Index (cdk 2.7.1 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

A

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.
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
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 variable in class org.openscience.cdk.smiles.SmiFlavor: Output canonical SMILES with stereochemistry, atomic masses.
absolute() - Static method in class org.openscience.cdk.smiles.SmilesGenerator: Create a absolute SMILES generator.
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<? 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(IChemObject) - Method in class org.openscience.cdk.io.iterator.event.DefaultEventChemObjectReader
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(IChemObject) - Method in class org.openscience.cdk.io.MDLRXNReader: Deprecated.
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MDLRXNV2000Reader
accepts(IChemObject) - Method in class org.openscience.cdk.io.MDLRXNV2000Reader
accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MDLRXNV3000Reader
accepts(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(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) - Method in class org.openscience.cdk.io.VASPReader
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
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.
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(IAtomContainer) - Method in class org.openscience.cdk.AtomContainer: Adds all atoms and electronContainers of a given atomcontainer to this container.
add(IAtomContainerSet) - Method in class org.openscience.cdk.AtomContainerSet: Adds all atomContainers in the AtomContainerSet to this container.
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(IAtomContainer) - Method in class org.openscience.cdk.ConformerContainer: Add a conformer to the end of the list.
add(int, IAtomContainer) - Method in class org.openscience.cdk.ConformerContainer
add(IMolecularFormulaSet) - Method in class org.openscience.cdk.debug.DebugAdductFormula: Adds all molecularFormulas in the AdductFormula to this chemObject.
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(IAtomContainerSet) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Adds all atomContainers in the AtomContainerSet 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(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugMolecularFormula: Adds an molecularFormula to this MolecularFormula.
add(IMolecularFormulaSet) - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet: Adds all molecularFormulas in the MolecularFormulaSet to this chemObject.
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(IReactionScheme) - Method in class org.openscience.cdk.debug.DebugReactionScheme: Add a Scheme of Reactions.
add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugRing: Adds all atoms and electronContainers of a given atomcontainer to this container.
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(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugStrand: Adds all atoms and electronContainers of a given atomcontainer to this container.
add(IAtomContainerSet) - Method in class org.openscience.cdk.debug.DebugSubstance: Adds all atomContainers in the AtomContainerSet to this container.
add(String) - Method in class org.openscience.cdk.depict.Abbreviations: Convenience method to add an abbreviation from a SMILES string.
add(IAtomContainer, String) - Method in class org.openscience.cdk.depict.Abbreviations: Add an abbreviation to the factory.
add(IMolecularFormulaSet) - Method in class org.openscience.cdk.formula.AdductFormula: Adds all molecularFormulas in the AdductFormula to this chemObject.
add(IMolecularFormula) - Method in class org.openscience.cdk.formula.MolecularFormula: Adds an molecularFormula to this MolecularFormula.
add(IMolecularFormulaSet) - Method in class org.openscience.cdk.formula.MolecularFormulaSet: Adds all molecularFormulas in the MolecularFormulaSet to this chemObject.
add(GIMatrix) - Method in class org.openscience.cdk.graph.invariant.GIMatrix: Addition from two matrices.
add(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Adds all atoms and electronContainers of a given atomcontainer to this container.
add(IAtomContainerSet) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet: Adds all atomContainers in the AtomContainerSet to this container.
add(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.ICrystal: Adds the atoms in the AtomContainer as cell content.
add(IMolecularFormula) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula: Adds an molecularFormula to this MolecularFormula.
add(IMolecularFormulaSet) - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet: Adds all molecularFormulas in the MolecularFormulaSet to this chemObject.
add(IReactionScheme) - Method in interface org.openscience.cdk.interfaces.IReactionScheme: Add a scheme of reactions.
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(IChemObject) - Method in class org.openscience.cdk.io.random.RandomAccessReader
add(T) - Method in class org.openscience.cdk.io.setting.SettingManager: Add a setting to the manager and return the instance to use.
add(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Adds all atoms and electronContainers of a given atomcontainer to this container.
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(double) - Method in class org.openscience.cdk.qsar.result.DoubleArrayResult
add(int) - Method in class org.openscience.cdk.qsar.result.IntegerArrayResult
add(IReactionScheme) - Method in class org.openscience.cdk.ReactionScheme: Add a Scheme of Reactions.
add(IRenderingElement) - Method in class org.openscience.cdk.renderer.elements.Bounds: Add the specified element bounds.
add(double, double) - Method in class org.openscience.cdk.renderer.elements.Bounds: Ensure the point x,y is included in the bounding box.
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.ElementGroup: Add a new element to the group.
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(IMolecularFormulaSet) - Method in class org.openscience.cdk.silent.AdductFormula: Adds all molecularFormulas in the AdductFormula to this chemObject.
add(IAtomContainer) - Method in class org.openscience.cdk.silent.AtomContainer: Adds all atoms and electronContainers of a given atomcontainer to this container.
add(IAtomContainerSet) - Method in class org.openscience.cdk.silent.AtomContainerSet: Adds all atomContainers in the AtomContainerSet to this container.
add(IMolecularFormula) - Method in class org.openscience.cdk.silent.MolecularFormula: Adds an molecularFormula to this MolecularFormula.
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.silent.ReactionScheme: Add a Scheme of Reactions.
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(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
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(Collection<? extends IAtomContainer>) - Method in class org.openscience.cdk.ConformerContainer
addAll(int, 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(IAtom) - Method in class org.openscience.cdk.AtomContainer: Adds an atom to this container.
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, IMonomer, IStrand) - Method in class org.openscience.cdk.BioPolymer: Adds the atom to a specified Strand and a specified Monomer.
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, IMonomer) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Adds the atom oAtom to a specified Monomer.
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, IMonomer, IStrand) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Adds the atom to a specified Strand and a specified Monomer.
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, IMonomer) - Method in class org.openscience.cdk.debug.DebugPolymer: Adds the atom oAtom to a specified Monomer.
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, IMonomer) - Method in class org.openscience.cdk.debug.DebugStrand: Adds the atom oAtom to a specific Monomer.
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, IStrand) - Method in interface org.openscience.cdk.interfaces.IBioPolymer: Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.
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) - Method in interface org.openscience.cdk.interfaces.ICrystal: Adds the atom to the crystal.
addAtom(IPDBAtom) - Method in interface org.openscience.cdk.interfaces.IPDBPolymer: Adds the atom oAtom without specifying a Monomer or a Strand.
addAtom(IPDBAtom, IMonomer, IStrand) - Method in interface org.openscience.cdk.interfaces.IPDBPolymer: Adds the atom to a specified Strand and a specified Monomer.
addAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.IPolymer: Adds the atom oAtom without specifying a Monomer.
addAtom(IAtom, IMonomer) - Method in interface org.openscience.cdk.interfaces.IPolymer: Adds the atom oAtom to a specified Monomer.
addAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.IStrand: Adds the atom oAtom without specifying a Monomer or a Strand.
addAtom(IAtom, IMonomer) - Method in interface org.openscience.cdk.interfaces.IStrand: Adds the atom oAtom to a specific Monomer.
addAtom(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Adds an atom to this container.
addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.Polymer: Adds the atom oAtom to a specified Monomer.
addAtom(IPDBAtom) - Method in class org.openscience.cdk.protein.data.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, IStrand) - Method in class org.openscience.cdk.protein.data.PDBPolymer: Adds the IPDBAtom oAtom to a specified Monomer of a specified Strand.
addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.protein.data.PDBStrand: Adds the atom oAtom to a specified Monomer.
addAtom(IAtom) - Method in class org.openscience.cdk.sgroup.Sgroup: Add an atom to this Sgroup.
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.silent.AtomContainer: Adds an atom to this container.
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(IAtom, IMonomer, IStrand) - Method in class org.openscience.cdk.silent.BioPolymer: Adds the atom to a specified Strand and a specified Monomer.
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.silent.PDBPolymer: Adds the atom oAtom to a specified Monomer.
addAtom(IPDBAtom, IMonomer, IStrand) - Method in class org.openscience.cdk.silent.PDBPolymer: Adds the IPDBAtom oAtom to a specified Monomer of a specified Strand.
addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.silent.Polymer: Adds the atom oAtom to a specified Monomer.
addAtom(IAtom) - Method in class org.openscience.cdk.silent.Strand: Adds the atom oAtom without specifying a Monomer or a Strand.
addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.silent.Strand: Adds the atom oAtom to a specific Monomer.
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.Strand: Adds the atom oAtom to a specific Monomer.
addAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.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) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Adds an atomContainer to this container.
addAtomContainer(IAtomContainer, double) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet: Adds an atomContainer to this container with the given multiplier.
addAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugSubstance: Adds an atomContainer to this container.
addAtomContainer(IAtomContainer, double) - Method in class org.openscience.cdk.debug.DebugSubstance: Adds an atomContainer to this container with the given multiplier.
addAtomContainer(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet: Adds an atomContainer to this container.
addAtomContainer(IAtomContainer, double) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet: Adds an atomContainer to this container with the given multiplier.
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.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(IBond) - Method in class org.openscience.cdk.AtomContainer: Adds a Bond to this AtomContainer.
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) - Method in class org.openscience.cdk.AtomContainer: Adds a bond to this container.
addBond(IBond) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Adds a Bond to this AtomContainer.
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) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Adds a bond to this container.
addBond(IBond) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Adds a Bond to this AtomContainer.
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) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Adds a bond to this container.
addBond(IBond) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Adds a Bond to this AtomContainer.
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) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Adds a bond to this container.
addBond(IBond) - Method in class org.openscience.cdk.debug.DebugCrystal: Adds a Bond to this AtomContainer.
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) - Method in class org.openscience.cdk.debug.DebugCrystal: Adds a bond to this container.
addBond(IBond) - Method in class org.openscience.cdk.debug.DebugMonomer: Adds a Bond to this AtomContainer.
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) - Method in class org.openscience.cdk.debug.DebugMonomer: Adds a bond to this container.
addBond(IBond) - Method in class org.openscience.cdk.debug.DebugPolymer: Adds a Bond to this AtomContainer.
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) - Method in class org.openscience.cdk.debug.DebugPolymer: Adds a bond to this container.
addBond(IBond) - Method in class org.openscience.cdk.debug.DebugRing: Adds a Bond to this AtomContainer.
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) - Method in class org.openscience.cdk.debug.DebugRing: Adds a bond to this container.
addBond(IBond) - Method in class org.openscience.cdk.debug.DebugStrand: Adds a Bond to this AtomContainer.
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) - Method in class org.openscience.cdk.debug.DebugStrand: Adds a bond to this container.
addBond(IBond) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Adds a Bond to this AtomContainer.
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) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Adds a bond to this container.
addBond(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Adds a Bond to this AtomContainer.
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) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Adds a bond to this container.
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.
addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.silent.AtomContainer: 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.
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, TextGroupElement.Position) - Method in class org.openscience.cdk.renderer.elements.TextGroupElement: Add a child text element.
addChild(String, String, TextGroupElement.Position) - Method in class org.openscience.cdk.renderer.elements.TextGroupElement: Add a child text element with a subscript.
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
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(IIsotope) - Method in class org.openscience.cdk.debug.DebugMolecularFormula: 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(IsotopeContainer) - Method in class org.openscience.cdk.formula.IsotopePattern: Add an isotope object.
addIsotope(IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormula: Adds an Isotope to this MolecularFormula one time.
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, int) - Method in class org.openscience.cdk.formula.MolecularFormulaRange: Adds an Isotope to this MolecularFormulaExpand in a number of maximum and minimum occurrences allowed.
addIsotope(IIsotope) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula: Adds an Isotope to this MolecularFormula one time.
addIsotope(IIsotope, int) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula: Adds an Isotope to this MolecularFormula in a number of occurrences.
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.silent.MolecularFormula: Adds an Isotope to this MolecularFormula in a number of occurrences.
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(ILonePair) - Method in class org.openscience.cdk.AtomContainer: Adds a lone pair to this AtomContainer.
addLonePair(int) - Method in class org.openscience.cdk.AtomContainer: Adds a LonePair to this Atom.
addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Adds a lone pair to this AtomContainer.
addLonePair(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Adds a LonePair to this Atom.
addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Adds a lone pair to this AtomContainer.
addLonePair(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Adds a LonePair to this Atom.
addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Adds a lone pair to this AtomContainer.
addLonePair(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Adds a LonePair to this Atom.
addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugCrystal: Adds a lone pair to this AtomContainer.
addLonePair(int) - Method in class org.openscience.cdk.debug.DebugCrystal: Adds a LonePair to this Atom.
addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugMonomer: Adds a lone pair to this AtomContainer.
addLonePair(int) - Method in class org.openscience.cdk.debug.DebugMonomer: Adds a LonePair to this Atom.
addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugPolymer: Adds a lone pair to this AtomContainer.
addLonePair(int) - Method in class org.openscience.cdk.debug.DebugPolymer: Adds a LonePair to this Atom.
addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugRing: Adds a lone pair to this AtomContainer.
addLonePair(int) - Method in class org.openscience.cdk.debug.DebugRing: Adds a LonePair to this Atom.
addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugStrand: Adds a lone pair to this AtomContainer.
addLonePair(int) - Method in class org.openscience.cdk.debug.DebugStrand: Adds a LonePair to this Atom.
addLonePair(ILonePair) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Adds a lone pair to this AtomContainer.
addLonePair(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Adds a LonePair to this Atom.
addLonePair(ILonePair) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Adds a lone pair to this AtomContainer.
addLonePair(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Adds a LonePair to this Atom.
addLonePair(ILonePair) - Method in class org.openscience.cdk.silent.AtomContainer: Adds a lone pair to this AtomContainer.
addLonePair(int) - Method in class org.openscience.cdk.silent.AtomContainer: Adds a LonePair to this Atom.
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, 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.
addMolecule(IAtomContainer) - Method in class org.openscience.cdk.layout.TemplateHandler: Adds a Molecule to the list of templates use by this TemplateHandler.
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(CDKRNode) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph: Deprecated.

Adds a new node to the CDKRGraph.
addNode(VFAtomMatcher, IAtom) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder: Deprecated.

Add and return a node for a query atom
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.
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.
addProduct(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugReaction: 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) - Method in interface org.openscience.cdk.interfaces.IReaction: 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) - Method in class org.openscience.cdk.Reaction: Adds a product to this reaction.
addProduct(IAtomContainer, Double) - 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.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, Double) - Method in class org.openscience.cdk.debug.DebugReaction: Adds a reactant to this reaction with a stoichiometry coefficient.
addReactant(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IReaction: Adds a reactant to this reaction.
addReactant(IAtomContainer, Double) - Method in interface org.openscience.cdk.interfaces.IReaction: Adds a reactant to this reaction with a stoichiometry coefficient.
addReactant(IAtomContainer) - Method in class org.openscience.cdk.Reaction: Adds a reactant to this reaction.
addReactant(IAtomContainer, Double) - Method in class org.openscience.cdk.Reaction: Adds a reactant to this reaction with a stoichiometry coefficient.
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.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, int) - Method in class org.openscience.cdk.reaction.ReactionChain: Added a IReaction for this chain in position.
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.
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(ISingleElectron) - Method in class org.openscience.cdk.AtomContainer: Adds a single electron to this AtomContainer.
addSingleElectron(int) - Method in class org.openscience.cdk.AtomContainer: Adds a SingleElectron to this Atom.
addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Adds a single electron to this AtomContainer.
addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid: Adds a SingleElectron to this Atom.
addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Adds a single electron to this AtomContainer.
addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer: Adds a SingleElectron to this Atom.
addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Adds a single electron to this AtomContainer.
addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer: Adds a SingleElectron to this Atom.
addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugCrystal: Adds a single electron to this AtomContainer.
addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugCrystal: Adds a SingleElectron to this Atom.
addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugMonomer: Adds a single electron to this AtomContainer.
addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugMonomer: Adds a SingleElectron to this Atom.
addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugPolymer: Adds a single electron to this AtomContainer.
addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugPolymer: Adds a SingleElectron to this Atom.
addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugRing: Adds a single electron to this AtomContainer.
addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugRing: Adds a SingleElectron to this Atom.
addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugStrand: Adds a single electron to this AtomContainer.
addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugStrand: Adds a SingleElectron to this Atom.
addSingleElectron(ISingleElectron) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Adds a single electron to this AtomContainer.
addSingleElectron(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: Adds a SingleElectron to this Atom.
addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Adds a single electron to this AtomContainer.
addSingleElectron(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Adds a LonePair to this Atom.
addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.silent.AtomContainer: Adds a single electron to this AtomContainer.
addSingleElectron(int) - Method in class org.openscience.cdk.silent.AtomContainer: Adds a SingleElectron to this Atom.
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() - Constructor for class org.openscience.cdk.formula.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 - Class in org.openscience.cdk.silent: Class defining an adduct object in a MolecularFormula.
AdductFormula() - Constructor for class org.openscience.cdk.silent.AdductFormula: Constructs an empty 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.
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
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(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() - Method in class org.openscience.cdk.group.PermutationGroup: Generate the whole group from the compact list of permutations.
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() - Static method in class org.openscience.cdk.renderer.SymbolVisibility: All atom symbols are visible.
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.
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
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(boolean) - Constructor for class org.openscience.cdk.ringsearch.AllRingsFinder: Deprecated.
turn logging off by setting the level in the logger implementation
AllRingsFinder() - Constructor for class org.openscience.cdk.ringsearch.AllRingsFinder: Default constructor using a threshold of AllRingsFinder.Threshold.PubChem_99.
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 - 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 - 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() - Constructor for class org.openscience.cdk.AminoAcid: Constructs a new AminoAcid.
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.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.
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.
ANTIMONY - Static variable in enum org.openscience.cdk.config.Elements
ANTIMONY - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
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(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(PermutationGroup.Backtracker) - Method in class org.openscience.cdk.group.PermutationGroup: Apply the backtracker to all permutations in the larger group.
apply(int[]) - Method in class org.openscience.cdk.isomorphism.SmartsStereoMatch: Deprecated.

Backwards compatible method from when we used GUAVA predicates.
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 - Static variable in enum org.openscience.cdk.config.Elements
Aromatic() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
aromatic() - Method in class org.openscience.cdk.smiles.SmilesGenerator: Deprecated.
configure with SmiFlavor
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.
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.
ArrowHeadWidth() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ArrowHeadWidth
ArrowHeadWidth() - Constructor for class org.openscience.cdk.renderer.generators.ReactionSceneGenerator.ArrowHeadWidth
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.interfaces.IElement
as - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
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(IAtom, IAtom) - Constructor for class org.openscience.cdk.Association: Constructs an association between two Atom's.
Association() - Constructor for class org.openscience.cdk.Association: Constructs an empty association.
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 - Class in org.openscience.cdk: Represents the idea of an chemical atom.
Atom() - Constructor for class org.openscience.cdk.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, int) - Constructor for class org.openscience.cdk.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(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, Point3d) - Constructor for class org.openscience.cdk.Atom: Constructs an Atom from an Element and a Point3d.
Atom(String, Point2d) - Constructor for class org.openscience.cdk.Atom: Constructs an Atom from an Element and a Point2d.
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 - Static variable in class org.openscience.cdk.libio.jena.CDK
atom - Variable in class org.openscience.cdk.LonePair: The atom with which this lone pair is associated.
Atom - Class in org.openscience.cdk.silent: Represents the idea of an chemical atom.
Atom() - Constructor for class org.openscience.cdk.silent.Atom: Constructs an completely unset Atom.
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.silent.Atom: Create a new atom with of the specified element and hydrogen count.
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.silent.Atom: Constructs an Atom from a string containing an element symbol and optionally the atomic mass, hydrogen count, and formal charge.
Atom(String, Point3d) - Constructor for class org.openscience.cdk.silent.Atom: Constructs an Atom from an Element and a Point3d.
Atom(String, Point2d) - Constructor for class org.openscience.cdk.silent.Atom: Constructs an Atom from an Element and a Point2d.
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 - 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_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 - Class in org.openscience.cdk: 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(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(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 - 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 - 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.silent.AtomContainer: Constructs an empty 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).
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 - Variable in class org.openscience.cdk.tools.HOSECodeGenerator: The molecular structure on which we work
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(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 - 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.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() - 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 - Variable in class org.openscience.cdk.silent.AtomContainerSet: Array of AtomContainers.
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() - Constructor for class org.openscience.cdk.AtomContainerSet: Constructs an empty AtomContainerSet.
AtomContainerSet - Class in org.openscience.cdk.silent: A set of AtomContainers.
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.
AtomicMass - Static variable in class org.openscience.cdk.graph.invariant.CanonOpts: Distinguish atoms based on atomic mass.
AtomicMass() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
AtomicMass - Static variable in class org.openscience.cdk.smiles.SmiFlavor: Output atomic mass on atoms.
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() - Constructor for class org.openscience.cdk.isomorphism.AtomMatcher
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.
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
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() - Method in class org.openscience.cdk.AtomContainer: Returns an Iterable for looping over all atoms in this container.
atoms - Variable in class org.openscience.cdk.Bond: A list of atoms participating in this bond.
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 - Variable in class org.openscience.cdk.fingerprint.CircularFingerprinter.FP
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 - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Internal array of atoms.
atoms() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Returns an Iterable for looping over all atoms in this container.
atoms - Variable in class org.openscience.cdk.isomorphism.matchers.QueryBond: A list of atoms participating in this query bond.
atoms() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond: Returns the Iterator to atoms making up this query bond.
atoms - Variable in class org.openscience.cdk.silent.AtomContainer: Internal array of atoms.
atoms() - Method in class org.openscience.cdk.silent.AtomContainer: Returns an Iterable for looping over all atoms in this container.
atoms - Variable in class org.openscience.cdk.silent.Bond: A list of atoms participating in this bond.
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, IAtomContainer) - Constructor for class org.openscience.cdk.signature.AtomSignature: Create an atom signature starting at atomIndex.
AtomSignature(IAtom, IAtomContainer) - Constructor for class org.openscience.cdk.signature.AtomSignature: Create an atom signature for the atom 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(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(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(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.
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(String) - Constructor for class org.openscience.cdk.AtomType: Constructor for the AtomType object.
AtomType(String, String) - Constructor for class org.openscience.cdk.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 - Static variable in class org.openscience.cdk.libio.jena.CDK
AtomType - Class in org.openscience.cdk.silent: The base class for atom types.
AtomType(String) - Constructor for class org.openscience.cdk.silent.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.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_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 - Static variable in interface org.openscience.cdk.interfaces.IStereoElement: Atropisomeric (e.g.
Atropisomeric - Class in org.openscience.cdk.stereo: Restricted axial rotation around Aryl-Aryl bonds.
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>, String) - Constructor for class org.openscience.cdk.iupac.parser.AttachedGroup: Creates a new instance of AttachedGroup with a Sting denoting the functional group
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
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.
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.
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 - Static variable in interface org.openscience.cdk.interfaces.IElement
b - Variable in class org.openscience.cdk.io.random.RandomAccessReader
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.
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 - 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 - Static variable in enum org.openscience.cdk.config.Elements
BERKELIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
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.
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() - Constructor for class org.openscience.cdk.BioPolymer: Constructs a new Polymer to store the Strands.
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.silent.BioPolymer: Constructs a new Polymer to store the Strands.
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(BitSet) - Constructor for class org.openscience.cdk.fingerprint.BitSetFingerprint
BitSetFingerprint() - Constructor for class org.openscience.cdk.fingerprint.BitSetFingerprint
BitSetFingerprint(int) - 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 - Static variable in enum org.openscience.cdk.config.Elements
BOHRIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
Bond - Class in org.openscience.cdk: 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(IAtom, IAtom) - Constructor for class org.openscience.cdk.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[]) - Constructor for class org.openscience.cdk.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, 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 - Static variable in class org.openscience.cdk.libio.jena.CDK
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.silent.Bond: Constructs an empty bond.
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.silent.Bond: Constructs a bond with a given order.
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.silent.Bond: Constructs a multi-center bond, with a specified order and no stereo information.
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.
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() - Constructor for class org.openscience.cdk.isomorphism.BondMatcher
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.
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() - Method in class org.openscience.cdk.Atom: Returns the bonds connected to this atom.
bonds - Variable in class org.openscience.cdk.AtomContainer: Internal array of bonds.
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 - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: Internal array of bonds.
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 - Variable in class org.openscience.cdk.silent.AtomContainer: Internal array of bonds.
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 - 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(double, double, double, double) - Constructor for class org.openscience.cdk.renderer.elements.Bounds: Specify the min/max coordinates of the bounding box.
Bounds() - Constructor for class org.openscience.cdk.renderer.elements.Bounds: An empty 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, 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.
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.
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 - 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.
buildBondMatrix() - Method in class org.openscience.cdk.graph.invariant.EquivalentClassPartitioner: Build bond 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.
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
BUT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.

C

C - Static variable in interface org.openscience.cdk.interfaces.IElement
c - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
C - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants: RegularExpression Id.
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 - Static variable in enum org.openscience.cdk.config.Elements
CADMIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
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
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, 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.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 >.
calcInvertedAxes(Vector3d, Vector3d, Vector3d) - Static method in class org.openscience.cdk.geometry.CrystalGeometryTools: Inverts three cell axes.
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, double, double, double, double) - Method in class org.openscience.cdk.math.qm.GaussiansBasis: Transfer equation the the calculation of the impulse
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>.
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(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter: Calculates the fingerprints for the given IAtomContainer, and stores them for subsequent retrieval.
calculate(IAtom, IAtom) - Method in interface org.openscience.cdk.geometry.IRDFWeightFunction: Calculates the weight for the interaction between the two atoms.
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) - Static method in class org.openscience.cdk.geometry.volume.VABCVolume: Calculates the volume for the given IAtomContainer.
calculate() - Method in class org.openscience.cdk.math.qm.ClosedShellJob
calculate() - Method in class org.openscience.cdk.math.qm.OneElectronJob
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, IRingSet) - 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, IRingSet) - 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
calculate(IAtom, IAtomContainer, IRingSet) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR
calculate(IAtom, IAtomContainer) - 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_topol
calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR
calculate(IAtom, IAtomContainer, IRingSet) - 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, IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor: The method returns if two atoms have pi-contact.
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(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(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.
calculate(IAtom, IAtomContainer) - Method in interface org.openscience.cdk.qsar.IAtomicDescriptor: Calculates the descriptor value for the given IAtom.
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 interface org.openscience.cdk.qsar.IBondDescriptor: Calculates the descriptor value for the given IBond.
calculate(IAtomContainer) - Method in interface org.openscience.cdk.qsar.IMolecularDescriptor: Calculates the descriptor value for the given IAtomContainer.
calculate(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.similarity.DistanceMoment: Evaluate the 3D similarity between two molecules.
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(BitSet, BitSet) - Static method in class org.openscience.cdk.similarity.Tanimoto: Evaluates Tanimoto coefficient for two bit sets.
calculate(IBitFingerprint, IBitFingerprint) - Static method in class org.openscience.cdk.similarity.Tanimoto: Evaluates Tanimoto coefficient for two IBitFingerprint.
calculate(double[], double[]) - Static method in class org.openscience.cdk.similarity.Tanimoto: Evaluates the continuous Tanimoto coefficient for two real valued vectors.
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(ICountFingerprint, ICountFingerprint) - Static method in class org.openscience.cdk.similarity.Tanimoto: Evaluate continuous Tanimoto coefficient for two feature, count fingerprint representations.
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(IReaction) - Static method in class org.openscience.cdk.renderer.AverageBondLengthCalculator: Calculate the average bond length for the bonds in a reaction.
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(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(IChemModel) - Static method in class org.openscience.cdk.renderer.BoundsCalculator: Calculate the bounding rectangle for a chem model.
calculateBounds(IReactionSet) - Static method in class org.openscience.cdk.renderer.BoundsCalculator: Calculate the bounding rectangle for a reaction set.
calculateBounds(IReaction) - Static method in class org.openscience.cdk.renderer.BoundsCalculator: Calculate the bounding rectangle for a reaction.
calculateBounds(IAtomContainerSet) - Static method in class org.openscience.cdk.renderer.BoundsCalculator: Calculate the bounding rectangle for a molecule set.
calculateBounds(IAtomContainer) - Static method in class org.openscience.cdk.renderer.BoundsCalculator: Calculate the bounding rectangle for an atom container.
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(IChemModel) - Method in class org.openscience.cdk.renderer.ChemModelRenderer: Given a chem model, 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.
calculateDiagramBounds(IAtomContainerSet) - Method in class org.openscience.cdk.renderer.MoleculeSetRenderer: Given a IChemObject, 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.
calculateGHEffectiveAtomPolarizability(IAtomContainer, IAtom, int, boolean) - Method in class org.openscience.cdk.charges.Polarizability: calculate effective atom polarizability.
calculateGHEffectiveAtomPolarizability(IAtomContainer, IAtom, boolean, int[][]) - 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, 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) - Method in class org.openscience.cdk.tools.SaturationChecker
calculateNumberOfImplicitHydrogens(IAtom, IAtomContainer, boolean) - 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.SmilesValencyChecker
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, Vector, double) - Method in class org.openscience.cdk.math.qm.GaussiansBasis: Calculates the core potential.
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>.
CALIFORNIUM - Static variable in enum org.openscience.cdk.config.Elements
CALIFORNIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
cancel() - Method in class org.openscience.cdk.formula.MolecularFormulaGenerator: Cancel the current search.
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.
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 - 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() - Constructor for class org.openscience.cdk.CDK
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.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() - 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(Reader) - Constructor for class org.openscience.cdk.io.rdf.CDKOWLReader: Creates a new CDKOWLReader sending output to the given Writer.
CDKOWLReader() - Constructor for class org.openscience.cdk.io.rdf.CDKOWLReader: Creates a new CDKOWLReader with an undefined input.
CDKOWLWriter - Class in org.openscience.cdk.io.rdf: Serializes the data model into CDK OWL.
CDKOWLWriter(Writer) - Constructor for class org.openscience.cdk.io.rdf.CDKOWLWriter: Creates a new CDKOWLWriter sending output to the given Writer.
CDKOWLWriter() - Constructor for class org.openscience.cdk.io.rdf.CDKOWLWriter: Creates a new CDKOWLWriter with an undefined output.
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(Writer) - Constructor for class org.openscience.cdk.io.CDKSourceCodeWriter: Constructs a new CDKSourceCodeWriter.
CDKSourceCodeWriter(OutputStream) - Constructor for class org.openscience.cdk.io.CDKSourceCodeWriter
CDKSourceCodeWriter() - Constructor for class org.openscience.cdk.io.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, Dimension) - Static method in class org.openscience.cdk.geometry.GeometryTools: Deprecated.

Centers the molecule in the given area.
center(IAtomContainer, double[]) - Static method in class org.openscience.cdk.geometry.GeometryUtil: Centers the molecule in the given area.
centerCode - Variable in class org.openscience.cdk.tools.HOSECodeGenerator
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.
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, IAtomContainer, List<String>) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks: Deprecated.
changeCharBonds(int, String, int, List<Integer>, 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_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.
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() - Constructor for class org.openscience.cdk.ChemFile: Constructs an empty ChemFile.
ChemFile - Class in org.openscience.cdk.silent: A Object containing a number of ChemSequences.
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() - Constructor for class org.openscience.cdk.ChemModel: Constructs an new ChemModel with a null setOfMolecules.
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.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>>, 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.
ChemModelRenderer(List<IGenerator<IAtomContainer>>, List<IGenerator<IReaction>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.ChemModelRenderer
chemModels - Variable in class org.openscience.cdk.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 - Variable in class org.openscience.cdk.silent.ChemSequence: Array of ChemModels.
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() - Constructor for class org.openscience.cdk.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 - Static variable in class org.openscience.cdk.libio.jena.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.silent.ChemObject: Constructs a new IChemObject.
ChemObject(IChemObject) - Constructor for class org.openscience.cdk.silent.ChemObject: Constructs a new IChemObject by copying the flags, and the identifier.
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() - Constructor for class org.openscience.cdk.ChemSequence: Constructs an empty ChemSequence.
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.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() - 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 - Variable in class org.openscience.cdk.silent.ChemFile: Array of ChemSquences.
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, TextGroupElement.Position) - Constructor for class org.openscience.cdk.renderer.elements.TextGroupElement.Child: Make a child element with the specified text and position.
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.
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.
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 - Static variable in enum org.openscience.cdk.config.Elements
CHLORO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
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(Reader) - Constructor for class org.openscience.cdk.io.CIFReader: Create an CIF like file reader.
CIFReader(InputStream) - Constructor for class org.openscience.cdk.io.CIFReader
CIFReader() - Constructor for class org.openscience.cdk.io.CIFReader
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.
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.
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.
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(IAtomContainer) - Static method in class org.openscience.cdk.qsar.AbstractMolecularDescriptor
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
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 - Class in org.openscience.cdk.renderer.elements.path: Indicates the closing point of the path.
Close() - Constructor for class org.openscience.cdk.renderer.elements.path.Close: Make a Close PathElement.
close() - Method in class org.openscience.cdk.renderer.elements.path.PathBuilder: Close the path.
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.
closeNodeScope(Node, int) - Method in class org.openscience.cdk.smiles.smarts.parser.JJTSMARTSParserState
closeNodeScope(Node, boolean) - 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(InputStream) - Constructor for class org.openscience.cdk.io.CMLReader: Reads CML from an java.io.InputStream, for example the FileInputStream.
CMLReader() - Constructor for class org.openscience.cdk.io.CMLReader
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(Writer) - Constructor for class org.openscience.cdk.io.CMLWriter: Constructs a new CMLWriter class.
CMLWriter(OutputStream) - Constructor for class org.openscience.cdk.io.CMLWriter
CMLWriter() - Constructor for class org.openscience.cdk.io.CMLWriter
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 - 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(Color) - Method in class org.openscience.cdk.renderer.elements.path.PathBuilder: Sets the color if this path.
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.
ColorByType() - Constructor for class org.openscience.cdk.renderer.generators.AtomNumberGenerator.ColorByType
ColorByType() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.ColorByType
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(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(IAtom, IAtom) - Method in class org.openscience.cdk.fingerprint.SimpleAtomComparator
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(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 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(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(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
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.
compareTo(Algorithm) - Method in enum org.openscience.cdk.smsd.interfaces.Algorithm: Deprecated.

Compares algorithm types.
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.
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).
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).
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(IAtom, IIsotope) - Method in class org.openscience.cdk.config.IsotopeFactory: Configures an atom to have all the data of the given isotope.
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.
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.
configureLog4j() - Static method in class org.openscience.cdk.tools.LoggingTool: Forces the LoggingTool to configure the Log4J toolkit.
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
CONSTANT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants: RegularExpression Id.
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.
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, 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, String, String) - Static method in class org.openscience.cdk.tools.diff.tree.StringDifference: Constructs a new IDifference object.
ConstructorKey() - Constructor for class org.openscience.cdk.DynamicFactory.ConstructorKey
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(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(IBond) - Method in class org.openscience.cdk.AtomContainer: True, if the AtomContainer contains the given bond object.
contains(ILonePair) - Method in class org.openscience.cdk.AtomContainer: True, if the AtomContainer contains the given LonePair object.
contains(ISingleElectron) - Method in class org.openscience.cdk.AtomContainer: True, if the AtomContainer contains the given SingleElectron object.
contains(IElectronContainer) - Method in class org.openscience.cdk.AtomContainer: True, if the AtomContainer contains the given ElectronContainer 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(Object) - Method in class org.openscience.cdk.ConformerContainer: Checks to see whether the specified conformer is currently stored.
contains(IIsotope) - Method in class org.openscience.cdk.debug.DebugAdductFormula: True, if the AdductFormula contains the given IIsotope object and not the instance.
contains(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugAdductFormula: True, if the AdductFormula contains the given IMolecularFormula object.
contains(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid: True, if the AtomContainer contains the given atom object.
contains(IBond) - Method in class org.openscience.cdk.debug.DebugAminoAcid: True, if the AtomContainer contains the given bond object.
contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugAminoAcid: True, if the AtomContainer contains the given LonePair object.
contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAminoAcid: True, if the AtomContainer contains the given SingleElectron object.
contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugAminoAcid: True, if the AtomContainer contains the given ElectronContainer object.
contains(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer: True, if the AtomContainer contains the given atom object.
contains(IBond) - Method in class org.openscience.cdk.debug.DebugAtomContainer: True, if the AtomContainer contains the given bond object.
contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugAtomContainer: True, if the AtomContainer contains the given LonePair object.
contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAtomContainer: True, if the AtomContainer contains the given SingleElectron object.
contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainer: True, if the AtomContainer contains the given ElectronContainer object.
contains(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer: True, if the AtomContainer contains the given atom object.
contains(IBond) - Method in class org.openscience.cdk.debug.DebugBioPolymer: True, if the AtomContainer contains the given bond object.
contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugBioPolymer: True, if the AtomContainer contains the given LonePair object.
contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugBioPolymer: True, if the AtomContainer contains the given SingleElectron object.
contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugBioPolymer: True, if the AtomContainer contains the given ElectronContainer 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(IBond) - Method in class org.openscience.cdk.debug.DebugCrystal: True, if the AtomContainer contains the given bond object.
contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugCrystal: True, if the AtomContainer contains the given LonePair object.
contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugCrystal: True, if the AtomContainer contains the given SingleElectron object.
contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugCrystal: True, if the AtomContainer contains the given ElectronContainer object.
contains(IAtom) - Method in class org.openscience.cdk.debug.DebugLonePair: Returns true if the given atom participates in this lone pair.
contains(IIsotope) - Method in class org.openscience.cdk.debug.DebugMolecularFormula: True, if the MolecularFormula contains the given IIsotope object and not the instance.
contains(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet: True, if the MolecularFormulaSet contains the given IMolecularFormula object.
contains(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer: True, if the AtomContainer contains the given atom object.
contains(IBond) - Method in class org.openscience.cdk.debug.DebugMonomer: True, if the AtomContainer contains the given bond object.
contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugMonomer: True, if the AtomContainer contains the given LonePair object.
contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugMonomer: True, if the AtomContainer contains the given SingleElectron object.
contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugMonomer: True, if the AtomContainer contains the given ElectronContainer object.
contains(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer: True, if the AtomContainer contains the given atom object.
contains(IBond) - Method in class org.openscience.cdk.debug.DebugPolymer: True, if the AtomContainer contains the given bond object.
contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugPolymer: True, if the AtomContainer contains the given LonePair object.
contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugPolymer: True, if the AtomContainer contains the given SingleElectron object.
contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugPolymer: True, if the AtomContainer contains the given ElectronContainer object.
contains(IAtom) - Method in class org.openscience.cdk.debug.DebugRing: True, if the AtomContainer contains the given atom object.
contains(IBond) - Method in class org.openscience.cdk.debug.DebugRing: True, if the AtomContainer contains the given bond object.
contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugRing: True, if the AtomContainer contains the given LonePair object.
contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugRing: True, if the AtomContainer contains the given SingleElectron object.
contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugRing: True, if the AtomContainer contains the given ElectronContainer 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(IBond) - Method in class org.openscience.cdk.debug.DebugStrand: True, if the AtomContainer contains the given bond object.
contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugStrand: True, if the AtomContainer contains the given LonePair object.
contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugStrand: True, if the AtomContainer contains the given SingleElectron object.
contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugStrand: True, if the AtomContainer contains the given ElectronContainer object.
contains(IIsotope) - Method in class org.openscience.cdk.formula.AdductFormula: True, if the AdductFormula contains the given IIsotope object and not the instance.
contains(IMolecularFormula) - Method in class org.openscience.cdk.formula.AdductFormula: True, if the AdductFormula contains the given IMolecularFormula object.
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(IMolecularFormula) - Method in class org.openscience.cdk.formula.MolecularFormulaSet: True, if the MolecularFormulaSet contains the given IMolecularFormula object.
contains(IIsotope) - Method in interface org.openscience.cdk.interfaces.IAdductFormula: True, if the AdductFormula contains the given IIsotope object.
contains(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: True, if the AtomContainer contains the given atom object.
contains(IBond) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: True, if the AtomContainer contains the given bond object.
contains(ILonePair) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: True, if the AtomContainer contains the given LonePair object.
contains(ISingleElectron) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: True, if the AtomContainer contains the given SingleElectron object.
contains(IElectronContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainer: True, if the AtomContainer contains the given ElectronContainer 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(IIsotope) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula: True, if the MolecularFormula contains the given IIsotope object.
contains(IMolecularFormula) - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet: True, if the IMolecularFormulaSet contains the given IMolecularFormula object.
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(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IRingSet: True, if this set contains the IAtomContainer.
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(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: True, if the AtomContainer contains the given bond object.
contains(ILonePair) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: True, if the AtomContainer contains the given LonePair object.
contains(ISingleElectron) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: True, if the AtomContainer contains the given SingleElectron object.
contains(IElectronContainer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer: True, if the AtomContainer contains the given ElectronContainer 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(IChemObject) - Method in interface org.openscience.cdk.renderer.selection.IChemObjectSelection: Determines if the IChemObject is part of the current selection.
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(IAtomContainer) - Method in class org.openscience.cdk.RingSet: Checks for presence of a ring in this RingSet.
contains(int) - Method in class org.openscience.cdk.signature.Orbit: Checks to see if the orbit contains this atom index.
contains(IIsotope) - Method in class org.openscience.cdk.silent.AdductFormula: True, if the AdductFormula contains the given IIsotope object and not the instance.
contains(IMolecularFormula) - Method in class org.openscience.cdk.silent.AdductFormula: True, if the AdductFormula contains the given IMolecularFormula object.
contains(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer: True, if the AtomContainer contains the given atom object.
contains(IBond) - Method in class org.openscience.cdk.silent.AtomContainer: True, if the AtomContainer contains the given bond object.
contains(ILonePair) - Method in class org.openscience.cdk.silent.AtomContainer: True, if the AtomContainer contains the given LonePair object.
contains(ISingleElectron) - Method in class org.openscience.cdk.silent.AtomContainer: True, if the AtomContainer contains the given SingleElectron object.
contains(IElectronContainer) - Method in class org.openscience.cdk.silent.AtomContainer: True, if the AtomContainer contains the given ElectronContainer 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(IIsotope) - Method in class org.openscience.cdk.silent.MolecularFormula: True, if the MolecularFormula contains the given IIsotope object and not the instance.
contains(IMolecularFormula) - Method in class org.openscience.cdk.silent.MolecularFormulaSet: True, if the MolecularFormulaSet contains the given IMolecularFormula object.
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(IAtomContainer) - Method in class org.openscience.cdk.silent.RingSet: Checks for presence of a ring in this RingSet.
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(IMolecularFormulaSet, IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaSetManipulator: True, if the IMolecularFormulaSet contains the given IMolecularFormula but not as 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(boolean, String) - Constructor for class org.openscience.cdk.libio.cml.Convertor: Constructs a CML convertor.
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
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.
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.
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(IAtom, double, IBond.Order, IAtomType) - Method in class org.openscience.cdk.tools.SmilesValencyChecker: 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.
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(TargetProperties) - 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(TargetProperties) - 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 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(IAtom) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.TargetProperties: Deprecated.
countNeighbors() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.INode: Deprecated.

Returns Neighbors count.
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(Object[]) - Method in interface org.openscience.cdk.DynamicFactory.Creator: Create a new instance with the provided object parameters.
create() - Method in class org.openscience.cdk.group.PartitionRefinement.AtomRefinerBuilder
create() - Method in class org.openscience.cdk.group.PartitionRefinement.BondRefinerBuilder
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, 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(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.smarts.SmartsPattern: Create a Pattern that will match the given smarts query.
create(String) - Static method in class org.openscience.cdk.smarts.SmartsPattern: Default SMARTS pattern constructor, passes in a null chem object builder.
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(String) - Static method in class org.openscience.cdk.smiles.smarts.SmartsPattern: Deprecated.

Default SMARTS pattern constructor, passes in a null chem object builder.
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, 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(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.
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(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(Class<?>) - Static method in class org.openscience.cdk.tools.LoggingTool: Creates a new LoggingTool for the given class.
create(Class<?>) - Static method in class org.openscience.cdk.tools.SystemOutLoggingTool: Creates a new SystemOutLoggingTool for the given class.
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(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.
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.
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(IChemFormat) - Method in class org.openscience.cdk.io.ReaderFactory: Creates a new IChemObjectReader based on the given IChemFormat.
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.
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 - Class in org.openscience.cdk: Class representing a molecular crystal.
Crystal() - Constructor for class org.openscience.cdk.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 - Variable in class org.openscience.cdk.silent.ChemModel: A Crystal.
Crystal - Class in org.openscience.cdk.silent: Class representing a molecular crystal.
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.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.