism: Deprecated.

initialize query and target molecules.
setChemObjectReader(ISimpleChemObjectReader) - Method in class org.openscience.cdk.io.random.RandomAccessReader
setChiCatHydrogen(double) - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges: Sets chi_cat value for hydrogen, because H poses a special problem due to lack of possible second ionisation.
setClassName(String) - Method in class org.openscience.cdk.dict.Entry
setClipboardContent(IAtomContainer) - Method in class org.openscience.cdk.renderer.RendererModel: Sets the atoms and bonds on the Renderer2D clipboard.
setClockwise(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom: Deprecated.
setCoefficients(Matrix) - Method in class org.openscience.cdk.math.qm.Orbitals: Set a coefficient matrix
setCoeffs(Map<Integer, Double>) - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor.JPlogPCalculator
setColumn(int, GIMatrix) - Method in class org.openscience.cdk.graph.invariant.GIMatrix: Sets the column of the matrix at the specified index to a new value.
setComputeRingFragments(boolean) - Method in class org.openscience.cdk.fragment.MurckoFragmenter: Sets whether to calculate ring fragments (true by default).
setConfigOrder(int) - Method in interface org.openscience.cdk.interfaces.IStereoElement: Set the configuration order of the stereochemistry.
setConsumer(Maygen.Consumer) - Method in class org.openscience.cdk.structgen.maygen.Maygen
setContractOnHetero(boolean) - Method in class org.openscience.cdk.depict.Abbreviations: Set whether abbreviations should be further contracted when they are connected to a heteroatom, for example -NH-Boc becomes -NHBoc.
setContractToSingleLabel(boolean) - Method in class org.openscience.cdk.depict.Abbreviations
setCountElectrons(int) - Method in class org.openscience.cdk.math.qm.Orbitals: Sets the count of electrons, which occupies the orbitals
setCovalentRadius(Double) - Method in class org.openscience.cdk.AtomRef: Sets the covalent radius for this AtomType.
setCovalentRadius(Double) - Method in class org.openscience.cdk.AtomType: Sets the covalent radius for this AtomType.
setCovalentRadius(Double) - Method in class org.openscience.cdk.debug.DebugAtom: Sets the covalent radius for this AtomType.
setCovalentRadius(Double) - Method in class org.openscience.cdk.debug.DebugAtomType: Sets the covalent radius for this AtomType.
setCovalentRadius(Double) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Sets the covalent radius for this AtomType.
setCovalentRadius(Double) - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Sets the covalent radius for this AtomType.
setCovalentRadius(Double) - Method in interface org.openscience.cdk.interfaces.IAtomType: Sets the covalent radius for this AtomType.
setCovalentRadius(Double) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Sets the covalent radius for this AtomType.
setCovalentRadius(Double) - Method in class org.openscience.cdk.silent.AtomType: Sets the covalent radius for this AtomType.
setCreator(String) - Method in class org.openscience.cdk.io.RssWriter
setCreatormap(Map) - Method in class org.openscience.cdk.io.RssWriter
setCrystal(ICrystal) - Method in class org.openscience.cdk.ChemModel: Sets the Crystal contained in this ChemModel.
setCrystal(ICrystal) - Method in class org.openscience.cdk.debug.DebugChemModel: Sets the Crystal contained in this ChemModel.
setCrystal(ICrystal) - Method in interface org.openscience.cdk.interfaces.IChemModel: Sets the Crystal contained in this ChemModel.
setCrystal(ICrystal) - Method in class org.openscience.cdk.silent.ChemModel: Sets the Crystal contained in this ChemModel.
setCurr(long) - Method in class org.openscience.cdk.smiles.InvPair: Set the value of the seed.
setDatemap(Map) - Method in class org.openscience.cdk.io.RssWriter
setDebugEnabled(boolean) - Method in class org.openscience.cdk.tools.SystemOutLoggingTool: Deprecated.
use SystemOutLoggingTool.setLevel(int)
setDebugStream(PrintStream) - Method in class org.openscience.cdk.iupac.parser.NomParserTokenManager: Set debug output.
setDebugStream(PrintStream) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager: Set debug output.
setDefaultReactions() - Method in class org.openscience.cdk.tools.StructureResonanceGenerator: Set the default reactions that must be presents to generate the resonance.
setDefaultRestrictions() - Method in class org.openscience.cdk.formula.MassToFormulaTool: Deprecated.

Set the default restrictions that must be presents in the molecular formula.
setDefinition(String) - Method in class org.openscience.cdk.dict.Entry
setDegree(int) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom: Deprecated.
setDescription(String) - Method in class org.openscience.cdk.dict.Entry
setDescription(String) - Method in class org.openscience.cdk.io.RssWriter
setDescriptorInstances(List<IDescriptor>) - Method in class org.openscience.cdk.qsar.DescriptorEngine: Set the list of Descriptor objects.
setDescriptorMetadata(String) - Method in class org.openscience.cdk.dict.Entry
setDescriptorSpecifications(List<IImplementationSpecification>) - Method in class org.openscience.cdk.qsar.DescriptorEngine: Set the list of DescriptorSpecification objects.
setDetails(String) - Method in class org.openscience.cdk.validate.ValidationTest
setDim(int[]) - Method in class org.openscience.cdk.tools.GridGenerator
setDimension(double[], boolean) - Method in class org.openscience.cdk.tools.GridGenerator: Method sets the maximal 3d dimensions to given min and max values.
setDimension(double, double) - Method in class org.openscience.cdk.tools.GridGenerator: Method sets the maximal 3d dimensions to given min and max values.
setDimension(double, double, double, double, double, double) - Method in class org.openscience.cdk.tools.GridGenerator: Method sets the maximal 3d dimensions to given min and max values.
setDirection(IReaction.Direction) - Method in class org.openscience.cdk.debug.DebugReaction: Sets the direction of the reaction.
setDirection(IReaction.Direction) - Method in interface org.openscience.cdk.interfaces.IReaction: Sets the direction of the reaction.
setDirection(IReaction.Direction) - Method in class org.openscience.cdk.Reaction: Sets the direction of the reaction.
setDirection(IReaction.Direction) - Method in class org.openscience.cdk.silent.Reaction: Sets the direction of the reaction.
setDisplay(IBond.Display) - Method in class org.openscience.cdk.Bond: Set the bond display style.
setDisplay(IBond.Display) - Method in class org.openscience.cdk.BondRef: Set the bond display style.
setDisplay(IBond.Display) - Method in interface org.openscience.cdk.interfaces.IBond: Set the bond display style.
setDisplay(IBond.Display) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Not used for query bonds.
setDisplay(IBond.Display) - Method in class org.openscience.cdk.silent.Bond: Set the bond display style.
setDisplayMode(int) - Method in class org.openscience.cdk.renderer.GraphRendererModel: Set the display mode
setDocumentProperty(String, String) - Method in class org.openscience.cdk.io.iterator.event.EventCMLHandler: Procedure required by the CDOInterface.
setDrawCenter(double, double) - Method in class org.openscience.cdk.renderer.AbstractRenderer: Set the point on the screen to draw the diagram.
setElectronCount(Integer) - Method in class org.openscience.cdk.BondRef: Sets the number of electrons in this electron container.
setElectronCount(Integer) - Method in class org.openscience.cdk.debug.DebugBond: Sets the number of electrons in this electron container.
setElectronCount(Integer) - Method in class org.openscience.cdk.debug.DebugElectronContainer: Sets the number of electrons in this electron container.
setElectronCount(Integer) - Method in class org.openscience.cdk.debug.DebugLonePair: Sets the number of electrons in this electron container.
setElectronCount(Integer) - Method in class org.openscience.cdk.debug.DebugSingleElectron: Sets the number of electrons in this electron container.
setElectronCount(Integer) - Method in class org.openscience.cdk.ElectronContainer: Sets the number of electrons in this electron container.
setElectronCount(Integer) - Method in interface org.openscience.cdk.interfaces.IElectronContainer: Sets the number of electrons in this electron container.
setElectronCount(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Sets the number of electrons in this bond
setElectronCount(Integer) - Method in class org.openscience.cdk.silent.ElectronContainer: Sets the number of electrons in this electron container.
setEnabled(String, boolean) - Method in class org.openscience.cdk.depict.Abbreviations: Set whether an abbreviation is enabled or disabled.
setEndChainID(Character) - Method in class org.openscience.cdk.debug.DebugPDBStructure: set the ending Chain identifier of this structure.
setEndChainID(Character) - Method in interface org.openscience.cdk.interfaces.IPDBStructure: set the ending Chain identifier of this structure.
setEndChainID(Character) - Method in class org.openscience.cdk.protein.data.PDBStructure: set the ending Chain identifier of this structure.
setEndChainID(Character) - Method in class org.openscience.cdk.silent.PDBStructure: set the ending Chain identifier of this structure.
setEndInsertionCode(Character) - Method in class org.openscience.cdk.debug.DebugPDBStructure: set the ending Code for insertion of residues of this structure.
setEndInsertionCode(Character) - Method in interface org.openscience.cdk.interfaces.IPDBStructure: set the ending Code for insertion of residues of this structure.
setEndInsertionCode(Character) - Method in class org.openscience.cdk.protein.data.PDBStructure: set the ending Code for insertion of residues of this structure.
setEndInsertionCode(Character) - Method in class org.openscience.cdk.silent.PDBStructure: set the ending Code for insertion of residues of this structure.
setEndSequenceNumber(Integer) - Method in class org.openscience.cdk.debug.DebugPDBStructure: set the ending sequence number of this structure.
setEndSequenceNumber(Integer) - Method in interface org.openscience.cdk.interfaces.IPDBStructure: set the ending sequence number of this structure.
setEndSequenceNumber(Integer) - Method in class org.openscience.cdk.protein.data.PDBStructure: set the ending sequence number of this structure.
setEndSequenceNumber(Integer) - Method in class org.openscience.cdk.silent.PDBStructure: set the ending sequence number of this structure.
setEqual(BinaryTree) - Method in class org.openscience.cdk.smsd.helper.BinaryTree: Deprecated.

Set equal node
setErrorHandler(IChemObjectReaderErrorHandler) - Method in class org.openscience.cdk.io.DefaultChemObjectReader: Sets an error handler that is sent events when file format issues occur.
setErrorHandler(IChemObjectReaderErrorHandler) - Method in interface org.openscience.cdk.io.IChemObjectReader: Sets an error handler that is sent events when file format issues occur.
setErrorHandler(IChemObjectReaderErrorHandler) - Method in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader: Sets an error handler that is sent events when file format issues occur.
setExactMass(Double) - Method in class org.openscience.cdk.AtomRef: Sets the ExactMass attribute of the Isotope object.
setExactMass(Double) - Method in class org.openscience.cdk.debug.DebugAtom: Sets the ExactMass attribute of the Isotope object.
setExactMass(Double) - Method in class org.openscience.cdk.debug.DebugAtomType: Sets the ExactMass attribute of the Isotope object.
setExactMass(Double) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Sets the ExactMass attribute of the Isotope object.
setExactMass(Double) - Method in class org.openscience.cdk.debug.DebugIsotope: Sets the ExactMass attribute of the Isotope object.
setExactMass(Double) - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Sets the ExactMass attribute of the Isotope object.
setExactMass(Double) - Method in class org.openscience.cdk.FragmentAtom
setExactMass(Double) - Method in interface org.openscience.cdk.interfaces.IIsotope: Sets the ExactMass attribute of the Isotope object.
setExactMass(Double) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Sets the ExactMass attribute of the Isotope object.
setExactMass(Double) - Method in class org.openscience.cdk.Isotope: Sets the ExactMass attribute of the Isotope object.
setExactMass(Double) - Method in class org.openscience.cdk.silent.FragmentAtom
setExactMass(Double) - Method in class org.openscience.cdk.silent.Isotope: Sets the ExactMass attribute of the Isotope object.
setExpanded(boolean) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Sets whether this atom is to be fully drawn and not just in the abbreviated form.
setExpanded(boolean) - Method in class org.openscience.cdk.FragmentAtom
setExpanded(boolean) - Method in interface org.openscience.cdk.interfaces.IFragmentAtom: Sets whether this atom is to be fully drawn and not just in the abbreviated form.
setExpanded(boolean) - Method in class org.openscience.cdk.silent.FragmentAtom
setExpression(Expr) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Set the atom-expression predicate for this query atom.
setExpression(Expr) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Set the bond expression for this query bond.
setExtendGrid(double) - Method in class org.openscience.cdk.tools.GridGenerator
setExtension(BitSet) - Method in class org.openscience.cdk.isomorphism.mcss.RNode: Sets the extension attribute of the RNode object.
setExtension(BitSet) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode: Deprecated.

Sets the extension attribute of the RNode object
setExternalSelectedPart(IAtomContainer) - Method in class org.openscience.cdk.renderer.RendererModel: Set externally selected atoms.
setFirstAttachmentPoint(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.RGroup
setFirstGraphSize(int) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Sets the size of the first of the two compared graphs.
setFirstGraphSize(int) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph: Deprecated.

Sets the size of the first of the two compared graphs.
setFlag(int, boolean) - Method in class org.openscience.cdk.ChemObject: Sets the value of some flag.
setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Sets the value of some flag.
setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugAtom: Sets the value of some flag.
setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Sets the value of some flag.
setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Sets the value of some flag.
setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugAtomType: Sets the value of some flag.
setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Sets the value of some flag.
setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugBond: Sets the value of some flag.
setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugChemFile: Sets the value of some flag.
setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugChemModel: Sets the value of some flag.
setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugChemObject: Sets the value of some flag.
setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugChemSequence: Sets the value of some flag.
setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugCrystal: Sets the value of some flag.
setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugElectronContainer: Sets the value of some flag.
setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugElement: Sets the value of some flag.
setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Sets the value of some flag.
setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugIsotope: Sets the value of some flag.
setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugLonePair: Sets the value of some flag.
setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugMapping: Sets the value of some flag.
setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugMonomer: Sets the value of some flag.
setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugPolymer: Sets the value of some flag.
setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Sets the value of some flag.
setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugReaction: Sets the value of some flag.
setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugReactionScheme: Sets the value of some flag.
setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugReactionSet: Sets the value of some flag.
setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugRing: Sets the value of some flag.
setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugSingleElectron: Sets the value of some flag.
setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugStrand: Sets the value of some flag.
setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugSubstance: Sets the value of some flag.
setFlag(int, boolean) - Method in interface org.openscience.cdk.interfaces.IChemObject: Sets the value of some flag.
setFlag(int, boolean) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject: Sets the value of some flag.
setFlag(int, boolean) - Method in class org.openscience.cdk.silent.ChemObject: Sets the value of some flag.
setFlags(boolean[]) - Method in class org.openscience.cdk.ChemObject: Sets the whole set of flags.
setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Sets the whole set of flags.
setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugAtom: Sets the whole set of flags.
setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Sets the whole set of flags.
setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Sets the whole set of flags.
setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugAtomType: Sets the whole set of flags.
setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Sets the whole set of flags.
setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugBond: Sets the whole set of flags.
setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugChemFile: Sets the whole set of flags.
setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugChemModel: Sets the whole set of flags.
setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugChemObject: Sets the whole set of flags.
setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugChemSequence: Sets the whole set of flags.
setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugCrystal: Sets the whole set of flags.
setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugElectronContainer: Sets the whole set of flags.
setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugElement: Sets the whole set of flags.
setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Sets the whole set of flags.
setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugIsotope: Sets the whole set of flags.
setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugLonePair: Sets the whole set of flags.
setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugMapping: Sets the whole set of flags.
setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugMonomer: Sets the whole set of flags.
setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugPolymer: Sets the whole set of flags.
setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Sets the whole set of flags.
setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugReaction: Sets the whole set of flags.
setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugReactionScheme: Sets the whole set of flags.
setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugReactionSet: Sets the whole set of flags.
setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugRing: Sets the whole set of flags.
setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugSingleElectron: Sets the whole set of flags.
setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugStrand: Sets the whole set of flags.
setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugSubstance: Sets the whole set of flags.
setFlags(boolean[]) - Method in interface org.openscience.cdk.interfaces.IChemObject: Sets the whole set of flags.
setFlags(boolean[]) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject: Sets the whole set of flags.
setFlags(boolean[]) - Method in class org.openscience.cdk.silent.ChemObject: Sets the whole set of flags.
setFlavor(int) - Method in class org.openscience.cdk.io.SMILESWriter
setFontForZoom(double) - Method in class org.openscience.cdk.renderer.font.AWTFontManager: For a particular zoom level, set the appropriate font size to use.
setFontForZoom(double) - Method in interface org.openscience.cdk.renderer.font.IFontManager: For a particular zoom level, set the appropriate font size to use.
setFontManager(IFontManager) - Method in class org.openscience.cdk.renderer.visitor.AWTDrawVisitor: The font manager must be set by any renderer that uses this class! This manager is needed to keep track of fonts of the right size.
setFontManager(IFontManager) - Method in interface org.openscience.cdk.renderer.visitor.IDrawVisitor: Sets the IFontManager this IDrawVisitor should use.
setFontName(String) - Method in class org.openscience.cdk.renderer.font.AbstractFontManager: Set the font name ('Arial', 'Times New Roman') and so on.
setFontName(String) - Method in interface org.openscience.cdk.renderer.font.IFontManager: Set the font name ('Arial', 'Times New Roman') and so on.
setFontStyle(IFontManager.FontStyle) - Method in class org.openscience.cdk.renderer.font.AbstractFontManager: Set the font style.
setFontStyle(IFontManager.FontStyle) - Method in interface org.openscience.cdk.renderer.font.IFontManager: Set the font style.
setForbidden(BitSet) - Method in class org.openscience.cdk.isomorphism.mcss.RNode: Sets the forbidden attribute of the RNode object.
setForbidden(BitSet) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode: Deprecated.

Sets the forbidden attribute of the RNode object
setForceFieldConfigurator(String, IChemObjectBuilder) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator: Constructor for the ForceFieldConfigurator object
setFormalCharge(Integer) - Method in class org.openscience.cdk.AtomRef: Sets the formal charge of this atom.
setFormalCharge(Integer) - Method in class org.openscience.cdk.AtomType: Sets the formal charge of this atom.
setFormalCharge(Integer) - Method in class org.openscience.cdk.debug.DebugAtom: Sets the formal charge of this atom.
setFormalCharge(Integer) - Method in class org.openscience.cdk.debug.DebugAtomType: Sets the formal charge of this atom.
setFormalCharge(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Sets the formal charge of this atom.
setFormalCharge(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Sets the formal charge of this atom.
setFormalCharge(Integer) - Method in interface org.openscience.cdk.interfaces.IAtomType: Sets the formal charge of this atom.
setFormalCharge(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Sets the formal charge of this atom.
setFormalCharge(Integer) - Method in class org.openscience.cdk.silent.AtomType: Sets the formal charge of this atom.
setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.AtomRef: Sets the formal neighbour count of this atom.
setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.AtomType: Sets the formal neighbour count of this atom.
setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.debug.DebugAtom: Sets the formal neighbour count of this atom.
setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.debug.DebugAtomType: Sets the formal neighbour count of this atom.
setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Sets the formal neighbour count of this atom.
setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Sets the formal neighbour count of this atom.
setFormalNeighbourCount(Integer) - Method in interface org.openscience.cdk.interfaces.IAtomType: Sets the formal neighbour count of this atom.
setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Sets the formal neighbour count of this atom.
setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.silent.AtomType: Sets the formal neighbour count of this atom.
setFormula(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen
setFormula(IMolecularFormula) - Method in class org.openscience.cdk.formula.IsotopeContainer: Set IMolecularFormula object of this container.
setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.Atom: Sets a point specifying the location of this atom in a Crystal unit cell.
setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.AtomRef: Sets a point specifying the location of this atom in a Crystal unit cell.
setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugAtom: Sets a point specifying the location of this atom in a Crystal unit cell.
setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Sets a point specifying the location of this atom in a Crystal unit cell.
setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Sets a point specifying the location of this atom in a Crystal unit cell.
setFractionalPoint3d(Point3d) - Method in interface org.openscience.cdk.interfaces.IAtom: Sets a point specifying the location of this atom in a Crystal unit cell.
setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Sets a point specifying the location of this atom in a Crystal unit cell.
setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.silent.Atom: Sets a point specifying the location of this atom in a Crystal unit cell.
setFragment(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Sets the fully expended form of the IFragmentAtom.
setFragment(IAtomContainer) - Method in class org.openscience.cdk.FragmentAtom
setFragment(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IFragmentAtom: Sets the fully expended form of the IFragmentAtom.
setFragment(IAtomContainer) - Method in class org.openscience.cdk.silent.FragmentAtom
setFuzzyFormula(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen
setGrid(double[][][]) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
setGrid(double[][][]) - Method in class org.openscience.cdk.tools.GridGenerator
setGroup(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.matchers.RGroup
setGroupInfo(int) - Method in interface org.openscience.cdk.interfaces.IStereoElement: Set the stereo group information - see class doc.
setHashPseudoAtoms(boolean) - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter: Set the hashPseudoAtoms for the base daylight/path fingerprint.
setHashPseudoAtoms(boolean) - Method in class org.openscience.cdk.fingerprint.Fingerprinter
setHCount(int) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom: Deprecated.
setHetAtom(Boolean) - Method in class org.openscience.cdk.debug.DebugPDBAtom: Mark the atom as a heteroatom.
setHetAtom(Boolean) - Method in interface org.openscience.cdk.interfaces.IPDBAtom: Mark the atom as a heteroatom.
setHetAtom(Boolean) - Method in class org.openscience.cdk.protein.data.PDBAtom
setHetAtom(Boolean) - Method in class org.openscience.cdk.silent.PDBAtom
setHighlightedAtom(IAtom) - Method in class org.openscience.cdk.renderer.RendererModel: Sets the atom currently highlighted.
setHighlightedBond(IBond) - Method in class org.openscience.cdk.renderer.RendererModel: Sets the Bond currently highlighted.
setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.AtomRef: Sets the hybridization of this atom.
setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.AtomType: Sets the hybridization of this atom.
setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.debug.DebugAtom: Sets the hybridization of this atom.
setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.debug.DebugAtomType: Sets the hybridization of this atom.
setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Sets the hybridization of this atom.
setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Sets the hybridization of this atom.
setHybridization(IAtomType.Hybridization) - Method in interface org.openscience.cdk.interfaces.IAtomType: Sets the hybridization of this atom.
setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Sets the hybridization of this atom.
setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.silent.AtomType: Sets the hybridization of this atom.
setHydrogens(int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Calling the generate function for each degree values after the hydrogen distribution.
setICode(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom: set the Code for insertion of residues of this atom.
setICode(String) - Method in class org.openscience.cdk.debug.DebugPDBMonomer: Sets the ICode of this monomer.
setICode(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom: set the Code for insertion of residues of this atom.
setICode(String) - Method in interface org.openscience.cdk.interfaces.IPDBMonomer: Sets the ICode of this monomer.
setICode(String) - Method in class org.openscience.cdk.protein.data.PDBAtom: set the Code for insertion of residues of this atom.
setICode(String) - Method in class org.openscience.cdk.protein.data.PDBMonomer
setICode(String) - Method in class org.openscience.cdk.silent.PDBAtom: set the Code for insertion of residues of this atom.
setICode(String) - Method in class org.openscience.cdk.silent.PDBMonomer
setID(String) - Method in class org.openscience.cdk.ChemObject: Sets the identifier (ID) of this object.
setID(String) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Sets the identifier (ID) of this object.
setID(String) - Method in class org.openscience.cdk.debug.DebugAtom: Sets the identifier (ID) of this object.
setID(String) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Sets the identifier (ID) of this object.
setID(String) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Sets the identifier (ID) of this object.
setID(String) - Method in class org.openscience.cdk.debug.DebugAtomType: Sets the identifier (ID) of this object.
setID(String) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Sets the identifier (ID) of this object.
setID(String) - Method in class org.openscience.cdk.debug.DebugBond: Sets the identifier (ID) of this object.
setID(String) - Method in class org.openscience.cdk.debug.DebugChemFile: Sets the identifier (ID) of this object.
setID(String) - Method in class org.openscience.cdk.debug.DebugChemModel: Sets the identifier (ID) of this object.
setID(String) - Method in class org.openscience.cdk.debug.DebugChemObject: Sets the identifier (ID) of this object.
setID(String) - Method in class org.openscience.cdk.debug.DebugChemSequence: Sets the identifier (ID) of this object.
setID(String) - Method in class org.openscience.cdk.debug.DebugCrystal: Sets the identifier (ID) of this object.
setID(String) - Method in class org.openscience.cdk.debug.DebugElectronContainer: Sets the identifier (ID) of this object.
setID(String) - Method in class org.openscience.cdk.debug.DebugElement: Sets the identifier (ID) of this object.
setID(String) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Sets the identifier (ID) of this object.
setID(String) - Method in class org.openscience.cdk.debug.DebugIsotope: Sets the identifier (ID) of this object.
setID(String) - Method in class org.openscience.cdk.debug.DebugLonePair: Sets the identifier (ID) of this object.
setID(String) - Method in class org.openscience.cdk.debug.DebugMapping: Sets the identifier (ID) of this object.
setID(String) - Method in class org.openscience.cdk.debug.DebugMonomer: Sets the identifier (ID) of this object.
setID(String) - Method in class org.openscience.cdk.debug.DebugPolymer: Sets the identifier (ID) of this object.
setID(String) - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Sets the identifier (ID) of this object.
setID(String) - Method in class org.openscience.cdk.debug.DebugReaction: Sets the identifier (ID) of this object.
setID(String) - Method in class org.openscience.cdk.debug.DebugReactionScheme: Sets the identifier (ID) of this object.
setID(String) - Method in class org.openscience.cdk.debug.DebugReactionSet: Sets the identifier (ID) of this object.
setID(String) - Method in class org.openscience.cdk.debug.DebugRing: Sets the identifier (ID) of this object.
setID(String) - Method in class org.openscience.cdk.debug.DebugSingleElectron: Sets the identifier (ID) of this object.
setID(String) - Method in class org.openscience.cdk.debug.DebugStrand: Sets the identifier (ID) of this object.
setID(String) - Method in class org.openscience.cdk.debug.DebugSubstance: Sets the identifier (ID) of this object.
setID(String) - Method in class org.openscience.cdk.dict.Entry
setID(String) - Method in interface org.openscience.cdk.interfaces.IChemObject: Sets the identifier (ID) of this object.
setID(String) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject: Sets the identifier (ID) of this object.
setID(String) - Method in class org.openscience.cdk.silent.ChemObject: Sets the identifier (ID) of this object.
setId1(int) - Method in class org.openscience.cdk.isomorphism.mcss.RMap: Sets the id1 attribute of the RMap object.
setId1(int) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMap: Deprecated.

Sets the id1 attribute of the CDKRMap object
setId2(int) - Method in class org.openscience.cdk.isomorphism.mcss.RMap: Sets the id2 attribute of the RMap object.
setId2(int) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMap: Deprecated.

Sets the id2 attribute of the CDKRMap object
setIDPolicy(int) - Static method in class org.openscience.cdk.tools.IDCreator: Alters the policy of ID generation.
setIgnoreAromaticBonds(boolean) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory: Deprecated.
"the use of aromatic bonds is strongly discouraged" - InChI FAQ, the InChI will fail for many compounds if ignore aromatic bonds is not enabled and the compound have aromatic flags.
setImagelink(String) - Method in class org.openscience.cdk.io.RssWriter
setImaginaryPart(double) - Method in class org.openscience.cdk.math.Complex: Sets the imaginary part of this value
setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.Atom: Sets the number of implicit hydrogen count of this atom.
setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.AtomRef: Sets the implicit hydrogen count of this atom.
setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.debug.DebugAtom: Sets the number of implicit hydrogen count of this atom.
setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Sets the number of implicit hydrogen count of this atom.
setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Sets the number of implicit hydrogen count of this atom.
setImplicitHydrogenCount(Integer) - Method in interface org.openscience.cdk.interfaces.IAtom: Sets the implicit hydrogen count of this atom.
setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Sets the number of implicit hydrogen count of this atom.
setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.silent.Atom: Sets the number of implicit hydrogen count of this atom.
setInchimap(Map) - Method in class org.openscience.cdk.io.RssWriter
setIndexCreated(boolean) - Method in class org.openscience.cdk.io.random.RandomAccessReader
setInputReader(Reader) - Method in class org.openscience.cdk.io.listener.TextGUIListener: Overwrites the default reader from which the input is taken.
setInputStream(InputStream) - Method in class org.openscience.cdk.config.CDKBasedAtomTypeConfigurator: Sets the file containing the configuration data.
setInputStream(InputStream) - Method in interface org.openscience.cdk.config.IAtomTypeConfigurator: Sets the file containing the configuration data.
setInputStream(InputStream) - Method in class org.openscience.cdk.config.OWLBasedAtomTypeConfigurator: Sets the file containing the configuration data.
setInputStream(InputStream) - Method in class org.openscience.cdk.config.TXTBasedAtomTypeConfigurator: Sets the file containing the configuration data.
setInputStream(InputStream) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator: Sets the inputStream attribute of the ForceFieldConfigurator object
setInputStream(InputStream) - Method in class org.openscience.cdk.modeling.builder3d.MM2BasedParameterSetReader: Sets the file containing the config data.
setInputStream(InputStream) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94BasedParameterSetReader: Sets the file containing the config data
setIntensity(double) - Method in class org.openscience.cdk.formula.IsotopeContainer: Set the intensity value of this container.
setInterrupted(boolean) - Method in class org.openscience.cdk.smiles.DeduceBondSystemTool: Deprecated.

Sets if the calculation should be interrupted.
setInterrupted(boolean) - Method in class org.openscience.cdk.smiles.FixBondOrdersTool: Deprecated.

Sets if the calculation should be interrupted.
setIsAromatic(boolean) - Method in class org.openscience.cdk.Atom: Mark this atom as being aromatic.
setIsAromatic(boolean) - Method in class org.openscience.cdk.AtomRef: Mark this atom as being aromatic.
setIsAromatic(boolean) - Method in class org.openscience.cdk.Bond: Mark this bond as being aromatic.
setIsAromatic(boolean) - Method in class org.openscience.cdk.BondRef: Mark this bond as being aromatic.
setIsAromatic(boolean) - Method in interface org.openscience.cdk.interfaces.IAtom: Mark this atom as being aromatic.
setIsAromatic(boolean) - Method in interface org.openscience.cdk.interfaces.IBond: Mark this bond as being aromatic.
setIsAromatic(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Mark this atom as being aromatic.
setIsAromatic(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Mark this bond as being aromatic.
setIsAromatic(boolean) - Method in class org.openscience.cdk.silent.Atom: Mark this atom as being aromatic.
setIsAromatic(boolean) - Method in class org.openscience.cdk.silent.Bond: Mark this bond as being aromatic.
setIsInRing(boolean) - Method in class org.openscience.cdk.Atom: Mark this atom as being in a ring.
setIsInRing(boolean) - Method in class org.openscience.cdk.AtomRef: Mark this atom as being in a ring.
setIsInRing(boolean) - Method in class org.openscience.cdk.Bond: Mark this bond as being in a ring.
setIsInRing(boolean) - Method in class org.openscience.cdk.BondRef: Mark this bond as being in a ring.
setIsInRing(boolean) - Method in interface org.openscience.cdk.interfaces.IAtom: Mark this atom as being in a ring.
setIsInRing(boolean) - Method in interface org.openscience.cdk.interfaces.IBond: Mark this bond as being in a ring.
setIsInRing(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Mark this atom as being in a ring.
setIsInRing(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Mark this bond as being in a ring.
setIsInRing(boolean) - Method in class org.openscience.cdk.silent.Atom: Mark this atom as being in a ring.
setIsInRing(boolean) - Method in class org.openscience.cdk.silent.Bond: Mark this bond as being in a ring.
setLabel(String) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Sets the label of this PseudoAtom.
setLabel(String) - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Sets the label of this PseudoAtom.
setLabel(String) - Method in class org.openscience.cdk.dict.Entry
setLabel(String) - Method in interface org.openscience.cdk.interfaces.IPseudoAtom: Sets the label of this PseudoAtom.
setLabel(String) - Method in class org.openscience.cdk.PseudoAtom: Sets the label of this PseudoAtom.
setLabel(String) - Method in class org.openscience.cdk.silent.PseudoAtom: Sets the label of this PseudoAtom.
setLast(long) - Method in class org.openscience.cdk.smiles.InvPair
setLatticeConstant(double) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
setLatticeConstant(double) - Method in class org.openscience.cdk.tools.GridGenerator
setLearningFromConnectivity(Set<Integer>, int[], int[], boolean[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: If matrix is not connected, setting learninfFromConnectivity global variables.
setLeft(IQueryAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom: Deprecated.
setLeft(IQueryBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond: Deprecated.
setLength(int) - Method in class org.openscience.cdk.iupac.parser.AttachedGroup: Setter for property length.
setLernenIndices(int, Permutation, int[][], int[], int[], int[], boolean[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Setting the nonCanonicalIndices global variable.
setLevel(int) - Method in interface org.openscience.cdk.tools.ILoggingTool: Set the level of this logger.
setLevel(int) - Method in class org.openscience.cdk.tools.SystemOutLoggingTool: Deprecated.

Set the level of this logger.
setLevel(IOSetting.Importance) - Method in class org.openscience.cdk.io.listener.SwingGUIListener
setLevel(IOSetting.Importance) - Method in class org.openscience.cdk.io.listener.TextGUIListener
setLine(int, GIMatrix) - Method in class org.openscience.cdk.graph.invariant.GIMatrix: Sets the line of the matrix at the specified index to a new value.
setLink(String) - Method in class org.openscience.cdk.io.RssWriter
setLinkageRadius(double) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
setLinkmap(Map) - Method in class org.openscience.cdk.io.RssWriter
setLocations(List<Token>) - Method in class org.openscience.cdk.iupac.parser.AttachedGroup: Setter for property locations.
setLoggingToolClass(Class<? extends ILoggingTool>) - Static method in class org.openscience.cdk.tools.LoggingToolFactory: Sets the ILoggingTool implementation to be used.
setLogical(Expr.Type, Expr, Expr) - Method in class org.openscience.cdk.isomorphism.matchers.Expr: Set the logical value of this atom expression.
setMapIdx(int) - Method in class org.openscience.cdk.Atom
setMapIdx(int) - Method in class org.openscience.cdk.AtomRef
setMapIdx(int) - Method in interface org.openscience.cdk.interfaces.IAtom: Set the map index for this atom.
setMapIdx(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Set the map index for this atom.
setMapIdx(int) - Method in class org.openscience.cdk.silent.Atom
setMappings(List<Map<Integer, Integer>>) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler: Deprecated.

Set mapping solutions
setMass(double) - Method in class org.openscience.cdk.formula.IsotopeContainer: Set the mass value of this container.
setMassNumber(Integer) - Method in class org.openscience.cdk.AtomRef: Sets the atomic mass of this element.
setMassNumber(Integer) - Method in class org.openscience.cdk.debug.DebugAtom: Sets the atomic mass of this element.
setMassNumber(Integer) - Method in class org.openscience.cdk.debug.DebugAtomType: Sets the atomic mass of this element.
setMassNumber(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Sets the atomic mass of this element.
setMassNumber(Integer) - Method in class org.openscience.cdk.debug.DebugIsotope: Sets the atomic mass of this element.
setMassNumber(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Sets the atomic mass of this element.
setMassNumber(Integer) - Method in interface org.openscience.cdk.interfaces.IIsotope: Sets the atomic mass of this element.
setMassNumber(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Sets the atomic mass of this element.
setMassNumber(Integer) - Method in class org.openscience.cdk.Isotope: Sets the atomic mass of this element.
setMassNumber(Integer) - Method in class org.openscience.cdk.silent.Isotope: Sets the atomic mass of this element.
setMatchBond(boolean) - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph: Deprecated.
setMatchBonds(boolean) - Method in class org.openscience.cdk.smsd.Isomorphism: Deprecated.
setMatchingAtoms(int[]) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom: Set the atoms of a target molecule that correspond to this group.
setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.AtomRef: Sets the MaxBondOrder attribute of the AtomType object.
setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.AtomType: Sets the MaxBondOrder attribute of the AtomType object.
setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.debug.DebugAtom: Sets the MaxBondOrder attribute of the AtomType object.
setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.debug.DebugAtomType: Sets the MaxBondOrder attribute of the AtomType object.
setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Sets the MaxBondOrder attribute of the AtomType object.
setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Sets the MaxBondOrder attribute of the AtomType object.
setMaxBondOrder(IBond.Order) - Method in interface org.openscience.cdk.interfaces.IAtomType: Sets the MaxBondOrder attribute of the AtomType object.
setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Sets the MaxBondOrder attribute of the AtomType object.
setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.silent.AtomType: Sets the MaxBondOrder attribute of the AtomType object.
setMaxGasteigerDamp(double) - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges: Sets the maxGasteigerDamp attribute of the GasteigerMarsiliPartialCharges object.
setMaxGasteigerIters(double) - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges: Sets the maxGasteigerIters attribute of the GasteigerMarsiliPartialCharges object.
setMaxGasteigerIters(int) - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges: Sets the maxGasteigerIters attribute of the GasteigerPEPEPartialCharges object.
setMaximalStructures(int) - Method in class org.openscience.cdk.tools.StructureResonanceGenerator: Set the number maximal of resonance structures to be found.
setMaximumNeighbors(int) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultMCSPlusAtomMatcher: Deprecated.
setMaximumNeighbors(int) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultRGraphAtomMatcher: Deprecated.
setMaximumNeighbors(int) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFAtomMatcher: Deprecated.
setMaxIteration(int) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Sets the maxIteration for the RGraph parsing.
setMaxIteration(int) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph: Deprecated.

Sets the maxIteration for the CDKRGraph parsing.
setMaxIterations(int) - Method in class org.openscience.cdk.charges.Electronegativity: set the maximum number of Iterations.
setMaxIterations(int) - Method in class org.openscience.cdk.charges.PiElectronegativity: set the maximum number of Iterations.
setMaxResonStruc(int) - Method in class org.openscience.cdk.charges.Electronegativity: set the maximum number of resonance structures.
setMaxResonStruc(int) - Method in class org.openscience.cdk.charges.PiElectronegativity: set the maximum number of resonance structures.
setMaxResoStruc(int) - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges: Sets the maximum resonance structures to be searched.
setMechanism(String) - Method in class org.openscience.cdk.dict.EntryReact: Set the mechanism of this reaction.
setMinimumFragmentSize(int) - Method in class org.openscience.cdk.fragment.ExhaustiveFragmenter: Set the minimum fragment size.
setMinIntensity(double) - Method in class org.openscience.cdk.formula.IsotopePatternGenerator: Set the minimum (normalised) intensity to generate.
setMinPSCluster(int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
setMinPSPocket(int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
setMinResolution(double) - Method in class org.openscience.cdk.formula.IsotopePatternGenerator: Set the minimum resolution at which peaks within this mass difference should be considered equivalent.
setMM2Parameters(IChemObjectBuilder) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator: Sets the parameters attribute of the ForceFieldConfigurator object, default is mm2 force field
setMMFF94Parameters(IChemObjectBuilder) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
setMode(int) - Method in class org.openscience.cdk.smarts.SmartsFragmentExtractor: Set the mode of SMARTS substructure selection
setModelCenter(double, double) - Method in class org.openscience.cdk.renderer.AbstractRenderer: Set the position of the center of the model.
setMolecule(IAtomContainer) - Method in class org.openscience.cdk.layout.AtomPlacer: Sets the molecule the AtomPlacer currently works with
setMolecule(IAtomContainer) - Method in class org.openscience.cdk.layout.RingPlacer
setMolecule(IAtomContainer) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator: Assings a molecule to be layed out.
setMolecule(IAtomContainer) - Method in class org.openscience.cdk.structgen.RandomGenerator: Assigns a starting structure to this generator.
setMolecule(IAtomContainer, boolean) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
setMolecule(IAtomContainer, boolean, Set<IAtom>, Set<IBond>) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator: Assigns a molecule to be laid out.
setMoleculeSet(IAtomContainerSet) - Method in class org.openscience.cdk.ChemModel: Sets the MoleculeSet of this ChemModel.
setMoleculeSet(IAtomContainerSet) - Method in class org.openscience.cdk.debug.DebugChemModel: Sets the MoleculeSet of this ChemModel.
setMoleculeSet(IAtomContainerSet) - Method in interface org.openscience.cdk.interfaces.IChemModel: Sets the IAtomContainerSet of this ChemModel.
setMoleculeSet(IAtomContainerSet) - Method in class org.openscience.cdk.silent.ChemModel: Sets the MoleculeSet of this ChemModel.
setMonoIsotope(IsotopeContainer) - Method in class org.openscience.cdk.formula.IsotopePattern: Set the mono isotope object.
setMonomerName(String) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Sets the name of the Monomer object.
setMonomerName(String) - Method in class org.openscience.cdk.debug.DebugMonomer: Sets the name of the Monomer object.
setMonomerName(String) - Method in interface org.openscience.cdk.interfaces.IMonomer: Set the name of the Monomer object.
setMonomerName(String) - Method in class org.openscience.cdk.Monomer: Sets the name of the Monomer object.
setMonomerName(String) - Method in class org.openscience.cdk.silent.Monomer: Sets the name of the Monomer object.
setMonomerType(String) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Sets the type of the Monomer object.
setMonomerType(String) - Method in class org.openscience.cdk.debug.DebugMonomer: Sets the type of the Monomer object.
setMonomerType(String) - Method in interface org.openscience.cdk.interfaces.IMonomer: Set the type of the Monomer object.
setMonomerType(String) - Method in class org.openscience.cdk.Monomer: Sets the type of the Monomer object.
setMonomerType(String) - Method in class org.openscience.cdk.silent.Monomer: Sets the type of the Monomer object.
setMultiMap(Map) - Method in class org.openscience.cdk.io.RssWriter
setMultiplier(int, Double) - Method in class org.openscience.cdk.AtomContainerSet: Sets the coefficient of a AtomContainer to a given value.
setMultiplier(int, Double) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Sets the coefficient of a AtomContainer to a given value.
setMultiplier(int, Double) - Method in class org.openscience.cdk.debug.DebugSubstance: Sets the coefficient of a AtomContainer to a given value.
setMultiplier(int, Double) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet: Sets the coefficient of a AtomContainer to a given value.
setMultiplier(int, Double) - Method in class org.openscience.cdk.silent.AtomContainerSet: Sets the coefficient of a AtomContainer to a given value.
setMultiplier(IAtomContainer, Double) - Method in class org.openscience.cdk.AtomContainerSet: Sets the coefficient of a AtomContainer to a given value.
setMultiplier(IAtomContainer, Double) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Sets the coefficient of a AtomContainer to a given value.
setMultiplier(IAtomContainer, Double) - Method in class org.openscience.cdk.debug.DebugSubstance: Sets the coefficient of a AtomContainer to a given value.
setMultiplier(IAtomContainer, Double) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet: Sets the coefficient of a AtomContainer to a given value.
setMultiplier(IAtomContainer, Double) - Method in class org.openscience.cdk.silent.AtomContainerSet: Sets the coefficient of a AtomContainer to a given value.
setMultipliers(Double[]) - Method in class org.openscience.cdk.AtomContainerSet: Sets the multipliers of the AtomContainers.
setMultipliers(Double[]) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Sets the multipliers of the AtomContainers.
setMultipliers(Double[]) - Method in class org.openscience.cdk.debug.DebugSubstance: Sets the multipliers of the AtomContainers.
setMultipliers(Double[]) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet: Sets the multipliers of the AtomContainers.
setMultipliers(Double[]) - Method in class org.openscience.cdk.silent.AtomContainerSet: Sets the multipliers of the AtomContainers.
setMultiThread(boolean) - Method in class org.openscience.cdk.structgen.maygen.Maygen
setName(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom: set the Atom name of this atom.
setName(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom: set the Atom name of this atom.
setName(String) - Method in class org.openscience.cdk.iupac.parser.AttachedGroup: Setter for property name.
setName(String) - Method in class org.openscience.cdk.libio.md.Residue
setName(String) - Method in class org.openscience.cdk.protein.data.PDBAtom: set the Atom name of this atom.
setName(String) - Method in class org.openscience.cdk.silent.PDBAtom: set the Atom name of this atom.
setNaturalAbundance(Double) - Method in class org.openscience.cdk.AtomRef: Sets the NaturalAbundance attribute of the Isotope object.
setNaturalAbundance(Double) - Method in class org.openscience.cdk.debug.DebugAtom: Sets the NaturalAbundance attribute of the Isotope object.
setNaturalAbundance(Double) - Method in class org.openscience.cdk.debug.DebugAtomType: Sets the NaturalAbundance attribute of the Isotope object.
setNaturalAbundance(Double) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Sets the NaturalAbundance attribute of the Isotope object.
setNaturalAbundance(Double) - Method in class org.openscience.cdk.debug.DebugIsotope: Sets the NaturalAbundance attribute of the Isotope object.
setNaturalAbundance(Double) - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Sets the NaturalAbundance attribute of the Isotope object.
setNaturalAbundance(Double) - Method in interface org.openscience.cdk.interfaces.IIsotope: Sets the NaturalAbundance attribute of the Isotope object.
setNaturalAbundance(Double) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Sets the NaturalAbundance attribute of the Isotope object.
setNaturalAbundance(Double) - Method in class org.openscience.cdk.Isotope: Sets the NaturalAbundance attribute of the Isotope object.
setNaturalAbundance(Double) - Method in class org.openscience.cdk.silent.Isotope: Sets the NaturalAbundance attribute of the Isotope object.
setNewMatrix(boolean) - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregor: Deprecated.

set a new Matrix.
setNoteComments(String[]) - Method in class org.openscience.cdk.fingerprint.model.Bayesian: Sets the comments for the model, which is a list of strings containing arbitrary content.
setNoteOrigin(String) - Method in class org.openscience.cdk.fingerprint.model.Bayesian: Provides an arbitrary string that briefly describes the model origin, which may include authors, data source keywords, or other pertinent information.
setNotEqual(BinaryTree) - Method in class org.openscience.cdk.smsd.helper.BinaryTree: Deprecated.

Set not equal node
setNoteTitle(String) - Method in class org.openscience.cdk.fingerprint.model.Bayesian: Provides an arbitrary title string that briefly summarises the model.
setNotification(boolean) - Method in class org.openscience.cdk.ChemObject
setNotification(boolean) - Method in class org.openscience.cdk.debug.DebugChemObject: Set a flag to use or not use notification.
setNotification(boolean) - Method in interface org.openscience.cdk.interfaces.IChemObject: Set a flag to use or not use notification.
setNotification(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
setNotification(boolean) - Method in class org.openscience.cdk.renderer.RendererModel: Dis- or enables sending around change notifications.
setNotification(boolean) - Method in class org.openscience.cdk.silent.ChemObject
setNS(String) - Method in class org.openscience.cdk.dict.Dictionary
setNumAtoms(int) - Method in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
setNumber(int) - Method in class org.openscience.cdk.libio.md.ChargeGroup
setNumber(int) - Method in class org.openscience.cdk.libio.md.Residue
setObjectProperty(String, String, String) - Method in class org.openscience.cdk.io.iterator.event.EventCMLHandler: Procedure required by the CDOInterface.
setOccupancy(Double) - Method in class org.openscience.cdk.debug.DebugPDBAtom: set the Occupancy of this atom.
setOccupancy(Double) - Method in interface org.openscience.cdk.interfaces.IPDBAtom: set the Occupancy of this atom.
setOccupancy(Double) - Method in class org.openscience.cdk.protein.data.PDBAtom: set the Occupancy of this atom.
setOccupancy(Double) - Method in class org.openscience.cdk.silent.PDBAtom: set the Occupancy of this atom.
setOccurrence(String) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList: Picky setter for occurrence fields.
setOfMolecules - Variable in class org.openscience.cdk.ChemModel: A MoleculeSet.
setOfMolecules - Variable in class org.openscience.cdk.silent.ChemModel: A MoleculeSet.
setOfReactions - Variable in class org.openscience.cdk.ChemModel: A ReactionSet.
setOfReactions - Variable in class org.openscience.cdk.silent.ChemModel: A ReactionSet.
seTolerance(double) - Method in class org.openscience.cdk.formula.IsotopePatternSimilarity: Set the tolerance of the mass accuracy.
setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom: Deprecated.
setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom: Deprecated.
use static utility methods to create logical atom matcher, LogicalOperatorAtom.and(org.openscience.cdk.isomorphism.matchers.IQueryAtom, org.openscience.cdk.isomorphism.matchers.IQueryAtom), LogicalOperatorAtom.or(org.openscience.cdk.isomorphism.matchers.IQueryAtom, org.openscience.cdk.isomorphism.matchers.IQueryAtom) or LogicalOperatorAtom.not(org.openscience.cdk.isomorphism.matchers.IQueryAtom).
setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond: Deprecated.
setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolAndChargeQueryAtom: Deprecated.
setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolChargeIDQueryAtom
setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom: Deprecated.
setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom: Deprecated.
setOrder(IBond.Order) - Method in class org.openscience.cdk.Bond: Sets the bond order of this bond.
setOrder(IBond.Order) - Method in class org.openscience.cdk.BondRef: Sets the bond order of this bond.
setOrder(IBond.Order) - Method in class org.openscience.cdk.debug.DebugBond: Sets the bond order of this bond.
setOrder(IBond.Order) - Method in interface org.openscience.cdk.interfaces.IBond: Sets the bond order of this bond.
setOrder(IBond.Order) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Sets the bond order of this query bond.
setOrder(IBond.Order) - Method in class org.openscience.cdk.silent.Bond: Sets the bond order of this bond.
setOutputWriter(Writer) - Method in class org.openscience.cdk.io.listener.PropertiesListener: Overwrites the default writer to which the output is directed.
setOutputWriter(Writer) - Method in class org.openscience.cdk.io.listener.TextGUIListener: Overwrites the default writer to which the output is directed.
setOverrideBondWidth(double) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator: Set the width to use for all bonds, overriding any standard bond widths.
setOverrideColor(Color) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator: Set the color to use for all bonds, overriding the standard bond colors.
setOxt(Boolean) - Method in class org.openscience.cdk.debug.DebugPDBAtom: Change the state of this atom in being the PDB OXT atom.
setOxt(Boolean) - Method in interface org.openscience.cdk.interfaces.IPDBAtom: Change the state of this atom in being the PDB OXT atom.
setOxt(Boolean) - Method in class org.openscience.cdk.protein.data.PDBAtom
setOxt(Boolean) - Method in class org.openscience.cdk.silent.PDBAtom
setParameter(boolean) - Method in interface org.openscience.cdk.reaction.type.parameters.IParameterReact: Set the parameter to take account.
setParameter(boolean) - Method in class org.openscience.cdk.reaction.type.parameters.ParameterReact: Set the parameter to take account.
setParameterList(List<IParameterReact>) - Method in interface org.openscience.cdk.reaction.IReactionProcess: Sets the parameters for this reaction.
setParameterList(List<IParameterReact>) - Method in class org.openscience.cdk.reaction.ReactionEngine: Returns the current parameter Map for this reaction.
setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.ChargeRule: Sets the parameters attribute of the ChargeRule object.
setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.ElementRule: Sets the parameters attribute of the ElementRule object.
setParameters(Object[]) - Method in interface org.openscience.cdk.formula.rules.IRule: Sets the parameters for this rule.
setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.IsotopePatternRule: Sets the parameters attribute of the IsotopePatternRule object.
setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.MMElementRule: Sets the parameters attribute of the MMElementRule object.
setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.NitrogenRule: Sets the parameters attribute of the NitrogenRule object.
setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.RDBERule: Sets the parameters attribute of the RDBE object.
setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.ToleranceRangeRule: Sets the parameters attribute of the ToleranceRangeRule object.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor: This descriptor does not have any parameter to be set.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor: This descriptor does have any parameter.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor: This descriptor does have any parameter.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor: This descriptor does have any parameter.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor: Sets the parameters attribute of the BondsToAtomDescriptor object
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor: This descriptor does have any parameter.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor: Sets the parameters attribute of the DistanceToAtomDescriptor object
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor: This descriptor does have any parameter.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor: This descriptor does have any parameter.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor: This descriptor does have any parameter.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor: This descriptor does have any parameter.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor: Deprecated.

This descriptor does have any parameter.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor: Sets the parameters attribute of the IsProtonInAromaticSystemDescriptor object
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInConjugatedPiSystemDescriptor: Sets the parameters attribute of the IsProtonInConjugatedPiSystemDescriptor object
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor: Sets the parameters attribute of the PartialPiChargeDescriptor object
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor: Sets the parameters attribute of the PartialSigmaChargeDescriptor object
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor: This descriptor does not have any parameter to be set.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor: This descriptor does not have any parameter to be set.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor: This descriptor does not have any parameter to be set.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor: Sets the parameters attribute of the PiElectronegativityDescriptor object
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor: This descriptor does have any parameter.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor: This descriptor does not have any parameter to be set.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R: Sets the parameters attribute of the RDFProtonDescriptor object
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR: Sets the parameters attribute of the RDFProtonDescriptor object
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol: Sets the parameters attribute of the RDFProtonDescriptor object
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR: Sets the parameters attribute of the RDFProtonDescriptor object
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR: Sets the parameters attribute of the RDFProtonDescriptor object
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor: Sets the parameters attribute of the SigmaElectronegativityDescriptor object
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor: Sets the parameters attribute of the StabilizationPlusChargeDescriptor object
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor: This descriptor does have any parameter.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor: Sets the parameters attribute of the PiContactDetectionDescriptor object.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptor
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor: This descriptor does have any parameter.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor: This descriptor does have any parameter.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor: This descriptor does have any parameter.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor: This descriptor does have any parameter.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor: Deprecated.

This descriptor does have any parameter.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor: Sets the parameters for this descriptor.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor: Sets the parameters attribute of the AminoAcidsCountDescriptor object.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor: Sets the parameters attribute of the APolDescriptor object.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor: Sets the parameters attribute of the AromaticAtomsCountDescriptor object.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor: Sets the parameters attribute of the AromaticBondsCountDescriptor object.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor: Sets the parameters attribute of the AtomCountDescriptor object.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor: Sets the parameters for this descriptor.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor: Sets the parameters attribute of the BCUTDescriptor object.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor: Sets the parameters attribute of the BondCountDescriptor object
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor: Sets the parameters attribute of the BPolDescriptor object
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor: Sets the parameters attribute of the GravitationalIndexDescriptor object.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor: Sets the parameters attribute of the CPSADescriptor object.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor: Sets the parameters attribute of the EccentricConnectivityIndexDescriptor object
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor: Sets the parameters for this descriptor.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalCSP3Descriptor: Sets the parameters for this descriptor.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor: Sets the parameters for this descriptor.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor: Sets the parameters attribute of the FragmentComplexityDescriptor object.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor: Sets the parameters attribute of the GravitationalIndexDescriptor object.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor: Sets the parameters attribute of the HBondAcceptorCountDescriptor object.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor: Sets the parameter of this HBondDonorCountDescriptor instance.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor: Sets the parameters attribute of the HybridizationRatioDescriptor object.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor: Deprecated.

Sets the parameters attribute of the IPMolecularLearningDescriptor object
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor: Sets the parameters attribute of the KappaShapeIndicesDescriptor object
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor: Sets the parameters attribute of the descriptor.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor: Sets the parameters attribute of the LargestChain object.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor: Sets the parameters attribute of the LargestPiSystemDescriptor object.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor: Sets the parameters attribute of the PetitjeanNumberDescriptor object
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor: Sets the parameters attribute of the LongestAliphaticChainDescriptor object.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor: This IDescriptor does not have any parameters.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor: Sets the parameters attribute of the WeightDescriptor object.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor: Sets the parameters attribute of the MomentOfInertiaDescriptor object.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor: Sets the parameters attribute of the PetitjeanNumberDescriptor object
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor: Sets the parameters attribute of the PetitjeanShapeIndexDescriptor object.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor: Sets the parameters attribute of the RotatableBondsCountDescriptor object
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor: Sets the parameters attribute of the RuleOfFiveDescriptor object.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor: Set parameters: ignored, there are none.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.SpiroAtomCountDescriptor: Sets the parameters for this descriptor.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor: Sets the parameters attribute of the TPSADescriptor object.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor: Sets the parameters for this descriptor.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor: Sets the parameters attribute of the VAdjMaDescriptor object
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor: Sets the parameters attribute of the WeightDescriptor object.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor: Sets the parameters attribute of the WeightedPathDescriptor object.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor: Sets the parameters attribute of the WHIMDescriptor object.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor: Sets the parameters attribute of the WienerNumbersDescriptor object.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor: Sets the parameters attribute of the XLogPDescriptor object.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor: Sets the parameters attribute of the ZagrebIndexDescriptor object.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor: Sets the parameters attribute of the TaeAminoAcidDescriptor object.
setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.substance.OxygenAtomCountDescriptor: Sets the parameters for this descriptor.
setParameters(Object[]) - Method in interface org.openscience.cdk.qsar.IDescriptor: Sets the parameters for this descriptor.
setParameters(String, String, String) - Method in class org.openscience.cdk.dict.EntryReact: Set the parameters of the reaction.
setParameters(Map<String, Object>) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator: Sets the parameters attribute of the ForceFieldConfigurator object
setParameterSet(Map) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D: Constructor for the setParameterSet object.
setParentMolecule(MDMolecule) - Method in class org.openscience.cdk.libio.md.ChargeGroup
setParentMolecule(MDMolecule) - Method in class org.openscience.cdk.libio.md.Residue
setPathLimit(int) - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter: Set the pathLimit for the base daylight/path fingerprint.
setPathLimit(int) - Method in class org.openscience.cdk.fingerprint.Fingerprinter
setPerceiveStereo(boolean) - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter: Sets whether stereochemistry should be re-perceived from 2D/3D coordinates.
setPerceiveStereo(boolean) - Method in class org.openscience.cdk.fingerprint.model.Bayesian: Sets whether stereochemistry should be re-perceived from 2D/3D coordinates.
setPermutation(int[]) - Method in class org.openscience.cdk.graph.Permutor: Set the currently used permutation.
setPermutation(int[]) - Method in class org.openscience.cdk.smsd.labelling.Permutor: Deprecated.

Set the currently used permutation.
setPharmacophoreQuery(PharmacophoreQuery) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher: Set a pharmacophore query.
setPocketSize(int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
setPoint2d(Point2d) - Method in class org.openscience.cdk.Atom: Sets a point specifying the location of this atom in a 2D space.
setPoint2d(Point2d) - Method in class org.openscience.cdk.AtomRef: Sets a point specifying the location of this atom in a 2D space.
setPoint2d(Point2d) - Method in class org.openscience.cdk.debug.DebugAtom: Sets a point specifying the location of this atom in a 2D space.
setPoint2d(Point2d) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Sets a point specifying the location of this atom in a 2D space.
setPoint2d(Point2d) - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Sets a point specifying the location of this atom in a 2D space.
setPoint2d(Point2d) - Method in interface org.openscience.cdk.interfaces.IAtom: Sets a point specifying the location of this atom in a 2D space.
setPoint2d(Point2d) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Sets a point specifying the location of this atom in a 2D space.
setPoint2d(Point2d) - Method in class org.openscience.cdk.silent.Atom: Sets a point specifying the location of this atom in a 2D space.
setPoint3d(Point3d) - Method in class org.openscience.cdk.Atom: Sets a point specifying the location of this atom in 3D space.
setPoint3d(Point3d) - Method in class org.openscience.cdk.AtomRef: Sets a point specifying the location of this atom in 3D space.
setPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugAtom: Sets a point specifying the location of this atom in 3D space.
setPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Sets a point specifying the location of this atom in 3D space.
setPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Sets a point specifying the location of this atom in 3D space.
setPoint3d(Point3d) - Method in interface org.openscience.cdk.interfaces.IAtom: Sets a point specifying the location of this atom in 3D space.
setPoint3d(Point3d) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Sets a point specifying the location of this atom in 3D space.
setPoint3d(Point3d) - Method in class org.openscience.cdk.silent.Atom: Sets a point specifying the location of this atom in 3D space.
setPrepare(boolean) - Method in class org.openscience.cdk.smarts.SmartsPattern: Sets whether the molecule should be "prepared" for a SMARTS match, including set ring flags and perceiving aromaticity.
setPrepare(boolean) - Method in class org.openscience.cdk.smiles.smarts.SmartsPattern: Deprecated.

Sets whether the molecule should be "prepared" for a SMARTS match, including set ring flags and perceiving aromaticity.
setPreservingAromaticity(boolean) - Method in class org.openscience.cdk.smiles.SmilesParser: Deprecated.
setPrime() - Method in class org.openscience.cdk.smiles.InvPair: Sets the prime number based on the current seed.
setPrimitive(Expr.Type) - Method in class org.openscience.cdk.isomorphism.matchers.Expr: Set the primitive value of this atom expression.
setPrimitive(Expr.Type, int) - Method in class org.openscience.cdk.isomorphism.matchers.Expr: Set the primitive value of this atom expression.
setProductCoefficient(IAtomContainer, Double) - Method in class org.openscience.cdk.debug.DebugReaction: Sets the coefficient of a a product to a given value.
setProductCoefficient(IAtomContainer, Double) - Method in interface org.openscience.cdk.interfaces.IReaction: Sets the coefficient of a a product to a given value.
setProductCoefficient(IAtomContainer, Double) - Method in class org.openscience.cdk.Reaction: Sets the coefficient of a a product to a given value.
setProductCoefficient(IAtomContainer, Double) - Method in class org.openscience.cdk.silent.Reaction: Sets the coefficient of a a product to a given value.
setProductCoefficients(Double[]) - Method in class org.openscience.cdk.debug.DebugReaction: Sets the coefficient of the products.
setProductCoefficients(Double[]) - Method in interface org.openscience.cdk.interfaces.IReaction: Sets the coefficient of the products.
setProductCoefficients(Double[]) - Method in class org.openscience.cdk.Reaction: Sets the coefficient of the products.
setProductCoefficients(Double[]) - Method in class org.openscience.cdk.silent.Reaction: Sets the coefficient of the products.
setProducts(IAtomContainerSet) - Method in class org.openscience.cdk.debug.DebugReaction: Assigns a MoleculeSet to the products of this reaction.
setProducts(IAtomContainerSet) - Method in interface org.openscience.cdk.interfaces.IReaction: Assigns a IAtomContaineSet to the products of this reaction.
setProducts(IAtomContainerSet) - Method in class org.openscience.cdk.Reaction: Assigns a MoleculeSet to the products of this reaction.
setProducts(IAtomContainerSet) - Method in class org.openscience.cdk.silent.Reaction: Assigns a MoleculeSet to the products of this reaction.
setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.ChemObject: Set the properties of this object to the provided map (shallow copy).
setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugChemObject: Set the properties of this object to the provided map (shallow copy).
setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugMolecularFormula: Sets the properties of this object.
setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.formula.MolecularFormula: Sets the properties of this object.
setProperties(Map<Object, Object>) - Method in interface org.openscience.cdk.interfaces.IChemObject: Set the properties of this object to the provided map (shallow copy).
setProperties(Map<Object, Object>) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula: Sets the properties of this object.I should integrate into ChemObject.
setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject: Set the properties of this object to the provided map (shallow copy).
setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.silent.ChemObject: Set the properties of this object to the provided map (shallow copy).
setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.silent.MolecularFormula: Sets the properties of this object.
setProperty(Object, Object) - Method in class org.openscience.cdk.ChemObject: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugAtom: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugAtomType: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugBond: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugChemFile: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugChemModel: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugChemObject: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugChemSequence: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugCrystal: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugElectronContainer: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugElement: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugIsotope: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugLonePair: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugMapping: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugMolecularFormula: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugMonomer: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugPolymer: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugReaction: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugReactionScheme: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugReactionSet: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugRing: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugSingleElectron: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugStrand: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugSubstance: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.formula.MolecularFormula: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in interface org.openscience.cdk.interfaces.IChemObject: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.silent.ChemObject: Sets a property for a IChemObject.
setProperty(Object, Object) - Method in class org.openscience.cdk.silent.MolecularFormula: Sets a property for a IChemObject.
setProtein(IBioPolymer) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
setProteinInterior(int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
setPublisher(String) - Method in class org.openscience.cdk.io.RssWriter
setQueryCacheSize(int) - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool: Deprecated.

Set the maximum size of the query cache.
setRandom(Random) - Static method in class org.openscience.cdk.math.RandomNumbersTool: Sets the base generator to be used by this class.
setRandomSeed(long) - Static method in class org.openscience.cdk.math.RandomNumbersTool: Sets the seed of this random number generator using a single long seed.
setRank(int) - Method in class org.openscience.cdk.graph.Permutor: Set the permutation to use, given its rank.
setRank(int) - Method in class org.openscience.cdk.smsd.labelling.Permutor: Deprecated.

Set the permutation to use, given its rank.
setRAtom(double) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
setRawContent(Object) - Method in class org.openscience.cdk.dict.Entry
setRdFields(Map<String, Object>) - Method in class org.openscience.cdk.io.MDLRXNWriter: Here you can set a map which will be used to build rd fields in the file.
setReactantCoefficient(IAtomContainer, Double) - Method in class org.openscience.cdk.debug.DebugReaction: Sets the coefficient of a a reactant to a given value.
setReactantCoefficient(IAtomContainer, Double) - Method in interface org.openscience.cdk.interfaces.IReaction: Sets the coefficient of a a reactant to a given value.
setReactantCoefficient(IAtomContainer, Double) - Method in class org.openscience.cdk.Reaction: Sets the coefficient of a a reactant to a given value.
setReactantCoefficient(IAtomContainer, Double) - Method in class org.openscience.cdk.silent.Reaction: Sets the coefficient of a a reactant to a given value.
setReactantCoefficients(Double[]) - Method in class org.openscience.cdk.debug.DebugReaction: Sets the coefficients of the reactants.
setReactantCoefficients(Double[]) - Method in interface org.openscience.cdk.interfaces.IReaction: Sets the coefficients of the reactants.
setReactantCoefficients(Double[]) - Method in class org.openscience.cdk.Reaction: Sets the coefficients of the reactants.
setReactantCoefficients(Double[]) - Method in class org.openscience.cdk.silent.Reaction: Sets the coefficients of the reactants.
setReactants(IAtomContainerSet) - Method in class org.openscience.cdk.debug.DebugReaction: Assigns a MoleculeSet to the reactants in this reaction.
setReactants(IAtomContainerSet) - Method in interface org.openscience.cdk.interfaces.IReaction: Assigns a IAtomContaineSet to the reactants in this reaction.
setReactants(IAtomContainerSet) - Method in class org.openscience.cdk.Reaction: Assigns a MoleculeSet to the reactants in this reaction.
setReactants(IAtomContainerSet) - Method in class org.openscience.cdk.silent.Reaction: Assigns a MoleculeSet to the reactants in this reaction.
SetReactionCenter - Class in org.openscience.cdk.reaction.type.parameters: Class extension of ParameterReact class which defines if a reaction is set already the reaction center in the reactants.
SetReactionCenter() - Constructor for class org.openscience.cdk.reaction.type.parameters.SetReactionCenter
setReactionMetadata(String) - Method in class org.openscience.cdk.dict.EntryReact
setReactions(List<IReactionProcess>) - Method in class org.openscience.cdk.tools.StructureResonanceGenerator: Set the reactions that must be used in the generation of the resonance.
setReactionSet(IReactionSet) - Method in class org.openscience.cdk.ChemModel: Sets the ReactionSet contained in this ChemModel.
setReactionSet(IReactionSet) - Method in class org.openscience.cdk.debug.DebugChemModel: Sets the ReactionSet contained in this ChemModel.
setReactionSet(IReactionSet) - Method in interface org.openscience.cdk.interfaces.IChemModel: Sets the ReactionSet contained in this ChemModel.
setReactionSet(IReactionSet) - Method in class org.openscience.cdk.silent.ChemModel: Sets the ReactionSet contained in this ChemModel.
setReader(InputStream) - Method in class org.openscience.cdk.io.CIFReader
setReader(InputStream) - Method in class org.openscience.cdk.io.CMLReader
setReader(InputStream) - Method in class org.openscience.cdk.io.CrystClustReader
setReader(InputStream) - Method in class org.openscience.cdk.io.CTXReader
setReader(InputStream) - Method in class org.openscience.cdk.io.GamessReader
setReader(InputStream) - Method in class org.openscience.cdk.io.Gaussian03Reader
setReader(InputStream) - Method in class org.openscience.cdk.io.Gaussian98Reader
setReader(InputStream) - Method in class org.openscience.cdk.io.GhemicalMMReader
setReader(InputStream) - Method in class org.openscience.cdk.io.HINReader
setReader(InputStream) - Method in interface org.openscience.cdk.io.IChemObjectReader: Sets the InputStream from which this ChemObjectReader should read the contents.
setReader(InputStream) - Method in class org.openscience.cdk.io.INChIPlainTextReader
setReader(InputStream) - Method in class org.openscience.cdk.io.INChIReader
setReader(InputStream) - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundASNReader
setReader(InputStream) - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader
setReader(InputStream) - Method in class org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader
setReader(InputStream) - Method in class org.openscience.cdk.io.iterator.IteratingSDFReader
setReader(InputStream) - Method in class org.openscience.cdk.io.iterator.IteratingSMILESReader
setReader(InputStream) - Method in class org.openscience.cdk.io.MDLReader: Deprecated.
setReader(InputStream) - Method in class org.openscience.cdk.io.MDLRXNReader: Deprecated.
setReader(InputStream) - Method in class org.openscience.cdk.io.MDLRXNV2000Reader
setReader(InputStream) - Method in class org.openscience.cdk.io.MDLRXNV3000Reader
setReader(InputStream) - Method in class org.openscience.cdk.io.MDLV2000Reader
setReader(InputStream) - Method in class org.openscience.cdk.io.MDLV3000Reader
setReader(InputStream) - Method in class org.openscience.cdk.io.Mol2Reader
setReader(InputStream) - Method in class org.openscience.cdk.io.Mopac7Reader
setReader(InputStream) - Method in class org.openscience.cdk.io.MoSSOutputReader: Sets the InputStream from which this ChemObjectReader should read the contents.
setReader(InputStream) - Method in class org.openscience.cdk.io.PCCompoundASNReader
setReader(InputStream) - Method in class org.openscience.cdk.io.PCCompoundXMLReader
setReader(InputStream) - Method in class org.openscience.cdk.io.PCSubstanceXMLReader
setReader(InputStream) - Method in class org.openscience.cdk.io.PDBReader
setReader(InputStream) - Method in class org.openscience.cdk.io.PMPReader
setReader(InputStream) - Method in class org.openscience.cdk.io.random.RandomAccessSDFReader
setReader(InputStream) - Method in class org.openscience.cdk.io.rdf.CDKOWLReader: Sets the InputStream from which this ChemObjectReader should read the contents.
setReader(InputStream) - Method in class org.openscience.cdk.io.RGroupQueryReader
setReader(InputStream) - Method in class org.openscience.cdk.io.ShelXReader
setReader(InputStream) - Method in class org.openscience.cdk.io.SMILESReader
setReader(InputStream) - Method in class org.openscience.cdk.io.VASPReader
setReader(InputStream) - Method in class org.openscience.cdk.io.XYZReader
setReader(InputStream) - Method in class org.openscience.cdk.io.ZMatrixReader
setReader(Reader) - Method in class org.openscience.cdk.io.CIFReader
setReader(Reader) - Method in class org.openscience.cdk.io.CMLReader: This method must not be used; XML reading requires the use of an InputStream.
setReader(Reader) - Method in class org.openscience.cdk.io.CrystClustReader
setReader(Reader) - Method in class org.openscience.cdk.io.CTXReader
setReader(Reader) - Method in class org.openscience.cdk.io.GamessReader
setReader(Reader) - Method in class org.openscience.cdk.io.Gaussian03Reader
setReader(Reader) - Method in class org.openscience.cdk.io.Gaussian98Reader: Sets the reader attribute of the Gaussian98Reader object.
setReader(Reader) - Method in class org.openscience.cdk.io.GhemicalMMReader
setReader(Reader) - Method in class org.openscience.cdk.io.HINReader
setReader(Reader) - Method in interface org.openscience.cdk.io.IChemObjectReader: Sets the Reader from which this ChemObjectReader should read the contents.
setReader(Reader) - Method in class org.openscience.cdk.io.INChIPlainTextReader
setReader(Reader) - Method in class org.openscience.cdk.io.INChIReader: This method must not be used; XML reading requires the use of an InputStream.
setReader(Reader) - Method in class org.openscience.cdk.io.iterator.event.EventCMLReader
setReader(Reader) - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundASNReader
setReader(Reader) - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader
setReader(Reader) - Method in class org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader
setReader(Reader) - Method in class org.openscience.cdk.io.iterator.IteratingSDFReader
setReader(Reader) - Method in class org.openscience.cdk.io.iterator.IteratingSMILESReader
setReader(Reader) - Method in class org.openscience.cdk.io.MDLReader: Deprecated.
setReader(Reader) - Method in class org.openscience.cdk.io.MDLRXNReader: Deprecated.
setReader(Reader) - Method in class org.openscience.cdk.io.MDLRXNV2000Reader
setReader(Reader) - Method in class org.openscience.cdk.io.MDLRXNV3000Reader
setReader(Reader) - Method in class org.openscience.cdk.io.MDLV2000Reader
setReader(Reader) - Method in class org.openscience.cdk.io.MDLV3000Reader
setReader(Reader) - Method in class org.openscience.cdk.io.Mol2Reader
setReader(Reader) - Method in class org.openscience.cdk.io.Mopac7Reader
setReader(Reader) - Method in class org.openscience.cdk.io.MoSSOutputReader: Sets the Reader from which this ChemObjectReader should read the contents.
setReader(Reader) - Method in class org.openscience.cdk.io.PCCompoundASNReader
setReader(Reader) - Method in class org.openscience.cdk.io.PCCompoundXMLReader
setReader(Reader) - Method in class org.openscience.cdk.io.PCSubstanceXMLReader
setReader(Reader) - Method in class org.openscience.cdk.io.PDBReader
setReader(Reader) - Method in class org.openscience.cdk.io.PMPReader
setReader(Reader) - Method in class org.openscience.cdk.io.random.RandomAccessSDFReader
setReader(Reader) - Method in class org.openscience.cdk.io.rdf.CDKOWLReader: Deprecated.
setReader(Reader) - Method in class org.openscience.cdk.io.RGroupQueryReader: Sets the input Reader.
setReader(Reader) - Method in class org.openscience.cdk.io.ShelXReader
setReader(Reader) - Method in class org.openscience.cdk.io.SMILESReader
setReader(Reader) - Method in class org.openscience.cdk.io.VASPReader
setReader(Reader) - Method in class org.openscience.cdk.io.XYZReader
setReader(Reader) - Method in class org.openscience.cdk.io.ZMatrixReader
setReaderMode(IChemObjectReader.Mode) - Method in class org.openscience.cdk.io.DefaultChemObjectReader
setReaderMode(IChemObjectReader.Mode) - Method in interface org.openscience.cdk.io.IChemObjectReader: Sets the reader mode.
setReaderMode(IChemObjectReader.Mode) - Method in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader
setReaderMode(IChemObjectReader.Mode) - Method in class org.openscience.cdk.io.random.DefaultRandomAccessChemObjectReader
setRealPart(double) - Method in class org.openscience.cdk.math.Complex: Sets the real part of this complex value
setRecord(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom: set one entire line from the PDB entry file which describe the IPDBAtom.
setRecord(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom: Set one entire line from the PDB entry file which describe the IPDBAtom.
setRecord(String) - Method in class org.openscience.cdk.protein.data.PDBAtom: set one entire line from the PDB entry file which describe the IPDBAtom.
setRecord(String) - Method in class org.openscience.cdk.silent.PDBAtom: set one entire line from the PDB entry file which describe the IPDBAtom.
setRendererModel(RendererModel) - Method in class org.openscience.cdk.renderer.visitor.AWTDrawVisitor: Sets the RendererModel this IDrawVisitor should use.
setRendererModel(RendererModel) - Method in interface org.openscience.cdk.renderer.visitor.IDrawVisitor: Sets the RendererModel this IDrawVisitor should use.
setRepresentation(String) - Method in class org.openscience.cdk.dict.EntryReact: Set the representation of the reaction.
setRequiredRGroupNumber(int) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
setResidues(List<Residue>) - Method in class org.openscience.cdk.libio.md.MDMolecule
setResName(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom: set the Residue name of this atom.
setResName(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom: set the Residue name of this atom.
setResName(String) - Method in class org.openscience.cdk.protein.data.PDBAtom: set the Residue name of this atom.
setResName(String) - Method in class org.openscience.cdk.silent.PDBAtom: set the Residue name of this atom.
setResSeq(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom: set the Residue sequence number of this atom.
setResSeq(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom: set the Residue sequence number of this atom.
setResSeq(String) - Method in interface org.openscience.cdk.interfaces.IPDBMonomer: Sets the sequence identifier of this monomer.
setResSeq(String) - Method in class org.openscience.cdk.protein.data.PDBAtom: set the Residue sequence number of this atom.
setResSeq(String) - Method in class org.openscience.cdk.protein.data.PDBMonomer
setResSeq(String) - Method in class org.openscience.cdk.silent.PDBAtom: set the Residue sequence number of this atom.
setResSeq(String) - Method in class org.openscience.cdk.silent.PDBMonomer
setRestH(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
setRestrictions(List<IRule>) - Method in class org.openscience.cdk.formula.MassToFormulaTool: Deprecated.

Set the restrictions that must be presents in the molecular formula.
setRGroupDefinitions(Map<Integer, IRGroupList>) - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery: Setter for the R-group definitions (substituents).
setRGroupDefinitions(Map<Integer, IRGroupList>) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
setRGroupNumber(int) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList: Setter for rGroupNumber, checks for valid range.
setRGroups(List<IRGroup>) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
setRight(IQueryAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom: Deprecated.
setRight(IQueryBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond: Deprecated.
setRingBond(IQueryBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RingIdentifierAtom: Deprecated.
setRingSet(IRingSet) - Method in class org.openscience.cdk.atomtype.EStateAtomTypeMatcher
setRingSet(IRingSet) - Method in class org.openscience.cdk.ChemModel: Sets the RingSet of this ChemModel.
setRingSet(IRingSet) - Method in class org.openscience.cdk.debug.DebugChemModel: Sets the RingSet of this ChemModel.
setRingSet(IRingSet) - Method in interface org.openscience.cdk.interfaces.IChemModel: Sets the RingSet of this ChemModel.
setRingSet(IRingSet) - Method in class org.openscience.cdk.silent.ChemModel: Sets the RingSet of this ChemModel.
setrMap(CDKRMap) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode: Deprecated.

Sets resolution map/graph
setRMap(RMap) - Method in class org.openscience.cdk.isomorphism.mcss.RNode: Sets the rMap attribute of the RNode object.
setRMap(CDKRMap) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode: Deprecated.

Sets the rMap attribute of the RNode object
setRootAttachmentPoints(Map<IAtom, Map<Integer, IBond>>) - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery: Setter for root attachment points = bonds that connect R pseudo-atoms to the scaffold.
setRootAttachmentPoints(Map<IAtom, Map<Integer, IBond>>) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
setRootStructure(IAtomContainer) - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery: Setter for the root structure of this R-Group.
setRootStructure(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
setRounding(boolean) - Method in class org.openscience.cdk.renderer.visitor.AWTDrawVisitor: Set whether we should we round coordinates to ints, this tries to circumvent graphical glitches from AWT where floating points are truncated (e.g.
setRSolvent(double) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
setScale(IAtomContainer) - Method in class org.openscience.cdk.renderer.AtomContainerRenderer: Set the scale for an IAtomContainer.
setScale(IAtomContainerSet) - Method in class org.openscience.cdk.renderer.MoleculeSetRenderer: Set the scale for an IAtomContainerSet.
setScale(IChemModel) - Method in class org.openscience.cdk.renderer.ChemModelRenderer: Set the scale for an IChemModel.
setScale(IReaction) - Method in class org.openscience.cdk.renderer.ReactionRenderer: Set the scale for an IReaction.
setScale(IReactionSet) - Method in class org.openscience.cdk.renderer.ReactionSetRenderer: Set the scale for an IReactionSet.
setScale(T) - Method in interface org.openscience.cdk.renderer.IRenderer: Set the scale for an IChemObject.
setSecondAttachmentPoint(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.RGroup
setSecondGraphSize(int) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Returns the size of the second of the two compared graphs.
setSecondGraphSize(int) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph: Deprecated.

Returns the size of the second of the two compared graphs.
setSegID(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom: set the Segment identifier, left-justified of this atom.
setSegID(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom: set the Segment identifier, left-justified of this atom.
setSegID(String) - Method in class org.openscience.cdk.protein.data.PDBAtom: set the Segment identifier, left-justified of this atom.
setSegID(String) - Method in class org.openscience.cdk.silent.PDBAtom: set the Segment identifier, left-justified of this atom.
setSelection(IChemObjectSelection) - Method in class org.openscience.cdk.renderer.RendererModel: Set the selected IChemObjects.
setSerial(Integer) - Method in class org.openscience.cdk.debug.DebugPDBAtom: set the Atom serial number of this atom.
setSerial(Integer) - Method in interface org.openscience.cdk.interfaces.IPDBAtom: set the Atom serial number of this atom.
setSerial(Integer) - Method in class org.openscience.cdk.protein.data.PDBAtom: set the Atom serial number of this atom.
setSerial(Integer) - Method in class org.openscience.cdk.silent.PDBAtom: set the Atom serial number of this atom.
setSetElement(boolean) - Method in class org.openscience.cdk.structgen.maygen.Maygen
setSetting(int) - Method in class org.openscience.cdk.io.setting.OptionIOSetting: Sets the setting for a certain question.
setSetting(String) - Method in class org.openscience.cdk.io.setting.BooleanIOSetting: Sets the setting for a certain question.
setSetting(String) - Method in class org.openscience.cdk.io.setting.IntegerIOSetting: Sets the setting for a certain question.
setSetting(String) - Method in class org.openscience.cdk.io.setting.IOSetting: Sets the setting for a certain question.
setSetting(String) - Method in class org.openscience.cdk.io.setting.OptionIOSetting: Sets the setting for a certain question.
setSetting(String) - Method in class org.openscience.cdk.io.setting.StringIOSetting: Sets the setting for a certain question.
setSingleOrDoubleFlags(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Assigns CDKConstants.SINGLE_OR_DOUBLE flags to the bonds of a container.
setSkip(boolean) - Method in class org.openscience.cdk.io.iterator.IteratingSDFReader: Indicate whether the reader should skip over SDF records that cause problems.
setSmarts(String) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom: Set the SMARTS for the group.
setSmarts(String) - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool: Deprecated.

Set a new SMARTS pattern.
setSolvantValue(int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
setSource(IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler: Deprecated.

Set source molecule
setSpaceGroup(String) - Method in class org.openscience.cdk.Crystal: Sets the space group of this crystal.
setSpaceGroup(String) - Method in class org.openscience.cdk.debug.DebugCrystal: Sets the space group of this crystal.
setSpaceGroup(String) - Method in interface org.openscience.cdk.interfaces.ICrystal: Sets the space group of this crystal.
setSpaceGroup(String) - Method in class org.openscience.cdk.silent.Crystal: Sets the space group of this crystal.
setStackLength(int) - Method in interface org.openscience.cdk.tools.ILoggingTool: Sets the number of StackTraceElements to be printed in DEBUG mode when calling debug(Throwable).
setStackLength(int) - Method in class org.openscience.cdk.tools.SystemOutLoggingTool: Deprecated.

Sets the number of StackTraceElements to be printed in DEBUG mode when calling debug(Throwable).
setStart(long) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
setStartChainID(Character) - Method in class org.openscience.cdk.debug.DebugPDBStructure: set the start Chain identifier of this structure.
setStartChainID(Character) - Method in interface org.openscience.cdk.interfaces.IPDBStructure: set the start Chain identifier of this structure.
setStartChainID(Character) - Method in class org.openscience.cdk.protein.data.PDBStructure: set the start Chain identifier of this structure.
setStartChainID(Character) - Method in class org.openscience.cdk.silent.PDBStructure: set the start Chain identifier of this structure.
setStartInsertionCode(Character) - Method in class org.openscience.cdk.debug.DebugPDBStructure: set the start Chain identifier of this structure.
setStartInsertionCode(Character) - Method in interface org.openscience.cdk.interfaces.IPDBStructure: set the start Chain identifier of this structure.
setStartInsertionCode(Character) - Method in class org.openscience.cdk.protein.data.PDBStructure: set the start Chain identifier of this structure.
setStartInsertionCode(Character) - Method in class org.openscience.cdk.silent.PDBStructure: set the start Chain identifier of this structure.
setStartSequenceNumber(Integer) - Method in class org.openscience.cdk.debug.DebugPDBStructure: set the start sequence number of this structure.
setStartSequenceNumber(Integer) - Method in interface org.openscience.cdk.interfaces.IPDBStructure: set the start sequence number of this structure.
setStartSequenceNumber(Integer) - Method in class org.openscience.cdk.protein.data.PDBStructure: set the start sequence number of this structure.
setStartSequenceNumber(Integer) - Method in class org.openscience.cdk.silent.PDBStructure: set the start sequence number of this structure.
setStepSize(int) - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges: Set the StepSize attribute of the GasteigerMarsiliPartialCharges object.
setStepSize(int) - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges: Set the StepSize attribute of the GasteigerMarsiliPartialCharges object.
setStereo(IBond.Stereo) - Method in class org.openscience.cdk.Bond: Sets the stereo descriptor for this bond.
setStereo(IBond.Stereo) - Method in class org.openscience.cdk.BondRef: Sets the stereo descriptor for this bond.
setStereo(IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugBond: Sets the stereo descriptor for this bond.
setStereo(IBond.Stereo) - Method in interface org.openscience.cdk.interfaces.IBond: Sets the stereo descriptor for this bond.
setStereo(IBond.Stereo) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Sets the stereo descriptor for this query bond.
setStereo(IBond.Stereo) - Method in class org.openscience.cdk.silent.Bond: Sets the stereo descriptor for this bond.
setStereo(ITetrahedralChirality.Stereo) - Method in interface org.openscience.cdk.interfaces.ITetrahedralChirality: Set the stereochemistry of this tetrahedral centre.
setStereo(ITetrahedralChirality.Stereo) - Method in class org.openscience.cdk.stereo.TetrahedralChirality
setStereoElements(List<IStereoElement>) - Method in class org.openscience.cdk.AtomContainer: Set the stereo elements - this will replace the existing instance with a new instance.
setStereoElements(List<IStereoElement>) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Set the stereo elements - this will replace the existing instance with a new instance.
setStereoElements(List<IStereoElement>) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Set the stereo elements - this will replace the existing instance with a new instance.
setStereoElements(List<IStereoElement>) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
setStereoElements(List<IStereoElement>) - Method in class org.openscience.cdk.silent.AtomContainer: Set the stereo elements - this will replace the existing instance with a new instance.
setStereoParity(Integer) - Method in class org.openscience.cdk.Atom: Sets the stereo parity for this atom.
setStereoParity(Integer) - Method in class org.openscience.cdk.AtomRef: Sets the stereo parity for this atom.
setStereoParity(Integer) - Method in class org.openscience.cdk.debug.DebugAtom: Sets the stereo parity for this atom.
setStereoParity(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Dummy method: the stereo parity is undefined, final.
setStereoParity(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Dummy method: the stereo parity is undefined, final.
setStereoParity(Integer) - Method in interface org.openscience.cdk.interfaces.IAtom: Deprecated.
use IStereoElements for storing stereochemistry
setStereoParity(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Sets the stereo parity for this atom.
setStereoParity(Integer) - Method in class org.openscience.cdk.PseudoAtom: Dummy method: the stereo parity is undefined, final.
setStereoParity(Integer) - Method in class org.openscience.cdk.silent.Atom: Sets the stereo parity for this atom.
setStereoParity(Integer) - Method in class org.openscience.cdk.silent.PseudoAtom: Dummy method: the stereo parity is undefined, final.
setStoreFormulas(boolean) - Method in class org.openscience.cdk.formula.IsotopePatternGenerator: When generating the isotope containers store the MF for each IsotopeContainer.
setStrandName(String) - Method in class org.openscience.cdk.debug.DebugStrand: Sets the name of the Strand object.
setStrandName(String) - Method in interface org.openscience.cdk.interfaces.IStrand: Set the name of the Strand object.
setStrandName(String) - Method in class org.openscience.cdk.silent.Strand: Sets the name of the Strand object.
setStrandName(String) - Method in class org.openscience.cdk.Strand: Sets the name of the Strand object.
setStrandType(String) - Method in class org.openscience.cdk.debug.DebugStrand: Sets the type of the Strand object.
setStrandType(String) - Method in interface org.openscience.cdk.interfaces.IStrand: Set the type of the Strand object.
setStrandType(String) - Method in class org.openscience.cdk.silent.Strand: Sets the type of the Strand object.
setStrandType(String) - Method in class org.openscience.cdk.Strand: Sets the type of the Strand object.
setStrict(boolean) - Method in class org.openscience.cdk.smiles.SmilesParser: Sets whether the parser is in strict mode.
setStructureType(String) - Method in class org.openscience.cdk.debug.DebugPDBStructure: set the Structure Type of this structure.
setStructureType(String) - Method in interface org.openscience.cdk.interfaces.IPDBStructure: set the Structure Type of this structure.
setStructureType(String) - Method in class org.openscience.cdk.protein.data.PDBStructure: set the Structure Type of this structure.
setStructureType(String) - Method in class org.openscience.cdk.silent.PDBStructure: set the Structure Type of this structure.
setSubgraph(List<Integer>) - Method in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
setSubscript(String) - Method in class org.openscience.cdk.sgroup.Sgroup: Set the subscript value.
setSwitchingAtom(IAtom) - Method in class org.openscience.cdk.libio.md.ChargeGroup
setSymbol(String) - Method in class org.openscience.cdk.AtomRef: Sets the element symbol of this element.
setSymbol(String) - Method in class org.openscience.cdk.debug.DebugAtom: Sets the element symbol of this element.
setSymbol(String) - Method in class org.openscience.cdk.debug.DebugAtomType: Sets the element symbol of this element.
setSymbol(String) - Method in class org.openscience.cdk.debug.DebugElement: Sets the element symbol of this element.
setSymbol(String) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Sets the element symbol of this element.
setSymbol(String) - Method in class org.openscience.cdk.debug.DebugIsotope: Sets the element symbol of this element.
setSymbol(String) - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Sets the element symbol of this element.
setSymbol(String) - Method in class org.openscience.cdk.Element: Sets the element symbol of this element.
setSymbol(String) - Method in interface org.openscience.cdk.interfaces.IElement: Sets the element symbol of this element.
setSymbol(String) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Sets the element symbol of this element.
setSymbol(String) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom
setSymbol(String) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryAtom: Sets the element symbol of this element.
setSymbol(String) - Method in class org.openscience.cdk.silent.Element: Sets the element symbol of this element.
setSymbol(String) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultMCSPlusAtomMatcher: Deprecated.
setSymbol(String) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultRGraphAtomMatcher: Deprecated.
setSymbol(String) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFAtomMatcher: Deprecated.
setSymbols(List<String>) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Setting the firstSymbols and symbols global variables for the initial sorted list of symbols.
setTabSize(int) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
setTabSize(int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
setTarget(IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler: Deprecated.

Set target molecule
setTempFactor(Double) - Method in class org.openscience.cdk.debug.DebugPDBAtom: set the Temperature factor of this atom.
setTempFactor(Double) - Method in interface org.openscience.cdk.interfaces.IPDBAtom: set the Temperature factor of this atom.
setTempFactor(Double) - Method in class org.openscience.cdk.protein.data.PDBAtom: set the Temperature factor of this atom.
setTempFactor(Double) - Method in class org.openscience.cdk.silent.PDBAtom: set the Temperature factor of this atom.
setTemplateHandler(TemplateHandler) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator: Deprecated.
substructure templates are no longer used for layout but those provided here will be converted to identity templates
setTimeManager(TimeManager) - Static method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlus: Deprecated.
setTimeManager(TimeManager) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS: Deprecated.
setTimeManager(TimeManager) - Static method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper: Deprecated.
setTimeManager(TimeManager) - Static method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper: Deprecated.
setTimeout(long) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Sets the time in milliseconds until the substructure search will be breaked.
setTimeout(long) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester: Sets the time in milliseconds until the substructure search will be breaked.
setTimeout(long) - Method in class org.openscience.cdk.ringsearch.AllRingsFinder: Deprecated.
use the new threshold (during construction)
setTimeOut(double) - Method in class org.openscience.cdk.smsd.global.TimeOut: Deprecated.

set cutoff value for time out eg.
setTimeoutFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler: Deprecated.

Set time out flag
setTimeOutFlag(boolean) - Method in class org.openscience.cdk.smsd.global.TimeOut: Deprecated.

Set true if timeout occures else false
setTimezone(String) - Method in class org.openscience.cdk.io.RssWriter
setting - Variable in class org.openscience.cdk.io.setting.IOSetting
SettingManager<T extends ISetting> - Class in org.openscience.cdk.io.setting: Provides dynamic management of settings.
SettingManager() - Constructor for class org.openscience.cdk.io.setting.SettingManager
setTitle(String) - Method in class org.openscience.cdk.AtomContainer: Modify the title of the record.
setTitle(String) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Modify the title of the record.
setTitle(String) - Method in class org.openscience.cdk.io.RssWriter
setTitle(String) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Modify the title of the record.
setTitle(String) - Method in class org.openscience.cdk.renderer.GraphRendererModel: Set the main title
setTitle(String) - Method in class org.openscience.cdk.silent.AtomContainer: Modify the title of the record.
setTitlemap(Map) - Method in class org.openscience.cdk.io.RssWriter
setTo(Permutation) - Method in class org.openscience.cdk.group.Permutation: Alter a permutation by setting it to the values in the other permutation.
setToolTipTextMap(Map<IAtom, String>) - Method in class org.openscience.cdk.renderer.RendererModel: Sets the toolTipTextMap.
setTransform(AffineTransform) - Method in interface org.openscience.cdk.renderer.elements.IRenderingVisitor: Sets the affine transformations used.
setTransform(AffineTransform) - Method in class org.openscience.cdk.renderer.visitor.AbstractAWTDrawVisitor: Sets a new affine transformation to convert world coordinates into screen coordinates.
setTsvoutput(boolean) - Method in class org.openscience.cdk.structgen.maygen.Maygen
setType(CTFileQueryBond.Type) - Method in class org.openscience.cdk.isomorphism.matchers.CTFileQueryBond: Deprecated.

Getter for bond type
setType(SgroupType) - Method in class org.openscience.cdk.sgroup.Sgroup: Set the type of the Sgroup.
setUnspecified(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom: Deprecated.
setup() - Method in class org.openscience.cdk.renderer.AbstractRenderer: Creates the transform using the scale, zoom, drawCenter, and modelCenter.
setup(IAtomContainer, Rectangle) - Method in class org.openscience.cdk.renderer.AtomContainerRenderer: Setup the transformations necessary to draw this Atom Container.
setup(IAtomContainerSet, Rectangle) - Method in class org.openscience.cdk.renderer.MoleculeSetRenderer: Setup the transformations necessary to draw this IAtomContainerSet.
setup(IChemModel, Rectangle) - Method in class org.openscience.cdk.renderer.ChemModelRenderer: Setup the transformations necessary to draw this Chem Model.
setup(IReaction, Rectangle) - Method in class org.openscience.cdk.renderer.ReactionRenderer: Setup the transformations necessary to draw this Reaction.
setup(IReactionSet, Rectangle) - Method in class org.openscience.cdk.renderer.ReactionSetRenderer: Setup the transformations necessary to draw this Reaction Set.
setup(T, Rectangle) - Method in interface org.openscience.cdk.renderer.IRenderer: Setup the transformations necessary to draw the IChemObject matching this IRenderer implementation.
setupTransformNatural(Rectangle2D) - Method in class org.openscience.cdk.renderer.AbstractRenderer: Set the transform for a non-fit to screen paint.
setupTransformToFit(Rectangle2D, Rectangle2D, double, boolean) - Method in class org.openscience.cdk.renderer.AbstractRenderer: Sets the transformation needed to draw the model on the canvas when the diagram needs to fit the screen.
setUseAromaticityFlag(boolean) - Method in class org.openscience.cdk.smiles.SmilesGenerator: Deprecated.
since 1.5.6, use SmilesGenerator.aromatic() - invoking this method does nothing
setUseIdentityTemplates(boolean) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator: Set whether identity templates are used.
setUseTemplates(boolean) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator: Deprecated.
always false, substructure templates are not used anymore
setValency(Integer) - Method in class org.openscience.cdk.AtomRef: Sets the the exact electron valency of the AtomType object.
setValency(Integer) - Method in class org.openscience.cdk.AtomType: Sets the the exact electron valency of the AtomType object.
setValency(Integer) - Method in class org.openscience.cdk.debug.DebugAtom: Sets the the exact electron valency of the AtomType object.
setValency(Integer) - Method in class org.openscience.cdk.debug.DebugAtomType: Sets the the exact electron valency of the AtomType object.
setValency(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom: Sets the the exact electron valency of the AtomType object.
setValency(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom: Sets the the exact electron valency of the AtomType object.
setValency(Integer) - Method in interface org.openscience.cdk.interfaces.IAtomType: Sets the the exact electron valency of the AtomType object.
setValency(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom: Sets the the exact electron valency of the AtomType object.
setValency(Integer) - Method in class org.openscience.cdk.silent.AtomType: Sets the the exact electron valency of the AtomType object.
setValue(Object) - Method in interface org.openscience.cdk.reaction.type.parameters.IParameterReact: Set the value of the parameter.
setValue(Object) - Method in class org.openscience.cdk.reaction.type.parameters.ParameterReact: Set the value of the parameter.
setValue(T) - Method in interface org.openscience.cdk.renderer.generators.IGeneratorParameter: Sets the value for this parameter.
setValue(T) - Method in class org.openscience.cdk.renderer.generators.parameter.AbstractGeneratorParameter: Sets the value for this parameter.
setValueAt(int, int, double) - Method in class org.openscience.cdk.graph.invariant.GIMatrix: Sets the value of the element at the given index.
setVanDerWaalsFile(String) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
setVerbose(boolean) - Method in class org.openscience.cdk.structgen.maygen.Maygen
setWriteAromaticBondTypes(boolean) - Method in class org.openscience.cdk.io.MDLV2000Writer: Convenience method to set the option for writing aromatic bond types.
setWriter(OutputStream) - Method in class org.openscience.cdk.io.CDKSourceCodeWriter
setWriter(OutputStream) - Method in class org.openscience.cdk.io.CMLWriter
setWriter(OutputStream) - Method in class org.openscience.cdk.io.CrystClustWriter
setWriter(OutputStream) - Method in class org.openscience.cdk.io.HINWriter
setWriter(OutputStream) - Method in interface org.openscience.cdk.io.IChemObjectWriter: Sets the OutputStream from which this ChemObjectWriter should write the contents.
setWriter(OutputStream) - Method in class org.openscience.cdk.io.MDLRXNWriter
setWriter(OutputStream) - Method in class org.openscience.cdk.io.MDLV2000Writer
setWriter(OutputStream) - Method in class org.openscience.cdk.io.MDLV3000Writer: Sets the OutputStream from which this ChemObjectWriter should write the contents.
setWriter(OutputStream) - Method in class org.openscience.cdk.io.Mol2Writer
setWriter(OutputStream) - Method in class org.openscience.cdk.io.PDBWriter
setWriter(OutputStream) - Method in class org.openscience.cdk.io.program.GaussianInputWriter
setWriter(OutputStream) - Method in class org.openscience.cdk.io.program.Mopac7Writer
setWriter(OutputStream) - Method in class org.openscience.cdk.io.rdf.CDKOWLWriter: Sets the OutputStream from which this ChemObjectWriter should write the contents.
setWriter(OutputStream) - Method in class org.openscience.cdk.io.RGroupQueryWriter: Sets the writer to given output stream.
setWriter(OutputStream) - Method in class org.openscience.cdk.io.RssWriter
setWriter(OutputStream) - Method in class org.openscience.cdk.io.SDFWriter
setWriter(OutputStream) - Method in class org.openscience.cdk.io.ShelXWriter
setWriter(OutputStream) - Method in class org.openscience.cdk.io.SMILESWriter
setWriter(OutputStream) - Method in class org.openscience.cdk.io.XYZWriter
setWriter(Writer) - Method in class org.openscience.cdk.io.CDKSourceCodeWriter
setWriter(Writer) - Method in class org.openscience.cdk.io.CMLWriter
setWriter(Writer) - Method in class org.openscience.cdk.io.CrystClustWriter
setWriter(Writer) - Method in class org.openscience.cdk.io.HINWriter
setWriter(Writer) - Method in interface org.openscience.cdk.io.IChemObjectWriter: Sets the Writer from which this ChemObjectWriter should write the contents.
setWriter(Writer) - Method in class org.openscience.cdk.io.MDLRXNWriter
setWriter(Writer) - Method in class org.openscience.cdk.io.MDLV2000Writer
setWriter(Writer) - Method in class org.openscience.cdk.io.MDLV3000Writer: Sets the Writer from which this ChemObjectWriter should write the contents.
setWriter(Writer) - Method in class org.openscience.cdk.io.Mol2Writer
setWriter(Writer) - Method in class org.openscience.cdk.io.PDBWriter
setWriter(Writer) - Method in class org.openscience.cdk.io.program.GaussianInputWriter
setWriter(Writer) - Method in class org.openscience.cdk.io.program.Mopac7Writer
setWriter(Writer) - Method in class org.openscience.cdk.io.rdf.CDKOWLWriter: Sets the Writer from which this ChemObjectWriter should write the contents.
setWriter(Writer) - Method in class org.openscience.cdk.io.RGroupQueryWriter: Sets the writer.
setWriter(Writer) - Method in class org.openscience.cdk.io.RssWriter
setWriter(Writer) - Method in class org.openscience.cdk.io.SDFWriter
setWriter(Writer) - Method in class org.openscience.cdk.io.ShelXWriter
setWriter(Writer) - Method in class org.openscience.cdk.io.SMILESWriter
setWriter(Writer) - Method in class org.openscience.cdk.io.XYZWriter
setWriteTitle(boolean) - Method in class org.openscience.cdk.io.SMILESWriter
setX(double, double) - Method in class org.openscience.cdk.renderer.GraphRendererModel: Sets the function area, which will painted
setXTitle(String) - Method in class org.openscience.cdk.renderer.GraphRendererModel: Set the title of the x axis
setY(double, double) - Method in class org.openscience.cdk.renderer.GraphRendererModel: Sets the function area, which will painted
setYTitle(String) - Method in class org.openscience.cdk.renderer.GraphRendererModel: Set the title of the y axis
setYZValues(int[], int[][], int[][]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Setting the y and z values for each block.
setZ(Integer) - Method in class org.openscience.cdk.Crystal: Sets the number of asymmetric parts in the unit cell.
setZ(Integer) - Method in class org.openscience.cdk.debug.DebugCrystal: Sets the number of asymmetric parts in the unit cell.
setZ(Integer) - Method in interface org.openscience.cdk.interfaces.ICrystal: Sets the number of assymmetric parts in the unit cell.
setZ(Integer) - Method in class org.openscience.cdk.silent.Crystal: Sets the number of asymmetric parts in the unit cell.
setZoom(double) - Method in class org.openscience.cdk.renderer.AbstractRenderer: Set the zoom, where 1.0 is 100% zoom.
setZoom(double) - Method in interface org.openscience.cdk.renderer.IRenderer: Set a new zoom factor.
setZoomToFit(double, double, double, double) - Method in class org.openscience.cdk.renderer.AbstractRenderer: Calculate and set the zoom factor needed to completely fit the diagram onto the screen bounds.
SEXTUPLE - org.openscience.cdk.interfaces.IBond.Order
Sg - Static variable in interface org.openscience.cdk.interfaces.IElement
Sgroup - Class in org.openscience.cdk.sgroup: Generic CTab Sgroup (substructure group) that stores all other types of group.
Sgroup() - Constructor for class org.openscience.cdk.sgroup.Sgroup: Create a new generic Sgroup.
SgroupBracket - Class in org.openscience.cdk.sgroup: Representation of an Sgroup bracket.
SgroupBracket(double, double, double, double) - Constructor for class org.openscience.cdk.sgroup.SgroupBracket: Create an Sgroup bracket.
SgroupBracket(SgroupBracket) - Constructor for class org.openscience.cdk.sgroup.SgroupBracket: Copy constructor.
SgroupBracketDepth() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.SgroupBracketDepth
SgroupFontScale() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.SgroupFontScale
SgroupKey - Enum in org.openscience.cdk.sgroup: Keys for indexing common Sgroup attributes.
SgroupManipulator - Class in org.openscience.cdk.tools.manipulator: Utilities related to Ctab Sgroups.
SgroupType - Enum in org.openscience.cdk.sgroup: Enumeration of Ctab Sgroup types.
shallowCopy() - Method in class org.openscience.cdk.ChemObject: Clones this IChemObject, but preserves references to Objects.
shallowCopy() - Method in class org.openscience.cdk.silent.ChemObject: Clones this IChemObject, but preserves references to Objects.
shapeOf(Shape, Color) - Static method in class org.openscience.cdk.renderer.elements.GeneralPath: Create a filled path of the specified Java 2D Shape and color.
SharingAnionReaction - Class in org.openscience.cdk.reaction.type: IReactionProcess which participate in movement resonance.
SharingAnionReaction() - Constructor for class org.openscience.cdk.reaction.type.SharingAnionReaction: Constructor of the SharingAnionReaction object.
SharingChargeDBReaction - Class in org.openscience.cdk.reaction.type: IReactionProcess which participate in movement resonance.
SharingChargeDBReaction() - Constructor for class org.openscience.cdk.reaction.type.SharingChargeDBReaction: Constructor of the SharingChargeDBReaction object.
SharingChargeSBReaction - Class in org.openscience.cdk.reaction.type: IReactionProcess which participate in movement resonance.
SharingChargeSBReaction() - Constructor for class org.openscience.cdk.reaction.type.SharingChargeSBReaction: Constructor of the SharingChargeSBReaction object.
SharingElectronMechanism - Class in org.openscience.cdk.reaction.mechanism: This mechanism displaces the charge (lonePair) because of deficiency of charge.
SharingElectronMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.SharingElectronMechanism
SharingLonePairReaction - Class in org.openscience.cdk.reaction.type: IReactionProcess which participate in movement resonance.
SharingLonePairReaction() - Constructor for class org.openscience.cdk.reaction.type.SharingLonePairReaction: Constructor of the SharingLonePairReaction object.
SHEET - Static variable in class org.openscience.cdk.protein.data.PDBStructure
SHEET - Static variable in class org.openscience.cdk.silent.PDBStructure
ShelXFormat - Class in org.openscience.cdk.io.formats: See here.
ShelXFormat() - Constructor for class org.openscience.cdk.io.formats.ShelXFormat
ShelXReader - Class in org.openscience.cdk.io: A reader for ShelX output (RES) files.
ShelXReader() - Constructor for class org.openscience.cdk.io.ShelXReader
ShelXReader(InputStream) - Constructor for class org.openscience.cdk.io.ShelXReader
ShelXReader(Reader) - Constructor for class org.openscience.cdk.io.ShelXReader: Create an ShelX file reader.
ShelXWriter - Class in org.openscience.cdk.io: Serializes a MoleculeSet or a Molecule object to ShelX code.
ShelXWriter() - Constructor for class org.openscience.cdk.io.ShelXWriter
ShelXWriter(OutputStream) - Constructor for class org.openscience.cdk.io.ShelXWriter
ShelXWriter(Writer) - Constructor for class org.openscience.cdk.io.ShelXWriter: Constructs a new ShelXWriter class.
shift(Rectangle, Rectangle) - Method in class org.openscience.cdk.renderer.AbstractRenderer: Determine the overlap of the diagram with the screen, and shift (if necessary) the diagram draw center.
shift(Rectangle, Rectangle) - Method in class org.openscience.cdk.renderer.MoleculeSetRenderer: Determine the overlap of the diagram with the screen, and shift (if necessary) the diagram draw center.
shiftContainer(IAtomContainer, double[], double[], double) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Shift the container horizontally to the right to make its bounds not overlap with the other bounds.
shiftContainer(IAtomContainer, Rectangle2D, Rectangle2D, double) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Shift the container horizontally to the right to make its bounds not overlap with the other bounds.
shiftDrawCenter(double, double) - Method in class org.openscience.cdk.renderer.AbstractRenderer: Move the draw center by dx and dy.
shiftDrawCenter(double, double) - Method in interface org.openscience.cdk.renderer.IRenderer: Set a new drawing center in screen coordinates.
shiftReactionVertical(IReaction, double[], double[], double) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Shift the containers in a reaction vertically upwards to not overlap with the reference rectangle.
shiftReactionVertical(IReaction, Rectangle2D, Rectangle2D, double) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Shift the containers in a reaction vertically upwards to not overlap with the reference Rectangle2D.
ShortestPathFingerprinter - Class in org.openscience.cdk.fingerprint: Generates a fingerprint for a given IAtomContainer.
ShortestPathFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.ShortestPathFingerprinter: Creates a fingerprint generator of length DEFAULT_SIZE
ShortestPathFingerprinter(int) - Constructor for class org.openscience.cdk.fingerprint.ShortestPathFingerprinter: Constructs a fingerprint generator that creates fingerprints of the given fingerprintLength, using a generation algorithm with shortest paths.
ShortestPaths - Class in org.openscience.cdk.graph: Find and reconstruct the shortest paths from a given start atom to any other connected atom.
ShortestPaths(IAtomContainer, IAtom) - Constructor for class org.openscience.cdk.graph.ShortestPaths: Create a new shortest paths tool for a single start atom.
ShortestPathWalker - Class in org.openscience.cdk.fingerprint
ShortestPathWalker(IAtomContainer) - Constructor for class org.openscience.cdk.fingerprint.ShortestPathWalker: Create a new shortest path walker for a given container.
shouldBeLinear(IAtom, IAtomContainer) - Static method in class org.openscience.cdk.layout.AtomPlacer: Deprecated.
ShowAromaticity() - Constructor for class org.openscience.cdk.renderer.generators.RingGenerator.ShowAromaticity
ShowAtomAtomMapping() - Constructor for class org.openscience.cdk.renderer.generators.MappingGenerator.ShowAtomAtomMapping
ShowAtomTypeNames() - Constructor for class org.openscience.cdk.renderer.generators.ExtendedAtomGenerator.ShowAtomTypeNames
showCarbon(IAtom, IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.AtomMassGenerator: Returns true if the mass number of this element is set and not equal the mass number of the most abundant isotope of this element.
showCarbon(IAtom, IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator: Checks a carbon atom to see if it should be shown.
ShowEndCarbons() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.ShowEndCarbons
ShowExplicitHydrogens() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.ShowExplicitHydrogens
ShowImplicitHydrogens() - Constructor for class org.openscience.cdk.renderer.generators.ExtendedAtomGenerator.ShowImplicitHydrogens
ShowMoleculeTitle() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ShowMoleculeTitle
ShowReactionBoxes() - Constructor for class org.openscience.cdk.renderer.generators.ReactionSceneGenerator.ShowReactionBoxes
ShowReactionTitle() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ShowReactionTitle
ShowTooltip() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ShowTooltip
Si - Static variable in interface org.openscience.cdk.interfaces.IElement
SI - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
SigmaElectronegativityDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic: Atomic descriptor that reflects that Gasteiger-Marsili sigma electronegativity.
SigmaElectronegativityDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor: Constructor for the SigmaElectronegativityDescriptor object
SignatureFingerprinter - Class in org.openscience.cdk.fingerprint: An implementation of a AtomSignature-based fingerprint.
SignatureFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.SignatureFingerprinter: Initialize the fingerprinter with a default signature depth of 1.
SignatureFingerprinter(int) - Constructor for class org.openscience.cdk.fingerprint.SignatureFingerprinter: Initialize the fingerprinter with a certain signature depth.
signatureForVertex(int) - Method in class org.openscience.cdk.signature.MoleculeSignature
SignatureQuotientGraph - Class in org.openscience.cdk.signature: A signature quotient graph has a vertex for every signature symmetry class and an edge for each bond in the molecule between atoms in their class.
SignatureQuotientGraph(IAtomContainer) - Constructor for class org.openscience.cdk.signature.SignatureQuotientGraph: Construct a quotient graph from the symmetry classes generated from the atom container.
SignatureQuotientGraph(IAtomContainer, int) - Constructor for class org.openscience.cdk.signature.SignatureQuotientGraph: Construct a quotient graph using symmetry classes defined by signatures of height height.
SignatureReactionCanoniser - Class in org.openscience.cdk.smsd.labelling: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
SignatureReactionCanoniser() - Constructor for class org.openscience.cdk.smsd.labelling.SignatureReactionCanoniser: Deprecated.
signatureStringForVertex(int) - Method in class org.openscience.cdk.signature.MoleculeSignature
signatureStringForVertex(int, int) - Method in class org.openscience.cdk.signature.MoleculeSignature
signedDistanceToPlane(Vector3d, Point3d, Point3d) - Static method in class org.openscience.cdk.stereo.StereoTool: Given a normalized normal for a plane, any point in that plane, and a point, will return the distance between the plane and that point.
SilentChemObjectBuilder - Class in org.openscience.cdk.silent: A factory class to provide implementation independent ICDKObjects.
SilentChemObjectBuilder() - Constructor for class org.openscience.cdk.silent.SilentChemObjectBuilder
Silicon - org.openscience.cdk.config.Elements
SILICON - Static variable in enum org.openscience.cdk.config.Elements
Silver - org.openscience.cdk.config.Elements
SILVER - Static variable in enum org.openscience.cdk.config.Elements
SILVER - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
similar(IMatrix) - Method in class org.openscience.cdk.math.IMatrix: Similar transformation Ut * M * U
similar(IMatrix, IMatrix) - Method in class org.openscience.cdk.math.IMatrix: Similar transformation Ut * M * U
similar(Matrix) - Method in class org.openscience.cdk.math.Matrix: Similar transformation Ut * M * U
SimpleAtomCanonicalizer - Class in org.openscience.cdk.fingerprint: This code returns a sorted set of atoms for a container according to its symbol and hybridization states.
SimpleAtomCanonicalizer() - Constructor for class org.openscience.cdk.fingerprint.SimpleAtomCanonicalizer
SimpleAtomComparator - Class in org.openscience.cdk.fingerprint: This code returns a sorted set of atoms for a container according to its symbol and hybridization states.
SimpleAtomComparator() - Constructor for class org.openscience.cdk.fingerprint.SimpleAtomComparator
SimpleBasisSet - Class in org.openscience.cdk.math.qm: This class will generate a simple base set for a atom container.
SimpleBasisSet(IAtom[]) - Constructor for class org.openscience.cdk.math.qm.SimpleBasisSet: Create a base set
SimpleBond() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
SimpleCharStream - Class in org.openscience.cdk.iupac.parser: An implementation of interface CharStream, where the stream is assumed to contain only ASCII characters (without unicode processing).
SimpleCharStream - Class in org.openscience.cdk.smiles.smarts.parser: An implementation of interface CharStream, where the stream is assumed to contain only ASCII characters (without unicode processing).
SimpleCharStream(InputStream) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream, int, int) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream, int, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream, int, int, int) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream, int, int, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream, String) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream, String) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream, String, int, int) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream, String, int, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream, String, int, int, int) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream: Constructor.
SimpleCharStream(InputStream, String, int, int, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Constructor.
SimpleCharStream(Reader) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream: Constructor.
SimpleCharStream(Reader) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Constructor.
SimpleCharStream(Reader, int, int) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream: Constructor.
SimpleCharStream(Reader, int, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Constructor.
SimpleCharStream(Reader, int, int, int) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream: Constructor.
SimpleCharStream(Reader, int, int, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Constructor.
SimpleCycle - Class in org.openscience.cdk.ringsearch.cyclebasis: Deprecated.
internal implemenation detail from SSSRFinder, do not use
SimpleCycle(UndirectedGraph, Collection) - Constructor for class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycle: Deprecated.

Constructs a cycle in a graph consisting of the specified edges.
SimpleCycle(UndirectedGraph, Set) - Constructor for class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycle: Deprecated.

Constructs a cycle in a graph consisting of the specified edges.
SimpleCycleBasis - Class in org.openscience.cdk.ringsearch.cyclebasis: Deprecated.
internal implemenation detail from SSSRFinder, do not use
SimpleCycleBasis(List<SimpleCycle>, List, UndirectedGraph) - Constructor for class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis: Deprecated.
SimpleCycleBasis(UndirectedGraph) - Constructor for class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis: Deprecated.
simplifyMolecularFormula(String) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator: Simplify the molecular formula.
SINGLE - org.openscience.cdk.interfaces.IBond.Order
SINGLE - org.openscience.cdk.isomorphism.matchers.CTFileQueryBond.Type: Deprecated.
SINGLE - org.openscience.cdk.renderer.elements.LineElement.LineType
SINGLE_ELECTRON_COUNT - Static variable in class org.openscience.cdk.CDKConstants: Used as property key for indicating the number of single electrons on the atom type.
SINGLE_OR_AROMATIC - org.openscience.cdk.isomorphism.matchers.CTFileQueryBond.Type: Deprecated.
SINGLE_OR_AROMATIC - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if the bond order (IBond.getOrder()) is single or the bond is marked as aromatic (IBond.isAromatic()).
SINGLE_OR_DOUBLE - org.openscience.cdk.isomorphism.matchers.CTFileQueryBond.Type: Deprecated.
SINGLE_OR_DOUBLE - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if the bond order (IBond.getOrder()) is single or double.
SINGLE_OR_DOUBLE - Static variable in class org.openscience.cdk.CDKConstants: Flag used for marking uncertainty of the bond order.
singleAtomCheck(String[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen
singleAtomCheckLengthIsBiggerThanOne(String[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen
SINGLEBOND - Static variable in class org.openscience.cdk.libio.jena.CDK
SingleElectron - Class in org.openscience.cdk.silent: A Single Electron is an orbital which is occupied by only one electron.
SingleElectron - Class in org.openscience.cdk: A Single Electron is an orbital which is occupied by only one electron.
SingleElectron() - Constructor for class org.openscience.cdk.silent.SingleElectron: Constructs an single electron orbital with an associated Atom.
SingleElectron() - Constructor for class org.openscience.cdk.SingleElectron: Constructs an single electron orbital with an associated Atom.
SingleElectron(IAtom) - Constructor for class org.openscience.cdk.silent.SingleElectron: Constructs an single electron orbital on an Atom.
SingleElectron(IAtom) - Constructor for class org.openscience.cdk.SingleElectron: Constructs an single electron orbital on an Atom.
singleElectronCount - Variable in class org.openscience.cdk.AtomContainer: Number of single electrons contained by this object.
singleElectronCount - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Number of single electrons contained by this object.
singleElectronCount - Variable in class org.openscience.cdk.silent.AtomContainer: Number of single electrons contained by this object.
SingleElectronDiff - Class in org.openscience.cdk.tools.diff: Compares two ISingleElectron classes.
singleElectrons - Variable in class org.openscience.cdk.AtomContainer: Internal array of single electrons.
singleElectrons - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Internal array of single electrons.
singleElectrons - Variable in class org.openscience.cdk.silent.AtomContainer: Internal array of single electrons.
singleElectrons() - Method in class org.openscience.cdk.AtomContainer: Returns an Iterable for looping over all single electrons in this container.
singleElectrons() - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns an Iterable for looping over all single electrons in this container.
singleElectrons() - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns an Iterable for looping over all single electrons in this container.
singleElectrons() - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns an Iterable for looping over all single electrons in this container.
singleElectrons() - Method in class org.openscience.cdk.debug.DebugCrystal: Returns an Iterable for looping over all single electrons in this container.
singleElectrons() - Method in class org.openscience.cdk.debug.DebugMonomer: Returns an Iterable for looping over all single electrons in this container.
singleElectrons() - Method in class org.openscience.cdk.debug.DebugPolymer: Returns an Iterable for looping over all single electrons in this container.
singleElectrons() - Method in class org.openscience.cdk.debug.DebugRing: Returns an Iterable for looping over all single electrons in this container.
singleElectrons() - Method in class org.openscience.cdk.debug.DebugStrand: Returns an Iterable for looping over all single electrons in this container.
singleElectrons() - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Returns an Iterable for looping over all single electrons in this container.
singleElectrons() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns an Iterable for looping over all single electrons in this container.
singleElectrons() - Method in class org.openscience.cdk.silent.AtomContainer: Returns an Iterable for looping over all single electrons in this container.
SingleMapping - Class in org.openscience.cdk.smsd.algorithm.single: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
SingleMapping() - Constructor for class org.openscience.cdk.smsd.algorithm.single.SingleMapping: Deprecated.

Default
SingleMappingHandler - Class in org.openscience.cdk.smsd.algorithm.single: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
SingleMappingHandler(boolean) - Constructor for class org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler: Deprecated.
SingleStructureRandomGenerator - Class in org.openscience.cdk.structgen: Randomly generates a single, connected, correctly bonded structure for a given molecular formula.
SingleStructureRandomGenerator() - Constructor for class org.openscience.cdk.structgen.SingleStructureRandomGenerator: Constructor for the SingleStructureRandomGenerator object.
SingleStructureRandomGenerator(long) - Constructor for class org.openscience.cdk.structgen.SingleStructureRandomGenerator: Constructor for the SingleStructureRandomGenerator object.
sitefinder() - Method in class org.openscience.cdk.protein.ProteinPocketFinder: Main method which calls the methods: assignProteinToGrid, GridScan, and FindPockets.
size - Variable in class org.openscience.cdk.math.IVector: Size of this vector
size - Variable in class org.openscience.cdk.math.Vector: The size of this vector
size() - Method in class org.openscience.cdk.ConformerContainer: Get the number of conformers stored.
size() - Method in class org.openscience.cdk.debug.DebugAdductFormula: Returns the number of MolecularFormulas in this AdductFormula.
size() - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet: Returns the number of MolecularFormulas in this MolecularFormulaSet.
size() - Method in class org.openscience.cdk.dict.Dictionary
size() - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
size() - Method in interface org.openscience.cdk.fingerprint.IBitFingerprint: Returns the size of the fingerprint, i.e., the number of hash bins.
size() - Method in interface org.openscience.cdk.fingerprint.ICountFingerprint: Returns the number of bits of this fingerprint.
size() - Method in class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
size() - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
size() - Method in class org.openscience.cdk.formula.AdductFormula: Returns the number of MolecularFormulas in this AdductFormula.
size() - Method in class org.openscience.cdk.formula.MolecularFormulaSet: Returns the number of MolecularFormulas in this MolecularFormulaSet.
size() - Method in class org.openscience.cdk.graph.AllCycles: Cardinality of the set.
size() - Method in class org.openscience.cdk.graph.EssentialCycles: Number of essential cycles.
size() - Method in class org.openscience.cdk.graph.MinimumCycleBasis: The number of the cycles in the minimum cycle basis.
size() - Method in class org.openscience.cdk.graph.RelevantCycles: The number of the relevant cycles.
size() - Method in class org.openscience.cdk.graph.TripletShortCycles: Size of the cycle basis, cardinality of the ESSSR.
size() - Method in class org.openscience.cdk.group.Partition: Gets the size of the partition, in terms of the number of cells.
size() - Method in class org.openscience.cdk.group.Permutation: Get the number of elements in the permutation.
size() - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet: Returns the number of MolecularFormulas in this IMolecularFormulaSet.
size() - Method in interface org.openscience.cdk.io.random.IRandomAccessChemObjectReader
size() - Method in class org.openscience.cdk.io.random.RandomAccessReader
size() - Method in class org.openscience.cdk.silent.AdductFormula: Returns the number of MolecularFormulas in this AdductFormula.
size() - Method in class org.openscience.cdk.silent.MolecularFormulaSet: Returns the number of MolecularFormulas in this MolecularFormulaSet.
skeleton(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Create a skeleton copy of the provided structure.
SKIP - net.sf.jniinchi.INCHI_RET
Sm - Static variable in interface org.openscience.cdk.interfaces.IElement
SM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
SMALL_FIRST - Static variable in class org.openscience.cdk.silent.RingSet: Flag to denote that the set is order with the smallest ring first?
SMALL_FIRST - Static variable in class org.openscience.cdk.tools.manipulator.RingSizeComparator: Flag to denote that the set is order with the smallest ring first
SMALLEST_RINGS - Static variable in class org.openscience.cdk.CDKConstants: A smallest set of smallest rings computed for this molecule.
SmallestRingAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
SmallestRingAtom(int, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.SmallestRingAtom: Deprecated.

Creates a matcher for specified ring size.
SmallestRingSize() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
SmallRingDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Small ring descriptors: these are based on enumeration of all the small rings (sizes 3 to 9) in a molecule, which can be obtained quickly and deterministically.
SmallRingDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor
smallRingSize(IAtom) - Static method in class org.openscience.cdk.graph.Cycles: Determine the smallest ring size an atom belongs to.
smallRingSize(IAtom, int) - Static method in class org.openscience.cdk.graph.Cycles: Determine the smallest ring size an atom belongs to.
smallRingSize(IBond) - Static method in class org.openscience.cdk.graph.Cycles: Determine the smallest ring size an bond belongs to.
smallRingSize(IBond, int) - Static method in class org.openscience.cdk.graph.Cycles: Determine the smallest ring size an bond belongs to.
smallRingSizes(IAtomContainer, int[]) - Static method in class org.openscience.cdk.graph.Cycles: Convenience method to determine the smallest ring size of every atom in the molecule.
Smarts - Class in org.openscience.cdk.smarts: Parse and generate the SMARTS query language.
Smarts() - Constructor for class org.openscience.cdk.smarts.Smarts
Smarts2MQLVisitor - Class in org.openscience.cdk.smiles.smarts.parser: Deprecated.
Smarts2MQLVisitor() - Constructor for class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
SMARTSAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
SMARTSAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom: Deprecated.
SMARTSBond - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
SMARTSBond(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.SMARTSBond: Deprecated.
SMARTSBond(IQueryAtom, IQueryAtom, IBond.Order, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.SMARTSBond: Deprecated.
SmartsDumpVisitor - Class in org.openscience.cdk.smiles.smarts.parser: Deprecated.
SmartsDumpVisitor() - Constructor for class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
SmartsExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
SMARTSFormat - Class in org.openscience.cdk.io.formats: See here.
SMARTSFormat() - Constructor for class org.openscience.cdk.io.formats.SMARTSFormat
SmartsFragmentExtractor - Class in org.openscience.cdk.smarts: Utility class to create SMARTS that match part (substructure) of a molecule.
SmartsFragmentExtractor(IAtomContainer) - Constructor for class org.openscience.cdk.smarts.SmartsFragmentExtractor: Create a new instance over the provided molecule.
SmartsMatchers - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
SmartsMatchers() - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.SmartsMatchers: Deprecated.
SMARTSParser - Class in org.openscience.cdk.smiles.smarts.parser: This parser implements a nearly complete subset of the SMARTS syntax as defined on the Daylight website.
SMARTSParser(InputStream) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SMARTSParser: Constructor with InputStream.
SMARTSParser(InputStream, String) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SMARTSParser: Constructor with InputStream and supplied encoding
SMARTSParser(Reader) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SMARTSParser: Constructor.
SMARTSParser(SMARTSParserTokenManager) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SMARTSParser: Constructor with generated Token Manager.
SMARTSParserConstants - Interface in org.openscience.cdk.smiles.smarts.parser: Token literal values and constants.
SMARTSParserDefaultVisitor - Class in org.openscience.cdk.smiles.smarts.parser
SMARTSParserDefaultVisitor() - Constructor for class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
SMARTSParserTokenManager - Class in org.openscience.cdk.smiles.smarts.parser: Token Manager.
SMARTSParserTokenManager(SimpleCharStream) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager: Constructor.
SMARTSParserTokenManager(SimpleCharStream, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager: Constructor.
SMARTSParserTreeConstants - Interface in org.openscience.cdk.smiles.smarts.parser
SMARTSParserVisitor - Interface in org.openscience.cdk.smiles.smarts.parser
SmartsPattern - Class in org.openscience.cdk.smarts: A Pattern for matching a single SMARTS query against multiple target compounds.
SmartsPattern - Class in org.openscience.cdk.smiles.smarts: Deprecated.
SMARTSQueryTool - Class in org.openscience.cdk.smiles.smarts: Deprecated.
use SmartsPattern
SMARTSQueryTool(String, IChemObjectBuilder) - Constructor for class org.openscience.cdk.smiles.smarts.SMARTSQueryTool: Deprecated.

Create a new SMARTS query tool for the specified SMARTS string.
SmartsQueryVisitor - Class in org.openscience.cdk.smiles.smarts.parser: Deprecated.
SmartsQueryVisitor(IChemObjectBuilder) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
SmartsResult - Class in org.openscience.cdk.smarts: The result of parsing a SMARTS.
SmartsStereoMatch - Class in org.openscience.cdk.isomorphism: Deprecated.
use QueryStereoFilter
SmartsStereoMatch(IAtomContainer, IAtomContainer) - Constructor for class org.openscience.cdk.isomorphism.SmartsStereoMatch: Deprecated.

Create a predicate for checking mappings between a provided query and target.
SmiFlavor - Class in org.openscience.cdk.smiles: Flags for customising SMILES generation.
SMILES - Static variable in class org.openscience.cdk.CDKConstants: The Daylight SMILES.
SMILESFIXFormat - Class in org.openscience.cdk.io.formats
SMILESFIXFormat() - Constructor for class org.openscience.cdk.io.formats.SMILESFIXFormat
SMILESFormat - Class in org.openscience.cdk.io.formats: See here.
SMILESFormat() - Constructor for class org.openscience.cdk.io.formats.SMILESFormat
SmilesGenerator - Class in org.openscience.cdk.smiles: SMILES [Weininger, David. Journal of Chemical Information and Computer Sciences. 1988. 28, Weininger, David et. al.. Journal of Chemical Information and Computer Sciences. 1989. 29] provides a compact representation of chemical structures and reactions.
SmilesGenerator() - Constructor for class org.openscience.cdk.smiles.SmilesGenerator: Deprecated.
use SmilesGenerator(int) configuring with SmiFlavor.
SmilesGenerator(int) - Constructor for class org.openscience.cdk.smiles.SmilesGenerator: Create a SMILES generator with the specified SmiFlavor.
SmilesParser - Class in org.openscience.cdk.smiles: Read molecules and reactions from a SMILES [?Authors?, SMILES Tutorial] string.
SmilesParser(IChemObjectBuilder) - Constructor for class org.openscience.cdk.smiles.SmilesParser: Create a new SMILES parser which will create IAtomContainers with the specified builder.
SmilesReactionCanoniser - Class in org.openscience.cdk.smsd.labelling: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
SmilesReactionCanoniser() - Constructor for class org.openscience.cdk.smsd.labelling.SmilesReactionCanoniser: Deprecated.
SMILESReader - Class in org.openscience.cdk.io: This Reader reads files which has one SMILES string on each line, where the format is given as below:
SMILESReader() - Constructor for class org.openscience.cdk.io.SMILESReader
SMILESReader(InputStream) - Constructor for class org.openscience.cdk.io.SMILESReader
SMILESReader(Reader) - Constructor for class org.openscience.cdk.io.SMILESReader: Construct a new reader from a Reader and a specified builder object.
SmilesValencyChecker - Class in org.openscience.cdk.tools: Small customization of ValencyHybridChecker suggested by Todd Martin specially tuned for SMILES parsing.
SmilesValencyChecker() - Constructor for class org.openscience.cdk.tools.SmilesValencyChecker
SmilesValencyChecker(String) - Constructor for class org.openscience.cdk.tools.SmilesValencyChecker
SMILESWriter - Class in org.openscience.cdk.io: Writes the SMILES strings to a plain text file.
SMILESWriter() - Constructor for class org.openscience.cdk.io.SMILESWriter
SMILESWriter(FileOutputStream) - Constructor for class org.openscience.cdk.io.SMILESWriter: Constructs a new SMILESWriter that can write an list of SMILES to a given OutputStream
SMILESWriter(OutputStream) - Constructor for class org.openscience.cdk.io.SMILESWriter
SMILESWriter(Writer) - Constructor for class org.openscience.cdk.io.SMILESWriter: Constructs a new SMILESWriter that can write a list of SMILES to a Writer
SMSDNormalizer - Class in org.openscience.cdk.normalize: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
SMSDNormalizer() - Constructor for class org.openscience.cdk.normalize.SMSDNormalizer: Deprecated.
Sn - Static variable in interface org.openscience.cdk.interfaces.IElement
SN - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
SNon - net.sf.jniinchi.INCHI_OPTION
Sodium - org.openscience.cdk.config.Elements
SODIUM - Static variable in enum org.openscience.cdk.config.Elements
SODIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Solid - org.openscience.cdk.interfaces.IBond.Display: A solid line (default).
sort() - Method in class org.openscience.cdk.signature.Orbit: Sorts the atom indices in this orbit.
sort(List<String>, Set<Map.Entry<String, Integer>>) - Method in class org.openscience.cdk.structgen.maygen.Maygen
sort(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator: Sorts the IAtomContainers in the given IAtomContainerSet by the following criteria with decreasing priority:
sort(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator: Sorts the rings in the set by size.
sortAndNormalizedByIntensity(IsotopePattern) - Static method in class org.openscience.cdk.formula.IsotopePatternManipulator: Return the isotope pattern sorted and normalized by intensity to the highest abundance.
sortAscending(List<String>) - Method in class org.openscience.cdk.structgen.maygen.Maygen: The initializer function, reading the formula to set the degrees, partition and file directory variables.
sortAtomContainers(Comparator<IAtomContainer>) - Method in class org.openscience.cdk.AtomContainerSet: Sort the AtomContainers and multipliers using a provided Comparator.
sortAtomContainers(Comparator<IAtomContainer>) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet: Sort the AtomContainers using a provided Comparator.
sortAtomContainers(Comparator<IAtomContainer>) - Method in class org.openscience.cdk.silent.AtomContainerSet: Sort the AtomContainers and multipliers using a provided Comparator
sortBy2DDistance(IAtom[], Point2d) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Sorts a Vector of atoms such that the 2D distances of the atom locations from a given point are smallest for the first atoms in the vector.
sortBy2DDistance(IAtom[], Point2d) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Sorts a Vector of atoms such that the 2D distances of the atom locations from a given point are smallest for the first atoms in the vector.
sortByIntensity(IsotopePattern) - Static method in class org.openscience.cdk.formula.IsotopePatternManipulator: Return the isotope pattern sorted by intensity to the highest abundance.
sortByMass(IsotopePattern) - Static method in class org.openscience.cdk.formula.IsotopePatternManipulator: Return the isotope pattern sorted by mass to the highest abundance.
sortResultsByEnergies() - Method in class org.openscience.cdk.smsd.filters.ChemicalFilters: Deprecated.

Sort MCS solution by bond breaking energy.
sortResultsByFragments() - Method in class org.openscience.cdk.smsd.filters.ChemicalFilters: Deprecated.

Sort solution by ascending order of the fragment count.
sortResultsByStereoAndBondMatch() - Method in class org.openscience.cdk.smsd.filters.ChemicalFilters: Deprecated.

Sort MCS solution by stereo and bond type matches.
sortWithPartition(int[], int[], String[], int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Sort arrays with partitions.
SP - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Square Planar (SP-4) (e.g.
SP1 - org.openscience.cdk.interfaces.IAtomType.Hybridization
SP2 - org.openscience.cdk.interfaces.IAtomType.Hybridization
SP3 - org.openscience.cdk.interfaces.IAtomType.Hybridization
SP3D1 - org.openscience.cdk.interfaces.IAtomType.Hybridization
SP3D2 - org.openscience.cdk.interfaces.IAtomType.Hybridization
SP3D3 - org.openscience.cdk.interfaces.IAtomType.Hybridization
SP3D4 - org.openscience.cdk.interfaces.IAtomType.Hybridization
SP3D5 - org.openscience.cdk.interfaces.IAtomType.Hybridization
SP4 - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Square Planar Configutation in 4 Shape
SPACE - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
SpanningTree - Class in org.openscience.cdk.graph: Spanning tree of a molecule.
SpanningTree(IAtomContainer) - Constructor for class org.openscience.cdk.graph.SpanningTree: Create a new spanning tree for the provided molecule.
SpartanFormat - Class in org.openscience.cdk.io.formats
SpartanFormat() - Constructor for class org.openscience.cdk.io.formats.SpartanFormat
specialCase() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Deal with special cases where the rules don't apply.
specialToken - Variable in class org.openscience.cdk.iupac.parser.Token: This field is used to access special tokens that occur prior to this token, but after the immediately preceding regular (non-special) token.
specialToken - Variable in class org.openscience.cdk.smiles.smarts.parser.Token: This field is used to access special tokens that occur prior to this token, but after the immediately preceding regular (non-special) token.
sphere - Variable in class org.openscience.cdk.tools.HOSECodeGenerator: Counter for the sphere in which we currently work.
sphereNodes - Variable in class org.openscience.cdk.tools.HOSECodeGenerator: Container for the nodes in a sphere.
spheres - Variable in class org.openscience.cdk.tools.HOSECodeGenerator: Here we store the spheres that we assemble, in order to parse them into a code later.
SPHERICAL_MATCHER - Static variable in class org.openscience.cdk.CDKConstants: Used as property key for indicating the HOSE code for a certain atom type.
SPIN_MULTIPLICITY - Static variable in class org.openscience.cdk.CDKConstants: Enumeration of all valid radical values.
spinMultiplicities - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
SpiroAtomCountDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Returns the number of spiro atoms.
SpiroAtomCountDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.SpiroAtomCountDescriptor: Creates a new SpiroAtomCountDescriptor.
splice(PathEdge) - Method in class org.openscience.cdk.smsd.ring.PathEdge: Deprecated.
SPLIT_MODE_BREADTH_FIRST - Static variable in class org.openscience.cdk.structgen.stochastic.operator.CrossoverMachine: Indicates that crossover is using SPLIT_MODE_BREADTH_FIRST mode.
SPLIT_MODE_DEPTH_FIRST - Static variable in class org.openscience.cdk.structgen.stochastic.operator.CrossoverMachine: Indicates that crossover is using SPLIT_MODE_DEPTH_FIRST mode.
SPLIT_MODE_RADNDOM - Static variable in class org.openscience.cdk.structgen.stochastic.operator.CrossoverMachine: Indicates that crossover is using SPLIT_MODE_RADNDOM mode.
splitAfter(int, int) - Method in class org.openscience.cdk.group.Partition: Splits this partition by taking the cell at cellIndex and making two new cells - the first with the the rest of the elements from that cell and the second with the singleton splitElement.
splitBefore(int, int) - Method in class org.openscience.cdk.group.Partition: Splits this partition by taking the cell at cellIndex and making two new cells - the first with the singleton splitElement and the second with the rest of the elements from that cell.
splitMolecule(IAtomContainer, IBond) - Static method in class org.openscience.cdk.fragment.FragmentUtils: Non destructively split a molecule into two parts at the specified bond.
SPU - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Square Planar Configutation in U Shape
SPXYZ - net.sf.jniinchi.INCHI_OPTION
SPY - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Square Pyramidal (SPY-5)
SPZ - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Square Planar Configutation in Z Shape
sqrt() - Method in class org.openscience.cdk.math.Quaternion
SQUARE - org.openscience.cdk.renderer.generators.BasicAtomGenerator.Shape
SQUARE_PLANAR - org.openscience.cdk.stereo.StereoTool.StereoClass
SquarePlanar - Class in org.openscience.cdk.stereo: Describes square planar configuration.
SquarePlanar - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Square Planar (SP-4) (e.g.
SquarePlanar(IAtom, IAtom[], int) - Constructor for class org.openscience.cdk.stereo.SquarePlanar: Create a square-planar configuration around a provided focus atom.
SquarePyramidal - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Square Pyramidal (SPY-5)
Sr - Static variable in interface org.openscience.cdk.interfaces.IElement
SR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
SRac - net.sf.jniinchi.INCHI_OPTION
SRel - net.sf.jniinchi.INCHI_OPTION
sssr(IAtomContainer) - Static method in class org.openscience.cdk.graph.Cycles: Find the smallest set of smallest rings (SSSR) - aka minimum cycle basis (MCB) of a molecule.
SSSRFinder - Class in org.openscience.cdk.ringsearch: Deprecated.
Use the Cycles API Cycles.sssr(IAtomContainer)
SSSRFinder(IAtomContainer) - Constructor for class org.openscience.cdk.ringsearch.SSSRFinder: Deprecated.

Constructs a SSSRFinder for a specified molecule.
st - Variable in class org.openscience.cdk.io.VASPReader
StabilizationCharges - Class in org.openscience.cdk.charges: The stabilization of the positive and the negative charge obtained (e.g in the polar breaking of a bond) is calculated from the sigma- and lone pair-electronegativity values of the atoms that are in conjugation to the atoms obtaining the charges.
StabilizationCharges() - Constructor for class org.openscience.cdk.charges.StabilizationCharges: Constructor for the StabilizationCharges object.
StabilizationPlusChargeDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic: The stabilization of the positive charge (e.g.) obtained in the polar breaking of a bond is calculated from the sigma- and lone pair-electronegativity values of the atoms that are in conjugation to the atoms obtaining the charges.
StabilizationPlusChargeDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor: Constructor for the StabilizationPlusChargeDescriptor object
StandardGenerator - Class in org.openscience.cdk.renderer.generators.standard: The standard generator creates IRenderingElements for the atoms and bonds of a structure diagram.
StandardGenerator(Font) - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator: Create a new standard generator that utilises the specified font to display atom symbols.
StandardGenerator.AnnotationColor - Class in org.openscience.cdk.renderer.generators.standard: The color of the atom numbers.
StandardGenerator.AnnotationDistance - Class in org.openscience.cdk.renderer.generators.standard: The distance of atom numbers from their parent atom as a percentage of bond length, default value is 0.25 (25%)
StandardGenerator.AnnotationFontScale - Class in org.openscience.cdk.renderer.generators.standard: Annotation font size relative to element symbols, default = 0.4 (40%).
StandardGenerator.AtomColor - Class in org.openscience.cdk.renderer.generators.standard: Defines the color of unselected atoms (and bonds).
StandardGenerator.BondSeparation - Class in org.openscience.cdk.renderer.generators.standard: Defines the ratio of the separation between lines in double bonds as a percentage of length (BasicSceneGenerator.BondLength).
StandardGenerator.DashSection - Class in org.openscience.cdk.renderer.generators.standard: The number of sections to render in a dashed 'unknown' bond, default = 4;
StandardGenerator.DelocalisedDonutsBondDisplay - Class in org.openscience.cdk.renderer.generators.standard: Render small delocalised rings as bonds/life buoys? This can sometimes be misleading for fused rings but is commonly used.
StandardGenerator.DeuteriumSymbol - Class in org.openscience.cdk.renderer.generators.standard: Display deuterium [2H] as 'D'.
StandardGenerator.FancyBoldWedges - Class in org.openscience.cdk.renderer.generators.standard: Modify bold wedges to be flush with adjacent bonds, default = true.
StandardGenerator.FancyHashedWedges - Class in org.openscience.cdk.renderer.generators.standard: Modify hashed wedges to be flush when there is a single adjacent bond, default = true.
StandardGenerator.ForceDelocalisedBondDisplay - Class in org.openscience.cdk.renderer.generators.standard: Indicate delocalised/aromatic bonds should always be rendered, even when there is a valid Kekule structure.
StandardGenerator.HashSpacing - Class in org.openscience.cdk.renderer.generators.standard: The preferred spacing between lines in hashed bonds.
StandardGenerator.Highlighting - Class in org.openscience.cdk.renderer.generators.standard: Parameter defines the style of highlight used to emphasis atoms and bonds.
StandardGenerator.HighlightStyle - Enum in org.openscience.cdk.renderer.generators.standard: Enumeration of highlight style.
StandardGenerator.OmitMajorIsotopes - Class in org.openscience.cdk.renderer.generators.standard: Whether Major Isotopes e.g.
StandardGenerator.OuterGlowWidth - Class in org.openscience.cdk.renderer.generators.standard: The width of outer glow as a percentage of stroke width.
StandardGenerator.PseudoFontStyle - Class in org.openscience.cdk.renderer.generators.standard: The default font style for pseudo-atoms, is Bold and Italic.
StandardGenerator.SgroupBracketDepth - Class in org.openscience.cdk.renderer.generators.standard: How "deep" are brackets drawn.
StandardGenerator.SgroupFontScale - Class in org.openscience.cdk.renderer.generators.standard: Scale Sgroup annotations relative to the normal font size (atom symbol).
StandardGenerator.StrokeRatio - Class in org.openscience.cdk.renderer.generators.standard: Defines the ratio of the stroke to the width of the stroke of the font used to depict atom symbols.
StandardGenerator.SymbolMarginRatio - Class in org.openscience.cdk.renderer.generators.standard: Defines the margin between an atom symbol and a connected bond based on the stroke width.
StandardGenerator.Visibility - Class in org.openscience.cdk.renderer.generators.standard: Defines which atoms have their symbol displayed.
StandardGenerator.WaveSpacing - Class in org.openscience.cdk.renderer.generators.standard: The spacing of waves (semi circles) drawn in wavy bonds with.
StandardGenerator.WedgeRatio - Class in org.openscience.cdk.renderer.generators.standard: Ratio of the wide end of wedge compared to the narrow end (stroke width).
StandardSubstructureSets - Class in org.openscience.cdk.fingerprint: Default sets of atom containers aimed for use with the substructure.
StandardSubstructureSets() - Constructor for class org.openscience.cdk.fingerprint.StandardSubstructureSets
Start() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser: Start ::= <ReactionExpression> <#_WS> ReactionExpression ::= <GroupExpression>? (">" <GroupExpression>? ">" <GroupExpression>?)? GroupExpression ::= ["("] <SmartsExpresion> [")"] ( "." ["("] <SmartsExpression> [")"] )* SmartsExpression ::= <AtomExpression> ( ( [ <LowAndBond> ] ( <Digit> | <AtomExpression> ) ) | ( "(" [ <LowAndBond> ] <SmartsExpression> ")" ) )* AtomExpression ::= ( "[" [ <AtomicMass> ] <LowAndExpression> [:<Digit>+] "]" ) | <ExplicitAtomExpression> LowAndBond ::= <OrBond> [ ";" <AndBond> ] OrBond ::= <ExplicitHighAndBond> [ "," <OrBond> ] ExplicitHighAndBond ::= <ImplicitHighAndBond> [ "&" <ExplicitHighAndBond> ] ImplicitHighAndBond ::= <NotBond> [ <ImplicitHighAndBond> ] NotBond ::= [ "!" ] <SimpleBond> SimpleBond ::= "/" | "\\" | "/?" | "\\?" | "=" | "#" | "~" | "@" ExplicitAtomExpression ::= [ "B" | "C" | "N" | "O" | "P" | "S" | "F" | "CL" | "BR" | "I" | "c" | "o" | "n" | "*" | "A" | "a" | "p" | "as" | "se" ] LowAndExpression ::= <OrExpression> ( ";" <LowAndExpression> )? OrExpression ::= <ExplicitHighAndExpression> ( "," <OrExpression> ) ? ExplicitHighAndExpression ::= <ImplicitHighAndExpression> ( "&" <ExplicitHighAndExpression> )? ImplicitHighAndExpression ::= <NotExpression> ( <ImplicitHighAndExpression> ) ? NotExpression ::= "!" ( <PrimitiveAtomExpression> | <RecursiveSmartsExpression> ) RecursiveSmartsExpression ::= "$" "(" <SmartsExpression> ")" PrimitiveAtomExpression ::= <AtomicMass> | <NonHydrogenElement> | "*" | "A" | "a" | "D" (<Digits>)? | "H" (<Digits>)? | "h" (<Digits>)? | "R" (<Digit>+)? | "r" (<Digit>+)? | "v" (<Digit>+)? | "#X" | "G" (<DIGIT>+) | "X" (<Digit>+)? | "x" (<Digit>+)? | "^" (<DIGIT>) | ("+" | "-") (<Digit>+)? | "#" (<Digit>+) | "@" | "@@" | <Digit>+ Digit ::= ( "0" - "9") NonHydrogenElement ::= [ "HE" | "LI" | "BE" | "NE" | "NA" | "MG" | "AL" | "SI" | "AR" | "CA" | "SC" | "TI" | "CR" | "MN" | "FE" | "CO" | "NI" | "CU" | "ZN" | "GA" | "GE" | "AS" | "SE" | "BR" | "KR" | "RB" | "SR" | "ZR" | "NB" | "MO" | "TC" | "RU" | "RH" | "PD" | "AG" | "CD" | "IN" | "SN" | "SB" | "TE" | "XE" | "CS" | "BA" | "LA" | "HF" | "TA" | "RE" | "OS" | "IR" | "PT" | "AU" | "HG" | "TL" | "PB" | "BI" | "PO" | "AT" | "RN" | "FR" | "RA" | "AC" | "TH" | "PA" | "B" | "C" | "N" | "O" | "F" | "P" | "S" | "K" | "V" | "Y" | "I" | "U" | "c" | "o" | "n" | "p" | "as" | "se" ]
startDocument() - Method in class org.openscience.cdk.config.atomtypes.AtomTypeHandler
startDocument() - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeHandler
startDocument() - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingHandler
startDocument() - Method in class org.openscience.cdk.config.isotopes.IsotopeHandler
startDocument() - Method in class org.openscience.cdk.dict.DictionaryHandler
startDocument() - Method in class org.openscience.cdk.io.cml.CDKConvention
startDocument() - Method in class org.openscience.cdk.io.cml.CMLCoreModule
startDocument() - Method in class org.openscience.cdk.io.cml.CMLHandler
startDocument() - Method in interface org.openscience.cdk.io.cml.ICMLModule
startDocument() - Method in class org.openscience.cdk.io.cml.MDLMolConvention
startDocument() - Method in class org.openscience.cdk.io.cml.PMPConvention
startDocument() - Method in class org.openscience.cdk.io.inchi.INChIHandler: Deprecated.
startDocument() - Method in class org.openscience.cdk.io.iterator.event.EventCMLHandler: Procedure required by the CDOInterface.
startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.config.atomtypes.AtomTypeHandler
startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeHandler
startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingHandler
startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.config.isotopes.IsotopeHandler
startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.dict.DictionaryHandler
startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.CMLHandler
startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.io.inchi.INChIHandler: Deprecated.

Implementation of the startElement() procedure overwriting the DefaultHandler interface.
startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.CDKConvention
startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.CMLCoreModule
startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.CMLReactionModule
startElement(CMLStack, String, String, String, Attributes) - Method in interface org.openscience.cdk.io.cml.ICMLModule
startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.JMOLANIMATIONConvention
startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.MDLMolConvention
startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.MDMoleculeConvention: Add parsing of elements in mdmolecule: mdmolecule chargeGroup id cgNumber atomArray switchingAtom residue id title resNumber atomArray
startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.PDBConvention
startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.PMPConvention
startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.QSARConvention
startMcGregorIteration(int, List<Integer>, List<Integer>) - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregor: Deprecated.

Start McGregor search and extend the mappings if possible.
startMcGregorIteration(int, Map<Integer, Integer>) - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregor: Deprecated.

Start McGregor search and extend the mappings if possible.
startObject(String) - Method in class org.openscience.cdk.io.iterator.event.EventCMLHandler: Procedure required by the CDOInterface.
startX - Variable in class org.openscience.cdk.renderer.elements.ArrowElement: X coordinate of the point where the arrow starts.
startY - Variable in class org.openscience.cdk.renderer.elements.ArrowElement: Y coordinate of the point where the arrow starts.
stateChanged(EventObject) - Method in interface org.openscience.cdk.event.ICDKChangeListener: Invoked when the target of the listener has changed its state.
stateChanged(EventObject) - Method in interface org.openscience.cdk.event.ICDKSelectionChangeListener: Invoked when the target of the listener has changed its state.
stateChanged(List) - Method in interface org.openscience.cdk.structgen.IStructureGenerationListener
stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.AtomContainer: Called by objects to notify objects that implemented this interface and registered with them as ChemObjectListeners.
stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.AtomContainerSet: Called by objects to which this object has registered as a listener.
stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.ChemFile: Called by objects to which this object has registered as a listener.
stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.ChemModel: Called by objects to which this object has registered as a listener.
stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.ChemSequence: Called by objects to which this object has registered as a listener.
stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Called by objects to notify objects that implemented this interface and registered with them as ChemObjectListeners.
stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Called by objects to notify objects that implemented this interface and registered with them as ChemObjectListeners.
stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugCrystal: Called by objects to notify objects that implemented this interface and registered with them as ChemObjectListeners.
stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugMonomer: Called by objects to notify objects that implemented this interface and registered with them as ChemObjectListeners.
stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugPolymer: Called by objects to notify objects that implemented this interface and registered with them as ChemObjectListeners.
stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugRing: Called by objects to notify objects that implemented this interface and registered with them as ChemObjectListeners.
stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugStrand: Called by objects to notify objects that implemented this interface and registered with them as ChemObjectListeners.
stateChanged(IChemObjectChangeEvent) - Method in interface org.openscience.cdk.interfaces.IChemObjectListener: Called by objects to notify objects that implemented this interface and registered with them as ChemObjectListeners.
stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Called by objects to which this object has registered as a listener.
stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.ReactionSet
stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.AtomContainer: Called by objects to notify objects that implemented this interface and registered with them as ChemObjectListeners.
stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.AtomContainerSet: Called by objects to which this object has registered as a listener.
stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.ChemFile: Called by objects to which this object has registered as a listener.
stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.ChemModel: Called by objects to which this object has registered as a listener.
stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.ChemSequence: Called by objects to which this object has registered as a listener.
stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.ReactionSet
STATIC_LEXER_ERROR - Static variable in error org.openscience.cdk.iupac.parser.TokenMgrError: An attempt was made to create a second instance of a static token manager.
STATIC_LEXER_ERROR - Static variable in error org.openscience.cdk.smiles.smarts.parser.TokenMgrError: An attempt was made to create a second instance of a static token manager.
staticFlag - Static variable in class org.openscience.cdk.iupac.parser.SimpleCharStream: Whether parser is static.
staticFlag - Static variable in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream: Whether parser is static.
stereo - Variable in class org.openscience.cdk.Bond: A descriptor the stereochemical orientation of this bond.
stereo - Variable in class org.openscience.cdk.isomorphism.matchers.QueryBond: A descriptor the stereochemical orientation of this query bond.
stereo - Variable in class org.openscience.cdk.silent.Bond: A descriptor the stereochemical orientation of this bond.
Stereo - Static variable in class org.openscience.cdk.smiles.SmiFlavor: Output supported stereochemistry types.
STEREO_ATOM_PARITY_MINUS - Static variable in class org.openscience.cdk.CDKConstants: A negative atom parity.
STEREO_ATOM_PARITY_PLUS - Static variable in class org.openscience.cdk.CDKConstants: A positive atom parity.
STEREO_ATOM_PARITY_UNDEFINED - Static variable in class org.openscience.cdk.CDKConstants: A undefined atom parity.
StereoBond - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
StereoBond(IChemObjectBuilder, StereoBond.Direction, boolean) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.StereoBond: Deprecated.
StereoBond.Direction - Enum in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
Stereocenters - Class in org.openscience.cdk.stereo: Find atoms which can support stereo chemistry based on the connectivity.
Stereocenters.Stereocenter - Enum in org.openscience.cdk.stereo: Defines the type of a stereocenter.
Stereocenters.Type - Enum in org.openscience.cdk.stereo
stereocenterType(int) - Method in class org.openscience.cdk.stereo.Stereocenters: Determine the type of stereocenter is the atom at index v.
stereochemistry() - Method in class org.openscience.cdk.isomorphism.Mappings: Deprecated.
Results now automatically consider stereo if it's present, to match without stereochemistry remove the stereo features.
STEREOCHEMISTRY - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if an atom or bond has the specified stereochemistry value, see (IStereoElement) for a list of values.
StereoCisTrans - Static variable in class org.openscience.cdk.smiles.SmiFlavor: Output cis-trans stereochemistry specified by directional \ of / bonds.
StereoElementFactory - Class in org.openscience.cdk.stereo: Create stereo elements for a structure with 2D and 3D coordinates.
StereoElementFactory(IAtomContainer, int[][], GraphUtil.EdgeToBondMap) - Constructor for class org.openscience.cdk.stereo.StereoElementFactory: Internal constructor.
stereoElements - Variable in class org.openscience.cdk.AtomContainer: Internal list of atom parities.
stereoElements - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Internal list of atom parities.
stereoElements - Variable in class org.openscience.cdk.silent.AtomContainer: Internal list of atom parities.
stereoElements() - Method in class org.openscience.cdk.AtomContainer: Returns the stereo elements defined for this atom container.
stereoElements() - Method in class org.openscience.cdk.debug.DebugAminoAcid: Returns the stereo elements defined for this atom container.
stereoElements() - Method in class org.openscience.cdk.debug.DebugAtomContainer: Returns the stereo elements defined for this atom container.
stereoElements() - Method in class org.openscience.cdk.debug.DebugBioPolymer: Returns the stereo elements defined for this atom container.
stereoElements() - Method in class org.openscience.cdk.debug.DebugCrystal: Returns the stereo elements defined for this atom container.
stereoElements() - Method in class org.openscience.cdk.debug.DebugMonomer: Returns the stereo elements defined for this atom container.
stereoElements() - Method in class org.openscience.cdk.debug.DebugPolymer: Returns the stereo elements defined for this atom container.
stereoElements() - Method in class org.openscience.cdk.debug.DebugRing: Returns the stereo elements defined for this atom container.
stereoElements() - Method in class org.openscience.cdk.debug.DebugStrand: Returns the stereo elements defined for this atom container.
stereoElements() - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Returns the stereo elements defined for this atom container.
stereoElements() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns the stereo elements defined for this atom container.
stereoElements() - Method in class org.openscience.cdk.silent.AtomContainer: Returns the stereo elements defined for this atom container.
StereoEncoder - Interface in org.openscience.cdk.hash.stereo: An encoder for stereo chemistry.
StereoEncoderFactory - Interface in org.openscience.cdk.hash.stereo: Describes a factory for stereo elements.
StereoExCisTrans - Static variable in class org.openscience.cdk.smiles.SmiFlavor
StereoExTetrahedral - Static variable in class org.openscience.cdk.smiles.SmiFlavor: Output extended tetrahedral stereochemistry on atoms as @ and @@.
stereoGiven - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
stereoParity - Variable in class org.openscience.cdk.Atom: A stereo parity descriptor for the stereochemistry of this atom.
stereoParity - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom: A stereo parity descriptor for the stereochemistry of this atom.
stereoParity - Variable in class org.openscience.cdk.silent.Atom: A stereo parity descriptor for the stereochemistry of this atom.
stereosAreOpposite(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.BondTools: Says if of four atoms connected two one atom the up and down bonds are opposite or not, i.
StereoTetrahedral - Static variable in class org.openscience.cdk.smiles.SmiFlavor: Output tetrahedral stereochemistry on atoms as @ and @@.
StereoTool - Class in org.openscience.cdk.stereo: Methods to determine or check the stereo class of a set of atoms.
StereoTool() - Constructor for class org.openscience.cdk.stereo.StereoTool
StereoTool.SquarePlanarShape - Enum in org.openscience.cdk.stereo: The shape that four atoms take in a plane.
StereoTool.StereoClass - Enum in org.openscience.cdk.stereo: Currently unused, but intended for the StereoTool to indicate what it 'means' by an assignment of some atoms to a class.
StereoTool.TetrahedralSign - Enum in org.openscience.cdk.stereo: The handedness of a tetrahedron, in terms of the point-plane distance of three of the corners, compared to the fourth.
storeAtomData() - Method in class org.openscience.cdk.io.cml.CMLCoreModule
storeAtomData() - Method in class org.openscience.cdk.io.cml.PDBConvention
storeBondData() - Method in class org.openscience.cdk.io.cml.CMLCoreModule
storeData() - Method in class org.openscience.cdk.io.cml.CMLCoreModule
storeData() - Method in class org.openscience.cdk.io.cml.PDBConvention
Strand - Class in org.openscience.cdk.silent: A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms.
Strand - Class in org.openscience.cdk: A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms.
Strand() - Constructor for class org.openscience.cdk.silent.Strand: Constructs a new Strand.
Strand() - Constructor for class org.openscience.cdk.Strand: Constructs a new Strand.
stream() - Method in class org.openscience.cdk.isomorphism.Mappings: Convert the Mappings to a Java 8 Stream.
strict - Variable in class org.openscience.cdk.stereo.StereoElementFactory
STRICT - org.openscience.cdk.io.IChemObjectReader.Mode: Fail on any format problem
StringDifference - Class in org.openscience.cdk.tools.diff.tree: IDifference between two String.
StringIOSetting - Class in org.openscience.cdk.io.setting: An class for a reader setting which must be of type String.
StringIOSetting(String, IOSetting.Importance, String, String) - Constructor for class org.openscience.cdk.io.setting.StringIOSetting
stroke - Variable in class org.openscience.cdk.renderer.elements.GeneralPath: The width of the stroke.
stroke - Variable in class org.openscience.cdk.renderer.elements.OvalElement: The stroke width.
StrokeRatio() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.StrokeRatio
Strontium - org.openscience.cdk.config.Elements
STRONTIUM - Static variable in enum org.openscience.cdk.config.Elements
STRONTIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
structgenATF - Variable in class org.openscience.cdk.tools.SmilesValencyChecker
StructGenAtomTypeGuesser - Class in org.openscience.cdk.atomtype: AtomTypeMatcher that finds an AtomType by matching the Atom's element symbol.
StructGenAtomTypeGuesser() - Constructor for class org.openscience.cdk.atomtype.StructGenAtomTypeGuesser: Constructor for the StructGenMatcher object.
StructGenMatcher - Class in org.openscience.cdk.atomtype: AtomTypeMatcher that finds an AtomType by matching the Atom's element symbol.
StructGenMatcher() - Constructor for class org.openscience.cdk.atomtype.StructGenMatcher: Constructor for the StructGenMatcher object.
StructureDiagramGenerator - Class in org.openscience.cdk.layout: Generates 2D coordinates for a molecule.
StructureDiagramGenerator() - Constructor for class org.openscience.cdk.layout.StructureDiagramGenerator: The empty constructor.
StructureDiagramGenerator(IAtomContainer) - Constructor for class org.openscience.cdk.layout.StructureDiagramGenerator: Creates an instance of this class while assigning a molecule to be layed out.
structureGenerator(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen: After the hydrogen distribution, calling the structure generator functions.
StructureResonanceGenerator - Class in org.openscience.cdk.tools: This class try to generate resonance structure for a determinate molecule.
StructureResonanceGenerator() - Constructor for class org.openscience.cdk.tools.StructureResonanceGenerator: Construct an instance of StructureResonanceGenerator.
StructureResonanceGenerator(boolean) - Constructor for class org.openscience.cdk.tools.StructureResonanceGenerator: Construct an instance of StructureResonanceGenerator.
sub(Complex) - Method in class org.openscience.cdk.math.Complex: Subtracs a complex value
sub(IMatrix) - Method in class org.openscience.cdk.math.IMatrix: Subtraktion from two matrices
sub(IMatrix, IMatrix) - Method in class org.openscience.cdk.math.IMatrix: Subtraktion from two matrices
sub(IVector) - Method in class org.openscience.cdk.math.IVector: Subtraction from two vectors
sub(IVector, IVector) - Method in class org.openscience.cdk.math.IVector: Subtraction from two vectors
sub(Matrix) - Method in class org.openscience.cdk.math.Matrix: Subtracts from two matrices.
sub(Quaternion) - Method in class org.openscience.cdk.math.Quaternion
sub(Vector) - Method in class org.openscience.cdk.math.Vector: Subtraktion from two vectors
subChain() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

The substituent part of the prefix
subgraph(int[][], int[]) - Static method in class org.openscience.cdk.graph.GraphUtil: Create a subgraph by specifying the vertices from the original graph to include in the subgraph.
subGraph - Variable in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
subList(int, int) - Method in class org.openscience.cdk.ConformerContainer
subquery() - Method in class org.openscience.cdk.isomorphism.matchers.Expr: Access the sub-query, only applicable to recursive types.
subscript - Variable in class org.openscience.cdk.renderer.elements.TextGroupElement.Child: A subscript (if any) for the child.
Substance - Class in org.openscience.cdk.silent: An implementation of the ISubstance interface.
Substance - Class in org.openscience.cdk: An implementation of the ISubstance interface.
Substance() - Constructor for class org.openscience.cdk.silent.Substance
Substance() - Constructor for class org.openscience.cdk.Substance
SubStructure - org.openscience.cdk.smsd.interfaces.Algorithm: Deprecated.

Substructure search will return all maps.
SubstructureFingerprinter - Class in org.openscience.cdk.fingerprint: IFingerprinter that gives a bit set which has a size equal to the number of substructures it was constructed from.
SubstructureFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.SubstructureFingerprinter: Set up the fingerprinter to use the fragments from StandardSubstructureSets.
SubstructureFingerprinter(String[]) - Constructor for class org.openscience.cdk.fingerprint.SubstructureFingerprinter: Set up the fingerprinter to use a user-defined set of fragments.
successor(int[], int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Calculation of the next index pair in a matrix.
SUCF - net.sf.jniinchi.INCHI_OPTION
suggest(Class<?>) - Method in class org.openscience.cdk.DynamicFactory: Provides a list of all possible constructor keys for the provided interface.
Sulfur - org.openscience.cdk.config.Elements
SULFUR - Static variable in enum org.openscience.cdk.config.Elements
sum(int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Summing entries of an array.
sum(int[], int) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Summing entries of a list until a given index.
suppressHydrogens() - Method in class org.openscience.cdk.hash.HashGeneratorMaker: Suppress any explicit hydrogens in the encoding of hash values.
suppressHydrogens(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: Suppress any explicit hydrogens in the provided container.
suppressQueryHydrogens(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
SUU - net.sf.jniinchi.INCHI_OPTION
SVG_FMT - Static variable in class org.openscience.cdk.depict.Depiction: Structured Vector Graphics (SVG) format key.
SVGFormat - Class in org.openscience.cdk.io.formats
SVGFormat() - Constructor for class org.openscience.cdk.io.formats.SVGFormat
svgStyleCache(String, double, SvgDrawVisitor, List<? extends IRenderingElement>) - Method in class org.openscience.cdk.depict.Depiction
SW - org.openscience.cdk.renderer.elements.TextGroupElement.Position
swap(int[], int, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen
swap(String[], int, int) - Method in class org.openscience.cdk.structgen.maygen.Maygen
SwingEventRelay - Class in org.openscience.cdk.controller
SwingEventRelay(JComponent) - Constructor for class org.openscience.cdk.controller.SwingEventRelay
SwingGUIListener - Class in org.openscience.cdk.io.listener: Allows processing of IOSetting quesions which are passed to the user by using Swing dialogs.
SwingGUIListener(Component, IOSetting.Importance) - Constructor for class org.openscience.cdk.io.listener.SwingGUIListener: 0 = ask no questions 3 = ask all questions
SwingMouseEventRelay - Class in org.openscience.cdk.controller
SwingMouseEventRelay(IMouseEventRelay) - Constructor for class org.openscience.cdk.controller.SwingMouseEventRelay
SwissArmyKnife - Class in org.openscience.cdk.tools: Deprecated.
SwissArmyKnife() - Constructor for class org.openscience.cdk.tools.SwissArmyKnife: Deprecated.
SwitchTo(int) - Method in class org.openscience.cdk.iupac.parser.NomParserTokenManager: Switch to specified lex state.
SwitchTo(int) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager: Switch to specified lex state.
SybylAtomTypeMatcher - Class in org.openscience.cdk.atomtype: Atom Type matcher for Sybyl atom types.
SybylDescriptorFormat - Class in org.openscience.cdk.io.formats: See here.
SybylDescriptorFormat() - Constructor for class org.openscience.cdk.io.formats.SybylDescriptorFormat
symbol - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom: The element symbol for this element as listed in the periodic table.
symbol() - Method in enum org.openscience.cdk.config.Elements: The element symbol, C for carbon, N for nitrogen, Na for sodium, etc.
SYMBOL - Static variable in class org.openscience.cdk.libio.jena.CDK
SymbolAndChargeQueryAtom - Class in org.openscience.cdk.isomorphism.matchers: Deprecated.
SymbolAndChargeQueryAtom(IAtom) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolAndChargeQueryAtom: Deprecated.
SymbolAndChargeQueryAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolAndChargeQueryAtom: Deprecated.
SymbolChargeIDQueryAtom - Class in org.openscience.cdk.isomorphism.matchers
SymbolChargeIDQueryAtom(IAtom) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolChargeIDQueryAtom
SymbolChargeIDQueryAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolChargeIDQueryAtom
SymbolMarginRatio() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.SymbolMarginRatio
SymbolQueryAtom - Class in org.openscience.cdk.isomorphism.matchers: Deprecated.
SymbolQueryAtom(IAtom) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom: Deprecated.
SymbolQueryAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom: Deprecated.
SymbolSetQueryAtom - Class in org.openscience.cdk.isomorphism.matchers: Deprecated.
Use new Expr(Element, 6).and(new Expr(Element, 8)) etc
SymbolSetQueryAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom: Deprecated.

Constructor for the SymbolSetQueryAtom object
SymbolVisibility - Class in org.openscience.cdk.renderer: Predicate that defines whether an atom symbol is displayed in a structure diagram.
SymbolVisibility() - Constructor for class org.openscience.cdk.renderer.SymbolVisibility
symmetry(IAtomContainer, int[][]) - Static method in class org.openscience.cdk.graph.invariant.Canon: Compute the symmetry classes for the provided structure.
symmetry(IAtomContainer, int[][], int) - Static method in class org.openscience.cdk.graph.invariant.Canon: Compute the symmetry classes for the provided structure.
SYSTEMID - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
SystemOutLoggingTool - Class in org.openscience.cdk.tools: Deprecated.
should not be used directly
SystemOutLoggingTool(Class<?>) - Constructor for class org.openscience.cdk.tools.SystemOutLoggingTool: Deprecated.

Constructs a ILoggingTool which produces log lines indicating them to be for the given Class.

T

T_BOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Ta - Static variable in interface org.openscience.cdk.interfaces.IElement
TA - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
tabSize - Variable in class org.openscience.cdk.iupac.parser.SimpleCharStream
tabSize - Variable in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
TaeAminoAcidDescriptor - Class in org.openscience.cdk.qsar.descriptors.protein: An implementation of the TAE descriptors for amino acids.
TaeAminoAcidDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor
Tanimoto - Class in org.openscience.cdk.similarity: Calculates the Tanimoto coefficient for a given pair of two fingerprint bitsets or real valued feature vectors.
Tantalum - org.openscience.cdk.config.Elements
TANTALUM - Static variable in enum org.openscience.cdk.config.Elements
TANTALUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
TargetProcessor - Class in org.openscience.cdk.smsd.algorithm.mcgregor: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
TargetProcessor(List<String>, List<String>, String[], int, int, List<Integer>, List<String>, int, List<Integer>, List<String>) - Constructor for class org.openscience.cdk.smsd.algorithm.mcgregor.TargetProcessor: Deprecated.
TargetProperties - Class in org.openscience.cdk.smsd.algorithm.vflib.builder: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
TargetProperties(IAtomContainer) - Constructor for class org.openscience.cdk.smsd.algorithm.vflib.builder.TargetProperties: Deprecated.
TautomerizationMechanism - Class in org.openscience.cdk.reaction.mechanism: This mechanism produces the tautomerization chemical reaction between two tautomers.
TautomerizationMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.TautomerizationMechanism
TautomerizationReaction - Class in org.openscience.cdk.reaction.type: IReactionProcess which produces a tautomerization chemical reaction.
TautomerizationReaction() - Constructor for class org.openscience.cdk.reaction.type.TautomerizationReaction: Constructor of the TautomerizationReaction object.
Tb - Static variable in interface org.openscience.cdk.interfaces.IElement
TB - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
TBPY - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Trigonal Bipyramidal (TBPY-5)
Tc - Static variable in interface org.openscience.cdk.interfaces.IElement
TC - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Te - Static variable in interface org.openscience.cdk.interfaces.IElement
TE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Technetium - org.openscience.cdk.config.Elements
TECHNETIUM - Static variable in enum org.openscience.cdk.config.Elements
TECHNETIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Tellurium - org.openscience.cdk.config.Elements
TELLURIUM - Static variable in enum org.openscience.cdk.config.Elements
TELLURIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
TEMPLATE_PATH - Static variable in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D
TemplateExtractor - Class in org.openscience.cdk.modeling.builder3d: Helper class that help setup a template library of CDK's Builder3D.
TemplateExtractor() - Constructor for class org.openscience.cdk.modeling.builder3d.TemplateExtractor
TemplateHandler - Class in org.openscience.cdk.layout: Helper class for Structure Diagram Generation.
TemplateHandler() - Constructor for class org.openscience.cdk.layout.TemplateHandler: Creates a new TemplateHandler without any default templates.
TemplateHandler(IChemObjectBuilder) - Constructor for class org.openscience.cdk.layout.TemplateHandler: Creates a new TemplateHandler with default templates loaded.
TemplateHandler3D - Class in org.openscience.cdk.modeling.builder3d: Helper class for ModelBuilder3D.
Tennessine - org.openscience.cdk.config.Elements
tensNoUnits() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Deal with fragments refering to the positioning of the base numbers (denoting their magnitude)
tensWithUnits() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Deals with numbers above 30 where the base numbers set appear twice.
Terbium - org.openscience.cdk.config.Elements
TERBIUM - Static variable in enum org.openscience.cdk.config.Elements
TERBIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Tessellate - Class in org.openscience.cdk.geometry.surface: Performs a tessellation of the unit sphere.
Tessellate() - Constructor for class org.openscience.cdk.geometry.surface.Tessellate
Tessellate(String, int) - Constructor for class org.openscience.cdk.geometry.surface.Tessellate
test(int[]) - Method in class org.openscience.cdk.isomorphism.SmartsStereoMatch: Deprecated.

Is the mapping of the stereochemistry in the query preserved in the target.
test(Permutation) - Method in class org.openscience.cdk.group.PermutationGroup: Test a permutation to see if it is in the group.
TestMoleculeFactory - Class in org.openscience.cdk.templates: This class contains methods for generating simple organic molecules and is copy of MoleculeFactory for use in tests.
TestMoleculeFactory() - Constructor for class org.openscience.cdk.templates.TestMoleculeFactory
TETR - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Tetracoordinate - org.openscience.cdk.stereo.Stereocenters.Type: A potentially stereogenic atom with 4 neighbors - tetrahedral centres.
Tetrahedral - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Tetrahedral (T-4) (e.g.
TETRAHEDRAL - org.openscience.cdk.stereo.StereoTool.StereoClass
TETRAHEDRAL_ANGLE - Static variable in class org.openscience.cdk.geometry.AtomTools
TETRAHEDRAL_ANGLE - Static variable in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
TetrahedralChirality - Class in org.openscience.cdk.stereo: Stereochemistry specification for tetravalent atoms.
TetrahedralChirality(IAtom, IAtom[], int) - Constructor for class org.openscience.cdk.stereo.TetrahedralChirality
TetrahedralChirality(IAtom, IAtom[], ITetrahedralChirality.Stereo) - Constructor for class org.openscience.cdk.stereo.TetrahedralChirality
TetrahedralElementEncoderFactory - Class in org.openscience.cdk.hash.stereo: Defines a stereo encoder factory for the hash code.
TetrahedralElementEncoderFactory() - Constructor for class org.openscience.cdk.hash.stereo.TetrahedralElementEncoderFactory
text - Variable in class org.openscience.cdk.renderer.elements.TextElement: The text to be displayed.
text - Variable in class org.openscience.cdk.renderer.elements.TextGroupElement.Child: The text of this child.
TextElement - Class in org.openscience.cdk.renderer.elements: Text element as used in the chemical drawing.
TextElement(double, double, String, Color) - Constructor for class org.openscience.cdk.renderer.elements.TextElement: Constructs a new TextElement with the content text to be drawn at position (x,y) in the color color.
TextGroupElement - Class in org.openscience.cdk.renderer.elements: A group of text elements, particularly the element symbol (eg: "C") surrounded by other annotations such as mass number, charge, etc.
TextGroupElement(double, double, String, Color) - Constructor for class org.openscience.cdk.renderer.elements.TextGroupElement: Make a text group at (x, y) with the text and color given.
TextGroupElement.Child - Class in org.openscience.cdk.renderer.elements: A string of text that should be shown around the parent.
TextGroupElement.Position - Enum in org.openscience.cdk.renderer.elements: Compass-point positions for text element annotation children.
TextGUIListener - Class in org.openscience.cdk.io.listener: Allows processing of IOSetting quesions which are passed to the user by using the System.out and System.in by default.
TextGUIListener(IOSetting.Importance) - Constructor for class org.openscience.cdk.io.listener.TextGUIListener
Th - Static variable in interface org.openscience.cdk.interfaces.IElement
TH - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Tetrahedral (T-4) (e.g.
TH - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Thallium - org.openscience.cdk.config.Elements
THALLIUM - Static variable in enum org.openscience.cdk.config.Elements
THALLIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
THIOPHENE_RING - Static variable in class org.openscience.cdk.tools.AtomTypeTools
Thorium - org.openscience.cdk.config.Elements
THORIUM - Static variable in enum org.openscience.cdk.config.Elements
THORIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Thulium - org.openscience.cdk.config.Elements
THULIUM - Static variable in enum org.openscience.cdk.config.Elements
THULIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Ti - Static variable in interface org.openscience.cdk.interfaces.IElement
TI - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
TimeManager - Class in org.openscience.cdk.smsd.tools: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
TimeManager() - Constructor for class org.openscience.cdk.smsd.tools.TimeManager: Deprecated.

Constructor for storing execution time
timeout(long) - Static method in exception org.openscience.cdk.exception.Intractable: Utility for creating a message which indicates an operation timed out after a given time in milliseconds, t.
timeout(String, long) - Static method in exception org.openscience.cdk.exception.Intractable: Utility for creating a message which indicates an operation timed out after a given time in milliseconds, t.
TimeOut - Class in org.openscience.cdk.smsd.global: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
TimeOut() - Constructor for class org.openscience.cdk.smsd.global.TimeOut: Deprecated.
Tin - org.openscience.cdk.config.Elements
TIN - Static variable in enum org.openscience.cdk.config.Elements
TIN - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
TinkerMM2Format - Class in org.openscience.cdk.io.formats: See here.
TinkerMM2Format() - Constructor for class org.openscience.cdk.io.formats.TinkerMM2Format
TinkerXYZFormat - Class in org.openscience.cdk.io.formats: See here.
TinkerXYZFormat() - Constructor for class org.openscience.cdk.io.formats.TinkerXYZFormat
Titanium - org.openscience.cdk.config.Elements
TITANIUM - Static variable in enum org.openscience.cdk.config.Elements
TITANIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
TITLE - Static variable in class org.openscience.cdk.CDKConstants: The title for a IChemObject.
TitleColor() - Constructor for class org.openscience.cdk.renderer.RendererModel.TitleColor
TitleFontScale() - Constructor for class org.openscience.cdk.renderer.RendererModel.TitleFontScale
Tl - Static variable in interface org.openscience.cdk.interfaces.IElement
TL - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
Tm - Static variable in interface org.openscience.cdk.interfaces.IElement
TM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
toAdjList(IAtomContainer) - Static method in class org.openscience.cdk.graph.GraphUtil: Create an adjacent list representation of the container.
toAdjList(IAtomContainer, GraphUtil.EdgeToBondMap) - Static method in class org.openscience.cdk.graph.GraphUtil: Create an adjacent list representation of the container and fill in the bondMap for quick lookup.
toAdjListSubgraph(IAtomContainer, Set<IBond>) - Static method in class org.openscience.cdk.graph.GraphUtil: Create an adjacent list representation of the container that only includes bonds that are in the set provided as an argument.
toArray() - Method in class org.openscience.cdk.ConformerContainer: Returns the conformers in the form of an array of IAtomContainers.
toArray() - Method in class org.openscience.cdk.isomorphism.Mappings: Mappings are lazily generated and best used in a loop.
toArray(IAtomContainer[]) - Method in class org.openscience.cdk.ConformerContainer
toArray(T[]) - Method in class org.openscience.cdk.io.setting.SettingManager: Compatibility method generates an array of ISetting objects.
toAtomBondMap() - Method in class org.openscience.cdk.isomorphism.Mappings: Convert the permutations to an atom-atom bond-bond map.
toAtomMap() - Method in class org.openscience.cdk.isomorphism.Mappings: Convert the permutations to a atom-atom map.
toBondMap() - Method in class org.openscience.cdk.isomorphism.Mappings: Convert the permutations to a bond-bond map.
toCanonicalSignatureString(int) - Method in class org.openscience.cdk.signature.MoleculeSignature: Make a canonical signature string of a given height.
toChemObjects() - Method in class org.openscience.cdk.isomorphism.Mappings: Obtain the chem objects (atoms and bonds) that have 'hit' in the target molecule.
toConfig(IDoubleBondStereochemistry.Conformation) - Static method in enum org.openscience.cdk.interfaces.IDoubleBondStereochemistry.Conformation
toConfig(ITetrahedralChirality.Stereo) - Static method in enum org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo
toConformation(int) - Static method in enum org.openscience.cdk.interfaces.IDoubleBondStereochemistry.Conformation
toCycleString() - Method in class org.openscience.cdk.group.Permutation: An easily-readable version of the permutation as a product of cycles.
toEpsStr() - Method in class org.openscience.cdk.depict.Depiction: Render the image to an EPS (Encapsulated PostScript) format string.
toFirst - org.openscience.cdk.renderer.elements.WedgeLineElement.Direction
TOGETHER - org.openscience.cdk.interfaces.IDoubleBondStereochemistry.Conformation
TOGETHER - Static variable in interface org.openscience.cdk.interfaces.IStereoElement
toIElement() - Method in enum org.openscience.cdk.config.Elements: Access an IElement instance of the chemical element.
toImg() - Method in class org.openscience.cdk.depict.Depiction: Render the depiction to a Java AWT BufferedImage.
token - Variable in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Current token.
token - Variable in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser: Current token.
Token - Class in org.openscience.cdk.iupac.parser: Describes the input token stream.
Token - Class in org.openscience.cdk.smiles.smarts.parser: Describes the input token stream.
Token() - Constructor for class org.openscience.cdk.iupac.parser.Token: No-argument constructor
Token() - Constructor for class org.openscience.cdk.smiles.smarts.parser.Token: No-argument constructor
Token(int) - Constructor for class org.openscience.cdk.iupac.parser.Token: Constructs a new token for the specified Image.
Token(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.Token: Constructs a new token for the specified Image.
Token(int, String) - Constructor for class org.openscience.cdk.iupac.parser.Token: Constructs a new token for the specified Image and Kind.
Token(int, String) - Constructor for class org.openscience.cdk.smiles.smarts.parser.Token: Constructs a new token for the specified Image and Kind.
token_source - Variable in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Generated Token Manager.
token_source - Variable in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser: Generated Token Manager.
tokenImage - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: Literal token values.
tokenImage - Variable in exception org.openscience.cdk.iupac.parser.ParseException: This is a reference to the "tokenImage" array of the generated parser within which the parse error occurred.
tokenImage - Variable in exception org.openscience.cdk.smiles.smarts.parser.ParseException: This is a reference to the "tokenImage" array of the generated parser within which the parse error occurred.
tokenImage - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: Literal token values.
TokenMgrError - Error in org.openscience.cdk.iupac.parser: Token Manager Error.
TokenMgrError - Error in org.openscience.cdk.smiles.smarts.parser: Token Manager Error.
TokenMgrError() - Constructor for error org.openscience.cdk.iupac.parser.TokenMgrError: No arg constructor.
TokenMgrError() - Constructor for error org.openscience.cdk.smiles.smarts.parser.TokenMgrError: No arg constructor.
TokenMgrError(boolean, int, int, int, String, int, int) - Constructor for error org.openscience.cdk.iupac.parser.TokenMgrError: Full Constructor.
TokenMgrError(boolean, int, int, int, String, int, int) - Constructor for error org.openscience.cdk.smiles.smarts.parser.TokenMgrError: Full Constructor.
TokenMgrError(String, int) - Constructor for error org.openscience.cdk.iupac.parser.TokenMgrError: Constructor with message and reason.
TokenMgrError(String, int) - Constructor for error org.openscience.cdk.smiles.smarts.parser.TokenMgrError: Constructor with message and reason.
ToleranceRangeRule - Class in org.openscience.cdk.formula.rules: This class validate if the mass from an IMolecularFormula is between the tolerance range give a experimental mass.
ToleranceRangeRule() - Constructor for class org.openscience.cdk.formula.rules.ToleranceRangeRule: Constructor for the ToleranceRangeRule object.
toMiddle() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager: Set the font size pointer to the middle of the range.
toModelCoordinates(double, double) - Method in class org.openscience.cdk.renderer.AbstractRenderer: Convert a point in screen space into a point in model space.
toModelCoordinates(double, double) - Method in interface org.openscience.cdk.renderer.IRenderer: Converts screen coordinates into model (or world) coordinates.
toMolecule(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator: Converts a reaction to an 'inlined' reaction stored as a molecule.
toPdfStr() - Method in class org.openscience.cdk.depict.Depiction: Render the image to an PDF format string.
toPermutation() - Method in class org.openscience.cdk.group.Partition: Converts the whole partition into a permutation.
TopologicalMatrix - Class in org.openscience.cdk.graph.matrix: Calculator for a topological matrix representation of this AtomContainer.
TopologicalMatrix() - Constructor for class org.openscience.cdk.graph.matrix.TopologicalMatrix
toPsStr() - Method in class org.openscience.cdk.depict.Depiction: Render the image to an PS (PostScript) format string.
toReaction(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator: Converts an 'inlined' reaction stored in a molecule back to a reaction.
toRingSet() - Method in class org.openscience.cdk.graph.Cycles: Convert the cycles to a IRingSet containing the IAtoms and IBonds of the input molecule.
toRotationMatrix() - Method in class org.openscience.cdk.math.Quaternion
toScreenCoordinates(double, double) - Method in class org.openscience.cdk.renderer.AbstractRenderer: Convert a point in model space into a point in screen space.
toScreenCoordinates(double, double) - Method in interface org.openscience.cdk.renderer.IRenderer: Converts model (or world) coordinates into screen coordinates.
toSecond - org.openscience.cdk.renderer.elements.WedgeLineElement.Direction
toStereo(int) - Static method in enum org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo
toString() - Method in class org.openscience.cdk.AminoAcid
toString() - Method in class org.openscience.cdk.Association: Returns a one line string representation of this Container.
toString() - Method in class org.openscience.cdk.Atom: Returns a one line string representation of this Atom.
toString() - Method in class org.openscience.cdk.AtomContainer: Returns a one line description of this IChemObject.
toString() - Method in class org.openscience.cdk.AtomContainerSet: Returns the String representation of this AtomContainerSet.
toString() - Method in class org.openscience.cdk.AtomRef
toString() - Method in class org.openscience.cdk.AtomType
toString() - Method in class org.openscience.cdk.BioPolymer
toString() - Method in class org.openscience.cdk.Bond: Returns a one line string representation of this Container.
toString() - Method in class org.openscience.cdk.BondRef
toString() - Method in class org.openscience.cdk.ChemFile: Returns a String representation of this class.
toString() - Method in class org.openscience.cdk.ChemModel: Returns a String representation of the contents of this IChemObject.
toString() - Method in class org.openscience.cdk.ChemSequence
toString() - Method in class org.openscience.cdk.Crystal: Returns a String representation of this crystal.
toString() - Method in class org.openscience.cdk.dict.DictRef
toString() - Method in class org.openscience.cdk.dict.Entry
toString() - Method in class org.openscience.cdk.DynamicFactory.ConstructorKey
toString() - Method in class org.openscience.cdk.ElectronContainer
toString() - Method in class org.openscience.cdk.Element
toString() - Method in class org.openscience.cdk.fingerprint.ShortestPathWalker
toString() - Method in class org.openscience.cdk.formula.IsotopeContainer
toString() - Method in class org.openscience.cdk.FragmentAtom
toString() - Method in class org.openscience.cdk.graph.Matching
toString() - Method in class org.openscience.cdk.graph.rebond.Bspt
toString() - Method in class org.openscience.cdk.graph.rebond.Point
toString() - Method in class org.openscience.cdk.group.DisjointSetForest
toString() - Method in class org.openscience.cdk.group.Partition
toString() - Method in class org.openscience.cdk.group.Permutation
toString() - Method in class org.openscience.cdk.group.PermutationGroup
toString() - Method in interface org.openscience.cdk.interfaces.IChemObject: Returns a one line description of this IChemObject.
toString() - Method in class org.openscience.cdk.io.cml.CMLModuleStack: Returns a String representation of the stack.
toString() - Method in class org.openscience.cdk.io.random.RandomAccessReader
toString() - Method in class org.openscience.cdk.isomorphism.matchers.Expr
toString() - Method in class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom: Deprecated.

The toString method
toString() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
toString() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Returns a one line string representation of this query bond.
toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AliphaticAtom: Deprecated.
toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AliphaticSymbolAtom: Deprecated.
toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AnyAtom: Deprecated.
toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AnyOrderQueryBond: Deprecated.
toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AromaticAtom: Deprecated.
toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AromaticOrSingleQueryBond: Deprecated.
toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AromaticQueryBond: Deprecated.
toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AromaticSymbolAtom: Deprecated.
toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.FormalChargeAtom: Deprecated.
toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.HybridizationNumberAtom: Deprecated.
toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ImplicitHCountAtom: Deprecated.
toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.MassAtom: Deprecated.
toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.NonCHHeavyAtom: Deprecated.
toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.OrderQueryBond: Deprecated.
toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.PeriodicGroupNumberAtom: Deprecated.
toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ReactionRoleQueryAtom: Deprecated.
toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.TotalHCountAtom: Deprecated.

Returns a one line description of this IChemObject.
toString() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolAndChargeQueryAtom: Deprecated.
toString() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolChargeIDQueryAtom
toString() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom: Deprecated.
toString() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom: Deprecated.

The toString method
toString() - Method in class org.openscience.cdk.isomorphism.mcss.RGraph: Returns a string representation of the RGraph.
toString() - Method in class org.openscience.cdk.isomorphism.mcss.RNode: Returns a string representation of the RNode.
toString() - Method in class org.openscience.cdk.Isotope: A string representation of this isotope.
toString() - Method in class org.openscience.cdk.iupac.parser.AttachedGroup: A debug string which represents the contents of the class.
toString() - Method in class org.openscience.cdk.iupac.parser.Token: Returns the image.
toString() - Method in class org.openscience.cdk.LonePair: Returns a one line string representation of this LonePair.
toString() - Method in class org.openscience.cdk.math.Complex: Create a string of the content of this class
toString() - Method in class org.openscience.cdk.math.IMatrix: Return a matrix as a string
toString() - Method in class org.openscience.cdk.math.IVector: Return a vector as a string
toString() - Method in class org.openscience.cdk.math.Matrix: Return a matrix as a String.
toString() - Method in class org.openscience.cdk.math.Quaternion
toString() - Method in class org.openscience.cdk.math.Vector: Return a vector as a string
toString() - Method in class org.openscience.cdk.Monomer
toString() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQuery: String representation of this query.
toString() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryAngleBond: String representation of an angle constraint.
toString() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryAtom: String representation of this pharmacophore group.
toString() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryBond: String representation of a distance constraint.
toString() - Method in class org.openscience.cdk.Polymer
toString() - Method in class org.openscience.cdk.protein.data.PDBAtom: Returns a one line string representation of this Atom.
toString() - Method in class org.openscience.cdk.protein.data.PDBMonomer: Returns a one line string representation of this Atom.
toString() - Method in class org.openscience.cdk.protein.data.PDBPolymer
toString() - Method in class org.openscience.cdk.protein.data.PDBStrand
toString() - Method in class org.openscience.cdk.PseudoAtom: Returns a one line string representation of this Atom.
toString() - Method in class org.openscience.cdk.qsar.result.BooleanResult
toString() - Method in class org.openscience.cdk.qsar.result.BooleanResultType
toString() - Method in class org.openscience.cdk.qsar.result.DoubleArrayResult
toString() - Method in class org.openscience.cdk.qsar.result.DoubleArrayResultType
toString() - Method in class org.openscience.cdk.qsar.result.DoubleResult
toString() - Method in class org.openscience.cdk.qsar.result.DoubleResultType
toString() - Method in interface org.openscience.cdk.qsar.result.IDescriptorResult: String representation of the result.
toString() - Method in class org.openscience.cdk.qsar.result.IntegerArrayResult
toString() - Method in class org.openscience.cdk.qsar.result.IntegerArrayResultType
toString() - Method in class org.openscience.cdk.qsar.result.IntegerResult
toString() - Method in class org.openscience.cdk.qsar.result.IntegerResultType
toString() - Method in class org.openscience.cdk.Reaction: Returns a one line string representation of this Atom.
toString() - Method in class org.openscience.cdk.ReactionSet
toString() - Method in class org.openscience.cdk.renderer.elements.Bounds
toString() - Method in class org.openscience.cdk.Ring
toString() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycle: Deprecated.
toString() - Method in class org.openscience.cdk.RingSet: Returns the String representation of this RingSet.
toString() - Method in class org.openscience.cdk.sgroup.SgroupBracket
toString() - Method in class org.openscience.cdk.signature.Orbit
toString() - Method in class org.openscience.cdk.silent.AminoAcid
toString() - Method in class org.openscience.cdk.silent.Atom: Returns a one line string representation of this Atom.
toString() - Method in class org.openscience.cdk.silent.AtomContainer: Returns a one line description of this IChemObject.
toString() - Method in class org.openscience.cdk.silent.AtomContainerSet: Returns the String representation of this AtomContainerSet.
toString() - Method in class org.openscience.cdk.silent.AtomType
toString() - Method in class org.openscience.cdk.silent.BioPolymer
toString() - Method in class org.openscience.cdk.silent.Bond: Returns a one line string representation of this Container.
toString() - Method in class org.openscience.cdk.silent.ChemFile: Returns a String representation of this class.
toString() - Method in class org.openscience.cdk.silent.ChemModel: Returns a String representation of the contents of this IChemObject.
toString() - Method in class org.openscience.cdk.silent.ChemSequence
toString() - Method in class org.openscience.cdk.silent.Crystal: Returns a String representation of this crystal.
toString() - Method in class org.openscience.cdk.silent.ElectronContainer
toString() - Method in class org.openscience.cdk.silent.Element
toString() - Method in class org.openscience.cdk.silent.FragmentAtom
toString() - Method in class org.openscience.cdk.silent.Isotope: A string representation of this isotope.
toString() - Method in class org.openscience.cdk.silent.LonePair: Returns a one line string representation of this LonePair.
toString() - Method in class org.openscience.cdk.silent.Monomer
toString() - Method in class org.openscience.cdk.silent.PDBAtom: Returns a one line string representation of this Atom.
toString() - Method in class org.openscience.cdk.silent.PDBMonomer: Returns a one line string representation of this Atom.
toString() - Method in class org.openscience.cdk.silent.PDBPolymer
toString() - Method in class org.openscience.cdk.silent.Polymer
toString() - Method in class org.openscience.cdk.silent.PseudoAtom: Returns a one line string representation of this Atom.
toString() - Method in class org.openscience.cdk.silent.Reaction: Returns a one line string representation of this Atom.
toString() - Method in class org.openscience.cdk.silent.ReactionSet
toString() - Method in class org.openscience.cdk.silent.Ring
toString() - Method in class org.openscience.cdk.silent.RingSet: Returns the String representation of this RingSet.
toString() - Method in class org.openscience.cdk.silent.SingleElectron: Returns a one line string representation of this SingleElectron.
toString() - Method in class org.openscience.cdk.silent.Strand
toString() - Method in class org.openscience.cdk.SingleElectron: Returns a one line string representation of this SingleElectron.
toString() - Method in class org.openscience.cdk.smiles.InvPair: String representation.
toString() - Method in class org.openscience.cdk.smiles.smarts.parser.Token: Returns the image.
toString() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph: Deprecated.

Returns a string representation of the CDKRGraph.
toString() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode: Deprecated.

Returns a string representation of the RNode
toString() - Method in class org.openscience.cdk.stereo.TetrahedralChirality: Returns a String representation of this chiral element.
toString() - Method in class org.openscience.cdk.Strand
toString() - Method in class org.openscience.cdk.tools.diff.tree.AtomTypeHybridizationDifference: Returns a String representation for this IDifference.
toString() - Method in class org.openscience.cdk.tools.diff.tree.BondOrderDifference: Returns a String representation for this IDifference.
toString() - Method in class org.openscience.cdk.tools.diff.tree.BooleanArrayDifference: Returns a String representation for this IDifference.
toString() - Method in class org.openscience.cdk.tools.diff.tree.BooleanDifference: Returns a String representation for this IDifference.
toString() - Method in class org.openscience.cdk.tools.diff.tree.ChemObjectDifference: Returns a String representation for this IDifference.
toString() - Method in class org.openscience.cdk.tools.diff.tree.DoubleDifference: Returns a String representation for this IDifference.
toString() - Method in class org.openscience.cdk.tools.diff.tree.IntegerDifference: Returns a String representation for this IDifference.
toString() - Method in class org.openscience.cdk.tools.diff.tree.Point2dDifference: Returns a String representation for this IDifference.
toString() - Method in class org.openscience.cdk.tools.diff.tree.Point3dDifference: Returns a String representation for this IDifference.
toString() - Method in class org.openscience.cdk.tools.diff.tree.StringDifference: Returns a String representation for this IDifference.
toString() - Method in class org.openscience.cdk.tools.FormatStringBuffer: Get the result of the formatting.
toString() - Method in class org.openscience.cdk.tools.GridGenerator
toString(IAtomContainer) - Method in class org.openscience.cdk.smsd.labelling.AtomContainerPrinter: Deprecated.
toSubstructures() - Method in class org.openscience.cdk.isomorphism.Mappings: Obtain the mapped substructures (atoms/bonds) of the target compound.
toSubstructuresStream() - Method in class org.openscience.cdk.isomorphism.Mappings: Obtain the mapped substructures (atoms/bonds) of the target compound.
toSvgStr() - Method in class org.openscience.cdk.depict.Depiction: Render the image to an SVG image.
toSvgStr(String) - Method in class org.openscience.cdk.depict.Depiction: Render the image to an SVG image.
TOTAL_CONNECTIONS - Static variable in class org.openscience.cdk.CDKConstants
TOTAL_DEGREE - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if the total degree (IAtom.getBondCount() + IAtom.getImplicitHydrogenCount()) of an atom equals the specified 'value'.
TOTAL_H_COUNT - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if the total hydrogen count of an atom equals the specified 'value'.
TOTAL_H_COUNT - Static variable in class org.openscience.cdk.CDKConstants
TotalConnectionAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
TotalConnectionAtom(int, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.TotalConnectionAtom: Deprecated.

Creates a new instance.
TotalConnectivity() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
TotalHCount() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
TotalHCountAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
TotalHCountAtom(int, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.TotalHCountAtom: Deprecated.
TotalRingConnectionAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
TotalRingConnectionAtom(int, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.TotalRingConnectionAtom: Deprecated.

Create a matcher for the number of rings an atom belongs to.
TotalValencyAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts: Deprecated.
TotalValencyAtom(int, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.TotalValencyAtom: Deprecated.

Match the valence of atom.
TowardsRingCenterProportion() - Constructor for class org.openscience.cdk.renderer.generators.BasicBondGenerator.TowardsRingCenterProportion
TPSADescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Calculation of topological polar surface area based on fragment contributions (TPSA) [Ertl, P. et. al.. J. Med. Chem.. 2000. 43].
TPSADescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor: Constructor for the TPSADescriptor object.
trace() - Method in class org.openscience.cdk.graph.invariant.GIMatrix: Returns the trace of this matrix, that is the sum of the elements of its diagonal.
TRACE - Static variable in interface org.openscience.cdk.tools.ILoggingTool: Trace, Debug, Info, Warn, Error, and Fatal messages will be emitted.
trace_enabled() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Trace enabled.
trace_enabled() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser: Trace enabled.
trackLineColumn - Variable in class org.openscience.cdk.iupac.parser.SimpleCharStream
trackLineColumn - Variable in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
training - Variable in class org.openscience.cdk.fingerprint.model.Bayesian
trainingActives - Variable in class org.openscience.cdk.fingerprint.model.Bayesian
trainingSize - Variable in class org.openscience.cdk.fingerprint.model.Bayesian
transform - Variable in class org.openscience.cdk.renderer.AbstractRenderer: Converts between model coordinates and screen coordinates.
transform - Variable in class org.openscience.cdk.renderer.visitor.AbstractAWTDrawVisitor: This is initially null, and must be set in the setTransform method!
transformPoint(double[]) - Method in class org.openscience.cdk.renderer.visitor.AbstractAWTDrawVisitor
transformPoint(double, double) - Method in class org.openscience.cdk.renderer.visitor.AbstractAWTDrawVisitor: Transforms a point according to the current affine transformation, converting a world coordinate into a screen coordinate.
translate2D(IAtomContainer, double, double) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Translates the given molecule by the given Vector.
translate2D(IAtomContainer, double, double) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Translates the given molecule by the given Vector.
translate2D(IAtomContainer, Vector2d) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Translates a molecule from the origin to a new point denoted by a vector.
translate2D(IAtomContainer, Vector2d) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Translates a molecule from the origin to a new point denoted by a vector.
translate2DCenterTo(IAtomContainer, Point2d) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Translates the geometric 2DCenter of the given AtomContainer container to the specified Point2d p.
translate2DCenterTo(IAtomContainer, Point2d) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Translates the geometric 2DCenter of the given AtomContainer container to the specified Point2d p.
translate2DCentreOfMassTo(IAtomContainer, Point2d) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Translates a molecule from the origin to a new point denoted by a vector.
translate2DCentreOfMassTo(IAtomContainer, Point2d) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Translates a molecule from the origin to a new point denoted by a vector.
translateAllPositive(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Adds an automatically calculated offset to the coordinates of all atoms such that all coordinates are positive and the smallest x or y coordinate is exactly zero.
translateAllPositive(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Adds an automatically calculated offset to the coordinates of all atoms such that all coordinates are positive and the smallest x or y coordinate is exactly zero.
transpose() - Method in class org.openscience.cdk.graph.invariant.GIMatrix: Returns the transpose of this matrix.
transpose() - Method in class org.openscience.cdk.math.IMatrix: Transpose a matrix
transpose() - Method in class org.openscience.cdk.math.Matrix: Transposes a matrix.
transpose(IMatrix) - Method in class org.openscience.cdk.math.IMatrix: Transpose a matrix
transversal(PermutationGroup) - Method in class org.openscience.cdk.group.PermutationGroup: Generate a transversal of a subgroup in this group.
traverse(IAtomContainer, IAtom, List<IBond>) - Static method in class org.openscience.cdk.fragment.FragmentUtils
travIndex - Variable in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
TRI - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Triangle - Class in org.openscience.cdk.geometry.surface: Representation of a triangle in 3D.
Triangle(Point3d, Point3d, Point3d) - Constructor for class org.openscience.cdk.geometry.surface.Triangle
Tricoordinate - org.openscience.cdk.stereo.Stereocenters.Type: A potentially stereogenic atom with 3 neighbors - one atom in a geometric centres or cumulated system (allene, cumulene).
TRIGONAL_BIPYRAMIDAL - org.openscience.cdk.stereo.StereoTool.StereoClass
TrigonalBipyramidal - Class in org.openscience.cdk.stereo: Describes a trigonal-bipyramidal configuration.
TrigonalBipyramidal - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Trigonal Bipyramidal (TBPY-5)
TrigonalBipyramidal(IAtom, IAtom[], int) - Constructor for class org.openscience.cdk.stereo.TrigonalBipyramidal: Create a new trigonal bipyramidal configuration.
TRIPLE - org.openscience.cdk.interfaces.IBond.Order
TRIPLE - org.openscience.cdk.isomorphism.matchers.CTFileQueryBond.Type: Deprecated.
TRIPLE - org.openscience.cdk.renderer.elements.LineElement.LineType
TRIPLEBOND - Static variable in class org.openscience.cdk.libio.jena.CDK
tripletShort() - Static method in class org.openscience.cdk.graph.Cycles: Create a cycle finder which will compute the triplet short cycles of a molecule.
tripletShort(IAtomContainer) - Static method in class org.openscience.cdk.graph.Cycles: Find the triplet short cycles of a molecule.
TripletShortCycles - Class in org.openscience.cdk.graph: Compute the shortest cycles through each vertex triple.
TripletShortCycles(MinimumCycleBasis, boolean) - Constructor for class org.openscience.cdk.graph.TripletShortCycles: Compute the cycles of the extended smallest set of smallest rings (ESSSR) for an existing minimum cycle basis.
True - org.openscience.cdk.stereo.Stereocenters.Stereocenter: Atom is a true stereo-centre.
TRUE - org.openscience.cdk.isomorphism.matchers.Expr.Type: Always returns true.
Ts - Static variable in interface org.openscience.cdk.interfaces.IElement
Tungsten - org.openscience.cdk.config.Elements
TUNGSTEN - Static variable in enum org.openscience.cdk.config.Elements
TUNGSTEN - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
TurboMoleFormat - Class in org.openscience.cdk.io.formats: See here.
TurboMoleFormat() - Constructor for class org.openscience.cdk.io.formats.TurboMoleFormat
TurboSubStructure - org.openscience.cdk.smsd.interfaces.Algorithm: Deprecated.

Substructure search will return first map.
TURN - Static variable in class org.openscience.cdk.protein.data.PDBStructure
TURN - Static variable in class org.openscience.cdk.silent.PDBStructure
twoOrThreeAttachLocations() - Method in class org.openscience.cdk.iupac.parser.NomParser: Deprecated.

Two or three attach locations specidied, handle the second and if needed, the third one here.
TXTBasedAtomTypeConfigurator - Class in org.openscience.cdk.config: AtomType list configurator that uses the AtomTypes originally defined in Jmol v5.
TXTBasedAtomTypeConfigurator() - Constructor for class org.openscience.cdk.config.TXTBasedAtomTypeConfigurator
type - Variable in class org.openscience.cdk.isomorphism.matchers.CTFileQueryBond: Deprecated.

The type of this bond.
type - Variable in class org.openscience.cdk.renderer.elements.path.PathElement: the type of the path element.
type - Variable in class org.openscience.cdk.renderer.elements.WedgeLineElement: The type of the bond (dashed, wedged, not defined).
type() - Method in class org.openscience.cdk.isomorphism.matchers.Expr: Access the type of the atom expression.
type() - Method in class org.openscience.cdk.renderer.elements.path.PathElement: Get the type of the path element.
type() - Method in enum org.openscience.cdk.smsd.interfaces.Algorithm: Deprecated.

Returns type of algorithm.
type(int) - Method in class org.openscience.cdk.DynamicFactory.ConstructorKey: Access the type of class at the given parameter index.
Type - Enum in org.openscience.cdk.renderer.elements.path: The type of the path elements.

U

U - Static variable in interface org.openscience.cdk.interfaces.IElement
U - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
U_SHAPE - org.openscience.cdk.stereo.StereoTool.SquarePlanarShape
Ullmann - Class in org.openscience.cdk.isomorphism: A structure pattern which utilises the Ullmann algorithm [Ullmann J R. Journal of the Association for Computing Machinery. 1976. 23].
unchorded(CycleFinder) - Static method in class org.openscience.cdk.graph.Cycles: Derive a new cycle finder that only provides cycles without a chord.
UNDEC - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
undoableEditHappened(UndoableEditEvent) - Method in class org.openscience.cdk.controller.UndoAdapter
UndoAdapter - Class in org.openscience.cdk.controller: An undo adapter for updating the state of the undo components according to the new state of the undo history list.
UndoAdapter(UndoManager) - Constructor for class org.openscience.cdk.controller.UndoAdapter
UNEXPECTED_END_OF_INPUT - Static variable in class org.openscience.cdk.io.GamessReader
UNEXPECTED_END_OF_INPUT - Static variable in class org.openscience.cdk.io.MDLRXNReader: Deprecated.
UNEXPECTED_END_OF_INPUT - Static variable in class org.openscience.cdk.io.MDLRXNV2000Reader
UniChemXYZFormat - Class in org.openscience.cdk.io.formats
UniChemXYZFormat() - Constructor for class org.openscience.cdk.io.formats.UniChemXYZFormat
UniColor - Class in org.openscience.cdk.renderer.color: Defines an atom color that draws as a single uniform color.
UniColor(Color) - Constructor for class org.openscience.cdk.renderer.color.UniColor: Create a uniform atom colorer.
unique() - Static method in class org.openscience.cdk.smiles.SmilesGenerator: Create a unique SMILES generator.
unique(List<IAtom>) - Static method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor
Unique - Static variable in class org.openscience.cdk.smiles.SmiFlavor: Output canonical SMILES without stereochemistry, atomic masses.
uniqueAtoms() - Method in class org.openscience.cdk.isomorphism.Mappings: Filter the mappings for those which cover a unique atoms in the target.
uniqueBonds() - Method in class org.openscience.cdk.isomorphism.Mappings: Filter the mappings for those which cover a unique set of bonds in the target.
unit(int) - Static method in class org.openscience.cdk.group.Partition: Create a unit partition - in other words, the coarsest possible partition where all the elements are in one cell.
unitcellparams - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
UNITS_MM - Static variable in class org.openscience.cdk.depict.Depiction: Units in MM (specific to SVG).
UNITS_PX - Static variable in class org.openscience.cdk.depict.Depiction: Units in PX (specific to SVG).
UniversalIsomorphismTester - Class in org.openscience.cdk.isomorphism: This class implements a multipurpose structure comparison tool.
UniversalIsomorphismTester() - Constructor for class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
UniversalSmiles - Static variable in class org.openscience.cdk.smiles.SmiFlavor: Output canonical SMILES with stereochemistry and atomic masses, This output uses the InChI labelling algorithm to generate a 'Universal SMILES' [O'Boyle, Noel. Journal of Cheminformatics. 2012. 4].
Unknown - org.openscience.cdk.config.Elements
UNKNOWN - net.sf.jniinchi.INCHI_RET
UNKNOWN_STEREO - Static variable in class org.openscience.cdk.isomorphism.matchers.Expr: Sentinel value for indicating the stereochemistry configuration is not yet known.
unmark(IChemObject) - Static method in class org.openscience.cdk.validate.ProblemMarker
unmarkWithError(IChemObject) - Static method in class org.openscience.cdk.validate.ProblemMarker
unmarkWithWarning(IChemObject) - Static method in class org.openscience.cdk.validate.ProblemMarker
unmarshal(Reader) - Static method in class org.openscience.cdk.dict.Dictionary
unmarshal(Reader) - Static method in class org.openscience.cdk.dict.OWLFile
unmarshal(Reader) - Static method in class org.openscience.cdk.dict.OWLReact
unmarshal(Element, String) - Static method in class org.openscience.cdk.dict.OWLFile
unmarshal(Element, String) - Static method in class org.openscience.cdk.dict.OWLReact
unmatch(int) - Method in class org.openscience.cdk.graph.Matching: Remove a matching for the specified vertex.
unmatched(int) - Method in class org.openscience.cdk.graph.Matching: Determine if a vertex is not matched.
unregisterAtomListeners(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: A method to remove AtomListeners.
unregisterElectronContainerListeners(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator: A method to remove ElectronContainerListeners.
unsaturate(IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker: Resets the bond orders of all atoms to 1.0.
unsaturateBonds(IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker: Resets the bond order of the Bond to 1.0.
unsaturateByDecreasingBondOrder(IBond) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
UNSATURATED - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if the atom is unsaturated.
UNSET - org.openscience.cdk.interfaces.IBond.Order
UNSET - Static variable in class org.openscience.cdk.CDKConstants
unspecified() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.StereoBond: Deprecated.
UnsupportedChemObjectException - Exception in org.openscience.cdk.exception
UnsupportedChemObjectException(String) - Constructor for exception org.openscience.cdk.exception.UnsupportedChemObjectException
UNUNBIUM - Static variable in enum org.openscience.cdk.config.Elements
UNUNHEXIUM - Static variable in enum org.openscience.cdk.config.Elements
Ununoctium - org.openscience.cdk.config.Elements: Deprecated.
Ununpentium - org.openscience.cdk.config.Elements: Deprecated.
UNUNPENTIUM - Static variable in enum org.openscience.cdk.config.Elements
UNUNQUADIUM - Static variable in enum org.openscience.cdk.config.Elements
Ununseptium - org.openscience.cdk.config.Elements: Deprecated.
Ununtrium - org.openscience.cdk.config.Elements: Deprecated.
UNUNTRIUM - Static variable in enum org.openscience.cdk.config.Elements
UP - org.openscience.cdk.interfaces.IBond.Stereo: A bond pointing up of which the start atom is the stereocenter and the end atom is above the drawing plane.
UP - org.openscience.cdk.isomorphism.matchers.smarts.StereoBond.Direction: Deprecated.
UP_INVERTED - org.openscience.cdk.interfaces.IBond.Stereo: A bond pointing up of which the end atom is the stereocenter and the start atom is above the drawing plane.
UP_OR_DOWN - org.openscience.cdk.interfaces.IBond.Stereo: A bond for which there is stereochemistry, we just do not know if it is UP or DOWN.
UP_OR_DOWN_INVERTED - org.openscience.cdk.interfaces.IBond.Stereo: A bond for which there is stereochemistry, we just do not know if it is UP or DOWN.
UP_OR_UNSPECIFIED_S_BOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
UP_S_BOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
UpdateLineColumn(char) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
UpdateLineColumn(char) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
updateView() - Method in interface org.openscience.cdk.controller.IViewEventRelay
updateView() - Method in class org.openscience.cdk.controller.SwingEventRelay
updateView() - Method in class org.openscience.cdk.controller.SwingMouseEventRelay
upperIndex(int, int, int[][], Permutation) - Method in class org.openscience.cdk.structgen.maygen.Maygen: We need to calculate upperIndex.
upperTriangularC(int[], int[][][], int[][][]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: c; upper triangular matrix like given in 3.2.1.
upperTriangularL(int[], int[][][], int[][][]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: l; upper triangular matrix like given in 3.2.1.
Uranium - org.openscience.cdk.config.Elements
URANIUM - Static variable in enum org.openscience.cdk.config.Elements
URANIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
URI - Static variable in class org.openscience.cdk.libio.jena.CDK
UseAntiAliasing() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.UseAntiAliasing
UseAromaticSymbols - Static variable in class org.openscience.cdk.smiles.SmiFlavor: Writes aromatic atoms as lower case letters.
UsedFontStyle() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.UsedFontStyle
useEssentialRings() - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool: Deprecated.

Indicates that ring properties should use the Essential Rings (default).
useRelevantRings() - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool: Deprecated.

Indicates that ring properties should use the Relevant Rings.
useSmallestSetOfSmallestRings() - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool: Deprecated.

Indicates that ring properties should use the Smallest Set of Smallest Rings.
using2DCoordinates(IAtomContainer) - Static method in class org.openscience.cdk.stereo.StereoElementFactory: Create a stereo element factory for creating stereo elements using 2D coordinates and depiction labels (up/down, wedge/hatch).
using3DCoordinates(IAtomContainer) - Static method in class org.openscience.cdk.stereo.StereoElementFactory: Create a stereo element factory for creating stereo elements using 3D coordinates and depiction labels (up/down, wedge/hatch).
usingThreshold(AllRingsFinder.Threshold) - Static method in class org.openscience.cdk.ringsearch.AllRingsFinder: Create an AllRingsFinder instance using the given threshold.

V

v - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
V - Static variable in interface org.openscience.cdk.interfaces.IElement
V - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
VABCDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Volume descriptor using the method implemented in the VABCVolume class.
VABCDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor
VABCVolume - Class in org.openscience.cdk.geometry.volume: Calculates the Van der Waals volume using the method proposed in [Zhao, Yuan H. et. al.. The Journal of Organic Chemistry. 2003. 68].
VABCVolume() - Constructor for class org.openscience.cdk.geometry.volume.VABCVolume
VAdjMaDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Vertex adjacency information (magnitude): 1 + log2 m where m is the number of heavy-heavy bonds.
VAdjMaDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor: Constructor for the VAdjMaDescriptor object
Valence() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
VALENCE - org.openscience.cdk.isomorphism.matchers.Expr.Type: True if the valence of an atom equals the specified 'value'.
validate(IMolecularFormula) - Method in class org.openscience.cdk.formula.rules.ChargeRule: Validate the charge of this IMolecularFormula.
validate(IMolecularFormula) - Method in class org.openscience.cdk.formula.rules.ElementRule: Validate the occurrence of this IMolecularFormula.
validate(IMolecularFormula) - Method in interface org.openscience.cdk.formula.rules.IRule: Analyze the validity for the given IMolecularFormula.
validate(IMolecularFormula) - Method in class org.openscience.cdk.formula.rules.IsotopePatternRule: Validate the isotope pattern of this IMolecularFormula.
validate(IMolecularFormula) - Method in class org.openscience.cdk.formula.rules.MMElementRule: Validate the occurrence of this IMolecularFormula.
validate(IMolecularFormula) - Method in class org.openscience.cdk.formula.rules.NitrogenRule: Validate the nitrogen rule of this IMolecularFormula.
validate(IMolecularFormula) - Method in class org.openscience.cdk.formula.rules.RDBERule: Validate the RDBRule of this IMolecularFormula.
validate(IMolecularFormula) - Method in class org.openscience.cdk.formula.rules.ToleranceRangeRule: Validate the Tolerance Range of this IMolecularFormula.
validate(IMolecularFormula, double) - Method in class org.openscience.cdk.formula.rules.RDBERule: Validate the ion state.
validateAtom(IAtom) - Method in class org.openscience.cdk.validate.AbstractValidator
validateAtom(IAtom) - Method in class org.openscience.cdk.validate.BasicValidator
validateAtom(IAtom) - Method in interface org.openscience.cdk.validate.IValidator
validateAtom(IAtom) - Method in class org.openscience.cdk.validate.ValidatorEngine
validateAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.validate.AbstractValidator
validateAtomContainer(IAtomContainer) - Method in interface org.openscience.cdk.validate.IValidator
validateAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.validate.ValidatorEngine
validateAtomType(IAtomType) - Method in class org.openscience.cdk.validate.AbstractValidator
validateAtomType(IAtomType) - Method in interface org.openscience.cdk.validate.IValidator
validateAtomType(IAtomType) - Method in class org.openscience.cdk.validate.ValidatorEngine
validateBond(IBond) - Method in class org.openscience.cdk.validate.AbstractValidator
validateBond(IBond) - Method in class org.openscience.cdk.validate.BasicValidator
validateBond(IBond) - Method in class org.openscience.cdk.validate.Geometry3DValidator
validateBond(IBond) - Method in interface org.openscience.cdk.validate.IValidator
validateBond(IBond) - Method in class org.openscience.cdk.validate.ValidatorEngine
validateChemFile(IChemFile) - Method in class org.openscience.cdk.validate.AbstractValidator
validateChemFile(IChemFile) - Method in class org.openscience.cdk.validate.CDKValidator
validateChemFile(IChemFile) - Method in interface org.openscience.cdk.validate.IValidator
validateChemFile(IChemFile) - Method in class org.openscience.cdk.validate.ValidatorEngine
validateChemModel(IChemModel) - Method in class org.openscience.cdk.validate.AbstractValidator
validateChemModel(IChemModel) - Method in interface org.openscience.cdk.validate.IValidator
validateChemModel(IChemModel) - Method in class org.openscience.cdk.validate.ValidatorEngine
validateChemObject(IChemObject) - Method in class org.openscience.cdk.validate.AbstractValidator
validateChemObject(IChemObject) - Method in class org.openscience.cdk.validate.DictionaryValidator
validateChemObject(IChemObject) - Method in interface org.openscience.cdk.validate.IValidator
validateChemObject(IChemObject) - Method in class org.openscience.cdk.validate.ValidatorEngine
validateChemSequence(IChemSequence) - Method in class org.openscience.cdk.validate.AbstractValidator
validateChemSequence(IChemSequence) - Method in class org.openscience.cdk.validate.CDKValidator
validateChemSequence(IChemSequence) - Method in interface org.openscience.cdk.validate.IValidator
validateChemSequence(IChemSequence) - Method in class org.openscience.cdk.validate.ValidatorEngine
validateCrystal(ICrystal) - Method in class org.openscience.cdk.validate.AbstractValidator
validateCrystal(ICrystal) - Method in interface org.openscience.cdk.validate.IValidator
validateCrystal(ICrystal) - Method in class org.openscience.cdk.validate.ValidatorEngine
validateElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.validate.AbstractValidator
validateElectronContainer(IElectronContainer) - Method in interface org.openscience.cdk.validate.IValidator
validateElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.validate.ValidatorEngine
validateElement(IElement) - Method in class org.openscience.cdk.validate.AbstractValidator
validateElement(IElement) - Method in interface org.openscience.cdk.validate.IValidator
validateElement(IElement) - Method in class org.openscience.cdk.validate.ValidatorEngine
validateFiveFold() - Method in class org.openscience.cdk.fingerprint.model.Bayesian: Produces a ROC validation set by partitioning the inputs into 5 groups, and performing five separate 80% in/20% out model simulations.
validateFormula(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen
validateFuzzyFormula(String) - Method in class org.openscience.cdk.structgen.maygen.Maygen
validateIsotope(IIsotope) - Method in class org.openscience.cdk.validate.AbstractValidator
validateIsotope(IIsotope) - Method in class org.openscience.cdk.validate.BasicValidator
validateIsotope(IIsotope) - Method in interface org.openscience.cdk.validate.IValidator
validateIsotope(IIsotope) - Method in class org.openscience.cdk.validate.ValidatorEngine
validateIsotopeExistence(IIsotope) - Method in class org.openscience.cdk.validate.BasicValidator
validateLeaveOneOut() - Method in class org.openscience.cdk.fingerprint.model.Bayesian: Produces an ROC validation set, using the inputs provided prior to the model building, using leave-one-out.
validateMolecule(IAtomContainer) - Method in class org.openscience.cdk.validate.AbstractValidator
validateMolecule(IAtomContainer) - Method in class org.openscience.cdk.validate.BasicValidator
validateMolecule(IAtomContainer) - Method in interface org.openscience.cdk.validate.IValidator
validateMolecule(IAtomContainer) - Method in class org.openscience.cdk.validate.ValidatorEngine
validateMoleculeSet(IAtomContainerSet) - Method in class org.openscience.cdk.validate.AbstractValidator
validateMoleculeSet(IAtomContainerSet) - Method in interface org.openscience.cdk.validate.IValidator
validateMoleculeSet(IAtomContainerSet) - Method in class org.openscience.cdk.validate.ValidatorEngine
validateReaction(IReaction) - Method in class org.openscience.cdk.validate.AbstractValidator
validateReaction(IReaction) - Method in class org.openscience.cdk.validate.BasicValidator
validateReaction(IReaction) - Method in interface org.openscience.cdk.validate.IValidator
validateReaction(IReaction) - Method in class org.openscience.cdk.validate.ValidatorEngine
validateReactionSet(IReactionSet) - Method in class org.openscience.cdk.validate.AbstractValidator
validateReactionSet(IReactionSet) - Method in interface org.openscience.cdk.validate.IValidator
validateReactionSet(IReactionSet) - Method in class org.openscience.cdk.validate.ValidatorEngine
validateThreeFold() - Method in class org.openscience.cdk.fingerprint.model.Bayesian: Produces a ROC validation set by partitioning the inputs into 3 groups, and performing three separate 66% in/33% out model simulations.
ValidationReport - Class in org.openscience.cdk.validate: A report on validation of chemical semantics.
ValidationReport() - Constructor for class org.openscience.cdk.validate.ValidationReport: Constructs a new empty ValidationReport.
ValidationTest - Class in org.openscience.cdk.validate: Error found during sematical validation of a IChemObject.
ValidationTest(IChemObject, String) - Constructor for class org.openscience.cdk.validate.ValidationTest
ValidationTest(IChemObject, String, String) - Constructor for class org.openscience.cdk.validate.ValidationTest
ValidatorEngine - Class in org.openscience.cdk.validate: Engine that performs the validation by traversing the IChemObject hierarchy.
ValidatorEngine() - Constructor for class org.openscience.cdk.validate.ValidatorEngine
value() - Method in class org.openscience.cdk.isomorphism.matchers.Expr: Access the value of this atom expression being tested.
valueOf(String) - Static method in enum net.sf.jniinchi.INCHI_OPTION: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.jniinchi.INCHI_RET: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.config.Elements: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.depict.Abbreviations.Option: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.formula.rules.MMElementRule.Database: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.formula.rules.MMElementRule.RangeMass: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.geometry.cip.CIPTool.CIP_CHIRALITY: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.geometry.GeometryTools.CoordinateCoverage: Deprecated.

Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.geometry.GeometryUtil.CoordinateCoverage: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.hash.BasicAtomEncoder: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.interfaces.IAtomType.Hybridization: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.interfaces.IBond.Display: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.interfaces.IBond.Order: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.interfaces.IBond.Stereo: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.interfaces.IDoubleBondStereochemistry.Conformation: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.interfaces.IReaction.Direction: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.io.IChemObjectReader.Mode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.io.MDLV2000Writer.SPIN_MULTIPLICITY: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.io.setting.IOSetting.Importance: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.isomorphism.matchers.CTFileQueryBond.Type: Deprecated.

Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.isomorphism.matchers.Expr.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.isomorphism.matchers.smarts.StereoBond.Direction: Deprecated.

Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.ReactionRole: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.renderer.elements.LineElement.LineType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.renderer.elements.path.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.renderer.elements.TextGroupElement.Position: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.renderer.elements.WedgeLineElement.Direction: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.renderer.elements.WedgeLineElement.TYPE: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.renderer.font.IFontManager.FontStyle: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.renderer.generators.BasicAtomGenerator.Shape: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.renderer.generators.standard.StandardGenerator.HighlightStyle: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.ringsearch.AllRingsFinder.Threshold: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.sgroup.SgroupKey: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.sgroup.SgroupType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.smsd.interfaces.Algorithm: Deprecated.

Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.stereo.Projection: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.stereo.Stereocenters.Stereocenter: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.stereo.Stereocenters.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.stereo.StereoTool.SquarePlanarShape: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.stereo.StereoTool.StereoClass: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.openscience.cdk.stereo.StereoTool.TetrahedralSign: Returns the enum constant of this type with the specified name.
values() - Static method in enum net.sf.jniinchi.INCHI_OPTION: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.jniinchi.INCHI_RET: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.config.Elements: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.depict.Abbreviations.Option: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.formula.rules.MMElementRule.Database: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.formula.rules.MMElementRule.RangeMass: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.geometry.cip.CIPTool.CIP_CHIRALITY: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.geometry.GeometryTools.CoordinateCoverage: Deprecated.

Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.geometry.GeometryUtil.CoordinateCoverage: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.hash.BasicAtomEncoder: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.interfaces.IAtomType.Hybridization: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.interfaces.IBond.Display: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.interfaces.IBond.Order: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.interfaces.IBond.Stereo: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.interfaces.IDoubleBondStereochemistry.Conformation: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.interfaces.IReaction.Direction: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.io.IChemObjectReader.Mode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.io.MDLV2000Writer.SPIN_MULTIPLICITY: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.io.setting.IOSetting.Importance: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.isomorphism.matchers.CTFileQueryBond.Type: Deprecated.

Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.isomorphism.matchers.Expr.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.isomorphism.matchers.smarts.StereoBond.Direction: Deprecated.

Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.ReactionRole: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.renderer.elements.LineElement.LineType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.renderer.elements.path.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.renderer.elements.TextGroupElement.Position: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.renderer.elements.WedgeLineElement.Direction: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.renderer.elements.WedgeLineElement.TYPE: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.renderer.font.IFontManager.FontStyle: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.renderer.generators.BasicAtomGenerator.Shape: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.renderer.generators.standard.StandardGenerator.HighlightStyle: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.ringsearch.AllRingsFinder.Threshold: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.sgroup.SgroupKey: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.sgroup.SgroupType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.smsd.interfaces.Algorithm: Deprecated.

Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.stereo.Projection: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.stereo.Stereocenters.Stereocenter: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.stereo.Stereocenters.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.stereo.StereoTool.SquarePlanarShape: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.stereo.StereoTool.StereoClass: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.openscience.cdk.stereo.StereoTool.TetrahedralSign: Returns an array containing the constants of this enum type, in the order they are declared.
Vanadium - org.openscience.cdk.config.Elements
VANADIUM - Static variable in enum org.openscience.cdk.config.Elements
VANADIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
VASPFormat - Class in org.openscience.cdk.io.formats
VASPFormat() - Constructor for class org.openscience.cdk.io.formats.VASPFormat
VASPReader - Class in org.openscience.cdk.io: Read output files generated with the VASP software.
VASPReader() - Constructor for class org.openscience.cdk.io.VASPReader
VASPReader(InputStream) - Constructor for class org.openscience.cdk.io.VASPReader
VASPReader(Reader) - Constructor for class org.openscience.cdk.io.VASPReader: Creates a new VASPReader instance.
vdwRadius() - Method in enum org.openscience.cdk.config.Elements: The van der Waals radius, r_w, of an atom is the radius of an imaginary hard sphere which can be used to model the atom.
VdWRadiusDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic: This class return the VdW radius of a given atom.
VdWRadiusDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor: Constructor for the VdWRadiusDescriptor object.
vector - Variable in class org.openscience.cdk.math.Vector: The content of this vector
Vector - Class in org.openscience.cdk.math: This class handles vectors.
Vector(double[]) - Constructor for class org.openscience.cdk.math.Vector: Constructs a vector with the content of a array
Vector(int) - Constructor for class org.openscience.cdk.math.Vector: Constructs a Vector with "size" elements
Vector(Tuple3d) - Constructor for class org.openscience.cdk.math.Vector: Constructs a Vector with a Tuple3d, Vector3d or Point3d
VentoFoggia - Class in org.openscience.cdk.isomorphism: A structure pattern which utilises the Vento-Foggia (VF) algorithm [Cordella Luigi P et. al.. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE. 2004. 26].
vertexAdded(GraphVertexChangeEvent) - Method in class org.openscience.cdk.graph.BiconnectivityInspector: Deprecated.
vertexColor() - Method in interface org.openscience.cdk.ringsearch.CyclicVertexSearch: Build an indexed lookup of vertex color.
vertexList() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycle: Deprecated.

Returns a list of the vertices contained in this cycle.
vertexRemoved(GraphVertexChangeEvent) - Method in class org.openscience.cdk.graph.BiconnectivityInspector: Deprecated.
vertexShort() - Static method in class org.openscience.cdk.graph.Cycles: Create a cycle finder which will compute the shortest cycles of each vertex in a molecule.
vertexShort(IAtomContainer) - Static method in class org.openscience.cdk.graph.Cycles: Find the vertex short cycles of a molecule.
VFAtomMatcher - Interface in org.openscience.cdk.smsd.algorithm.matchers: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
VFBondMatcher - Interface in org.openscience.cdk.smsd.algorithm.matchers: Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
VFLibMCS - org.openscience.cdk.smsd.interfaces.Algorithm: Deprecated.

VF Lib based MCS algorithm.
VFlibMCSHandler - Class in org.openscience.cdk.smsd.algorithm.vflib: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
VFlibMCSHandler() - Constructor for class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler: Deprecated.

Constructor for an extended VF Algorithm for the MCS search
VFlibSubStructureHandler - Class in org.openscience.cdk.smsd.algorithm.vflib: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
VFlibSubStructureHandler() - Constructor for class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler: Deprecated.

Constructor for an extended VF Algorithm for the MCS search
VFlibTurboHandler - Class in org.openscience.cdk.smsd.algorithm.vflib: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
VFlibTurboHandler() - Constructor for class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler: Deprecated.

Constructor for an extended VF Algorithm for the MCS search
VFMapper - Class in org.openscience.cdk.smsd.algorithm.vflib.map: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
VFMapper(IAtomContainer, boolean) - Constructor for class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper: Deprecated.
VFMapper(IQuery) - Constructor for class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper: Deprecated.
VFMCSMapper - Class in org.openscience.cdk.smsd.algorithm.vflib.map: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
VFMCSMapper(IAtomContainer, boolean) - Constructor for class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper: Deprecated.
VFMCSMapper(IQuery) - Constructor for class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper: Deprecated.
VFQueryBuilder - Class in org.openscience.cdk.smsd.algorithm.vflib.builder: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
VFQueryBuilder() - Constructor for class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder: Deprecated.

Constructor for VF Query Builder
VFState - Class in org.openscience.cdk.smsd.algorithm.vflib.map: Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
VFState(IQuery, TargetProperties) - Constructor for class org.openscience.cdk.smsd.algorithm.vflib.map.VFState: Deprecated.

Initialise the VFState with query and target
Vibration - Class in org.openscience.cdk: A molecular vibration composed of a set of atom vectors.
Vibration(String) - Constructor for class org.openscience.cdk.Vibration: Create a vibration identified by the label.
VicinitySampler - Class in org.openscience.cdk.structgen: The VicinitySampler is a generator of constitutional isomers.
VicinitySampler() - Constructor for class org.openscience.cdk.structgen.VicinitySampler
ViewmolFormat - Class in org.openscience.cdk.io.formats: See here.
ViewmolFormat() - Constructor for class org.openscience.cdk.io.formats.ViewmolFormat
Visibility() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.Visibility
visible(IAtom, List<IBond>, RendererModel) - Method in class org.openscience.cdk.renderer.generators.standard.SelectionVisibility: Determine if an atom with the specified bonds is visible.
visible(IAtom, List<IBond>, RendererModel) - Method in class org.openscience.cdk.renderer.SymbolVisibility: Determine if an atom with the specified bonds is visible.
visit(IRenderingElement) - Method in interface org.openscience.cdk.renderer.elements.IRenderingVisitor: Translates a IRenderingElement into a widget toolkit specific rendering element.
visit(IRenderingElement) - Method in class org.openscience.cdk.renderer.visitor.AWTDrawVisitor: Translates a IRenderingElement into a widget toolkit specific rendering element.
visit(ASTAliphatic, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTAliphatic, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTAliphatic, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTAliphatic, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTAliphatic, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTAnyAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTAnyAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTAnyAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTAnyAtom, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTAnyAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTAromatic, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTAromatic, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTAromatic, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTAromatic, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTAromatic, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTAtomicMass, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTAtomicMass, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTAtomicMass, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTAtomicMass, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTAtomicMass, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTAtomicNumber, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTAtomicNumber, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTAtomicNumber, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTAtomicNumber, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTAtomicNumber, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTAtom, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTCharge, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTCharge, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTCharge, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTCharge, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTCharge, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTChirality, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTChirality, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTChirality, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTChirality, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTChirality, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTElement, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTElement, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTElement, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTElement, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTElement, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTExplicitAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTExplicitAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTExplicitAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTExplicitAtom, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTExplicitAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTExplicitConnectivity, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTExplicitConnectivity, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTExplicitConnectivity, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTExplicitConnectivity, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTExplicitConnectivity, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTExplicitHighAndBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTExplicitHighAndBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTExplicitHighAndBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTExplicitHighAndBond, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTExplicitHighAndBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTExplicitHighAndExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTExplicitHighAndExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTExplicitHighAndExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTExplicitHighAndExpression, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTExplicitHighAndExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTGroup, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTGroup, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTGroup, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTGroup, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTGroup, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTHybrdizationNumber, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTHybrdizationNumber, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTHybrdizationNumber, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTHybrdizationNumber, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTHybrdizationNumber, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTImplicitHCount, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTImplicitHCount, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTImplicitHCount, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTImplicitHCount, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTImplicitHCount, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTImplicitHighAndBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTImplicitHighAndBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTImplicitHighAndBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTImplicitHighAndBond, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTImplicitHighAndBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTImplicitHighAndExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTImplicitHighAndExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTImplicitHighAndExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTImplicitHighAndExpression, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTImplicitHighAndExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTLowAndBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTLowAndBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTLowAndBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTLowAndBond, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTLowAndBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTLowAndExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTLowAndExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTLowAndExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTLowAndExpression, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTLowAndExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTNonCHHeavyAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTNonCHHeavyAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTNonCHHeavyAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTNonCHHeavyAtom, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTNonCHHeavyAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTNotBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTNotBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTNotBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTNotBond, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTNotBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTNotExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTNotExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTNotExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTNotExpression, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTNotExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTOrBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTOrBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTOrBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTOrBond, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTOrBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTOrExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTOrExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTOrExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTOrExpression, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTOrExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTPeriodicGroupNumber, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTPeriodicGroupNumber, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTPeriodicGroupNumber, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTPeriodicGroupNumber, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTPeriodicGroupNumber, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTPrimitiveAtomExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTReaction, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTReaction, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTReaction, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTReaction, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTReaction, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTRecursiveSmartsExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTRecursiveSmartsExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTRecursiveSmartsExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTRecursiveSmartsExpression, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTRecursiveSmartsExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTRingConnectivity, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTRingConnectivity, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTRingConnectivity, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTRingConnectivity, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTRingConnectivity, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTRingIdentifier, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTRingIdentifier, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTRingIdentifier, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTRingIdentifier, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTRingIdentifier, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTRingMembership, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTRingMembership, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTRingMembership, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTRingMembership, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTRingMembership, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTSimpleBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTSimpleBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTSimpleBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTSimpleBond, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTSimpleBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTSmallestRingSize, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTSmallestRingSize, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTSmallestRingSize, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTSmallestRingSize, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTSmallestRingSize, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTSmarts, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTSmarts, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTSmarts, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTSmarts, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTSmarts, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTStart, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTStart, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTStart, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTStart, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTStart, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTTotalConnectivity, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTTotalConnectivity, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTTotalConnectivity, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTTotalConnectivity, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTTotalConnectivity, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTTotalHCount, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTTotalHCount, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTTotalHCount, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTTotalHCount, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTTotalHCount, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(ASTValence, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(ASTValence, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(ASTValence, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(ASTValence, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(ASTValence, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visit(SimpleNode, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor: Deprecated.
visit(SimpleNode, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor: Deprecated.
visit(SimpleNode, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor
visit(SimpleNode, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
visit(SimpleNode, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor: Deprecated.
visitChildren(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.ElementGroup: Visit the members of the group.
visited - Variable in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
visited(VisitedAtoms) - Method in class org.openscience.cdk.geometry.cip.VisitedAtoms: Adds all atoms from the visitedAtoms list to the current list.
visited(IAtom) - Method in class org.openscience.cdk.geometry.cip.VisitedAtoms: Marks the given atom as visited.
VISITED - Static variable in class org.openscience.cdk.CDKConstants: Flag is set if chemobject has been visited.
VisitedAtoms - Class in org.openscience.cdk.geometry.cip: Helper class for the CIPTool to keep track of which atoms have already been visited.
VisitedAtoms() - Constructor for class org.openscience.cdk.geometry.cip.VisitedAtoms: Creates a new empty list of visited IAtoms.

W

W - org.openscience.cdk.renderer.elements.TextGroupElement.Position
W - Static variable in interface org.openscience.cdk.interfaces.IElement
W - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
warn(Object) - Method in interface org.openscience.cdk.tools.ILoggingTool: Shows WARN output for the Object.
warn(Object) - Method in class org.openscience.cdk.tools.SystemOutLoggingTool: Deprecated.

Shows WARN output for the Object.
warn(Object, Object...) - Method in interface org.openscience.cdk.tools.ILoggingTool: Shows WARN output for the given Object's.
warn(Object, Object...) - Method in class org.openscience.cdk.tools.SystemOutLoggingTool: Deprecated.

Shows WARN output for the given Object's.
WARN - Static variable in interface org.openscience.cdk.tools.ILoggingTool: Warn, Error, and Fatal messages will be emitted.
warning(SAXParseException) - Method in class org.openscience.cdk.io.cml.CMLErrorHandler: Outputs a SAXParseException warning to the logger.
WARNING - net.sf.jniinchi.INCHI_RET
WARNING_MARKER - Static variable in class org.openscience.cdk.validate.ProblemMarker
WarnOnEmptyStructure - net.sf.jniinchi.INCHI_OPTION
WaveSpacing() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.WaveSpacing
Wavy - org.openscience.cdk.interfaces.IBond.Display: A wavy line.
WedgeBegin - org.openscience.cdk.interfaces.IBond.Display: Display as a bold wedge, with the narrow end towards the begin atom of the bond (IBond.getBegin()).
WEDGED - org.openscience.cdk.renderer.elements.WedgeLineElement.TYPE
WedgedHashBegin - org.openscience.cdk.interfaces.IBond.Display: Display as a hashed wedge, with the narrow end towards the begin atom of the bond (IBond.getBegin()).
WedgedHashEnd - org.openscience.cdk.interfaces.IBond.Display: Display as a hashed wedge, with the narrow end towards the end atom of the bond (IBond.getEnd()).
WedgeEnd - org.openscience.cdk.interfaces.IBond.Display: Display as a bold wedge, with the narrow end towards the end atom of the bond (IBond.getEnd()).
WedgeLineElement - Class in org.openscience.cdk.renderer.elements: A 'wedge' is a triangle aligned along a bond that indicates stereochemistry.
WedgeLineElement(double, double, double, double, double, WedgeLineElement.TYPE, WedgeLineElement.Direction, Color) - Constructor for class org.openscience.cdk.renderer.elements.WedgeLineElement: Make a wedge between the points (x1, y1) and (x2, y2) with a certain width, direction, dash, and color.
WedgeLineElement(LineElement, WedgeLineElement.TYPE, WedgeLineElement.Direction, Color) - Constructor for class org.openscience.cdk.renderer.elements.WedgeLineElement: Make a wedge along the given line element.
WedgeLineElement.Direction - Enum in org.openscience.cdk.renderer.elements: 'toFirst' means that the wedge gets thicker in the direction of the first point in the line.
WedgeLineElement.TYPE - Enum in org.openscience.cdk.renderer.elements: If the bond is dashed ,wedged, or "up_or_down", i.e., not defined.
WedgeRatio() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.WedgeRatio
WedgeWidth() - Constructor for class org.openscience.cdk.renderer.generators.BasicBondGenerator.WedgeWidth
weight() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycle: Deprecated.

Returns the sum of the weights of all edges in this cycle.
WeightDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: IDescriptor based on the weight of atoms of a certain element type.
WeightDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor: Constructor for the WeightDescriptor object.
WeightedPathDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Evaluates the weighted path descriptors.
WeightedPathDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor
WEIGHTS_CURR - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor
WEIGHTS_PLANTE_2018 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor
weightVector() - Method in class org.openscience.cdk.ringsearch.cyclebasis.CycleBasis: Deprecated.
weightVector() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis: Deprecated.
WHIMDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Holistic descriptors described by Todeschini et al [Todeschini, R. and Gramatica, P.. Persepectives in Drug Discovery and Design. 1998. null].
WHIMDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor
width - Variable in class org.openscience.cdk.renderer.elements.ArrowElement: Width of the arrow line.
width - Variable in class org.openscience.cdk.renderer.elements.LineElement: The width of the line.
width - Variable in class org.openscience.cdk.renderer.elements.RectangleElement: The width of the rectangle.
width() - Method in class org.openscience.cdk.graph.invariant.GIMatrix: Returns the number of columns of the matrix.
width() - Method in class org.openscience.cdk.renderer.elements.Bounds: Specifies the width of the bounding box.
WienerNumbersDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: This descriptor calculates the Wiener numbers.
WienerNumbersDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor: Constructor for the WienerNumbersDescriptor object.
Wildcard - Static variable in interface org.openscience.cdk.interfaces.IElement: Wildcard atom is atomic number 0
WILDCARD - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
WILEY - org.openscience.cdk.formula.rules.MMElementRule.Database: Wiley mass spectral database.
WillDrawAtomNumbers() - Constructor for class org.openscience.cdk.renderer.generators.AtomNumberGenerator.WillDrawAtomNumbers
WIND_EVEN_ODD - Static variable in class org.openscience.cdk.renderer.elements.GeneralPath
WIND_NON_ZERO - Static variable in class org.openscience.cdk.renderer.elements.GeneralPath
winding - Variable in class org.openscience.cdk.renderer.elements.GeneralPath: Winding rule for determining path interior.
winding() - Method in class org.openscience.cdk.stereo.ExtendedTetrahedral: The winding of the peripherals, when viewed from the first atom.
with(Abbreviations.Option) - Method in class org.openscience.cdk.depict.Abbreviations: Convenience method to enable an option.
withAnnotationColor(Color) - Method in class org.openscience.cdk.depict.DepictionGenerator: Set the color annotations (e.g.
withAnnotationScale(double) - Method in class org.openscience.cdk.depict.DepictionGenerator: Set the size of annotations relative to atom symbols.
withAromaticDisplay() - Method in class org.openscience.cdk.depict.DepictionGenerator: When aromaticity is set on bonds, display this in the diagram.
withAtomClasses() - Method in class org.openscience.cdk.smiles.SmilesGenerator: Deprecated.
configure with SmiFlavor
withAtomColors() - Method in class org.openscience.cdk.depict.DepictionGenerator: Color atom symbols using typical colors, oxygens are red, nitrogens are blue, etc.
withAtomColors(IAtomColorer) - Method in class org.openscience.cdk.depict.DepictionGenerator: Color atom symbols using provided colorer.
withAtomMapHighlight() - Method in class org.openscience.cdk.depict.DepictionGenerator: Adds to the highlight the coloring of reaction atom-maps.
withAtomMapHighlight(Color[]) - Method in class org.openscience.cdk.depict.DepictionGenerator: Adds to the highlight the coloring of reaction atom-maps.
withAtomMapNumbers() - Method in class org.openscience.cdk.depict.DepictionGenerator: Display atom-atom mapping numbers on a reaction.
withAtomNumbers() - Method in class org.openscience.cdk.depict.DepictionGenerator: Display atom numbers on the molecule or reaction.
withAtomValues() - Method in class org.openscience.cdk.depict.DepictionGenerator: Display atom values on the molecule or reaction.
withBackgroundColor(Color) - Method in class org.openscience.cdk.depict.DepictionGenerator: Change the background color.
withCapacity(int) - Static method in class org.openscience.cdk.graph.Matching: Create an empty matching with the specified capacity.
withCarbonSymbols() - Method in class org.openscience.cdk.depict.DepictionGenerator: Display atom symbols for all atoms in the molecule.
withDeuteriumSymbol(boolean) - Method in class org.openscience.cdk.depict.DepictionGenerator: Indicate whether ²H should be rendered as 'D'.
withFillToFit() - Method in class org.openscience.cdk.depict.DepictionGenerator: Resize depictions to fill all available space (only if a size is specified).
withHighlight(Iterable<? extends IChemObject>, Color) - Method in class org.openscience.cdk.depict.DepictionGenerator: Highlight the provided set of atoms and bonds in the depiction in the specified color.
withMappedRxnAlign(boolean) - Method in class org.openscience.cdk.depict.DepictionGenerator: Specifies that reactions with atom-atom mappings should have their reactants/product coordinates aligned.
withMargin(double) - Method in class org.openscience.cdk.depict.DepictionGenerator: Specify a desired size of margin.
withMolTitle() - Method in class org.openscience.cdk.depict.DepictionGenerator: Display a molecule title with each depiction.
without(Abbreviations.Option) - Method in class org.openscience.cdk.depict.Abbreviations: Convenience method to disable an option.
withOuterGlowHighlight() - Method in class org.openscience.cdk.depict.DepictionGenerator: Highlights are shown as an outer glow around the atom symbols and bonds rather than recoloring.
withOuterGlowHighlight(double) - Method in class org.openscience.cdk.depict.DepictionGenerator: Highlights are shown as an outer glow around the atom symbols and bonds rather than recoloring.
withPadding(double) - Method in class org.openscience.cdk.depict.DepictionGenerator: Specify a desired size of padding for molecule sets and reactions.
withParam(Class<T>, U) - Method in class org.openscience.cdk.depict.DepictionGenerator: Low-level option method to set a rendering model parameter.
withRxnTitle() - Method in class org.openscience.cdk.depict.DepictionGenerator: Display a reaction title with the depiction.
withSize(double, double) - Method in class org.openscience.cdk.depict.DepictionGenerator: Specify a desired size of depiction.
withSpaceFor(IAtomContainer) - Static method in class org.openscience.cdk.graph.GraphUtil.EdgeToBondMap: Create a map with enough space for all the bonds in the molecule, container.
withStrictMode() - Method in class org.openscience.cdk.stereo.StereoElementFactory: Enables stricter stereochemistry checking, specifically tetrahedral centres may not be created from inverse down wedges (i.e.
withTerminalCarbons() - Method in class org.openscience.cdk.depict.DepictionGenerator: Display atom symbols for terminal carbons (i.e.
withTitleColor(Color) - Method in class org.openscience.cdk.depict.DepictionGenerator: Set the color titles will appear in.
withTitleScale(double) - Method in class org.openscience.cdk.depict.DepictionGenerator: Set the size of titles compared to atom symbols.
withZoom(double) - Method in class org.openscience.cdk.depict.DepictionGenerator: Specify a desired zoom factor - this changes the base size of a depiction and is used for uniformly making depictions bigger.
Wnumber - net.sf.jniinchi.INCHI_OPTION
write(IChemObject) - Method in class org.openscience.cdk.io.CDKSourceCodeWriter
write(IChemObject) - Method in class org.openscience.cdk.io.CMLWriter: Serializes the IChemObject to CML and redirects it to the output Writer.
write(IChemObject) - Method in class org.openscience.cdk.io.CrystClustWriter: Serializes the IChemObject to CrystClust format and redirects it to the output Writer.
write(IChemObject) - Method in class org.openscience.cdk.io.HINWriter
write(IChemObject) - Method in interface org.openscience.cdk.io.IChemObjectWriter: Writes the content of "object" to output.
write(IChemObject) - Method in class org.openscience.cdk.io.MDLRXNWriter: Writes a IChemObject to the MDL RXN file formated output.
write(IChemObject) - Method in class org.openscience.cdk.io.MDLV2000Writer: Writes a IChemObject to the MDL molfile formated output.
write(IChemObject) - Method in class org.openscience.cdk.io.MDLV3000Writer: Writes a molecule to the V3000 format.
write(IChemObject) - Method in class org.openscience.cdk.io.Mol2Writer
write(IChemObject) - Method in class org.openscience.cdk.io.PDBWriter
write(IChemObject) - Method in class org.openscience.cdk.io.program.GaussianInputWriter
write(IChemObject) - Method in class org.openscience.cdk.io.program.Mopac7Writer: Writes the content of "object" to output.
write(IChemObject) - Method in class org.openscience.cdk.io.rdf.CDKOWLWriter: Writes the content of "object" to output.
write(IChemObject) - Method in class org.openscience.cdk.io.RGroupQueryWriter: The actual writing of the output.
write(IChemObject) - Method in class org.openscience.cdk.io.RssWriter: Writes a IChemObject to the MDL molfile formated output.
write(IChemObject) - Method in class org.openscience.cdk.io.SDFWriter: Writes a IChemObject to the MDL SD file formated output.
write(IChemObject) - Method in class org.openscience.cdk.io.ShelXWriter: Serializes the IChemObject to ShelX and redirects it to the output Writer.
write(IChemObject) - Method in class org.openscience.cdk.io.SMILESWriter: Writes the content from object to output.
write(IChemObject) - Method in class org.openscience.cdk.io.XYZWriter
writeAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.io.SMILESWriter: Writes the content from molecule to output.
writeAtomContainerSet(IAtomContainerSet) - Method in class org.openscience.cdk.io.SMILESWriter: Writes a list of molecules to an OutputStream.
writeChemModel(IAtomContainerSet, String, String) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor
writeCrystal(ICrystal) - Method in class org.openscience.cdk.io.PDBWriter
writeGridInPmeshFormat(String) - Method in class org.openscience.cdk.tools.GridGenerator: Method transforms the grid into pmesh format.
writeGridInPmeshFormat(String, double) - Method in class org.openscience.cdk.tools.GridGenerator: Method transforms the grid into pmesh format.
writeMolecule(IAtomContainer) - Method in class org.openscience.cdk.io.MDLV2000Writer: Writes a Molecule to an OutputStream in MDL sdf format.
writeMolecule(IAtomContainer) - Method in class org.openscience.cdk.io.Mol2Writer: Writes a single frame in XYZ format to the Writer.
writeMolecule(IAtomContainer) - Method in class org.openscience.cdk.io.PDBWriter: Writes a single frame in PDB format to the Writer.
writeMolecule(IAtomContainer) - Method in class org.openscience.cdk.io.program.GaussianInputWriter: Writes a molecule for input for Gaussian.
writeMolecule(IAtomContainer) - Method in class org.openscience.cdk.io.XYZWriter: writes a single frame in XYZ format to the Writer.
writePharmacophoreDefinition(List<PharmacophoreQuery>, OutputStream) - Static method in class org.openscience.cdk.pharmacophore.PharmacophoreUtils: Write out one or more pharmacophore queries in the CDK XML format.
writePharmacophoreDefinition(PharmacophoreQuery[], OutputStream) - Static method in class org.openscience.cdk.pharmacophore.PharmacophoreUtils: Write out one or more pharmacophore queries in the CDK XML format.
writePharmacophoreDefinition(PharmacophoreQuery, OutputStream) - Static method in class org.openscience.cdk.pharmacophore.PharmacophoreUtils: Write out one or more pharmacophore queries in the CDK XML format.
writePocketsToPMesh(String) - Method in class org.openscience.cdk.protein.ProteinPocketFinder: Method writes the pockets to pmesh format.
WriterFactory - Class in org.openscience.cdk.io: Helper tool to create IChemObjectWriters.
WriterFactory() - Constructor for class org.openscience.cdk.io.WriterFactory: Constructs a ChemObjectIOInstantionTests.
writeSingleAtom(int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Writing the single atom molecule in a output file.
writeTo(String) - Method in class org.openscience.cdk.depict.Depiction: Write the depiction to the provided file path, the format is determined by the path suffix.
writeTo(String, File) - Method in class org.openscience.cdk.depict.Depiction: Write the depiction to the provided output stream.
writeTo(String, OutputStream) - Method in class org.openscience.cdk.depict.Depiction: Write the depiction to the provided output stream.
writeTo(String, String) - Method in class org.openscience.cdk.depict.Depiction: Write the depiction to the provided file path.
writeXMLDeclaration() - Method in class org.openscience.cdk.io.cml.CustomSerializer: Overwrite the Serializer.writeXMLDeclaration() method, and have it not output the XML declaration.
WS - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
wValues(Set<Integer>, int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: Finding the W values of neighbors in the former connectivity partition.

X

x - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
X - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
x2 - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
x3 - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
xCoord - Variable in class org.openscience.cdk.renderer.elements.OvalElement: The x-coordinate of the center of the oval.
xCoord - Variable in class org.openscience.cdk.renderer.elements.RectangleElement: The x-coordinate of the center of the rectangle.
xCoord - Variable in class org.openscience.cdk.renderer.elements.TextElement: The x coordinate where the text should be displayed.
Xe - Static variable in interface org.openscience.cdk.interfaces.IElement
XE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
XEDFormat - Class in org.openscience.cdk.io.formats
XEDFormat() - Constructor for class org.openscience.cdk.io.formats.XEDFormat
Xenon - org.openscience.cdk.config.Elements
XENON - Static variable in enum org.openscience.cdk.config.Elements
xfract - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
XLogPDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Prediction of logP based on the atom-type method called XLogP.
XLogPDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor: Constructor for the XLogPDescriptor object.
XMLIsotopeFactory - Class in org.openscience.cdk.config: Used to store and return data of a particular isotope.
XYZFormat - Class in org.openscience.cdk.io.formats
XYZFormat() - Constructor for class org.openscience.cdk.io.formats.XYZFormat
XYZReader - Class in org.openscience.cdk.io: Reads an object from XYZ formated input.
XYZReader() - Constructor for class org.openscience.cdk.io.XYZReader
XYZReader(InputStream) - Constructor for class org.openscience.cdk.io.XYZReader
XYZReader(Reader) - Constructor for class org.openscience.cdk.io.XYZReader: Construct a new reader from a Reader type object.
XYZWriter - Class in org.openscience.cdk.io
XYZWriter() - Constructor for class org.openscience.cdk.io.XYZWriter
XYZWriter(OutputStream) - Constructor for class org.openscience.cdk.io.XYZWriter
XYZWriter(Writer) - Constructor for class org.openscience.cdk.io.XYZWriter: Constructor.

Y

Y - Static variable in interface org.openscience.cdk.interfaces.IElement
Y - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
y2 - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
y3 - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
YasaraFormat - Class in org.openscience.cdk.io.formats: See here.
YasaraFormat() - Constructor for class org.openscience.cdk.io.formats.YasaraFormat
Yb - Static variable in interface org.openscience.cdk.interfaces.IElement
YB - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
yCoord - Variable in class org.openscience.cdk.renderer.elements.OvalElement: The y-coordinate of the center of the oval.
yCoord - Variable in class org.openscience.cdk.renderer.elements.RectangleElement: The y-coordinate of the center of the rectangle.
yCoord - Variable in class org.openscience.cdk.renderer.elements.TextElement: The y coordinate where the text should be displayed.
yfract - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
YL - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
YN - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Ytterbium - org.openscience.cdk.config.Elements
YTTERBIUM - Static variable in enum org.openscience.cdk.config.Elements
YTTERBIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Yttrium - org.openscience.cdk.config.Elements
YTTRIUM - Static variable in enum org.openscience.cdk.config.Elements
YTTRIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.

Z

Z - org.openscience.cdk.geometry.cip.CIPTool.CIP_CHIRALITY
Z - org.openscience.cdk.interfaces.IBond.Stereo: Indication that this double bond has a Z configuration.
Z_SHAPE - org.openscience.cdk.stereo.StereoTool.SquarePlanarShape
z3 - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
ZagrebIndexDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular: Zagreb index: the sum of the squares of atom degree over all heavy atoms i.
ZagrebIndexDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor: Constructor for the ZagrebIndexDescriptor object.
zero(int[]) - Method in class org.openscience.cdk.structgen.maygen.Maygen: For a row given by index, checking whether it is in maximal form or not.
zero(int, int) - Static method in class org.openscience.cdk.graph.invariant.GIMatrix: Returns a null matrix (with zeros everywhere) of given dimensions.
zfract - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
Zinc - org.openscience.cdk.config.Elements
ZINC - Static variable in enum org.openscience.cdk.config.Elements
ZINC - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
ZindoFormat - Class in org.openscience.cdk.io.formats: See here.
ZindoFormat() - Constructor for class org.openscience.cdk.io.formats.ZindoFormat
Zirconium - org.openscience.cdk.config.Elements
ZIRCONIUM - Static variable in enum org.openscience.cdk.config.Elements
ZIRCONIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
zmatrixChainToCartesian(IAtomContainer, boolean) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D: Takes the given Z Matrix coordinates and converts them to cartesian coordinates.
ZMatrixFormat - Class in org.openscience.cdk.io.formats
ZMatrixFormat() - Constructor for class org.openscience.cdk.io.formats.ZMatrixFormat
ZMatrixReader - Class in org.openscience.cdk.io: It reads Z matrices like in Gaussian input files.
ZMatrixReader() - Constructor for class org.openscience.cdk.io.ZMatrixReader
ZMatrixReader(InputStream) - Constructor for class org.openscience.cdk.io.ZMatrixReader
ZMatrixReader(Reader) - Constructor for class org.openscience.cdk.io.ZMatrixReader: Constructs a ZMatrixReader from a Reader that contains the data to be parsed.
zmatrixToCartesian(double[], int[], double[], int[], double[], int[]) - Static method in class org.openscience.cdk.geometry.ZMatrixTools: Takes the given Z Matrix coordinates and converts them to cartesian coordinates.
ZMatrixTools - Class in org.openscience.cdk.geometry: A set of static utility classes for dealing with Z matrices.
ZMatrixTools() - Constructor for class org.openscience.cdk.geometry.ZMatrixTools
Zn - Static variable in interface org.openscience.cdk.interfaces.IElement
ZN - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
ZoomFactor() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ZoomFactor
Zr - Static variable in interface org.openscience.cdk.interfaces.IElement
ZR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.

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