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
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.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
 
accepts(IChemObject) - Method in class org.openscience.cdk.io.MDLRXNReader
 
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
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
Add a container (that) to this container, if "that" container has atoms, bonds, or electron containers already in "this" they are not added.
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
Add a container (that) to this container, if "that" container has atoms, bonds, or electron containers already in "this" they are not added.
add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainer
Add a container (that) to this container, if "that" container has atoms, bonds, or electron containers already in "this" they are not added.
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
Add a container (that) to this container, if "that" container has atoms, bonds, or electron containers already in "this" they are not added.
add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugCrystal
Add a container (that) to this container, if "that" container has atoms, bonds, or electron containers already in "this" they are not added.
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
Add a container (that) to this container, if "that" container has atoms, bonds, or electron containers already in "this" they are not added.
add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugPolymer
Add a container (that) to this container, if "that" container has atoms, bonds, or electron containers already in "this" they are not added.
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
Add a container (that) to this container, if "that" container has atoms, bonds, or electron containers already in "this" they are not added.
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
Add a container (that) to this container, if "that" container has atoms, bonds, or electron containers already in "this" they are not added.
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
Add a container (that) to this container, if "that" container has atoms, bonds, or electron containers already in "this" they are not added.
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 a bond 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.
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 LonePair 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 LonePair 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 LonePair 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 LonePair 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 LonePair 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 LonePair 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 LonePair 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 LonePair 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 LonePair 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 LonePair 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
Add a symbol to this QueryAtom
addSymbol(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom
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.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.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
This matcher any non-aromatic atom.
AliphaticAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AliphaticAtom
Creates a new instance
AliphaticSymbolAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
This smarts atom matches aliphatic atom with element symbol specified.
AliphaticSymbolAtom(String, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AliphaticSymbolAtom
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.
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
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. , Atomic physicochemical parameters for three-dimensional structure-directed quantitative structure-activity relationships. I. Partition coefficients as a measure of hydrophobicity, Journal of Computational Chemistry, 1986, 7:565-577, doi:10.1002/jcc.540070419, Ghose, A.K. and Crippen, G.M. , Atomic physicochemical parameters for three-dimensional-structure-directed quantitative structure-activity relationships. 2. Modeling dispersive and hydrophobic interactions, Journal of Chemical Information and Computer Science, 1987, 27:21-35, doi:10.1021/ci00053a005].
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.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(IQueryAtom, IQueryAtom) - Static method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom
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.
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
This matcher any Atom including explicit hydrogens.
AnyAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AnyAtom
Creates a new instance
AnyAtom() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
 
AnyOrderQueryBond - Class in org.openscience.cdk.isomorphism.matchers.smarts
This matches a bond of any order.
AnyOrderQueryBond(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AnyOrderQueryBond
 
AnyOrderQueryBond(IQueryAtom, IQueryAtom, IBond.Order, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AnyOrderQueryBond
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.ComponentGrouping
Does the mapping respected the component grouping specified by the query.
apply(int[]) - Method in class org.openscience.cdk.isomorphism.SmartsStereoMatch
Is the mapping of the stereochemistry in the query preserved in the target.
applyTo(Permutation) - Method in interface org.openscience.cdk.group.PermutationGroup.Backtracker
Do something to the permutation
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
This matcher any aromatic atom.
AromaticAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AromaticAtom
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.
AromaticityCalculator() - Constructor for class org.openscience.cdk.aromaticity.AromaticityCalculator
Deprecated.
 
AromaticOrSingleQueryBond - Class in org.openscience.cdk.isomorphism.matchers.smarts
This matches an aromatic or a single bond, used when no bond is specified between an atom.
AromaticOrSingleQueryBond(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AromaticOrSingleQueryBond
Creates a new instance.
AromaticOrSingleQueryBond(IQueryAtom, IQueryAtom, IBond.Order, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AromaticOrSingleQueryBond
Creates a new instance
AromaticQueryBond - Class in org.openscience.cdk.isomorphism.matchers.smarts
This matches an aromatic bond.
AromaticQueryBond(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AromaticQueryBond
Creates a new instance.
AromaticQueryBond(IQueryAtom, IQueryAtom, IBond.Order, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AromaticQueryBond
Creates a new instance
AromaticSymbolAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
This class matches aromatic atom with element symbol specified.
AromaticSymbolAtom(String, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AromaticSymbolAtom
 
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.
ARSENIC - Static variable in enum org.openscience.cdk.config.Elements
 
ARSENIC - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
as - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
AS - Static variable in interface org.openscience.cdk.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.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.
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() - 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
Generate SMILES with the major isotopes, only omit mass numbers when it is unset.
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
This matches an atom using the atomic number.
AtomicNumberAtom(int, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AtomicNumberAtom
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.AtomColorer() - Constructor for class org.openscience.cdk.renderer.generators.AtomNumberGenerator.AtomColorer
 
AtomNumberGenerator.AtomNumberTextColor - Class in org.openscience.cdk.renderer.generators
Color to draw the atom numbers with.
AtomNumberGenerator.AtomNumberTextColor() - Constructor for class org.openscience.cdk.renderer.generators.AtomNumberGenerator.AtomNumberTextColor
 
AtomNumberGenerator.ColorByType - Class in org.openscience.cdk.renderer.generators
Boolean to indicate of the AtomNumberGenerator.AtomColorer scheme will be used.
AtomNumberGenerator.ColorByType() - Constructor for class org.openscience.cdk.renderer.generators.AtomNumberGenerator.ColorByType
 
AtomNumberGenerator.Offset - Class in org.openscience.cdk.renderer.generators
Offset vector in screen space coordinates where the atom number label will be placed.
AtomNumberGenerator.Offset() - Constructor for class org.openscience.cdk.renderer.generators.AtomNumberGenerator.Offset
 
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.
AtomNumberGenerator.WillDrawAtomNumbers() - Constructor for class org.openscience.cdk.renderer.generators.AtomNumberGenerator.WillDrawAtomNumbers
 
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.
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.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., The signature molecular descriptor. 1. Using extended valence sequences in QSAR and QSPR studies., Journal of Chemical Information and Computer Sciences, 2003, 43:707-720, Faulon, J. L., Collins, M. J., and Carr, R. D., The Signature Molecular Descriptor. 4. Canonizing Molecules Using Extended Valence Sequences, Journal of Chemical Information and Computer Sciences, 2004, 44:427-436] 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
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
 
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.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., The autocorrelation of a topological structure: A new molecular descriptor, Nouveau Journal de Chimie, 1980, ?:359-360].
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 - 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.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
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.AtomColor() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.AtomColor
 
BasicAtomGenerator.AtomColorer - Class in org.openscience.cdk.renderer.generators
IAtomColorer used to draw elements.
BasicAtomGenerator.AtomColorer() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.AtomColorer
 
BasicAtomGenerator.AtomRadius - Class in org.openscience.cdk.renderer.generators
Magic number with unknown units that defines the radius around an atom, e.g.
BasicAtomGenerator.AtomRadius() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.AtomRadius
 
BasicAtomGenerator.ColorByType - Class in org.openscience.cdk.renderer.generators
Boolean property that triggers atoms to be colored by type when set to true.
BasicAtomGenerator.ColorByType() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.ColorByType
 
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.CompactAtom() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.CompactAtom
 
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.CompactShape() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.CompactShape
 
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.KekuleStructure() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.KekuleStructure
 
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.ShowEndCarbons() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.ShowEndCarbons
 
BasicAtomGenerator.ShowExplicitHydrogens - Class in org.openscience.cdk.renderer.generators
Boolean property that triggers explicit hydrogens to be drawn if set to true.
BasicAtomGenerator.ShowExplicitHydrogens() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.ShowExplicitHydrogens
 
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.BondDistance() - Constructor for class org.openscience.cdk.renderer.generators.BasicBondGenerator.BondDistance
 
BasicBondGenerator.BondWidth - Class in org.openscience.cdk.renderer.generators
The width on screen of a bond.
BasicBondGenerator.BondWidth() - Constructor for class org.openscience.cdk.renderer.generators.BasicBondGenerator.BondWidth
 
BasicBondGenerator.DefaultBondColor - Class in org.openscience.cdk.renderer.generators
The color to draw bonds if not other color is given.
BasicBondGenerator.DefaultBondColor() - Constructor for class org.openscience.cdk.renderer.generators.BasicBondGenerator.DefaultBondColor
 
BasicBondGenerator.TowardsRingCenterProportion - Class in org.openscience.cdk.renderer.generators
The proportion to move in towards the ring center.
BasicBondGenerator.TowardsRingCenterProportion() - Constructor for class org.openscience.cdk.renderer.generators.BasicBondGenerator.TowardsRingCenterProportion
 
BasicBondGenerator.WedgeWidth - Class in org.openscience.cdk.renderer.generators
The width on screen of the fat end of a wedge bond.
BasicBondGenerator.WedgeWidth() - Constructor for class org.openscience.cdk.renderer.generators.BasicBondGenerator.WedgeWidth
 
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
basicInvariants(IAtomContainer, 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.ArrowHeadWidth() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ArrowHeadWidth
 
BasicSceneGenerator.BackgroundColor - Class in org.openscience.cdk.renderer.generators
The background color of the drawn image.
BasicSceneGenerator.BackgroundColor() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.BackgroundColor
 
BasicSceneGenerator.BondLength - Class in org.openscience.cdk.renderer.generators
The length on the screen of a typical bond.
BasicSceneGenerator.BondLength() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.BondLength
 
BasicSceneGenerator.FitToScreen - Class in org.openscience.cdk.renderer.generators
If true, the scale is set such that the diagram fills the whole screen.
BasicSceneGenerator.FitToScreen() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.FitToScreen
 
BasicSceneGenerator.FontName - Class in org.openscience.cdk.renderer.generators
Font to use for text.
BasicSceneGenerator.FontName() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.FontName
 
BasicSceneGenerator.ForegroundColor - Class in org.openscience.cdk.renderer.generators
The foreground color, with which objects are drawn.
BasicSceneGenerator.ForegroundColor() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ForegroundColor
 
BasicSceneGenerator.Margin - Class in org.openscience.cdk.renderer.generators
Area on each of the four margins to keep empty.
BasicSceneGenerator.Margin() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.Margin
 
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.Scale() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.Scale
 
BasicSceneGenerator.ShowMoleculeTitle - Class in org.openscience.cdk.renderer.generators
Determines if the molecule's title is depicted.
BasicSceneGenerator.ShowMoleculeTitle() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ShowMoleculeTitle
 
BasicSceneGenerator.ShowReactionTitle - Class in org.openscience.cdk.renderer.generators
Determines if the reaction's title is depicted.
BasicSceneGenerator.ShowReactionTitle() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ShowReactionTitle
 
BasicSceneGenerator.ShowTooltip - Class in org.openscience.cdk.renderer.generators
Determines if tooltips are to be shown.
BasicSceneGenerator.ShowTooltip() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ShowTooltip
 
BasicSceneGenerator.UseAntiAliasing - Class in org.openscience.cdk.renderer.generators
If set to true, uses anti-aliasing for drawing.
BasicSceneGenerator.UseAntiAliasing() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.UseAntiAliasing
 
BasicSceneGenerator.UsedFontStyle - Class in org.openscience.cdk.renderer.generators
The font style to use for text.
BasicSceneGenerator.UsedFontStyle() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.UsedFontStyle
 
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.
BasicSceneGenerator.ZoomFactor() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ZoomFactor
 
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.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
Utility class that finds the shortest bond path between two atoms using a breadth first search.
BGFFormat - Class in org.openscience.cdk.io.formats
 
BGFFormat() - Constructor for class org.openscience.cdk.io.formats.BGFFormat
 
BI - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
biconnectedSets() - Method in class org.openscience.cdk.graph.BiconnectivityInspector
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
Finds the biconnected components of a graph.
BiconnectivityInspector(UndirectedGraph) - Constructor for class org.openscience.cdk.graph.BiconnectivityInspector
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.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.
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
 
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.
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.debug.DebugAminoAcid
Returns an Iterable for looping over all bonds in this container.
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.IAtomContainer
Returns an Iterable for looping over all bonds in this container.
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 - 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.
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.
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 booleans.
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
 
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.
BoundsGenerator.BoundsColor() - Constructor for class org.openscience.cdk.renderer.generators.BoundsGenerator.BoundsColor
 
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.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.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.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>.
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.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.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.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 weight of specified element 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
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
Evaluate the surface.
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 and Weininger, Arthur and Weininger, Joseph L., SMILES 2. Algorithm for Generation of Unique SMILES Notation, Journal of Chemical Information and Computer Sciences, 1989, 29:97-101].
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.
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
 
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.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.
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
 
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.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
center(IAtomContainer, Dimension) - Static method in class org.openscience.cdk.geometry.GeometryTools
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.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
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
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.
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
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
 
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
This matches an atom with chirality property.
ChiralityAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom
Creates a new instance
chiralityMatches(IAtom, int, int) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom
Check if the atom-based chirality of the target matches.
chiralityMatches(IAtom, int, int) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom
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. and Ingold, C. and Prelog, V., Specification of Molecular Chirality, Angew. Chem. Int. Ed., 1966, 5:385-415].
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
 
CircularFingerprinter.FP(int, int, int[]) - Constructor for class org.openscience.cdk.fingerprint.CircularFingerprinter.FP
 
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.
 
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 AtomContainer object and its content.
clone() - Method in class org.openscience.cdk.AtomContainerSet
Clones this AtomContainerSet and its content.
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.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 AtomContainer object and its content.
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 AtomContainer object and its content.
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 AtomContainer object and its content.
clone() - Method in class org.openscience.cdk.debug.DebugPolymer
Clones this AtomContainer object and its content.
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 AtomContainer object and its content.
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 AtomContainer object and its content.
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
 
clone() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolChargeIDQueryAtom
 
clone() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom
 
clone() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom
 
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 AtomContainer object and its content.
clone() - Method in class org.openscience.cdk.Polymer
 
clone() - Method in class org.openscience.cdk.protein.data.PDBMonomer
Clones this AtomContainer object and its content.
clone() - Method in class org.openscience.cdk.protein.data.PDBPolymer
Clones this AtomContainer object and its content.
clone() - Method in class org.openscience.cdk.PseudoAtom
 
clone() - Method in class org.openscience.cdk.Reaction
Clones this Reaction and its content.
clone() - Method in class org.openscience.cdk.ReactionScheme
Clones this ReactionScheme object and its content.
clone() - Method in class org.openscience.cdk.ReactionSet
Clones this ReactionSet and the contained Reactions too.
clone() - Method in class org.openscience.cdk.Ring
Clones this AtomContainer object and its content.
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 AtomContainer object and its content.
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 AtomContainer object and its content.
clone() - Method in class org.openscience.cdk.silent.PDBMonomer
Clones this AtomContainer object and its content.
clone() - Method in class org.openscience.cdk.silent.PDBPolymer
Clones this AtomContainer object and its content.
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 AtomContainer object and its content.
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
 
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
 
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.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., Processing CML Conventions in Java, 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
 
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.
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
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
 
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.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
ComponentGrouping - Class in org.openscience.cdk.isomorphism
A predicate for verifying component level grouping in query/target structure matching.
ComponentGrouping(IAtomContainer, IAtomContainer) - Constructor for class org.openscience.cdk.isomorphism.ComponentGrouping
Create a predicate to match components for the provided query and target.
ComponentGrouping(int[], int[]) - Constructor for class org.openscience.cdk.isomorphism.ComponentGrouping
Create a predicate to match components for the provided query (grouping) and target (connected components).
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., Algorithm 97: Shortest path, Commun. ACM, 1962, 5:345, doi:10.1145/367766.368168].
computeFloydAPSP(double[][]) - Static method in class org.openscience.cdk.graph.PathTools
All-Pairs-Shortest-Path computation based on Floyd's algorithm [Floyd, R.W., Algorithm 97: Shortest path, Commun. ACM, 1962, 5:345, doi:10.1145/367766.368168].
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.
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(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(IAtom) - Method in class org.openscience.cdk.stereo.DoubleBondStereochemistry
Does the stereo element contain the provided atom.
contains(IAtom) - Method in class org.openscience.cdk.stereo.ExtendedTetrahedral
Does the stereo element contain the provided atom.
contains(IAtom) - Method in class org.openscience.cdk.stereo.TetrahedralChirality
Does the stereo element contain the provided atom.
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.
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
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, rcov, 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.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(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.smiles.smarts.SmartsPattern
Create a Pattern that will match the given smarts query.
create(String) - Static method in class org.openscience.cdk.smiles.smarts.SmartsPattern
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(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 wildcard atoms and wildcard bonds.
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 AnyAtoms / Aromatic Atoms and OrderQueryBonds / AromaticQueryBonds.
createAnyAtomForPseudoAtomQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
Creates a QueryAtomContainer with SymbolQueryAtom's and OrderQueryBond's.
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 SymbolQueryAtom's, AromaticQueryBond's and OrderQueryBond's.
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
 
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
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 SymbolQueryAtom's and OrderQueryBond's.
createSymbolAndChargeQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
Creates a QueryAtomContainer with SymbolAncChargeQueryAtom's and OrderQueryBond's.
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.CrystClustFormat
 
CrystClustReader - Class in org.openscience.cdk.io
 
CrystClustReader() - Constructor for class org.openscience.cdk.io.CrystClustReader
 
CrystClustReader(Reader) - Constructor for class org.openscience.cdk.io.CrystClustReader
 
CrystClustReader(InputStream) - Constructor for class org.openscience.cdk.io.CrystClustReader
 
CrystClustWriter - Class in org.openscience.cdk.io
Rather stupid file format used for storing crystal information.
CrystClustWriter(Writer) - Constructor for class org.openscience.cdk.io.CrystClustWriter
Constructs a new CrystClustWriter class.
CrystClustWriter(OutputStream) - Constructor for class org.openscience.cdk.io.CrystClustWriter
 
CrystClustWriter() - Constructor for class org.openscience.cdk.io.CrystClustWriter
 
CS - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
CTAB_SGROUPS - Static variable in class org.openscience.cdk.CDKConstants
Key to store/fetch CTab Sgroups from Molfiles.
CTFileQueryBond - Class in org.openscience.cdk.isomorphism.matchers
Captures query bond types defined in the CTFile.
CTFileQueryBond(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.CTFileQueryBond
 
CTFileQueryBond.Type - Enum in org.openscience.cdk.isomorphism.matchers
 
CTXFormat - Class in org.openscience.cdk.io.formats
 
CTXFormat() - Constructor for class org.openscience.cdk.io.formats.CTXFormat
 
CTXReader - Class in org.openscience.cdk.io
Reader that extracts information from the IDENT, NAME, ATOMS and BONDS blocks in CTX files.
CTXReader() - Constructor for class org.openscience.cdk.io.CTXReader
 
CTXReader(Reader) - Constructor for class org.openscience.cdk.io.CTXReader
 
CTXReader(InputStream) - Constructor for class org.openscience.cdk.io.CTXReader
 
CU - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
CubicTo - Class in org.openscience.cdk.renderer.elements.path
A cubic curve in the path.
CubicTo(Point2d, Point2d, Point2d) - Constructor for class org.openscience.cdk.renderer.elements.path.CubicTo
Make a cubic curve path element.
CubicTo(double[]) - Constructor for class org.openscience.cdk.renderer.elements.path.CubicTo
Make a cubic curve path element.
CubicTo(double, double, double, double, double, double) - Constructor for class org.openscience.cdk.renderer.elements.path.CubicTo
Make a cubic curve path element.
cubicTo(Point2d, Point2d, Point2d) - Method in class org.openscience.cdk.renderer.elements.path.PathBuilder
Make a cubic curve in the path, with two control points.
curChar - Variable in class org.openscience.cdk.iupac.parser.NomParserTokenManager
 
curChar - Variable in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager
 
CURIUM - Static variable in enum org.openscience.cdk.config.Elements
 
CURIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
curRef - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
 
current() - Method in class org.openscience.cdk.io.cml.CMLModuleStack
Returns the last added entry.
currentAtom - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
 
currentBond - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
 
currentChars - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
 
currentChemFile - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
 
currentChemModel - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
 
currentChemSequence - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
 
CurrentElement - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
 
currentFontIndex - Variable in class org.openscience.cdk.renderer.font.AbstractFontManager
 
currentMolecule - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
 
currentMoleculeSet - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
 
currentMonomer - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
 
currentReaction - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
 
currentReactionSet - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
 
currentRecord - Variable in class org.openscience.cdk.io.random.RandomAccessReader
 
currentStrand - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
 
currentToken - Variable in exception org.openscience.cdk.iupac.parser.ParseException
This is the last token that has been consumed successfully.
currentToken - Variable in exception org.openscience.cdk.smiles.smarts.parser.ParseException
This is the last token that has been consumed successfully.
customize(IAtom, Object) - Method in interface org.openscience.cdk.libio.cml.ICMLCustomizer
Customized the nodeToAdd for the given Atom.
customize(IBond, Object) - Method in interface org.openscience.cdk.libio.cml.ICMLCustomizer
Customized the nodeToAdd for the given IBond.
customize(IAtomContainer, Object) - Method in interface org.openscience.cdk.libio.cml.ICMLCustomizer
Customized the nodeToAdd for the given Molecule.
customize(IBond, Object) - Method in class org.openscience.cdk.libio.cml.MDMoleculeCustomizer
No customization for bonds.
customize(IAtom, Object) - Method in class org.openscience.cdk.libio.cml.MDMoleculeCustomizer
Customize Atom.
customize(IAtomContainer, Object) - Method in class org.openscience.cdk.libio.cml.MDMoleculeCustomizer
Customize Molecule.
customize(IAtom, Object) - Method in class org.openscience.cdk.libio.cml.PDBAtomCustomizer
 
customize(IAtomContainer, Object) - Method in class org.openscience.cdk.libio.cml.PDBAtomCustomizer
 
customize(IBond, Object) - Method in class org.openscience.cdk.libio.cml.PDBAtomCustomizer
 
customize(IBond, Object) - Method in class org.openscience.cdk.libio.cml.QSARCustomizer
 
customize(IAtom, Object) - Method in class org.openscience.cdk.libio.cml.QSARCustomizer
 
customize(IAtomContainer, Object) - Method in class org.openscience.cdk.libio.cml.QSARCustomizer
 
customizeJob() - Method in class org.openscience.cdk.io.iterator.IteratingSDFReader
 
customizeJob() - Method in class org.openscience.cdk.io.MDLReader
Deprecated.
 
customizeJob() - Method in class org.openscience.cdk.io.MDLV2000Reader
 
customizeJob() - Method in class org.openscience.cdk.io.MDLV2000Writer
 
customizeJob() - Method in class org.openscience.cdk.io.PDBReader
 
customizeJob() - Method in class org.openscience.cdk.io.SDFWriter
 
customizeJob() - Method in class org.openscience.cdk.io.SMILESWriter
 
CustomSerializer - Class in org.openscience.cdk.io.cml
Custom Serializer with the sole purpose and functionality to not output the XML declaration.
CustomSerializer(OutputStream) - Constructor for class org.openscience.cdk.io.cml.CustomSerializer
Instantiates a new CustomSerializer using the matching Serializer.Serializer(OutputStream).
CustomSerializer(OutputStream, String) - Constructor for class org.openscience.cdk.io.cml.CustomSerializer
Instantiates a new CustomSerializer using the matching Serializer.Serializer(OutputStream, String).
Cx2dCoordinates - Static variable in class org.openscience.cdk.smiles.SmiFlavor
Output 2D coordinates.
Cx3dCoordinates - Static variable in class org.openscience.cdk.smiles.SmiFlavor
Output 3D coordinates.
CxAtomLabel - Static variable in class org.openscience.cdk.smiles.SmiFlavor
Output atom labels, atom labels are specified by IPseudoAtom.getLabel().
CxAtomValue - Static variable in class org.openscience.cdk.smiles.SmiFlavor
Output atom values, atom values are specified by IPseudoAtom.getLabel().
CxCoordinates - Static variable in class org.openscience.cdk.smiles.SmiFlavor
Output either 2D/3D coordinates.
CxFragmentGroup - Static variable in class org.openscience.cdk.smiles.SmiFlavor
Output fragment grouping for reactions.
CxMulticenter - Static variable in class org.openscience.cdk.smiles.SmiFlavor
Output multicenter bonds, positional variation is specified with Sgroups of the type SgroupType.ExtMulticenter.
CxPolymer - Static variable in class org.openscience.cdk.smiles.SmiFlavor
Output polymer repeat units is specified with Sgroups.
CxRadical - Static variable in class org.openscience.cdk.smiles.SmiFlavor
Output radicals, radicals are specified by IAtomContainer.getConnectedSingleElectronsCount(IAtom)
CxSmiles - Static variable in class org.openscience.cdk.smiles.SmiFlavor
Output CXSMILES layers.
CxSmilesGenerator - Class in org.openscience.cdk.smiles
 
CxSmilesGenerator() - Constructor for class org.openscience.cdk.smiles.CxSmilesGenerator
 
CxSmilesWithCoords - Static variable in class org.openscience.cdk.smiles.SmiFlavor
Output CXSMILES layers and coordinates.
cycle(int[][], int[]) - Static method in class org.openscience.cdk.graph.GraphUtil
Arrange the vertices in a simple cyclic path.
cycle() - Method in class org.openscience.cdk.iupac.parser.NomParser
Deprecated.
Deals with cyclic main chains.
CycleBasis - Class in org.openscience.cdk.ringsearch.cyclebasis
Deprecated.
internal implemenation detail from SSSRFinder, do not use
CycleBasis(UndirectedGraph) - Constructor for class org.openscience.cdk.ringsearch.cyclebasis.CycleBasis
Deprecated.
Constructs a minimum cycle basis of a graph.
CycleFinder - Interface in org.openscience.cdk.graph
Defines a method to find the cycles of a molecule.
Cycles - Class in org.openscience.cdk.graph
A utility class for storing and computing the cycles of a chemical graph.
cycles() - Method in class org.openscience.cdk.ringsearch.cyclebasis.CycleBasis
Deprecated.
Returns the cycles that form the cycle basis.
cycles() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis
Deprecated.
 
cyclic(int) - Method in interface org.openscience.cdk.ringsearch.CyclicVertexSearch
Returns true if the vertex v is in a cycle.
cyclic(int, int) - Method in interface org.openscience.cdk.ringsearch.CyclicVertexSearch
Is the edge between the two vertices u and v in a cycle?
cyclic() - Method in interface org.openscience.cdk.ringsearch.CyclicVertexSearch
The set of cyclic vertices.
cyclic(int, int) - Method in class org.openscience.cdk.ringsearch.RingSearch
Determine whether the edge between the vertices u and v is cyclic.
cyclic(IAtom) - Method in class org.openscience.cdk.ringsearch.RingSearch
Determine whether the provided atom belongs to a ring (is cyclic).
cyclic(IBond) - Method in class org.openscience.cdk.ringsearch.RingSearch
Determine whether the bond is cyclic.
cyclic(int) - Method in class org.openscience.cdk.ringsearch.RingSearch
Determine whether the vertex at index i is a cyclic vertex.
cyclic() - Method in class org.openscience.cdk.ringsearch.RingSearch
Construct a set of vertices which belong to any cycle (ring).
CyclicVertexSearch - Interface in org.openscience.cdk.ringsearch
Describes a search to identify vertices which belong to elementary cycles and if those cycles are isolated or are part of a fused system.
CYCLO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.

D

D - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
D_BOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
DaltonFormat - Class in org.openscience.cdk.io.formats
 
DaltonFormat() - Constructor for class org.openscience.cdk.io.formats.DaltonFormat
 
DARMSTADTIUM - Static variable in enum org.openscience.cdk.config.Elements
 
DASH - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
DataFeatures - Class in org.openscience.cdk.tools
Class with constants for possible data features defined in the a Data Feature Ontology.
DataFeatures() - Constructor for class org.openscience.cdk.tools.DataFeatures
 
DataFeaturesTool - Class in org.openscience.cdk.tools
Utility that helps determine which data features are present.
DataFeaturesTool() - Constructor for class org.openscience.cdk.tools.DataFeaturesTool
 
daylight() - Static method in class org.openscience.cdk.aromaticity.ElectronDonation
Electron donation model closely mirroring the Daylight model for use in generating SMILES.
dBlockMetals() - Method in class org.openscience.cdk.iupac.parser.NomParser
Deprecated.
 
DeAromatizationTool - Class in org.openscience.cdk.tools
Deprecated.
the newer Kekulization provides a faster, more generic and comprehensive algorithm.
DeAromatizationTool() - Constructor for class org.openscience.cdk.tools.DeAromatizationTool
Deprecated.
 
deAromatize(IRing) - Static method in class org.openscience.cdk.tools.DeAromatizationTool
Deprecated.
Methods that takes a ring of which all bonds are aromatic, and assigns single and double bonds.
Dearomatize(IAtomContainer) - Static method in class org.openscience.cdk.tools.DeAromatizationTool
Deprecated.
 
Dearomatize566Rings(IRingSet) - Static method in class org.openscience.cdk.tools.DeAromatizationTool
Deprecated.
 
Dearomatize56Rings(IRingSet) - Static method in class org.openscience.cdk.tools.DeAromatizationTool
Deprecated.
 
Dearomatize5Ring(IRingSet) - Static method in class org.openscience.cdk.tools.DeAromatizationTool
Deprecated.
 
Dearomatize666Rings(IRingSet) - Static method in class org.openscience.cdk.tools.DeAromatizationTool
Deprecated.
 
Dearomatize66Rings(IRingSet) - Static method in class org.openscience.cdk.tools.DeAromatizationTool
Deprecated.
 
Dearomatize6Ring(IRingSet) - Static method in class org.openscience.cdk.tools.DeAromatizationTool
Deprecated.
 
DEBUG - Static variable in class org.openscience.cdk.graph.PathTools
Boolean with which debugging can be turned on.
debug - Static variable in class org.openscience.cdk.layout.AtomPlacer
 
debug - Static variable in class org.openscience.cdk.ringsearch.RingPartitioner
Debugging on/off
debug(Object) - Method in interface org.openscience.cdk.tools.ILoggingTool
Shows DEBUG output for the Object.
debug(Object, Object...) - Method in interface org.openscience.cdk.tools.ILoggingTool
Shows DEBUG output for the given Object's.
debug(Object) - Method in class org.openscience.cdk.tools.LoggingTool
Shows DEBUG output for the Object.
debug(Object, Object...) - Method in class org.openscience.cdk.tools.LoggingTool
Shows DEBUG output for the given Object's.
debug - Static variable in class org.openscience.cdk.tools.SwissArmyKnife
Deprecated.
 
debug(Object) - Method in class org.openscience.cdk.tools.SystemOutLoggingTool
Shows DEBUG output for the Object.
debug(Object, Object...) - Method in class org.openscience.cdk.tools.SystemOutLoggingTool
Shows DEBUG output for the given Object's.
DebugAdductFormula - Class in org.openscience.cdk.debug
Debugging implementation of IAdductFormula.
DebugAdductFormula() - Constructor for class org.openscience.cdk.debug.DebugAdductFormula
 
DebugAdductFormula(IMolecularFormula) - Constructor for class org.openscience.cdk.debug.DebugAdductFormula
 
DebugAminoAcid - Class in org.openscience.cdk.debug
Debugging data class.
DebugAminoAcid() - Constructor for class org.openscience.cdk.debug.DebugAminoAcid
 
DebugAtom - Class in org.openscience.cdk.debug
Debugging data class.
DebugAtom() - Constructor for class org.openscience.cdk.debug.DebugAtom
 
DebugAtom(String) - Constructor for class org.openscience.cdk.debug.DebugAtom
 
DebugAtom(String, Point2d) - Constructor for class org.openscience.cdk.debug.DebugAtom
 
DebugAtom(String, Point3d) - Constructor for class org.openscience.cdk.debug.DebugAtom
 
DebugAtom(IElement) - Constructor for class org.openscience.cdk.debug.DebugAtom
 
DebugAtomContainer - Class in org.openscience.cdk.debug
Debugging data class.
DebugAtomContainer() - Constructor for class org.openscience.cdk.debug.DebugAtomContainer
 
DebugAtomContainer(int, int, int, int) - Constructor for class org.openscience.cdk.debug.DebugAtomContainer
 
DebugAtomContainer(IAtomContainer) - Constructor for class org.openscience.cdk.debug.DebugAtomContainer
 
DebugAtomContainerSet - Class in org.openscience.cdk.debug
Debugging data class.
DebugAtomContainerSet() - Constructor for class org.openscience.cdk.debug.DebugAtomContainerSet
 
DebugAtomType - Class in org.openscience.cdk.debug
Debugging data class.
DebugAtomType(String) - Constructor for class org.openscience.cdk.debug.DebugAtomType
 
DebugAtomType(String, String) - Constructor for class org.openscience.cdk.debug.DebugAtomType
 
DebugAtomType(IElement) - Constructor for class org.openscience.cdk.debug.DebugAtomType
 
DebugBioPolymer - Class in org.openscience.cdk.debug
Debugging data class.
DebugBioPolymer() - Constructor for class org.openscience.cdk.debug.DebugBioPolymer
 
DebugBond - Class in org.openscience.cdk.debug
Debugging data class.
DebugBond() - Constructor for class org.openscience.cdk.debug.DebugBond
 
DebugBond(IAtom, IAtom) - Constructor for class org.openscience.cdk.debug.DebugBond
 
DebugBond(IAtom, IAtom, IBond.Order) - Constructor for class org.openscience.cdk.debug.DebugBond
 
DebugBond(IAtom, IAtom, IBond.Order, IBond.Stereo) - Constructor for class org.openscience.cdk.debug.DebugBond
 
DebugBond(IAtom[]) - Constructor for class org.openscience.cdk.debug.DebugBond
 
DebugBond(IAtom[], IBond.Order) - Constructor for class org.openscience.cdk.debug.DebugBond
 
DebugChemFile - Class in org.openscience.cdk.debug
Debugging data class.
DebugChemFile() - Constructor for class org.openscience.cdk.debug.DebugChemFile
 
DebugChemModel - Class in org.openscience.cdk.debug
Debugging data class.
DebugChemModel() - Constructor for class org.openscience.cdk.debug.DebugChemModel
 
DebugChemObject - Class in org.openscience.cdk.debug
Debugging data class.
DebugChemObject(IChemObject) - Constructor for class org.openscience.cdk.debug.DebugChemObject
 
DebugChemObject() - Constructor for class org.openscience.cdk.debug.DebugChemObject
 
DebugChemObjectBuilder - Class in org.openscience.cdk.debug
A helper class to instantiate a IChemObject for the original CDK implementation.
DebugChemSequence - Class in org.openscience.cdk.debug
Debugging data class.
DebugChemSequence() - Constructor for class org.openscience.cdk.debug.DebugChemSequence
 
DebugCrystal - Class in org.openscience.cdk.debug
Debugging data class.
DebugCrystal() - Constructor for class org.openscience.cdk.debug.DebugCrystal
 
DebugCrystal(IAtomContainer) - Constructor for class org.openscience.cdk.debug.DebugCrystal
 
DebugElectronContainer - Class in org.openscience.cdk.debug
Debugging data class.
DebugElectronContainer() - Constructor for class org.openscience.cdk.debug.DebugElectronContainer
 
DebugElement - Class in org.openscience.cdk.debug
Debugging data class.
DebugElement() - Constructor for class org.openscience.cdk.debug.DebugElement
 
DebugElement(String) - Constructor for class org.openscience.cdk.debug.DebugElement
 
DebugElement(String, int) - Constructor for class org.openscience.cdk.debug.DebugElement
 
DebugElement(IElement) - Constructor for class org.openscience.cdk.debug.DebugElement
 
DebugFragmentAtom - Class in org.openscience.cdk.debug
Class to represent an IPseudoAtom which embeds an IAtomContainer.
DebugFragmentAtom() - Constructor for class org.openscience.cdk.debug.DebugFragmentAtom
 
debuggCheckPSPEvent() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
 
DebugIsotope - Class in org.openscience.cdk.debug
Debugging data class.
DebugIsotope(String) - Constructor for class org.openscience.cdk.debug.DebugIsotope
 
DebugIsotope(int, String, int, double, double) - Constructor for class org.openscience.cdk.debug.DebugIsotope
 
DebugIsotope(int, String, double, double) - Constructor for class org.openscience.cdk.debug.DebugIsotope
 
DebugIsotope(String, int) - Constructor for class org.openscience.cdk.debug.DebugIsotope
 
DebugIsotope(IElement) - Constructor for class org.openscience.cdk.debug.DebugIsotope
 
DebugLonePair - Class in org.openscience.cdk.debug
Debugging data class.
DebugLonePair() - Constructor for class org.openscience.cdk.debug.DebugLonePair
 
DebugLonePair(IAtom) - Constructor for class org.openscience.cdk.debug.DebugLonePair
 
DebugMapping - Class in org.openscience.cdk.debug
Debugging data class.
DebugMapping(IChemObject, IChemObject) - Constructor for class org.openscience.cdk.debug.DebugMapping
 
DebugMolecularFormula - Class in org.openscience.cdk.debug
Debugging implementation of IMolecularFormula.
DebugMolecularFormula() - Constructor for class org.openscience.cdk.debug.DebugMolecularFormula
 
DebugMolecularFormulaSet - Class in org.openscience.cdk.debug
Debugging implementation of IMolecularFormulaSet.
DebugMolecularFormulaSet() - Constructor for class org.openscience.cdk.debug.DebugMolecularFormulaSet
 
DebugMolecularFormulaSet(IMolecularFormula) - Constructor for class org.openscience.cdk.debug.DebugMolecularFormulaSet
 
DebugMonomer - Class in org.openscience.cdk.debug
Debugging data class.
DebugMonomer() - Constructor for class org.openscience.cdk.debug.DebugMonomer
 
DebugPDBAtom - Class in org.openscience.cdk.debug
Debugging data class.
DebugPDBAtom(IElement) - Constructor for class org.openscience.cdk.debug.DebugPDBAtom
 
DebugPDBAtom(String) - Constructor for class org.openscience.cdk.debug.DebugPDBAtom
 
DebugPDBAtom(String, Point3d) - Constructor for class org.openscience.cdk.debug.DebugPDBAtom
 
DebugPDBMonomer - Class in org.openscience.cdk.debug
Debugging data class.
DebugPDBMonomer() - Constructor for class org.openscience.cdk.debug.DebugPDBMonomer
 
DebugPDBPolymer - Class in org.openscience.cdk.debug
Debugging data class.
DebugPDBPolymer() - Constructor for class org.openscience.cdk.debug.DebugPDBPolymer
 
DebugPDBStructure - Class in org.openscience.cdk.debug
Debugging data class.
DebugPDBStructure() - Constructor for class org.openscience.cdk.debug.DebugPDBStructure
 
DebugPolymer - Class in org.openscience.cdk.debug
Debugging data class.
DebugPolymer() - Constructor for class org.openscience.cdk.debug.DebugPolymer
 
DebugPseudoAtom - Class in org.openscience.cdk.debug
Debugging data class.
DebugPseudoAtom() - Constructor for class org.openscience.cdk.debug.DebugPseudoAtom
 
DebugPseudoAtom(IElement) - Constructor for class org.openscience.cdk.debug.DebugPseudoAtom
 
DebugPseudoAtom(String) - Constructor for class org.openscience.cdk.debug.DebugPseudoAtom
 
DebugPseudoAtom(String, Point2d) - Constructor for class org.openscience.cdk.debug.DebugPseudoAtom
 
DebugPseudoAtom(String, Point3d) - Constructor for class org.openscience.cdk.debug.DebugPseudoAtom
 
DebugReaction - Class in org.openscience.cdk.debug
Debugging data class.
DebugReaction() - Constructor for class org.openscience.cdk.debug.DebugReaction
 
DebugReactionScheme - Class in org.openscience.cdk.debug
Debugging data class.
DebugReactionScheme() - Constructor for class org.openscience.cdk.debug.DebugReactionScheme
 
DebugReactionSet - Class in org.openscience.cdk.debug
Debugging data class.
DebugReactionSet() - Constructor for class org.openscience.cdk.debug.DebugReactionSet
 
DebugRing - Class in org.openscience.cdk.debug
Debugging data class.
DebugRing() - Constructor for class org.openscience.cdk.debug.DebugRing
 
DebugRing(int, String) - Constructor for class org.openscience.cdk.debug.DebugRing
 
DebugRing(int) - Constructor for class org.openscience.cdk.debug.DebugRing
 
DebugRing(IAtomContainer) - Constructor for class org.openscience.cdk.debug.DebugRing
 
DebugRingSet - Class in org.openscience.cdk.debug
Debugging data class.
DebugRingSet() - Constructor for class org.openscience.cdk.debug.DebugRingSet
 
DebugSingleElectron - Class in org.openscience.cdk.debug
Debugging data class.
DebugSingleElectron() - Constructor for class org.openscience.cdk.debug.DebugSingleElectron
 
DebugSingleElectron(IAtom) - Constructor for class org.openscience.cdk.debug.DebugSingleElectron
 
DebugStrand - Class in org.openscience.cdk.debug
Debugging data class.
DebugStrand() - Constructor for class org.openscience.cdk.debug.DebugStrand
 
debugStream - Variable in class org.openscience.cdk.iupac.parser.NomParserTokenManager
Debug output.
debugStream - Variable in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager
Debug output.
DebugSubstance - Class in org.openscience.cdk.debug
Debugging data class.
DebugSubstance() - Constructor for class org.openscience.cdk.debug.DebugSubstance
 
DEC - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
decideBondOrder(IAtomContainer, boolean) - Method in class org.openscience.cdk.tools.AtomTypeAwareSaturationChecker
This method decides the bond order on bonds that has the SINGLE_OR_DOUBLE-flag raised.
decideBondOrder(IAtomContainer) - Method in class org.openscience.cdk.tools.AtomTypeAwareSaturationChecker
This method decides the bond order on bonds that has the SINGLE_OR_DOUBLE-flag raised.
DECIMAL_FORMAT - Static variable in class org.openscience.cdk.io.MDLV3000Writer
 
decode(String) - Static method in class org.openscience.cdk.fingerprint.PubchemFingerprinter
Returns a fingerprint from a Base64 encoded Pubchem fingerprint.
decreaseBondOrder(IBond.Order) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
Returns the IBond.Order one lower.
decreaseBondOrder(IBond) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
Decrease the order of a bond.
decreaseFontSize() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
Move the font size pointer down.
DeduceBondSystemTool - Class in org.openscience.cdk.smiles
Deprecated.
Use the newer Kekulization
DeduceBondSystemTool() - Constructor for class org.openscience.cdk.smiles.DeduceBondSystemTool
Deprecated.
Constructor for the DeduceBondSystemTool object.
DeduceBondSystemTool(AllRingsFinder) - Constructor for class org.openscience.cdk.smiles.DeduceBondSystemTool
Deprecated.
Constructor for the DeduceBondSystemTool object accepting a custom AllRingsFinder.
DEFAULT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
Lexical state.
DEFAULT - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
Lexical state.
Default - Static variable in class org.openscience.cdk.smiles.SmiFlavor
Default SMILES output write Stereochemistry, Atomic Mass, and CXSMILES layers.
DEFAULT_BOND_LENGTH - Static variable in class org.openscience.cdk.layout.StructureDiagramGenerator
 
DEFAULT_BOND_LENGTH_H - Static variable in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
 
DEFAULT_BOND_VECTOR - Static variable in class org.openscience.cdk.layout.StructureDiagramGenerator
 
DEFAULT_LOGGING_TOOL_CLASS - Static variable in class org.openscience.cdk.tools.LoggingToolFactory
Default logging tool.
DEFAULT_MM_MARGIN - Static variable in class org.openscience.cdk.depict.DepictionGenerator
Default margin for vector graphics formats.
DEFAULT_OCCURRENCE - Static variable in class org.openscience.cdk.isomorphism.matchers.RGroupList
Default value for occurrence field.
DEFAULT_PADDING_FACTOR - Static variable in class org.openscience.cdk.depict.Depiction
When no fixed padding value is specified we use margin multiplied by this value.
DEFAULT_PX_MARGIN - Static variable in class org.openscience.cdk.depict.DepictionGenerator
Default margin for raster graphics formats.
DEFAULT_SCALE - Static variable in class org.openscience.cdk.renderer.AtomContainerRenderer
The default scale is used when the model is empty.
DEFAULT_SEARCH_DEPTH - Static variable in class org.openscience.cdk.fingerprint.Fingerprinter
The default search depth used to create the fingerprints.
DEFAULT_SIZE - Static variable in class org.openscience.cdk.fingerprint.Fingerprinter
The default length of created fingerprints.
DEFAULT_SIZE - Static variable in class org.openscience.cdk.fingerprint.ShortestPathFingerprinter
The default length of created fingerprints.
DEFAULT_STACK_LENGTH - Static variable in interface org.openscience.cdk.tools.ILoggingTool
Default number of StackTraceElements to be printed by debug(Exception).
DEFAULT_STACK_LENGTH - Variable in class org.openscience.cdk.tools.LoggingTool
Default number of StackTraceElements to be printed by debug(Exception).
defaultAngles - Static variable in class org.openscience.cdk.layout.RingPlacer
Default ring start angles.
DefaultBondMatcher - Class in org.openscience.cdk.smsd.algorithm.matchers
Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
DefaultBondMatcher() - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultBondMatcher
Deprecated.
Constructor
DefaultBondMatcher(IAtomContainer, IBond, boolean) - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultBondMatcher
Deprecated.
Constructor
DefaultBondMatcher(IQueryBond) - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultBondMatcher
Deprecated.
Constructor
DefaultChemObjectBuilder - Class in org.openscience.cdk
A factory class to provide implementation independent ICDKObjects.
DefaultChemObjectReader - Class in org.openscience.cdk.io
Abstract class that ChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners.
DefaultChemObjectReader() - Constructor for class org.openscience.cdk.io.DefaultChemObjectReader
 
DefaultChemObjectWriter - Class in org.openscience.cdk.io
Abstract class that ChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners.
DefaultChemObjectWriter() - Constructor for class org.openscience.cdk.io.DefaultChemObjectWriter
 
DefaultEventChemObjectReader - Class in org.openscience.cdk.io.iterator.event
Abstract class that IteratingChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners.
DefaultEventChemObjectReader() - Constructor for class org.openscience.cdk.io.iterator.event.DefaultEventChemObjectReader
 
DefaultIteratingChemObjectReader<T extends IChemObject> - Class in org.openscience.cdk.io.iterator
Abstract class that IteratingChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners.
DefaultIteratingChemObjectReader() - Constructor for class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader
 
DefaultMatcher - Class in org.openscience.cdk.smsd.algorithm.matchers
Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
DefaultMatcher() - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultMatcher
Deprecated.
 
DefaultMCSPlusAtomMatcher - Class in org.openscience.cdk.smsd.algorithm.matchers
Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
DefaultMCSPlusAtomMatcher() - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultMCSPlusAtomMatcher
Deprecated.
Constructor
DefaultMCSPlusAtomMatcher(IAtomContainer, IAtom, boolean) - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultMCSPlusAtomMatcher
Deprecated.
Constructor
DefaultMCSPlusAtomMatcher(IQueryAtom, IQueryAtomContainer) - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultMCSPlusAtomMatcher
Deprecated.
Constructor
DefaultMCSPlusAtomMatcher(IAtomContainer, IAtom, int, boolean) - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultMCSPlusAtomMatcher
Deprecated.
Constructor
DefaultRandomAccessChemObjectReader - Class in org.openscience.cdk.io.random
Abstract class that IRandomAccessChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners.
DefaultRandomAccessChemObjectReader() - Constructor for class org.openscience.cdk.io.random.DefaultRandomAccessChemObjectReader
 
DefaultRGraphAtomMatcher - Class in org.openscience.cdk.smsd.algorithm.matchers
Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
DefaultRGraphAtomMatcher() - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultRGraphAtomMatcher
Deprecated.
Constructor
DefaultRGraphAtomMatcher(IAtomContainer, IAtom, boolean) - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultRGraphAtomMatcher
Deprecated.
Constructor
DefaultRGraphAtomMatcher(IAtomContainer, IAtom, int, boolean) - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultRGraphAtomMatcher
Deprecated.
Constructor
DefaultVFAtomMatcher - Class in org.openscience.cdk.smsd.algorithm.matchers
Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
DefaultVFAtomMatcher() - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFAtomMatcher
Deprecated.
Constructor
DefaultVFAtomMatcher(IAtomContainer, IAtom, boolean) - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFAtomMatcher
Deprecated.
Constructor
DefaultVFAtomMatcher(IQueryAtom, IQueryAtomContainer) - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFAtomMatcher
Deprecated.
Constructor
DefaultVFAtomMatcher(IAtomContainer, IAtom, int, boolean) - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFAtomMatcher
Deprecated.
Constructor
DefaultVFBondMatcher - Class in org.openscience.cdk.smsd.algorithm.matchers
Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
DefaultVFBondMatcher() - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFBondMatcher
Deprecated.
Constructor
DefaultVFBondMatcher(IAtomContainer, IBond, boolean) - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFBondMatcher
Deprecated.
Constructor
DefaultVFBondMatcher(IQueryBond) - Constructor for class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFBondMatcher
Deprecated.
Constructor
defineLigancyFourChirality(IAtomContainer, int, int, int, int, int, ITetrahedralChirality.Stereo) - Static method in class org.openscience.cdk.geometry.cip.CIPTool
Creates a ligancy for chirality around a single chiral atom, where the involved atoms are identified by there index in the IAtomContainer.
defineLigand(IAtomContainer, VisitedAtoms, int, int) - Static method in class org.openscience.cdk.geometry.cip.CIPTool
Creates a ligand attached to a single chiral atom, where the involved atoms are identified by there index in the IAtomContainer.
depict(IAtomContainer) - Method in class org.openscience.cdk.depict.DepictionGenerator
Depict a single molecule.
depict(Iterable<IAtomContainer>) - Method in class org.openscience.cdk.depict.DepictionGenerator
Depict a set of molecules, they will be depicted in a grid.
depict(Iterable<IAtomContainer>, int, int) - Method in class org.openscience.cdk.depict.DepictionGenerator
Depict a set of molecules, they will be depicted in a grid with the specified number of rows and columns.
depict(IReaction) - Method in class org.openscience.cdk.depict.DepictionGenerator
Depict a reaction.
Depiction - Class in org.openscience.cdk.depict
Base class of a pre-rendered depiction.
DepictionGenerator - Class in org.openscience.cdk.depict
A high-level API for depicting molecules and reactions.
DepictionGenerator() - Constructor for class org.openscience.cdk.depict.DepictionGenerator
Create a depiction generator using the standard sans-serif system font.
DepictionGenerator(Font) - Constructor for class org.openscience.cdk.depict.DepictionGenerator
Create a depiction generator that will render atom labels using the specified AWT font.
depth(int) - Method in class org.openscience.cdk.hash.HashGeneratorMaker
Specify the depth of the hash generator.
depthFirstTargetSearch(IAtomContainer, IAtom, IAtom, IAtomContainer) - Static method in class org.openscience.cdk.graph.PathTools
Recursively performs a depth first search in a molecular graphs contained in the AtomContainer molecule, starting at the root atom and returning when it hits the target atom.
DESCRIPTION - Static variable in class org.openscience.cdk.CDKConstants
A description for a IChemObject.
description() - Method in enum org.openscience.cdk.smsd.interfaces.Algorithm
Deprecated.
Returns short description of the algorithm.
DescriptorEngine - Class in org.openscience.cdk.qsar
A class that provides access to automatic descriptor calculation and more.
DescriptorEngine(List<String>, IChemObjectBuilder) - Constructor for class org.openscience.cdk.qsar.DescriptorEngine
Instantiates the DescriptorEngine.
DescriptorEngine(Class<? extends IDescriptor>, IChemObjectBuilder) - Constructor for class org.openscience.cdk.qsar.DescriptorEngine
Create a descriptor engine for all descriptor types.
DescriptorException - Exception in org.openscience.cdk.qsar
Exception that is thrown by descriptor routines when a problem has occurred.
DescriptorException(String) - Constructor for exception org.openscience.cdk.qsar.DescriptorException
Constructs a new DescriptorException with the given message.
DescriptorException(String, String) - Constructor for exception org.openscience.cdk.qsar.DescriptorException
Constructs a new DescriptorException with from the supplied descriptor name and associated message.
DescriptorSpecification - Class in org.openscience.cdk.qsar
Class that is used to distribute descriptor specifications.
DescriptorSpecification(String, String, String, String) - Constructor for class org.openscience.cdk.qsar.DescriptorSpecification
Container for specifying the type of descriptor.
DescriptorSpecification(String, String, String) - Constructor for class org.openscience.cdk.qsar.DescriptorSpecification
Container for specifying the type of descriptor.
DescriptorValue - Class in org.openscience.cdk.qsar
Class that is used to store descriptor values as IChemObject properties.
DescriptorValue(DescriptorSpecification, String[], Object[], IDescriptorResult, String[]) - Constructor for class org.openscience.cdk.qsar.DescriptorValue
Construct a descriptor value object, representing the numeric values as well as parameters and provenance.
DescriptorValue(DescriptorSpecification, String[], Object[], IDescriptorResult, String[], Exception) - Constructor for class org.openscience.cdk.qsar.DescriptorValue
Construct a descriptor value object, representing the numeric values as well as parameters and provenance.
deserialise(String) - Static method in class org.openscience.cdk.fingerprint.model.Bayesian
Converts a given string into a Bayesian model instance, or throws an exception if it is not valid.
deserialise(BufferedReader) - Static method in class org.openscience.cdk.fingerprint.model.Bayesian
Reads the incoming stream and attempts to convert it into an instantiated model.
destroyBondOrder(IBond.Order) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
Deprecated.
use IBond.Order.numeric().doubleValue() instead
detect(IAtomContainer) - Static method in class org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector
Detect all conjugated pi systems in an AtomContainer.
detectAromaticity(IAtomContainer) - Static method in class org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector
Deprecated.
 
detectAromaticity(IAtomContainer) - Static method in class org.openscience.cdk.aromaticity.DoubleBondAcceptingAromaticityDetector
Deprecated.
 
determinant() - Method in class org.openscience.cdk.graph.invariant.GIMatrix
Returns the determinant of this matrix.
DI - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
diagonal() - Method in class org.openscience.cdk.graph.invariant.GIMatrix
Returns a matrix containing all of the diagonal elements of this matrix and zero (0) everywhere else.
diagonalAxisScanXYZ(int, int, int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
Method performs a scan; works only for cubic grids!
diagonalAxisScanXZY(int, int, int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
Method performs a scan; works only for cubic grids!
diagonalAxisScanYXZ(int, int, int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
Method performs a scan; works only for cubic grids!
diagonalAxisScanYZX(int, int, int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
Method performs a scan; works only for cubic grids!
diagonalize(int) - Method in class org.openscience.cdk.math.Matrix
Diagonalize this matrix with the Jacobi algorithm.
Dictionary - Class in org.openscience.cdk.dict
Dictionary with entries.
Dictionary() - Constructor for class org.openscience.cdk.dict.Dictionary
 
DictionaryDatabase - Class in org.openscience.cdk.dict
Database of dictionaries listing entries with compounds, fragments and entities.
DictionaryDatabase() - Constructor for class org.openscience.cdk.dict.DictionaryDatabase
 
DictionaryHandler - Class in org.openscience.cdk.dict
Class for unmarshalling a dictionary schema file.
DictionaryHandler() - Constructor for class org.openscience.cdk.dict.DictionaryHandler
 
DictionaryValidator - Class in org.openscience.cdk.validate
Validates the existence of references to dictionaries.
DictionaryValidator(DictionaryDatabase) - Constructor for class org.openscience.cdk.validate.DictionaryValidator
 
DictRef - Class in org.openscience.cdk.dict
Object that can be used as key in IChemObject.setProperty(key, value) to denote that this property is a dictionary reference for this IChemObject.
DictRef(String, String) - Constructor for class org.openscience.cdk.dict.DictRef
 
DICTREF - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
 
DICTREFPROPERTYNAME - Static variable in class org.openscience.cdk.dict.DictionaryDatabase
 
diff(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.AtomContainerDiff
Compare two IChemObject classes and return the difference as a String.
diff(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.AtomDiff
Compare two IChemObject classes and return the difference as a String.
diff(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.AtomTypeDiff
Compare two IChemObject classes and return the difference as a String.
diff(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.BondDiff
Compare two IChemObject classes and return the difference as a String.
diff(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.ChemObjectDiff
Compare two IChemObject classes and return the difference as a String.
diff(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.ElectronContainerDiff
Compare two IChemObject classes and return the difference as a String.
diff(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.ElementDiff
Compare two IChemObject classes and return the difference as a String.
diff(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.IsotopeDiff
Compare two IChemObject classes and return the difference as a String.
diff(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.LonePairDiff
Compare two IChemObject classes and return the difference as a String.
diff(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.SingleElectronDiff
Compare two IChemObject classes and return the difference as a String.
difference(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.AtomContainerDiff
Compare two IChemObject classes and return the difference as an IDifference.
difference(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.AtomDiff
Compare two IChemObject classes and return the difference as an IDifference.
difference(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.AtomTypeDiff
Compare two IChemObject classes and return the difference as an IDifference.
difference(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.BondDiff
Compare two IChemObject classes and return the difference as an IDifference.
difference(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.ChemObjectDiff
Compare two IChemObject classes and return the difference as an IDifference.
difference(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.ElectronContainerDiff
Compare two IChemObject classes and return the difference as an IDifference.
difference(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.ElementDiff
Compare two IChemObject classes and return the difference as an IDifference.
difference(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.IsotopeDiff
Compare two IChemObject classes and return the difference as an IDifference.
difference(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.LonePairDiff
Compare two IChemObject classes and return the difference as an IDifference.
difference(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.SingleElectronDiff
Compare two IChemObject classes and return the difference as an IDifference.
differences(BitSet, BitSet) - Static method in class org.openscience.cdk.fingerprint.FingerprinterTool
List all differences between the two bit vectors.
differences - Variable in class org.openscience.cdk.tools.diff.tree.AbstractDifferenceList
 
DIGIT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
DIGIT - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
dim - Variable in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
 
direction(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.StereoBond
 
direction - Variable in class org.openscience.cdk.renderer.elements.ArrowElement
Boolean that is true if the arrow points from start to end, false if from end to start.
direction - Variable in class org.openscience.cdk.renderer.elements.WedgeLineElement
The direction indicates which way the wedge gets thicker.
disable_tracing() - Method in class org.openscience.cdk.iupac.parser.NomParser
Deprecated.
Disable tracing.
disable_tracing() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
Disable tracing.
disconnected(SymbolVisibility) - Static method in class org.openscience.cdk.renderer.generators.standard.SelectionVisibility
Display the atom symbol if is disconnected from any other selected atoms or bonds.
DiscretePartitionRefiner - Interface in org.openscience.cdk.group
A mechanism for refining partitions of graph-like objects.
DisjointSetForest - Class in org.openscience.cdk.group
Implementation of a union-find data structure, largely copied from code due to Derrick Stolee.
DisjointSetForest(int) - Constructor for class org.openscience.cdk.group.DisjointSetForest
Initialize a disjoint set forest with a number of elements.
displace(IAtomContainer, Vector, Vector) - Method in class org.openscience.cdk.layout.OverlapResolver
Deprecated.
Makes a small displacement to some atoms or rings in the given atomcontainer.
displayArray(int[]) - Static method in class org.openscience.cdk.graph.invariant.HuLuIndexTool
Lists a 1D array to the System console.
displayArray(double[]) - Static method in class org.openscience.cdk.graph.invariant.HuLuIndexTool
Lists a 1D array to the System console.
displayMatrix(double[][]) - Static method in class org.openscience.cdk.graph.invariant.HuLuIndexTool
Lists a 2D double matrix to the System console.
displayMatrix(int[][]) - Static method in class org.openscience.cdk.graph.invariant.HuLuIndexTool
Lists a 2D int matrix to the System console.
distanceCalculator(int[], double) - Static method in class org.openscience.cdk.geometry.GeometryTools
Gets the coordinates of two points (that represent a bond) and calculates for each the coordinates of two new points that have the given distance vertical to the bond.
distanceCalculator(double[], double) - Static method in class org.openscience.cdk.geometry.GeometryTools
 
distanceCalculator(int[], double) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Gets the coordinates of two points (that represent a bond) and calculates for each the coordinates of two new points that have the given distance vertical to the bond.
distanceCalculator(double[], double) - Static method in class org.openscience.cdk.geometry.GeometryUtil
 
DistanceMoment - Class in org.openscience.cdk.similarity
Fast similarity measure for 3D structures.
DistanceMoment() - Constructor for class org.openscience.cdk.similarity.DistanceMoment
 
distanceTo(int) - Method in class org.openscience.cdk.graph.ShortestPaths
Access the distance to the provided end vertex.
distanceTo(IAtom) - Method in class org.openscience.cdk.graph.ShortestPaths
Access the distance to the provided end atom.
DistanceToAtomDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
This class returns the 3D distance between two atoms.
DistanceToAtomDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor
Constructor for the DistanceToAtomDescriptor object
distributePartners(IAtom, IAtomContainer, Point2d, IAtomContainer, double) - Method in class org.openscience.cdk.layout.AtomPlacer
Distribute the bonded atoms (neighbours) of an atom such that they fill the remaining space around an atom in a geometrically nice way.
div(Complex) - Method in class org.openscience.cdk.math.Complex
Div this value by a complex value
div(Quaternion) - Method in class org.openscience.cdk.math.Quaternion
 
DMol3Format - Class in org.openscience.cdk.io.formats
 
DMol3Format() - Constructor for class org.openscience.cdk.io.formats.DMol3Format
 
DN_OR_UNSPECIFIED_S_BOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
DN_S_BOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
DO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
DOCK5Format - Class in org.openscience.cdk.io.formats
See here.
DOCK5Format() - Constructor for class org.openscience.cdk.io.formats.DOCK5Format
 
doCrossover(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.structgen.stochastic.operator.CrossoverMachine
Performs the n point crossover of two IAtomContainer.
doctypeDecl(String, String, String) - Method in class org.openscience.cdk.dict.DictionaryHandler
 
doctypeDecl(String, String, String) - Method in class org.openscience.cdk.io.cml.CMLHandler
 
doctypeDecl(String, String, String) - Method in class org.openscience.cdk.io.inchi.INChIHandler
 
DOLLAR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
Done() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
Reset buffer when finished.
Done() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
Reset buffer when finished.
dot(IVector) - Method in class org.openscience.cdk.math.IVector
Multiplication from two vectors
dot(Vector) - Method in class org.openscience.cdk.math.Vector
Multiplikation from two vectors
doTessellate() - Method in class org.openscience.cdk.geometry.surface.Tessellate
 
DoubleArrayResult - Class in org.openscience.cdk.qsar.result
 
DoubleArrayResult() - Constructor for class org.openscience.cdk.qsar.result.DoubleArrayResult
 
DoubleArrayResult(int) - Constructor for class org.openscience.cdk.qsar.result.DoubleArrayResult
 
DoubleArrayResultType - Class in org.openscience.cdk.qsar.result
IDescriptorResult type for booleans.
DoubleArrayResultType(int) - Constructor for class org.openscience.cdk.qsar.result.DoubleArrayResultType
 
DOUBLEBOND - Static variable in class org.openscience.cdk.libio.jena.CDK
 
DoubleBondAcceptingAromaticityDetector - Class in org.openscience.cdk.aromaticity
DoubleBondAcceptingAromaticityDetector() - Constructor for class org.openscience.cdk.aromaticity.DoubleBondAcceptingAromaticityDetector
Deprecated.
 
DoubleBondElementEncoderFactory - Class in org.openscience.cdk.hash.stereo
Defines a stereo encoder factory for the hash code.
DoubleBondElementEncoderFactory() - Constructor for class org.openscience.cdk.hash.stereo.DoubleBondElementEncoderFactory
 
DoubleBondStereochemistry - Class in org.openscience.cdk.stereo
Stereochemistry specification for double bonds.
DoubleBondStereochemistry(IBond, IBond[], IDoubleBondStereochemistry.Conformation) - Constructor for class org.openscience.cdk.stereo.DoubleBondStereochemistry
Creates a new double bond stereo chemistry.
DoubleDifference - Class in org.openscience.cdk.tools.diff.tree
IDifference between two Double.
DoubleResult - Class in org.openscience.cdk.qsar.result
 
DoubleResult(double) - Constructor for class org.openscience.cdk.qsar.result.DoubleResult
 
DoubleResultType - Class in org.openscience.cdk.qsar.result
IDescriptorResult type for booleans.
DoubleResultType() - Constructor for class org.openscience.cdk.qsar.result.DoubleResultType
 
doubleValue() - Method in class org.openscience.cdk.qsar.result.DoubleResult
 
downcast() - Method in class org.openscience.cdk.sgroup.Sgroup
Downcast this, maybe generic, Sgroup to a specific concrete implementation.
draw(IDrawVisitor, double, Bounds, Rectangle2D) - Method in class org.openscience.cdk.depict.Depiction
Low-level draw method used by other rendering methods.
drawCenter - Variable in class org.openscience.cdk.renderer.AbstractRenderer
The center of the desired position on screen to draw.
DUBNIUM - Static variable in enum org.openscience.cdk.config.Elements
 
DUBNIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
DUMMY - Static variable in enum org.openscience.cdk.config.Elements
These instances are for backards compatability.
DUMMY_POINTER - Static variable in class org.openscience.cdk.CDKConstants
Flag used for JUnit testing the pointer functionality.
dump() - Method in class org.openscience.cdk.graph.rebond.Bspt
 
dumpClasspath() - Method in interface org.openscience.cdk.tools.ILoggingTool
Outputs the system property for java.class.path.
dumpClasspath() - Method in class org.openscience.cdk.tools.LoggingTool
Outputs the system property for java.class.path.
dumpClasspath() - Method in class org.openscience.cdk.tools.SystemOutLoggingTool
Outputs the system property for java.class.path.
dumpSystemProperties() - Method in interface org.openscience.cdk.tools.ILoggingTool
Outputs system properties for the operating system and the java version.
dumpSystemProperties() - Method in class org.openscience.cdk.tools.LoggingTool
Outputs system properties for the operating system and the java version.
dumpSystemProperties() - Method in class org.openscience.cdk.tools.SystemOutLoggingTool
Outputs system properties for the operating system and the java version.
duplicate() - Method in class org.openscience.cdk.math.IMatrix
Copy a matrix
duplicate(IMatrix) - Method in class org.openscience.cdk.math.IMatrix
Copy a matrix
duplicate() - Method in class org.openscience.cdk.math.IVector
Copy a vector
duplicate(IVector) - Method in class org.openscience.cdk.math.IVector
Copy a vector
duplicate() - Method in class org.openscience.cdk.math.Matrix
Copies a matrix.
duplicate() - Method in class org.openscience.cdk.math.Vector
Copy a vector
DY - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
DynamicFactory - Class in org.openscience.cdk
A factory class for constructing ICDKObject and IChemObject implementations.
DynamicFactory(DynamicFactory.InterfaceProvider, int) - Constructor for class org.openscience.cdk.DynamicFactory
Create a new default factory with an expected number of registered classes and an interface provider.
DynamicFactory(int) - Constructor for class org.openscience.cdk.DynamicFactory
Create a new default factory with an expected number of registered classes and a default interface provider.
DynamicFactory.BasicCreator<T> - Class in org.openscience.cdk
A simple creator that helps in creating an anonymous classes for a creator.
DynamicFactory.BasicCreator(Class<T>) - Constructor for class org.openscience.cdk.DynamicFactory.BasicCreator
Create a basic constructor with a given declaring class.
DynamicFactory.ConstructorKey - Class in org.openscience.cdk
A class which encapsulates the information about an interface (of this implementation) and the parameter types of the constructor.
DynamicFactory.ConstructorKey() - Constructor for class org.openscience.cdk.DynamicFactory.ConstructorKey
 
DynamicFactory.CreationModifier<T> - Interface in org.openscience.cdk
An interface that allows posterior modification of an instance after it has been created.
DynamicFactory.Creator<T> - Interface in org.openscience.cdk
An interface that wraps object creation via the DynamicFactory.Creator.create(Object[]) method.
DynamicFactory.DefaultInterfaceProvider - Class in org.openscience.cdk
A default interface provider implementation that simply returns the classes from Class.getInterfaces().
DynamicFactory.DefaultInterfaceProvider() - Constructor for class org.openscience.cdk.DynamicFactory.DefaultInterfaceProvider
 
DynamicFactory.InterfaceProvider - Interface in org.openscience.cdk
An interface that can provide which interfaces the given class implements.
DYSPROSIUM - Static variable in enum org.openscience.cdk.config.Elements
 
DYSPROSIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.

E

E - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
EccentricConnectivityIndexDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
A topological descriptor combining distance and adjacency information.
EccentricConnectivityIndexDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor
 
edgeAdded(GraphEdgeChangeEvent) - Method in class org.openscience.cdk.graph.BiconnectivityInspector
 
EdgeBuilder - Class in org.openscience.cdk.smsd.algorithm.vflib.builder
Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
EdgeBuilder(NodeBuilder, NodeBuilder, VFBondMatcher) - Constructor for class org.openscience.cdk.smsd.algorithm.vflib.builder.EdgeBuilder
Deprecated.
 
edgeRemoved(GraphEdgeChangeEvent) - Method in class org.openscience.cdk.graph.BiconnectivityInspector
 
edges() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis
Deprecated.
 
edges() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder
Deprecated.
Returns edges of the query.
edges() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQuery
Deprecated.
Returns edges of the query.
edgeShort() - Static method in class org.openscience.cdk.graph.Cycles
Create a cycle finder which will compute the shortest cycles of each vertex in a molecule.
edgeShort(IAtomContainer) - Static method in class org.openscience.cdk.graph.Cycles
Find the edge short cycles of a molecule.
EffectiveAtomPolarizabilityDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
Effective polarizability of a heavy atom Name Default Description no parameters
EffectiveAtomPolarizabilityDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor
Constructor for the EffectiveAtomPolarizabilityDescriptor object
effectiveCharges(IAtomContainer) - Method in class org.openscience.cdk.forcefield.mmff.Mmff
Assign the effective formal charges used by MMFF in calculating the final partial charge values.
EICOS - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
EINSTEINIUM - Static variable in enum org.openscience.cdk.config.Elements
 
EINSTEINIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
EL_ATOM_CONFORMER - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_ATOM_CONFORMER_X - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_ATOM_CONFORMER_XE - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_ATOM_CONFORMER_Y - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_ATOM_CONFORMER_YE - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_ATOM_CONFORMER_Z - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_ATOM_CONFORMER_ZE - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_ATOMBLOCK - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_ATOMINT - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_ATOMINT_AID - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_ATOMINT_VALUE - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_ATOMSCHARGE - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_ATOMSELEMENT - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_BONDBLOCK - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_BONDID1 - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_BONDID2 - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_BONDORDER - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_COORDINATES_AID - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_COORDINATES_AIDE - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_COORDINATESBLOCK - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_ELEMENT - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_PCCOMPOUND - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_PCCOMPOUND_CID - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_PCCOMPOUND_ID - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_PCCOMPOUNDS - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_PCID_ID - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_PCSUBSTANCE - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_PCSUBSTANCE_SID - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_PROPS_BVAL - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_PROPS_FVAL - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_PROPS_INFODATA - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_PROPS_SVAL - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_PROPS_URNLABEL - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_PROPS_URNNAME - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
EL_PROPSBLOCK - Static variable in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
ElectronContainer - Class in org.openscience.cdk
Base class for entities containing electrons, like bonds, orbitals, lone-pairs.
ElectronContainer() - Constructor for class org.openscience.cdk.ElectronContainer
Constructs an empty ElectronContainer.
ElectronContainer - Class in org.openscience.cdk.silent
Base class for entities containing electrons, like bonds, orbitals, lone-pairs.
ElectronContainer() - Constructor for class org.openscience.cdk.silent.ElectronContainer
Constructs an empty ElectronContainer.
ElectronContainerDiff - Class in org.openscience.cdk.tools.diff
Compares two IChemObject classes.
electronContainers() - Method in class org.openscience.cdk.AtomContainer
Returns an Iterable for looping over all electron containers in this container.
electronContainers() - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns an Iterable for looping over all electron containers in this container.
electronContainers() - Method in class org.openscience.cdk.debug.DebugAtomContainer
Returns an Iterable for looping over all electron containers in this container.
electronContainers() - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns an Iterable for looping over all electron containers in this container.
electronContainers() - Method in class org.openscience.cdk.debug.DebugCrystal
Returns an Iterable for looping over all electron containers in this container.
electronContainers() - Method in class org.openscience.cdk.debug.DebugMonomer
Returns an Iterable for looping over all electron containers in this container.
electronContainers() - Method in class org.openscience.cdk.debug.DebugPolymer
Returns an Iterable for looping over all electron containers in this container.
electronContainers() - Method in class org.openscience.cdk.debug.DebugRing
Returns an Iterable for looping over all electron containers in this container.
electronContainers() - Method in class org.openscience.cdk.debug.DebugStrand
Returns an Iterable for looping over all electron containers in this container.
electronContainers() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Returns an Iterable for looping over all electron containers in this container.
electronContainers() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Returns an Iterable for looping over all electron containers in this container.
electronContainers() - Method in class org.openscience.cdk.silent.AtomContainer
Returns an Iterable for looping over all electron containers in this container.
electronCount - Variable in class org.openscience.cdk.Association
Number of electrons in the association.
electronCount - Variable in class org.openscience.cdk.ElectronContainer
Number of electrons in the ElectronContainer.
electronCount - Variable in class org.openscience.cdk.isomorphism.matchers.QueryBond
Number of electrons in the ElectronContainer.
electronCount - Variable in class org.openscience.cdk.LonePair
Number of electrons in the lone pair.
electronCount - Variable in class org.openscience.cdk.silent.ElectronContainer
Number of electrons in the ElectronContainer.
electronCount - Variable in class org.openscience.cdk.silent.LonePair
Number of electrons in the lone pair.
electronCount - Variable in class org.openscience.cdk.silent.SingleElectron
Number of electron for this class is defined as one.
electronCount - Variable in class org.openscience.cdk.SingleElectron
Number of electron for this class is defined as one.
ElectronDonation - Class in org.openscience.cdk.aromaticity
Defines an electron donation model for perceiving aromatic systems.
ElectronDonation() - Constructor for class org.openscience.cdk.aromaticity.ElectronDonation
 
Electronegativity - Class in org.openscience.cdk.charges
Calculation of the electronegativity of orbitals of a molecule by the method Gasteiger based on electronegativity is given by X = a + bq + c(q*q).
Electronegativity() - Constructor for class org.openscience.cdk.charges.Electronegativity
Constructor for the PiElectronegativity object.
Electronegativity(int, int) - Constructor for class org.openscience.cdk.charges.Electronegativity
Constructor for the Electronegativity object.
electronegativity() - Method in enum org.openscience.cdk.config.Elements
Electronegativity, symbol χ, is a chemical property that describes the tendency of an atom or a functional group to attract electrons (or electron density) towards itself.
ElectronImpactNBEReaction - Class in org.openscience.cdk.reaction.type
IReactionProcess which make an electron impact for for Non-Bonding Electron Lost.
ElectronImpactNBEReaction() - Constructor for class org.openscience.cdk.reaction.type.ElectronImpactNBEReaction
Constructor of the ElectronImpactNBEReaction object.
ElectronImpactPDBReaction - Class in org.openscience.cdk.reaction.type
IReactionProcess which make an electron impact for pi-Bond Dissociation.
ElectronImpactPDBReaction() - Constructor for class org.openscience.cdk.reaction.type.ElectronImpactPDBReaction
Constructor of the ElectronImpactPDBReaction object.
ElectronImpactSDBReaction - Class in org.openscience.cdk.reaction.type
IReactionProcess which make an electron impact for Sigma Bond Dissociation.
ElectronImpactSDBReaction() - Constructor for class org.openscience.cdk.reaction.type.ElectronImpactSDBReaction
Constructor of the ElectronImpactSDBReaction object.
electronValency - Variable in class org.openscience.cdk.AtomType
The electron Valency of this atom with CDKConstants.UNSET as default.
electronValency - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom
The electron Valency of this atom with CDKConstants.UNSET as default.
electronValency - Variable in class org.openscience.cdk.silent.AtomType
The electron Valency of this atom with CDKConstants.UNSET as default.
Element - Class in org.openscience.cdk
Implements the idea of an element in the periodic table.
Element() - Constructor for class org.openscience.cdk.Element
Constructs an empty Element.
Element(IElement) - Constructor for class org.openscience.cdk.Element
Constructs an empty by copying the symbol, atomic number, flags, and identifier from the given IElement.
Element(String) - Constructor for class org.openscience.cdk.Element
Constructs an Element with a given element symbol.
Element(String, Integer) - Constructor for class org.openscience.cdk.Element
Constructs an Element with a given element symbol, atomic number and atomic mass.
ELEMENT - Static variable in class org.openscience.cdk.libio.jena.CDK
 
element() - Method in class org.openscience.cdk.renderer.elements.MarkedElement
Access the element of which the id and classes apply.
Element - Class in org.openscience.cdk.silent
Implements the idea of an element in the periodic table.
Element() - Constructor for class org.openscience.cdk.silent.Element
Constructs an empty Element.
Element(IElement) - Constructor for class org.openscience.cdk.silent.Element
Constructs an empty by copying the symbol, atomic number, flags, and identifier from the given IElement.
Element(String) - Constructor for class org.openscience.cdk.silent.Element
Constructs an Element with a given element symbol.
Element(String, Integer) - Constructor for class org.openscience.cdk.silent.Element
Constructs an Element with a given element symbol, atomic number and atomic mass.
elemental() - Method in class org.openscience.cdk.hash.HashGeneratorMaker
Discriminate elements.
ElementComparator - Class in org.openscience.cdk.tools
Compares elements based on the order commonly used in molecular formula.
ElementComparator() - Constructor for class org.openscience.cdk.tools.ElementComparator
 
ElementDiff - Class in org.openscience.cdk.tools.diff
Compares two IElement classes.
ElementGroup - Class in org.openscience.cdk.renderer.elements
A group of rendering elements, of any type.
ElementGroup() - Constructor for class org.openscience.cdk.renderer.elements.ElementGroup
Create an empty element group.
ElementRule - Class in org.openscience.cdk.formula.rules
This class validate if the occurrence of the IElements in the IMolecularFormula are into a limits.
ElementRule() - Constructor for class org.openscience.cdk.formula.rules.ElementRule
Constructor for the ElementRule object.
Elements - Enum in org.openscience.cdk.config
Enumeration of chemical elements.
elements - Variable in class org.openscience.cdk.renderer.elements.GeneralPath
The elements in the path.
elements(Class<E>) - Method in interface org.openscience.cdk.renderer.selection.IChemObjectSelection
Returns a Collection of all selected IChemObjects of the given type.
elements(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
Get a list of all Elements which are contained molecular.
elementTitle - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
 
elementType(int) - Method in class org.openscience.cdk.stereo.Stereocenters
Obtain the type of stereo element support for atom at index v.
elid - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
 
elimination(Matrix, Vector) - Static method in class org.openscience.cdk.math.Matrix
Solves a linear equation system with Gauss elimination.
elsym - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
 
eltitles - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
 
embedText(Font, String, Color, double) - Static method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator
Make an embedded text label for display in a CDK renderer.
EMPTY - Static variable in interface org.openscience.cdk.hash.stereo.StereoEncoder
empty stereo encoder when no stereo can be perceived
EMPTY - Static variable in interface org.openscience.cdk.hash.stereo.StereoEncoderFactory
Empty factory for when stereo encoding is not required
EMPTY_SELECTION - Static variable in class org.openscience.cdk.renderer.selection.AbstractSelection
Static implementation of an empty selection.
EN - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
enable_tracing() - Method in class org.openscience.cdk.iupac.parser.NomParser
Deprecated.
Enable tracing.
enable_tracing() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
Enable tracing.
encode(IAtom, IAtomContainer) - Method in interface org.openscience.cdk.hash.AtomEncoder
Encode an invariant attribute of the given atom.
encode(AtomEncoder) - Method in class org.openscience.cdk.hash.HashGeneratorMaker
Add a custom encoder to the hash generator which will be built.
encode(long[], long[]) - Method in interface org.openscience.cdk.hash.stereo.StereoEncoder
Encode one or more stereo elements based on the current invariants.
encodePaths(IAtomContainer, int, BitSet, int) - Method in class org.openscience.cdk.fingerprint.Fingerprinter
 
endColumn - Variable in class org.openscience.cdk.iupac.parser.Token
The column number of the last character of this Token.
endColumn - Variable in class org.openscience.cdk.smiles.smarts.parser.Token
The column number of the last character of this Token.
endDocument() - Method in class org.openscience.cdk.io.cml.CMLCoreModule
 
endDocument() - Method in class org.openscience.cdk.io.cml.CMLHandler
Calling this procedure signals the end of the XML document.
endDocument() - Method in interface org.openscience.cdk.io.cml.ICMLModule
 
endDocument() - Method in class org.openscience.cdk.io.cml.PDBConvention
 
endDocument() - Method in class org.openscience.cdk.io.inchi.INChIHandler
 
endDocument() - Method in class org.openscience.cdk.io.iterator.event.EventCMLHandler
Procedure required by the CDOInterface.
endElement(String, String, String) - Method in class org.openscience.cdk.config.atomtypes.AtomTypeHandler
endElement(String, String, String) - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeHandler
endElement(String, String, String) - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingHandler
endElement(String, String, String) - Method in class org.openscience.cdk.config.isotopes.IsotopeHandler
endElement(String, String, String) - Method in class org.openscience.cdk.dict.DictionaryHandler
 
endElement(CMLStack, String, String, String) - Method in class org.openscience.cdk.io.cml.CMLCoreModule
 
endElement(String, String, String) - Method in class org.openscience.cdk.io.cml.CMLHandler
 
endElement(CMLStack, String, String, String) - Method in class org.openscience.cdk.io.cml.CMLReactionModule
 
endElement(CMLStack, String, String, String) - Method in interface org.openscience.cdk.io.cml.ICMLModule
 
endElement(CMLStack, String, String, String) - Method in class org.openscience.cdk.io.cml.JMOLANIMATIONConvention
 
endElement(CMLStack, String, String, String) - Method in class org.openscience.cdk.io.cml.MDMoleculeConvention
Finish up parsing of elements in mdmolecule.
endElement(CMLStack, String, String, String) - Method in class org.openscience.cdk.io.cml.PDBConvention
 
endElement(CMLStack, String, String, String) - Method in class org.openscience.cdk.io.cml.QSARConvention
 
endElement(String, String, String) - Method in class org.openscience.cdk.io.inchi.INChIHandler
 
endFunctionalGroups() - Method in class org.openscience.cdk.iupac.parser.NomParser
Deprecated.
Functional groups which occur at the end of the main chain and need a connecting "an".
endLine - Variable in class org.openscience.cdk.iupac.parser.Token
The line number of the last character of this Token.
endLine - Variable in class org.openscience.cdk.smiles.smarts.parser.Token
The line number of the last character of this Token.
endObject(String) - Method in class org.openscience.cdk.io.iterator.event.EventCMLHandler
Procedure required by the CDOInterface.
endsWith(ICMLModule) - Method in class org.openscience.cdk.io.cml.CMLModuleStack
Convenience method to check the last added elements.
endsWith(ICMLModule, ICMLModule) - Method in class org.openscience.cdk.io.cml.CMLModuleStack
Convenience method to check the last two added elements.
endsWith(ICMLModule, ICMLModule, ICMLModule) - Method in class org.openscience.cdk.io.cml.CMLModuleStack
Convenience method to check the last three added elements.
endX - Variable in class org.openscience.cdk.renderer.elements.ArrowElement
X coordinate of the point where the arrow ends.
endY - Variable in class org.openscience.cdk.renderer.elements.ArrowElement
Y coordinate of the point where the arrow ends.
ensemble() - Method in class org.openscience.cdk.hash.HashGeneratorMaker
Given the current configuration create an EnsembleHashGenerator.
EnsembleHashGenerator - Interface in org.openscience.cdk.hash
A hash function which generates a single 64-bit hash code for a set of molecules (ensemble).
enter(Permutation) - Method in class org.openscience.cdk.group.PermutationGroup
Enter the permutation g into this group.
Entry - Class in org.openscience.cdk.dict
Entry in a Dictionary.
Entry(String, String) - Constructor for class org.openscience.cdk.dict.Entry
 
Entry(String) - Constructor for class org.openscience.cdk.dict.Entry
 
Entry() - Constructor for class org.openscience.cdk.dict.Entry
 
EntryReact - Class in org.openscience.cdk.dict
Entry in a Dictionary for reactions.
EntryReact(String, String) - Constructor for class org.openscience.cdk.dict.EntryReact
Constructor of the EntryReact.
EntryReact(String) - Constructor for class org.openscience.cdk.dict.EntryReact
Constructor of the EntryReact.
enumeration() - Method in class org.openscience.cdk.graph.rebond.Bspt
 
enumHemiSphere(Bspt.Tuple, double) - Method in class org.openscience.cdk.graph.rebond.Bspt
 
enumNear(Bspt.Tuple, double) - Method in class org.openscience.cdk.graph.rebond.Bspt
 
enumSphere(Bspt.Tuple, double) - Method in class org.openscience.cdk.graph.rebond.Bspt
 
EnzymeResidueLocator - Class in org.openscience.cdk
Atom that represents part of an residue in an enzyme, like Arg255.
EnzymeResidueLocator(String) - Constructor for class org.openscience.cdk.EnzymeResidueLocator
Constructs an EnzymeResidueLocator from a String containing the locator.
EnzymeResidueLocator(IAtom) - Constructor for class org.openscience.cdk.EnzymeResidueLocator
Constructs an EnzymeResidueLocator from an existing Atom.
EOF - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
End of File.
EOF - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
End of File.
EOL - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
eol - Variable in exception org.openscience.cdk.iupac.parser.ParseException
The end of line string for this machine.
eol - Variable in exception org.openscience.cdk.smiles.smarts.parser.ParseException
The end of line string for this machine.
equals(Object) - Method in class org.openscience.cdk.DynamicFactory.ConstructorKey
equals(Object) - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
 
equals(Object) - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
 
equals(GIMatrix) - Method in class org.openscience.cdk.graph.invariant.GIMatrix
Verifies if two given matrix are equal or not.
equals(Object) - Method in class org.openscience.cdk.group.Partition
equals(Object) - Method in class org.openscience.cdk.group.Permutation
equals(Object) - Method in class org.openscience.cdk.io.formats.AbstractResourceFormat
 
equals(Object) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
 
equals(Object) - Method in class org.openscience.cdk.isomorphism.mcss.RMap
The equals method.
equals(Object) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom
 
equals(Object) - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycle
Deprecated.
 
equals(Object) - Method in class org.openscience.cdk.smiles.InvPair
Check whether this instance equals another instance.
equals(Object) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMap
Deprecated.
The equals method.
equivalenceClasses() - Method in class org.openscience.cdk.ringsearch.cyclebasis.CycleBasis
Deprecated.
Returns the connected components of this cycle basis, in regard to matroid theory.
equivalenceClasses() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis
Deprecated.
 
EquivalentClassPartitioner - Class in org.openscience.cdk.graph.invariant
An algorithm for topological symmetry.
EquivalentClassPartitioner() - Constructor for class org.openscience.cdk.graph.invariant.EquivalentClassPartitioner
Constructor for the TopologicalEquivalentClass object.
EquivalentClassPartitioner(IAtomContainer) - Constructor for class org.openscience.cdk.graph.invariant.EquivalentClassPartitioner
Constructor for the TopologicalEquivalentClass object.
ER - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
ERBIUM - Static variable in enum org.openscience.cdk.config.Elements
 
ERBIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
error(SAXParseException) - Method in class org.openscience.cdk.io.cml.CMLErrorHandler
Outputs a SAXParseException error to the logger.
error(Object) - Method in interface org.openscience.cdk.tools.ILoggingTool
Shows ERROR output for the Object.
error(Object, Object...) - Method in interface org.openscience.cdk.tools.ILoggingTool
Shows ERROR output for the given Object's.
error(Object) - Method in class org.openscience.cdk.tools.LoggingTool
Shows ERROR output for the Object.
error(Object, Object...) - Method in class org.openscience.cdk.tools.LoggingTool
Shows ERROR output for the given Object's.
error(Object) - Method in class org.openscience.cdk.tools.SystemOutLoggingTool
Shows ERROR output for the Object.
error(Object, Object...) - Method in class org.openscience.cdk.tools.SystemOutLoggingTool
Shows ERROR output for the given Object's.
ERROR_MARKER - Static variable in class org.openscience.cdk.validate.ProblemMarker
 
errorHandler - Variable in class org.openscience.cdk.io.DefaultChemObjectReader
 
errorHandler - Variable in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader
 
ES - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
essential() - Static method in class org.openscience.cdk.graph.Cycles
Create a cycle finder which will compute the essential cycles of a molecule.
essential(IAtomContainer) - Static method in class org.openscience.cdk.graph.Cycles
Find the essential cycles of a molecule.
ESSENTIAL_RINGS - Static variable in class org.openscience.cdk.CDKConstants
The essential rings computed for this molecule.
EssentialCycles - Class in org.openscience.cdk.graph
Determine the uniquely defined essential cycles of a graph.
EssentialCycles(int[][]) - Constructor for class org.openscience.cdk.graph.EssentialCycles
Determine the essential cycles given a graph.
essentialCycles() - Method in class org.openscience.cdk.ringsearch.cyclebasis.CycleBasis
Deprecated.
Returns the essential cycles of this cycle basis.
essentialCycles() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis
Deprecated.
 
EStateAtomTypeMatcher - Class in org.openscience.cdk.atomtype
Determines the EState atom types.
EStateAtomTypeMatcher() - Constructor for class org.openscience.cdk.atomtype.EStateAtomTypeMatcher
 
EStateFingerprinter - Class in org.openscience.cdk.fingerprint
This fingerprinter generates 79 bit fingerprints using the E-State fragments.
EStateFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.EStateFingerprinter
 
EStateFragments - Class in org.openscience.cdk.config.fragments
A class representing the 79 E-state atom types in terms of SMARTS.
EStateFragments() - Constructor for class org.openscience.cdk.config.fragments.EStateFragments
 
estimates - Variable in class org.openscience.cdk.fingerprint.model.Bayesian
 
ETH - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
EU - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
EUROPIUM - Static variable in enum org.openscience.cdk.config.Elements
 
EUROPIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
EventCMLHandler - Class in org.openscience.cdk.io.iterator.event
CDO object needed as interface with the JCFL library for reading CML in a event based manner.
EventCMLHandler(DefaultEventChemObjectReader, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.event.EventCMLHandler
Constructs an iterating-abled CDO.
EventCMLReader - Class in org.openscience.cdk.io.iterator.event
Reads a molecule in CML 1.x and 2.0 format.
EventCMLReader(Reader, IReaderListener, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.event.EventCMLReader
Define this CMLReader to take the input from a java.io.Reader class.
EX - Static variable in class org.openscience.cdk.math.Vector
Unary vector in 3 dimensional space
ExactMapping - Class in org.openscience.cdk.smsd.algorithm.mcsplus
Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
ExactMapping() - Constructor for class org.openscience.cdk.smsd.algorithm.mcsplus.ExactMapping
Deprecated.
 
exactMass - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom
Exact mass of this isotope.
exactMass - Variable in class org.openscience.cdk.Isotope
Exact mass of this isotope.
exactMass - Variable in class org.openscience.cdk.silent.Isotope
Exact mass of this isotope.
exactMasses - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
 
ExhaustiveFragmenter - Class in org.openscience.cdk.fragment
Generate fragments exhaustively.
ExhaustiveFragmenter() - Constructor for class org.openscience.cdk.fragment.ExhaustiveFragmenter
Instantiate fragmenter with default minimum fragment size.
ExhaustiveFragmenter(int) - Constructor for class org.openscience.cdk.fragment.ExhaustiveFragmenter
Instantiate fragmenter with user specified minimum fragment size.
exhaustStringTokenizer(StringTokenizer) - Method in class org.openscience.cdk.io.MDLV3000Reader
 
ExpandBuff(boolean) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
 
ExpandBuff(boolean) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
 
expectedTokenSequences - Variable in exception org.openscience.cdk.iupac.parser.ParseException
Each entry in this array is an array of integers.
expectedTokenSequences - Variable in exception org.openscience.cdk.smiles.smarts.parser.ParseException
Each entry in this array is an array of integers.
ExplicitAtomExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
 
ExplicitConnectionAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
Match an atom with the defined degree.
ExplicitConnectionAtom(int, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.ExplicitConnectionAtom
Create a query atom for matching the degree of an atom.
ExplicitConnectivity() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
 
ExplicitHighAndBond() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
 
ExplicitHighAndExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
 
exponentialDouble(double) - Static method in class org.openscience.cdk.math.RandomNumbersTool
Generates a random double from an Exponential distribution with the specified mean value.
ExtAtomContainerManipulator - Class in org.openscience.cdk.smsd.tools
Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
ExtAtomContainerManipulator() - Constructor for class org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator
Deprecated.
 
ExtendedAtomGenerator - Class in org.openscience.cdk.renderer.generators
A generator for atoms with mass, charge, etc.
ExtendedAtomGenerator() - Constructor for class org.openscience.cdk.renderer.generators.ExtendedAtomGenerator
 
ExtendedAtomGenerator.ShowAtomTypeNames - Class in org.openscience.cdk.renderer.generators
Boolean that indicates if atom type names should be given instead of element symbols.
ExtendedAtomGenerator.ShowAtomTypeNames() - Constructor for class org.openscience.cdk.renderer.generators.ExtendedAtomGenerator.ShowAtomTypeNames
 
ExtendedAtomGenerator.ShowImplicitHydrogens - Class in org.openscience.cdk.renderer.generators
Boolean that indicates if implicit hydrogens should be depicted.
ExtendedAtomGenerator.ShowImplicitHydrogens() - Constructor for class org.openscience.cdk.renderer.generators.ExtendedAtomGenerator.ShowImplicitHydrogens
 
ExtendedFingerprinter - Class in org.openscience.cdk.fingerprint
Generates an extended fingerprint for a given IAtomContainer, that extends the Fingerprinter with additional bits describing ring features.
ExtendedFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.ExtendedFingerprinter
Creates a fingerprint generator of length DEFAULT_SIZE and with a search depth of DEFAULT_SEARCH_DEPTH.
ExtendedFingerprinter(int) - Constructor for class org.openscience.cdk.fingerprint.ExtendedFingerprinter
 
ExtendedFingerprinter(int, int) - Constructor for class org.openscience.cdk.fingerprint.ExtendedFingerprinter
Constructs a fingerprint generator that creates fingerprints of the given size, using a generation algorithm with the given search depth.
ExtendedTetrahedral - Class in org.openscience.cdk.stereo
Extended tetrahedral configuration.
ExtendedTetrahedral(IAtom, IAtom[], ITetrahedralChirality.Stereo) - Constructor for class org.openscience.cdk.stereo.ExtendedTetrahedral
Create an extended tetrahedral stereo element for the provided 'focus' and 'peripherals' in the given 'winding'.
extractMapping(List<List<Integer>>, List<Integer>, List<Integer>) - Static method in class org.openscience.cdk.smsd.algorithm.mcsplus.ExactMapping
Deprecated.
 
extractSubstructure(IAtomContainer, int...) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
Extract a substructure from an atom container, in the form of a new cloned atom container with only the atoms with indices in atomIndices and bonds that connect these atoms.
extractTopReactions(IReactionScheme) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator
Extract a set of Reactions which are in top of a IReactionScheme.
extractUniqueRingSystemsFromFile(String) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor
 
EY - Static variable in class org.openscience.cdk.math.Vector
Unary vector in 3 dimensional space
EZ - Static variable in class org.openscience.cdk.math.Vector
Unary vector in 3 dimensional space

F

F - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
faculty(int) - Static method in class org.openscience.cdk.tools.SwissArmyKnife
Deprecated.
Calculates the faculty for a given integer.
fatal(Object) - Method in interface org.openscience.cdk.tools.ILoggingTool
Shows FATAL output for the Object.
fatal(Object) - Method in class org.openscience.cdk.tools.LoggingTool
Shows FATAL output for the Object.
fatal(Object) - Method in class org.openscience.cdk.tools.SystemOutLoggingTool
Shows FATAL output for the Object.
fatalError(SAXParseException) - Method in class org.openscience.cdk.io.cml.CMLErrorHandler
Outputs as fatal SAXParseException error to the logger.
fBlockMetals() - Method in class org.openscience.cdk.iupac.parser.NomParser
Deprecated.
 
FE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
FenskeHall_ZMatrixFormat - Class in org.openscience.cdk.io.formats
 
FenskeHall_ZMatrixFormat() - Constructor for class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
 
FERMIUM - Static variable in enum org.openscience.cdk.config.Elements
 
FERMIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
fieldVal - Variable in class org.openscience.cdk.io.VASPReader
 
FiguerasSSSRFinder - Class in org.openscience.cdk.ringsearch
Deprecated.
Use SSSRFinder instead (exact algorithm).
FiguerasSSSRFinder() - Constructor for class org.openscience.cdk.ringsearch.FiguerasSSSRFinder
Deprecated.
 
fill - Variable in class org.openscience.cdk.renderer.elements.GeneralPath
Fill the shape instead of drawing outline.
fill - Variable in class org.openscience.cdk.renderer.elements.OvalElement
If true, draw the oval as filled.
FillBuff() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
 
FillBuff() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
 
filled - Variable in class org.openscience.cdk.renderer.elements.RectangleElement
If true, the rectangle is drawn as filled.
filter(Predicate<int[]>) - Method in class org.openscience.cdk.isomorphism.Mappings
Filter the mappings and keep only those which match the provided predicate (Guava).
filter(List<List<Integer>>) - Static method in class org.openscience.cdk.smsd.filters.PostFilter
Deprecated.
Creates a new instance of Post Filter and removes redundant mapping(s).
filterAtoms(int, Collection<List<IAtom>>, Collection<IAtom>) - Method in class org.openscience.cdk.smsd.ring.RingFilter
Deprecated.
 
filterAtoms(IAtomContainer, Collection<IAtom>) - Method in class org.openscience.cdk.smsd.ring.RingFilter
Deprecated.
 
finalize() - Method in class org.openscience.cdk.io.random.RandomAccessReader
 
FinalMappings - Class in org.openscience.cdk.smsd.helper
Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
FinalMappings() - Constructor for class org.openscience.cdk.smsd.helper.FinalMappings
Deprecated.
 
find(IAtomContainer) - Method in interface org.openscience.cdk.graph.CycleFinder
Find the cycles of the provided molecule.
find(IAtomContainer, int) - Method in interface org.openscience.cdk.graph.CycleFinder
Find the cycles of the provided molecule.
find(IAtomContainer, int[][], int) - Method in interface org.openscience.cdk.graph.CycleFinder
Find the cycles of the provided molecule when an adjacent relation (graph) is already available.
findAllRings(IAtomContainer) - Method in class org.openscience.cdk.ringsearch.AllRingsFinder
Compute all rings in the given IAtomContainer.
findAllRings(IAtomContainer, int) - Method in class org.openscience.cdk.ringsearch.AllRingsFinder
Compute all rings up to and including the maxRingSize.
findAllRingsInIsolatedRingSystem(IAtomContainer) - Method in class org.openscience.cdk.ringsearch.AllRingsFinder
Compute all rings in the given IAtomContainer.
findAllRingsInIsolatedRingSystem(IAtomContainer, int) - Method in class org.openscience.cdk.ringsearch.AllRingsFinder
Compute all rings up to an including the maxRingSize.
findBonds(IAtomContainer) - Method in class org.openscience.cdk.aromaticity.Aromaticity
Find the bonds of a molecule which this model determined were aromatic.
findChemFormats(int) - Method in class org.openscience.cdk.io.WriterFactory
Finds IChemFormats that provide a container for serialization for the given features.
findClosestByBond(IAtomContainer, IAtom, int) - Static method in class org.openscience.cdk.graph.PathTools
Returns the atoms which are closest to an atom in an AtomContainer by bonds.
findClosestInSpace(IAtomContainer, IAtom, int) - Static method in class org.openscience.cdk.geometry.GeometryTools
Returns the atoms which are closes to an atom in an AtomContainer by distance in 3d.
findClosestInSpace(IAtomContainer, IAtom, int) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Returns the atoms which are closes to an atom in an AtomContainer by distance in 3d.
findEquivalenceClasses() - Method in class org.openscience.cdk.ringsearch.SSSRFinder
Deprecated.
Finds the "interchangeability" equivalence classes.
findEssentialRings() - Method in class org.openscience.cdk.ringsearch.SSSRFinder
Deprecated.
Finds the Set of Essential Rings.
findGridBoundaries() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
Method determines the minimum and maximum values of a coordinate space up to 3D space.
findHeavyAtomsInChain(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
Count and find first heavy atom(s) (non Hydrogens) in a chain.
findIdentical(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.Pattern
Create a pattern which can be used to find molecules which are the same as the query structure.
findIdentical(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.VentoFoggia
Create a pattern which can be used to find molecules which are the same as the query structure.
findIdentical(IAtomContainer, AtomMatcher, BondMatcher) - Static method in class org.openscience.cdk.isomorphism.VentoFoggia
Create a pattern which can be used to find molecules which are the same as the query structure.
findMappedBonds(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
Collect the set of bonds that mapped in both a reactant and a product.
findMatchingAtomType(IAtomContainer, IAtom) - Method in class org.openscience.cdk.atomtype.CDKAtomTypeMatcher
Method that assigns an atom type to a given atom belonging to an atom container.
findMatchingAtomType(IAtomContainer, IAtom) - Method in class org.openscience.cdk.atomtype.EStateAtomTypeMatcher
 
findMatchingAtomType(IAtomContainer, IAtom) - Method in interface org.openscience.cdk.atomtype.IAtomTypeMatcher
Method that assigns an atom type to a given atom belonging to an atom container.
findMatchingAtomType(IAtomContainer, IAtom) - Method in class org.openscience.cdk.atomtype.MM2AtomTypeMatcher
Deprecated.
Assign the mm2 atom type to a given atom.
findMatchingAtomType(IAtomContainer, IAtom) - Method in class org.openscience.cdk.atomtype.MMFF94AtomTypeMatcher
Deprecated.
Assign the mmff94 atom type to a given atom.
findMatchingAtomType(IAtomContainer, IAtom) - Method in class org.openscience.cdk.atomtype.StructGenMatcher
Finds the AtomType matching the Atom's element symbol, formal charge and hybridization state.
findMatchingAtomType(IAtomContainer, IAtom) - Method in class org.openscience.cdk.atomtype.SybylAtomTypeMatcher
Sybyl atom type perception for a single atom.
findMatchingAtomTypes(IAtomContainer) - Method in class org.openscience.cdk.atomtype.CDKAtomTypeMatcher
Method that assigns atom types to atoms in the given atom container.
findMatchingAtomTypes(IAtomContainer) - Method in class org.openscience.cdk.atomtype.EStateAtomTypeMatcher
 
findMatchingAtomTypes(IAtomContainer) - Method in interface org.openscience.cdk.atomtype.IAtomTypeMatcher
Method that assigns atom types to atoms in the given atom container.
findMatchingAtomTypes(IAtomContainer) - Method in class org.openscience.cdk.atomtype.MM2AtomTypeMatcher
Deprecated.
 
findMatchingAtomTypes(IAtomContainer) - Method in class org.openscience.cdk.atomtype.MMFF94AtomTypeMatcher
Deprecated.
 
findMatchingAtomTypes(IAtomContainer) - Method in class org.openscience.cdk.atomtype.StructGenMatcher
 
findMatchingAtomTypes(IAtomContainer) - Method in class org.openscience.cdk.atomtype.SybylAtomTypeMatcher
Method that assigns atom types to atoms in the given atom container.
findPathBetween(Graph, Object, Object) - Static method in class org.openscience.cdk.graph.BFSShortestPath
 
findPathes(IAtomContainer, int) - Method in class org.openscience.cdk.fingerprint.Fingerprinter
findRelevantRings() - Method in class org.openscience.cdk.ringsearch.SSSRFinder
Deprecated.
Finds the Set of Relevant Rings.
findRings(IAtomContainer) - Method in class org.openscience.cdk.smsd.ring.HanserRingFinder
Deprecated.
Returns a collection of rings.
findRings(IAtomContainer) - Method in interface org.openscience.cdk.smsd.ring.RingFinder
Deprecated.
Returns Collection of atoms in Rings based on Hanser Ring Finding method
findSSSR(IAtomContainer) - Method in class org.openscience.cdk.ringsearch.FiguerasSSSRFinder
Deprecated.
Finds the Smallest Set of Smallest Rings.
findSSSR() - Method in class org.openscience.cdk.ringsearch.SSSRFinder
Deprecated.
Finds a Smallest Set of Smallest Rings.
findSubstructure(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.Pattern
Create a pattern which can be used to find molecules which contain the query structure.
findSubstructure(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.Ullmann
Create a pattern which can be used to find molecules which contain the query structure.
findSubstructure(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.VentoFoggia
Create a pattern which can be used to find molecules which contain the query structure.
findSubstructure(IAtomContainer, AtomMatcher, BondMatcher) - Static method in class org.openscience.cdk.isomorphism.VentoFoggia
Create a pattern which can be used to find molecules which contain the query structure.
findTerminalAtoms(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.stereo.ExtendedTetrahedral
Helper method to locate two terminal atoms in a container for a given focus.
findTerminalAtoms(IAtomContainer) - Method in class org.openscience.cdk.stereo.ExtendedTetrahedral
Helper method to locate two terminal atoms in a container for this extended tetrahedral element.
findTopoEquivClass(double[]) - Method in class org.openscience.cdk.graph.invariant.EquivalentClassPartitioner
Find the topological equivalent class for the given weight.
Fingerprinter - Class in org.openscience.cdk.fingerprint
Generates a fingerprint for a given AtomContainer.
Fingerprinter() - Constructor for class org.openscience.cdk.fingerprint.Fingerprinter
Creates a fingerprint generator of length DEFAULT_SIZE and with a search depth of DEFAULT_SEARCH_DEPTH.
Fingerprinter(int) - Constructor for class org.openscience.cdk.fingerprint.Fingerprinter
 
Fingerprinter(int, int) - Constructor for class org.openscience.cdk.fingerprint.Fingerprinter
Constructs a fingerprint generator that creates fingerprints of the given size, using a generation algorithm with the given search depth.
FingerprinterTool - Class in org.openscience.cdk.fingerprint
Tool with helper methods for IFingerprint.
FingerprinterTool() - Constructor for class org.openscience.cdk.fingerprint.FingerprinterTool
 
FingerprintFormat - Class in org.openscience.cdk.io.formats
 
FingerprintFormat() - Constructor for class org.openscience.cdk.io.formats.FingerprintFormat
 
fireChange() - Method in class org.openscience.cdk.renderer.RendererModel
Notifies registered listeners of certain changes that have occurred in this model.
fireFrameRead() - Method in class org.openscience.cdk.io.DefaultChemObjectReader
Sends a frame read event to the registered ReaderListeners.
fireFrameRead() - Method in class org.openscience.cdk.io.iterator.event.DefaultEventChemObjectReader
Sends a frame read event to the registered ReaderListeners.
fireIOSettingQuestion(IOSetting) - Method in class org.openscience.cdk.io.ChemObjectIO
fireIOSettingQuestion(IOSetting) - Method in class org.openscience.cdk.io.random.DefaultRandomAccessChemObjectReader
 
first() - Method in interface org.openscience.cdk.io.random.IRandomAccessChemObjectReader
 
first() - Method in class org.openscience.cdk.io.random.RandomAccessReader
 
first() - Method in class org.openscience.cdk.isomorphism.Mappings
Obtain the first match - if there is no first match an empty array is returned.
firstIndexOfDifference(Permutation) - Method in class org.openscience.cdk.group.Permutation
Find an r such that this[r] != other[r].
firstIsIdentity() - Method in interface org.openscience.cdk.group.DiscretePartitionRefiner
Check that the first refined partition is the identity.
firstPointX - Variable in class org.openscience.cdk.renderer.elements.LineElement
The x-coordinate of the first point.
firstPointY - Variable in class org.openscience.cdk.renderer.elements.LineElement
The y-coordinate of the first point.
FIVE_SECOND_TIMEOUT - Static variable in class org.openscience.cdk.inchi.JniInChIInputAdapter
 
fixAromaticBondOrders(IAtomContainer) - Method in class org.openscience.cdk.smiles.DeduceBondSystemTool
Deprecated.
Added missing bond orders based on atom type information.
fixAromaticityForXLogP(IAtomContainer) - Static method in class org.openscience.cdk.tools.CDKUtilities
Deprecated.
 
FixBondOrdersTool - Class in org.openscience.cdk.smiles
Deprecated.
FixBondOrdersTool() - Constructor for class org.openscience.cdk.smiles.FixBondOrdersTool
Deprecated.
Constructor for the FixBondOrdersTool object.
fixNitroGroups2(IAtomContainer) - Static method in class org.openscience.cdk.tools.CDKUtilities
Deprecated.
 
fixSmiles(String) - Static method in class org.openscience.cdk.tools.CDKUtilities
Deprecated.
 
fixSulphurH(IAtomContainer) - Static method in class org.openscience.cdk.tools.CDKUtilities
Deprecated.
 
FLAG_MASKS - Static variable in class org.openscience.cdk.CDKConstants
 
FLEROVIUM - Static variable in enum org.openscience.cdk.config.Elements
 
flipCoin(double) - Static method in class org.openscience.cdk.math.RandomNumbersTool
Returns a boolean value based on a biased coin toss.
FLUORINE - Static variable in enum org.openscience.cdk.config.Elements
 
FLUORO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
FM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
FMFDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
An implementation of the FMF descriptor characterizing complexity of a molecule.
FMFDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor
 
focus() - Method in class org.openscience.cdk.stereo.ExtendedTetrahedral
The central atom in the cumulated system.
fontManager - Variable in class org.openscience.cdk.renderer.AbstractRenderer
Font managers change the font size depending on the zoom.
forAny() - Static method in class org.openscience.cdk.isomorphism.AtomMatcher
Atoms are always compatible.
forAny() - Static method in class org.openscience.cdk.isomorphism.BondMatcher
All bonds are compatible.
forAtoms() - Static method in class org.openscience.cdk.group.PartitionRefinement
 
forBonds() - Method in class org.openscience.cdk.group.PartitionRefinement
 
ForceFieldConfigurator - Class in org.openscience.cdk.modeling.builder3d
Reads in a force field configuration file, set the atom types into a vector, and the data into a hashtable Therefore, it uses the class MM2BasedParameterSetReader.
ForceFieldConfigurator() - Constructor for class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
Constructor for the ForceFieldConfigurator object
forElement() - Static method in class org.openscience.cdk.isomorphism.AtomMatcher
Atoms are compatible if they are the same element.
formalCharge - Variable in class org.openscience.cdk.AtomType
The formal charge of the atom with CDKConstants.UNSET as default.
formalCharge - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom
The formal charge of the atom with CDKConstants.UNSET as default.
formalCharge - Variable in class org.openscience.cdk.renderer.elements.AtomSymbolElement
The formal charge.
formalCharge - Variable in class org.openscience.cdk.silent.AtomType
The formal charge of the atom with CDKConstants.UNSET as default.
FormalChargeAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
This matcher checks the formal charge of the Atom.
FormalChargeAtom(int, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.FormalChargeAtom
Creates a new instance
formalCharges - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
 
formalNeighbourCount - Variable in class org.openscience.cdk.AtomType
The formal number of neighbours this atom type can have with CDKConstants_UNSET as default.
formalNeighbourCount - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom
The formal number of neighbours this atom type can have with CDKConstants_UNSET as default.
formalNeighbourCount - Variable in class org.openscience.cdk.silent.AtomType
The formal number of neighbours this atom type can have with CDKConstants_UNSET as default.
format() - Method in class org.openscience.cdk.io.formats.IChemFormatMatcher.MatchResult
What was the format which matched if there was a match (IChemFormatMatcher.MatchResult.matched()).
format(char) - Method in class org.openscience.cdk.tools.FormatStringBuffer
Format a char.
format(float) - Method in class org.openscience.cdk.tools.FormatStringBuffer
Format a float.
format(double) - Method in class org.openscience.cdk.tools.FormatStringBuffer
Format a double.
format(int) - Method in class org.openscience.cdk.tools.FormatStringBuffer
Format a float.
format(long) - Method in class org.openscience.cdk.tools.FormatStringBuffer
Format a float.
format(String) - Method in class org.openscience.cdk.tools.FormatStringBuffer
Format a String.
formatCount() - Method in class org.openscience.cdk.io.WriterFactory
 
FormatFactory - Class in org.openscience.cdk.io
A factory for recognizing chemical file formats.
FormatFactory() - Constructor for class org.openscience.cdk.io.FormatFactory
Constructs a ReaderFactory which tries to detect the format in the first 65536 chars.
FormatFactory(int) - Constructor for class org.openscience.cdk.io.FormatFactory
Constructs a ReaderFactory which tries to detect the format in the first given number of chars.
formatMDLFloat(float) - Static method in class org.openscience.cdk.io.MDLV2000Writer
Formats a float to fit into the connectiontable and changes it to a String.
formatMDLInt(int, int) - Static method in class org.openscience.cdk.io.MDLV2000Writer
Formats an integer to fit into the connection table and changes it to a String.
formatMDLString(String, int) - Static method in class org.openscience.cdk.io.MDLV2000Writer
Formats a String to fit into the connectiontable.
FormatStringBuffer - Class in org.openscience.cdk.tools
A class for formatting output similar to the C printf command.
FormatStringBuffer(String) - Constructor for class org.openscience.cdk.tools.FormatStringBuffer
Create a new FormatStringBuffer.
FORMULA - Static variable in class org.openscience.cdk.CDKConstants
The Molecular Formula Identifier.
formula - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
 
formulaCounter - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
 
formulaGenerator - Variable in class org.openscience.cdk.formula.MolecularFormulaGenerator
The chosen implementation
forOrder() - Static method in class org.openscience.cdk.isomorphism.BondMatcher
Bonds are compatible if they are both aromatic or their orders are equal.
forQuery() - Static method in class org.openscience.cdk.isomorphism.AtomMatcher
Atoms are compatible if the second atom (atom2) is accepted by the IQueryAtom, atom1.
forQuery() - Static method in class org.openscience.cdk.isomorphism.BondMatcher
Bonds are compatible if the first bond1 (an IQueryBond) matches the second, bond2.
forStrictOrder() - Static method in class org.openscience.cdk.isomorphism.BondMatcher
Bonds are compatible if they are both aromatic or their orders are equal and they are non-aromatic.
FortranFormat - Class in org.openscience.cdk.math
Converts a String representation of a Fortran double to a double.
FortranFormat() - Constructor for class org.openscience.cdk.math.FortranFormat
 
forVectorGraphics(Graphics2D) - Static method in class org.openscience.cdk.renderer.visitor.AWTDrawVisitor
Create a draw visitor that will be rendering to a vector graphics output.
FourierGridBasis - Class in org.openscience.cdk.math.qm
At this time this class does not work correcly.
FourierGridBasis(int, double, double, IFunction) - Constructor for class org.openscience.cdk.math.qm.FourierGridBasis
 
FP_SIZE - Static variable in class org.openscience.cdk.fingerprint.PubchemFingerprinter
Number of bits in this fingerprint.
FR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
fractionalPoint3d - Variable in class org.openscience.cdk.Atom
A 3 point specifying the location of this atom in a crystal unit cell.
fractionalPoint3d - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom
A 3 point specifying the location of this atom in a crystal unit cell.
fractionalPoint3d - Variable in class org.openscience.cdk.silent.Atom
A 3 point specifying the location of this atom in a crystal unit cell.
FractionalPSADescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
Polar surface area expressed as a ratio to molecular size.
FractionalPSADescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor
 
fractionalToCartesian(Vector3d, Vector3d, Vector3d, Point3d) - Static method in class org.openscience.cdk.geometry.CrystalGeometryTools
 
fractionalToCartesian(ICrystal) - Static method in class org.openscience.cdk.geometry.CrystalGeometryTools
Creates Cartesian coordinates for all Atoms in the Crystal.
FragmentAtom - Class in org.openscience.cdk
Class to represent an IPseudoAtom which embeds an IAtomContainer.
FragmentAtom() - Constructor for class org.openscience.cdk.FragmentAtom
 
FragmentAtom - Class in org.openscience.cdk.silent
Class to represent an IPseudoAtom which embeds an IAtomContainer.
FragmentAtom() - Constructor for class org.openscience.cdk.silent.FragmentAtom
 
FragmentComplexityDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
Class that returns the complexity of a system.
FragmentComplexityDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor
Constructor for the FragmentComplexityDescriptor object.
FragmentUtils - Class in org.openscience.cdk.fragment
Helper methods for fragmentation algorithms.
FragmentUtils() - Constructor for class org.openscience.cdk.fragment.FragmentUtils
 
frameRead(ReaderEvent) - Method in interface org.openscience.cdk.io.listener.IReaderListener
Indicates that a new frame has been read.
frameRead(ReaderEvent) - Method in class org.openscience.cdk.io.listener.PropertiesListener
 
frameRead(ReaderEvent) - Method in class org.openscience.cdk.io.listener.SwingGUIListener
 
frameRead(ReaderEvent) - Method in class org.openscience.cdk.io.listener.TextGUIListener
 
FRANCIUM - Static variable in enum org.openscience.cdk.config.Elements
 
FRANCIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
from(int) - Method in class org.openscience.cdk.graph.AllPairsShortestPaths
Access the shortest paths object for provided start vertex.
from(IAtom) - Method in class org.openscience.cdk.graph.AllPairsShortestPaths
Access the shortest paths object for provided start atom.
fromRotationMatrix(Matrix) - Static method in class org.openscience.cdk.math.Quaternion
 
fromSignatureString(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.signature.MoleculeSignature
Builder for molecules (rather, for atom containers) from signature strings.
fromString(String) - Static method in class org.openscience.cdk.group.Partition
Parse a string like "[0,2|1,3]" to form the partition; cells are separated by '|' characters and elements within the cell by commas.
functionalGroupPrefix() - Method in class org.openscience.cdk.iupac.parser.NomParser
Deprecated.
The functional group part of the prefix
FURAN_RING - Static variable in class org.openscience.cdk.tools.AtomTypeTools
 
fused() - Method in interface org.openscience.cdk.ringsearch.CyclicVertexSearch
Construct the sets of vertices which belong to fused cycle systems (share at least one edge).
fused() - Method in class org.openscience.cdk.ringsearch.RingSearch
Construct the sets of vertices which belong to fused ring systems.
fusedRingFragments() - Method in class org.openscience.cdk.ringsearch.RingSearch
Construct a list of IAtomContainers which only contain fused rings.

G

G - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
GA - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
GADOLINIUM - Static variable in enum org.openscience.cdk.config.Elements
 
GADOLINIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
GALLIUM - Static variable in enum org.openscience.cdk.config.Elements
 
GALLIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
GamessFormat - Class in org.openscience.cdk.io.formats
See here.
GamessFormat() - Constructor for class org.openscience.cdk.io.formats.GamessFormat
 
GamessReader - Class in org.openscience.cdk.io
A reader for GAMESS log file.
GamessReader(Reader) - Constructor for class org.openscience.cdk.io.GamessReader
Constructs a new "GamessReader" object given a "Reader" object as input.
GamessReader(InputStream) - Constructor for class org.openscience.cdk.io.GamessReader
 
GamessReader() - Constructor for class org.openscience.cdk.io.GamessReader
 
GasteigerMarsiliPartialCharges - Class in org.openscience.cdk.charges
The calculation of the Gasteiger Marsili (PEOE) partial charges is based on [Gasteiger, J. and Marsili, M., Iterative partial equalization of orbital elektronegativity - a rapid access to atomic charges, Tetrahedron, 1980, 36:3219-3288].
GasteigerMarsiliPartialCharges() - Constructor for class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
Constructor for the GasteigerMarsiliPartialCharges object.
GasteigerPEPEPartialCharges - Class in org.openscience.cdk.charges
The calculation of the Gasteiger (PEPE) partial charges is based on [Saller, H., Quantitative Emperische Modelle fur Elektronische Effekte in Pi-Systemen und fur die Chemische Reaktivitat, 1985, Thecn. Univ. Munchen].
GasteigerPEPEPartialCharges() - Constructor for class org.openscience.cdk.charges.GasteigerPEPEPartialCharges
Constructor for the GasteigerPEPEPartialCharges object.
Gaussian03Format - Class in org.openscience.cdk.io.formats
See here.
Gaussian03Format() - Constructor for class org.openscience.cdk.io.formats.Gaussian03Format
 
Gaussian03Reader - Class in org.openscience.cdk.io
A reader for Gaussian03 output.
Gaussian03Reader(Reader) - Constructor for class org.openscience.cdk.io.Gaussian03Reader
 
Gaussian03Reader(InputStream) - Constructor for class org.openscience.cdk.io.Gaussian03Reader
 
Gaussian03Reader() - Constructor for class org.openscience.cdk.io.Gaussian03Reader
 
Gaussian90Format - Class in org.openscience.cdk.io.formats
 
Gaussian90Format() - Constructor for class org.openscience.cdk.io.formats.Gaussian90Format
 
Gaussian92Format - Class in org.openscience.cdk.io.formats
 
Gaussian92Format() - Constructor for class org.openscience.cdk.io.formats.Gaussian92Format
 
Gaussian94Format - Class in org.openscience.cdk.io.formats
 
Gaussian94Format() - Constructor for class org.openscience.cdk.io.formats.Gaussian94Format
 
Gaussian95Format - Class in org.openscience.cdk.io.formats
 
Gaussian95Format() - Constructor for class org.openscience.cdk.io.formats.Gaussian95Format
 
Gaussian98Format - Class in org.openscience.cdk.io.formats
 
Gaussian98Format() - Constructor for class org.openscience.cdk.io.formats.Gaussian98Format
 
Gaussian98Reader - Class in org.openscience.cdk.io
A reader for Gaussian98 output.
Gaussian98Reader() - Constructor for class org.openscience.cdk.io.Gaussian98Reader
Constructor for the Gaussian98Reader object
Gaussian98Reader(InputStream) - Constructor for class org.openscience.cdk.io.Gaussian98Reader
 
Gaussian98Reader(Reader) - Constructor for class org.openscience.cdk.io.Gaussian98Reader
Create an Gaussian98 output reader.
gaussianDouble(double) - Static method in class org.openscience.cdk.math.RandomNumbersTool
Generates a random double from a Gaussian distribution with the specified deviation.
gaussianFloat(float) - Static method in class org.openscience.cdk.math.RandomNumbersTool
Generates a random float from a Gaussian distribution with the specified deviation.
GaussianInputFormat - Class in org.openscience.cdk.io.formats
See here.
GaussianInputFormat() - Constructor for class org.openscience.cdk.io.formats.GaussianInputFormat
 
GaussianInputWriter - Class in org.openscience.cdk.io.program
File writer thats generates input files for Gaussian calculation jobs.
GaussianInputWriter(Writer) - Constructor for class org.openscience.cdk.io.program.GaussianInputWriter
Constructs a new writer that produces input files to run a Gaussian QM job.
GaussianInputWriter(OutputStream) - Constructor for class org.openscience.cdk.io.program.GaussianInputWriter
 
GaussianInputWriter() - Constructor for class org.openscience.cdk.io.program.GaussianInputWriter
 
GaussiansBasis - Class in org.openscience.cdk.math.qm
This class contains the information to use gauss function as a base for calculation of quantum mechanics.
GaussiansBasis() - Constructor for class org.openscience.cdk.math.qm.GaussiansBasis
 
GaussiansBasis(int[], int[], int[], double[], Vector[], IAtom[]) - Constructor for class org.openscience.cdk.math.qm.GaussiansBasis
Set up basis with gauss funktions f(x,y,z) = (x-rx)^nx * (y-ry)^ny * (z-rz)^nz * exp(-alpha*(r-ri)^2).
GaussJordan() - Method in class org.openscience.cdk.graph.invariant.GIMatrix
Gauss-Jordan algorithm.
GD - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
GE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
GeneralPath - Class in org.openscience.cdk.renderer.elements
A path of rendering elements from the elements.path package.
GeneralPath(List<PathElement>, Color) - Constructor for class org.openscience.cdk.renderer.elements.GeneralPath
Make a path from a list of path elements.
generate(IAtomContainer) - Method in class org.openscience.cdk.depict.Abbreviations
Find all enabled abbreviations in the provided molecule.
generate(double) - Method in class org.openscience.cdk.formula.MassToFormulaTool
Deprecated.
Method that actually does the work of extracting the molecular formula.
generate(IAtomContainer) - Method in interface org.openscience.cdk.hash.AtomHashGenerator
Generate invariant 64-bit hash codes for the atoms of the molecule.
generate(Set<IAtomContainer>) - Method in interface org.openscience.cdk.hash.EnsembleHashGenerator
Generate invariant 64-bit hash code for an ensemble of molecules.
generate(IAtomContainer) - Method in interface org.openscience.cdk.hash.MoleculeHashGenerator
Generate invariant 64-bit hash code for a molecule.
generate(String) - Static method in class org.openscience.cdk.iupac.parser.NomParser
Deprecated.
Parses the chemical name and returns the built molecule.
generate(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.iupac.parser.NomParser
Deprecated.
Parses the chemical name and returns the built molecule.
generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.AtomContainerBoundsGenerator
Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.AtomNumberGenerator
Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator
Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IAtomContainer, IAtom, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator
Generate the rendering element(s) for a particular atom.
generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IBond, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
Generate rendering element(s) for the current bond, including ring elements if this bond is part of a ring.
generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicGenerator
Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator
Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IReaction, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BoundsGenerator
Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IAtomContainer, IAtom, RendererModel) - Method in class org.openscience.cdk.renderer.generators.ExtendedAtomGenerator
Generate the rendering element(s) for a particular atom.
generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.HighlightGenerator
Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(T, RendererModel) - Method in interface org.openscience.cdk.renderer.generators.IGenerator
Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.LonePairGenerator
Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IReaction, RendererModel) - Method in class org.openscience.cdk.renderer.generators.MappingGenerator
Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IReaction, RendererModel) - Method in class org.openscience.cdk.renderer.generators.ProductsBoxGenerator
Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.RadicalGenerator
Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IReaction, RendererModel) - Method in class org.openscience.cdk.renderer.generators.ReactantsBoxGenerator
Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IReaction, RendererModel) - Method in class org.openscience.cdk.renderer.generators.ReactionArrowGenerator
Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IReaction, RendererModel) - Method in class org.openscience.cdk.renderer.generators.ReactionBoxGenerator
Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IReaction, RendererModel) - Method in class org.openscience.cdk.renderer.generators.ReactionPlusGenerator
Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IReaction, RendererModel) - Method in class org.openscience.cdk.renderer.generators.ReactionSceneGenerator
Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator
Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
generate(int[]) - Method in class org.openscience.cdk.smarts.SmartsFragmentExtractor
Generate a SMARTS for the substructure formed of the provided atoms.
generate() - Method in class org.openscience.cdk.structgen.SingleStructureRandomGenerator
Generates a random structure based on the atoms in the given IAtomContainer.
generate(IAtomContainerSet) - Method in class org.openscience.cdk.structgen.stochastic.PartialFilledStructureMerger
Randomly generates a single, connected, correctly bonded structure from a number of fragments.
generate3DCoordinates(IAtomContainer, boolean) - Method in class org.openscience.cdk.modeling.builder3d.ModelBuilder3D
Generate 3D coordinates with force field information.
generateAtomContainerFromInchi(IChemObjectBuilder) - Method in class org.openscience.cdk.inchi.InChIToStructure
Gets structure from InChI, and converts InChI library data structure into an IAtomContainer.
generateBond(IBond, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
Generate stereo or bond elements for this bond.
generateBondElement(IBond, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
Generate rendering elements for a bond, without ring elements but considering the type of the bond (single, double, triple).
generateBondElement(IBond, IBond.Order, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
Generate a LineElement or an ElementGroup of LineElements for this bond.
generateCompactElement(IAtom, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator
Generate a compact element for an atom, such as a circle or a square, rather than text element.
GenerateCompatibilityGraph - Class in org.openscience.cdk.smsd.algorithm.mcsplus
Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
GenerateCompatibilityGraph() - Constructor for class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
Deprecated.
Default constructor added
GenerateCompatibilityGraph(IAtomContainer, IAtomContainer, boolean) - Constructor for class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
Deprecated.
Generates a compatibility graph between two molecules
generateCoordinates(IAtomContainer) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
Convenience method for generating 2D coordinates.
generateCoordinates(IReaction) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
Convenience method to generate 2D coordinates for a reaction.
generateCoordinates(Vector2d) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
The main method of this StructurDiagramGenerator.
generateCoordinates() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
The main method of this StructurDiagramGenerator.
generateCSetCopy(int, List<String>) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
Deprecated.
 
generateCTabCopy(IAtomContainer) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
Deprecated.
 
generateDiagram(T) - Method in class org.openscience.cdk.renderer.AbstractRenderer
The main method of the renderer, that uses each of the generators to create a different set of IRenderingElements grouped together into a tree.
generateDiagram(T) - Method in interface org.openscience.cdk.renderer.IRenderer
Internal method to generate the intermediate format.
generateDiagram(IAtomContainerSet) - Method in class org.openscience.cdk.renderer.MoleculeSetRenderer
The main method of the renderer, that uses each of the generators to create a different set of IRenderingElements grouped together into a tree.
generateDiagram(IReaction) - Method in class org.openscience.cdk.renderer.ReactionRenderer
The main method of the renderer, that uses each of the generators to create a different set of IRenderingElements grouped together into a tree.
generateElement(IAtom, int, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator
Generate an atom symbol element.
generateExperimentalCoordinates() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
generateExperimentalCoordinates(Vector2d) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
generateFragments(IAtomContainer) - Method in class org.openscience.cdk.fragment.ExhaustiveFragmenter
Generate fragments for the input molecule.
generateFragments(IAtomContainer) - Method in interface org.openscience.cdk.fragment.IFragmenter
Generate fragments for the input molecule.
generateFragments(IAtomContainer) - Method in class org.openscience.cdk.fragment.MurckoFragmenter
Perform the fragmentation procedure.
generateGrid() - Method in class org.openscience.cdk.tools.GridGenerator
Main method creates a grid between given boundaries (dimensions).
generateInnerElement(IBond, IRing, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
Make the inner ring bond, which is slightly shorter than the outer bond.
generateMersenneTwisterRandomNumber(int, long) - Method in class org.openscience.cdk.fingerprint.RandomNumber
Mersenne Twister Random Number for a hashcode within a range between 0 to n.
generateMoments(IAtomContainer) - Static method in class org.openscience.cdk.similarity.DistanceMoment
Evaluate the 12 descriptors used to characterize the 3D shape of a molecule.
generateOrderEle() - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
Returns the Elements ordered according to (approximate) probability of occurrence.
generateParseException() - Method in class org.openscience.cdk.iupac.parser.NomParser
Deprecated.
Generate ParseException.
generateParseException() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
Generate ParseException.
generateRingElements(IBond, IRing, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
Generate ring elements, such as inner-ring bonds or ring stereo elements.
generateRingElements(IBond, IRing, RendererModel) - Method in class org.openscience.cdk.renderer.generators.RingGenerator
Generate ring elements, such as inner-ring bonds or ring stereo elements.
generators - Variable in class org.openscience.cdk.renderer.AbstractRenderer
Generators for diagram elements.
Generic - Static variable in class org.openscience.cdk.smiles.SmiFlavor
Output non-canonical SMILES without stereochemistry, atomic masses.
generic() - Static method in class org.openscience.cdk.smiles.SmilesGenerator
Create a generator for generic SMILES.
geometricCenterAllPlacedAtoms(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
Calculates the geometric center of all placed atoms in the atomcontainer.
GeometricCumulativeDoubleBondFactory - Class in org.openscience.cdk.hash.stereo
Stereo encoder factory for 2D and 3D cumulative double bonds.
GeometricCumulativeDoubleBondFactory() - Constructor for class org.openscience.cdk.hash.stereo.GeometricCumulativeDoubleBondFactory
 
GeometricDoubleBondEncoderFactory - Class in org.openscience.cdk.hash.stereo
A stereo encoder factory encoding double bond configurations by 2D and 3D coordinates.
GeometricDoubleBondEncoderFactory() - Constructor for class org.openscience.cdk.hash.stereo.GeometricDoubleBondEncoderFactory
 
GeometricTetrahedralEncoderFactory - Class in org.openscience.cdk.hash.stereo
A stereo encoder factory for tetrahedral centres.
GeometricTetrahedralEncoderFactory() - Constructor for class org.openscience.cdk.hash.stereo.GeometricTetrahedralEncoderFactory
 
Geometry3DValidator - Class in org.openscience.cdk.validate
Validates the 3D geometry of the model.
Geometry3DValidator() - Constructor for class org.openscience.cdk.validate.Geometry3DValidator
 
GeometryTools - Class in org.openscience.cdk.geometry
A set of static utility classes for geometric calculations and operations.
GeometryTools() - Constructor for class org.openscience.cdk.geometry.GeometryTools
 
GeometryTools.CoordinateCoverage - Enum in org.openscience.cdk.geometry
Provides the coverage of coordinates for this molecule.
GeometryUtil - Class in org.openscience.cdk.geometry
A set of static utility classes for geometric calculations and operations.
GeometryUtil.CoordinateCoverage - Enum in org.openscience.cdk.geometry
Provides the coverage of coordinates for this molecule.
GERMAINIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
GERMANIUM - Static variable in enum org.openscience.cdk.config.Elements
 
get(int) - Method in class org.openscience.cdk.ConformerContainer
Get the conformer at a specified position.
get(int) - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
 
get(int) - Method in interface org.openscience.cdk.fingerprint.IBitFingerprint
Returns the value of the bit with the specified index.
get(int) - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
 
get(int, int) - Method in class org.openscience.cdk.graph.GraphUtil.EdgeToBondMap
Access the bond store at the end points v and w.
get(int) - Method in class org.openscience.cdk.group.DisjointSetForest
Get the value of the forest at this index - note that this will not necessarily give the set for that element : use DisjointSetForest.getSets() after union-ing elements.
get(int) - Method in class org.openscience.cdk.group.Permutation
Get the value at this index.
get(int, int) - Method in class org.openscience.cdk.group.PermutationGroup
Get one of the permutations that make up the compact representation.
get(String) - Method in class org.openscience.cdk.io.setting.SettingManager
Access the setting stored for given name.
get(String, Class<S>) - Method in class org.openscience.cdk.io.setting.SettingManager
Convenience method that allows specification of return ISetting type so that you can nest the call to access the setting value.
get(int) - Method in class org.openscience.cdk.qsar.result.DoubleArrayResult
The first double is at index = 0;
get(int) - Method in class org.openscience.cdk.qsar.result.IntegerArrayResult
The first int is at index = 0.
get(Class<T>) - Method in class org.openscience.cdk.renderer.RendererModel
Returns the IGeneratorParameter for the active IRenderer.
get2DCenter() - Method in class org.openscience.cdk.Bond
Returns the geometric 2D center of the bond.
get2DCenter() - Method in class org.openscience.cdk.debug.DebugBond
Returns the geometric 2D center of the bond.
get2DCenter(Iterable<IAtom>) - Static method in class org.openscience.cdk.geometry.GeometryTools
Calculates the center of the given atoms and returns it as a Point2d.
get2DCenter(Iterator<IAtom>) - Static method in class org.openscience.cdk.geometry.GeometryTools
Calculates the center of the given atoms and returns it as a Point2d.
get2DCenter(IRingSet) - Static method in class org.openscience.cdk.geometry.GeometryTools
Returns the geometric center of all the rings in this ringset.
get2DCenter(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
Returns the geometric center of all the atoms in the atomContainer.
get2DCenter(Iterable<IAtom>) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Calculates the center of the given atoms and returns it as a Point2d.
get2DCenter(Iterator<IAtom>) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Calculates the center of the given atoms and returns it as a Point2d.
get2DCenter(IRingSet) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Returns the geometric center of all the rings in this ringset.
get2DCenter(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Returns the geometric center of all the atoms in the atomContainer.
get2DCenter() - Method in interface org.openscience.cdk.interfaces.IBond
Returns the geometric 2D center of the bond.
get2DCenter() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
Returns the geometric 2D center of the query bond.
get2DCenter() - Method in class org.openscience.cdk.silent.Bond
Returns the geometric 2D center of the bond.
get2DCentreOfMass(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
Calculates the center of mass for the Atoms in the AtomContainer for the 2D coordinates.
get2DCentreOfMass(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Calculates the center of mass for the Atoms in the AtomContainer for the 2D coordinates.
get2DCoordinateCoverage(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
Determines the coverage of this IAtomContainer's 2D coordinates.
get2DCoordinateCoverage(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Determines the coverage of this IAtomContainer's 2D coordinates.
get2DDimension(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
Returns the java.awt.Dimension of a molecule.
get2DDimension(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Returns the dimension of a molecule (width/height).
get3DCenter() - Method in class org.openscience.cdk.Bond
Returns the geometric 3D center of the bond.
get3DCenter() - Method in class org.openscience.cdk.debug.DebugBond
Returns the geometric 3D center of the bond.
get3DCenter(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
Returns the geometric center of all the atoms in this atomContainer.
get3DCenter(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Returns the geometric center of all the atoms in this atomContainer.
get3DCenter() - Method in interface org.openscience.cdk.interfaces.IBond
Returns the geometric 3D center of the bond.
get3DCenter() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
Returns the geometric 3D center of the query bond.
get3DCenter() - Method in class org.openscience.cdk.silent.Bond
Returns the geometric 3D center of the bond.
get3DCentreOfMass(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
Calculates the center of mass for the Atoms in the AtomContainer for the 2D coordinates.
get3DCentreOfMass(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Calculates the center of mass for the Atoms in the AtomContainer.
get3DCoordinateCoverage(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
Determines the coverage of this IAtomContainer's 3D coordinates.
get3DCoordinateCoverage(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Determines the coverage of this IAtomContainer's 3D coordinates.
get3DCoordinatesForLigands(IAtom, IAtomContainer, IAtomContainer, IAtom, int, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
Adds 3D coordinates for singly-bonded ligands of a reference atom (A).
get3DCoordinatesForSP2Ligands(IAtom, IAtomContainer, IAtomContainer, IAtom, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
Main method for the calculation of the ligand coordinates for sp2 atoms.
get3DCoordinatesForSP3Ligands(IAtom, IAtomContainer, IAtomContainer, IAtom, int, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
Main method for the calculation of the ligand coordinates for sp3 atoms.
get3DCoordinatesForSPLigands(IAtom, IAtomContainer, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
 
getA() - Method in class org.openscience.cdk.Crystal
Gets the A unit cell axes in Cartesian coordinates as a three element double array.
getA() - Method in class org.openscience.cdk.debug.DebugCrystal
Gets the A unit cell axes in Cartesian coordinates as a three element double array.
getA() - Method in interface org.openscience.cdk.interfaces.ICrystal
Gets the A unit cell axes in carthesian coordinates as a three element double array.
getA() - Method in class org.openscience.cdk.silent.Crystal
Gets the A unit cell axes in Cartesian coordinates as a three element double array.
getAgents() - Method in class org.openscience.cdk.debug.DebugReaction
Returns a MoleculeSet containing the agents in this reaction.
getAgents() - Method in interface org.openscience.cdk.interfaces.IReaction
Returns a IAtomContaineSet containing the agents in this reaction.
getAgents() - Method in class org.openscience.cdk.Reaction
Returns a MoleculeSet containing the agents in this reaction.
getAgents() - Method in class org.openscience.cdk.silent.Reaction
Returns a MoleculeSet containing the agents in this reaction.
getAllAgents(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
 
getAllAtomContainers(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
Returns all the AtomContainer's of a MoleculeSet.
getAllAtomContainers(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator
Returns all the AtomContainer's of a ChemFile.
getAllAtomContainers(IChemModel) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
Returns all the AtomContainer's of a ChemModel.
getAllAtomContainers(IChemSequence) - Static method in class org.openscience.cdk.tools.manipulator.ChemSequenceManipulator
Returns all the AtomContainer's of a ChemSequence.
getAllAtomContainers(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
Returns all the AtomContainer's of a MoleculeSet.
getAllAtomContainers(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
Returns all the AtomContainer's of a Reaction.
getAllAtomContainers(IReactionScheme, IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator
Get all molecule objects from a set of Reactions given a IAtomContainerSet to add.
getAllAtomContainers(IReactionScheme) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator
get all AtomContainers object from a set of Reactions.
getAllAtomContainers(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
Returns all the AtomContainer's of a Reaction.
getAllAtomContainers(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator
Returns all the AtomContainer's in a RingSet.
getAllAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler
Deprecated.
Returns all plausible mappings between query and target molecules.
getAllAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler
Deprecated.
Returns all plausible mappings between query and target molecules.
getAllAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler
Deprecated.
Returns all plausible mappings between query and target molecules.
getAllAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler
Deprecated.
Returns all plausible mappings between query and target molecules.
getAllAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler
Deprecated.
Returns all plausible mappings between query and target molecules.
getAllAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler
Deprecated.
Returns all plausible mappings between query and target molecules.
getAllAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler
Deprecated.
Returns all plausible mappings between query and target molecules.
getAllAtomMapping() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
Deprecated.
Returns all plausible mappings between query and target molecules Each map in the list has atom-atom equivalence of the mappings between query and target molecule i.e.
getAllAtomMapping() - Method in interface org.openscience.cdk.smsd.interfaces.IMCSBase
Deprecated.
Returns all plausible mappings between query and target molecules.
getAllAtomMapping() - Method in class org.openscience.cdk.smsd.Isomorphism
Deprecated.
Returns all plausible mappings between query and target molecules Each map in the list has atom-atom equivalence of the mappings between query and target molecule i.e.
getAllAtomRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>, boolean) - Static method in class org.openscience.cdk.geometry.GeometryTools
Return the RMSD between the 2 aligned molecules.
getAllAtomRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>, boolean) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Return the RMSD between the 2 aligned molecules.
getAllAtomTypes() - Method in class org.openscience.cdk.config.AtomTypeFactory
Gets the allAtomTypes attribute of the AtomTypeFactory object.
getAllBondMaps() - Method in class org.openscience.cdk.smsd.Isomorphism
Deprecated.
 
getAllChemModels(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator
Get a list of all ChemModels inside an IChemFile.
getAllChemObjects(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
Does not recursively return the contents of the AtomContainer.
getAllChemObjects(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator
Returns a List of all IChemObject inside a ChemFile.
getAllChemObjects(IChemModel) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
Retrieve a List of all ChemObject objects within an IChemModel.
getAllChemObjects(IChemSequence) - Static method in class org.openscience.cdk.tools.manipulator.ChemSequenceManipulator
Returns a List of all IChemObject inside a ChemSequence.
getAllChemObjects(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
 
getAllChemObjects(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
 
getAllChemObjects(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
 
getAllConfigurations() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
Produces all combinations of the root structure (scaffold) with the R-groups substituted in valid ways, using each R-group's definitions and conditions.
getAllConfigurations() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
 
getAllFormulas() - Method in class org.openscience.cdk.formula.MolecularFormulaGenerator
Generates a IMolecularFormulaSet by repeatedly calling MolecularFormulaGenerator.getNextFormula() until all possible formulas are generated.
getAllIDs(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
 
getAllIDs(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
 
getAllIDs(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator
 
getAllIDs(IChemModel) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
 
getAllIDs(IChemSequence) - Static method in class org.openscience.cdk.tools.manipulator.ChemSequenceManipulator
 
getAllIDs(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
 
getAllIDs(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
 
getAllIDs(IReactionScheme) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator
Get all ID of this IReactionSet.
getAllIDs(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
 
getAllInOneContainer(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator
Puts all rings of a ringSet in a single atomContainer
getAllMapping() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler
Deprecated.
Returns all plausible mappings between query and target molecules.
getAllMapping() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler
Deprecated.
Returns all plausible mappings between query and target molecules.
getAllMapping() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler
Deprecated.
Returns all plausible mappings between query and target molecules.
getAllMapping() - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler
Deprecated.
Returns all plausible mappings between query and target molecules.
getAllMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler
Deprecated.
Returns all plausible mappings between query and target molecules.
getAllMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler
Deprecated.
Returns all plausible mappings between query and target molecules.
getAllMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler
Deprecated.
Returns all plausible mappings between query and target molecules.
getAllMapping() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
Deprecated.
Returns all plausible mappings between query and target molecules Each map in the list has atom-atom equivalence index of the mappings between query and target molecule i.e.
getAllMapping() - Method in interface org.openscience.cdk.smsd.interfaces.IMCSBase
Deprecated.
Returns all plausible mappings between query and target molecules.
getAllMapping() - Method in class org.openscience.cdk.smsd.Isomorphism
Deprecated.
Returns all plausible mappings between query and target molecules Each map in the list has atom-atom equivalence index of the mappings between query and target molecule i.e.
getAllMaximum(List<List<CDKRMap>>) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
Deprecated.
 
getAllMolecules(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
Get all molecule of a IReaction: reactants + products.
getAllMolecules(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
get all Molecules object from a set of Reactions.
getAllPaths(IAtomContainer, IAtom, IAtom) - Static method in class org.openscience.cdk.graph.PathTools
Get a list of all the paths between two atoms.
getAllProducts(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
get all products of a IReaction
getAllReactants(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
get all reactants of a IReaction
getAllReactions(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator
Get a list of all IReaction inside an IChemFile.
getAllReactions(IReactionScheme) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator
Get all IReaction's object from a given IReactionScheme.
getAllRgroupQueryAtoms() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
Returns all R# type atoms (pseudo atoms) found in the root structure.
getAllRings() - Method in class org.openscience.cdk.graph.SpanningTree
All basic rings and the all pairs of basic rings share at least one edge combined.
getAllSurfaceAreas() - Method in class org.openscience.cdk.geometry.surface.NumericalSurface
Get an array containing the accessible surface area for each atom.
getAllSurfacePoints() - Method in class org.openscience.cdk.geometry.surface.NumericalSurface
Get an array of all the points on the molecular surface.
getAltLoc() - Method in class org.openscience.cdk.debug.DebugPDBAtom
get the Alternate location indicator of this atom.
getAltLoc() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
get the Alternate location indicator of this atom.
getAltLoc() - Method in class org.openscience.cdk.protein.data.PDBAtom
get the Alternate location indicator of this atom.
getAltLoc() - Method in class org.openscience.cdk.silent.PDBAtom
get the Alternate location indicator of this atom.
getAngle(double, double) - Static method in class org.openscience.cdk.geometry.GeometryTools
Gets the angle attribute of the GeometryTools class.
getAngle(double, double) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Gets the angle attribute of the GeometryTools class.
getAngleData(String, String, String, String) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94ParametersCall
Gets the angle parameter set.
getAngleRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>) - Static method in class org.openscience.cdk.geometry.GeometryTools
Return the variation of each angle value between the 2 aligned molecules.
getAngleRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Return the variation of each angle value between the 2 aligned molecules.
getAngleValue(String, String, String) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
Gets the angleKey attribute of the AtomPlacer3D object.
getAngleValue(String, String, String) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
Gets the angleKey attribute of the AtomPlacer3D object.
getArrayValue() - Method in class org.openscience.cdk.graph.invariant.GIMatrix
Returns the internal representation of the matrix, that is an array of double objects.
getAtom(int) - Method in class org.openscience.cdk.AtomContainer
Get the atom at position number in [0,..].
getAtom(int) - Method in class org.openscience.cdk.Bond
Returns an Atom from this bond.
getAtom(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid
Get the atom at position number in [0,..].
getAtom(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer
Get the atom at position number in [0,..].
getAtom(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Get the atom at position number in [0,..].
getAtom(int) - Method in class org.openscience.cdk.debug.DebugBond
Returns an Atom from this bond.
getAtom(int) - Method in class org.openscience.cdk.debug.DebugCrystal
Get the atom at position number in [0,..].
getAtom() - Method in class org.openscience.cdk.debug.DebugLonePair
Returns the associated Atom.
getAtom(int) - Method in class org.openscience.cdk.debug.DebugMonomer
Get the atom at position number in [0,..].
getAtom(int) - Method in class org.openscience.cdk.debug.DebugPolymer
Get the atom at position number in [0,..].
getAtom(int) - Method in class org.openscience.cdk.debug.DebugRing
Get the atom at position number in [0,..].
getAtom() - Method in class org.openscience.cdk.debug.DebugSingleElectron
Returns the associated Atom.
getAtom(int) - Method in class org.openscience.cdk.debug.DebugStrand
Get the atom at position number in [0,..].
getAtom(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Get the atom at position number in [0,..].
getAtom(int) - Method in interface org.openscience.cdk.interfaces.IBond
Returns an Atom from this bond.
getAtom() - Method in interface org.openscience.cdk.interfaces.ILonePair
Returns the associated Atom.
getAtom() - Method in interface org.openscience.cdk.interfaces.ISingleElectron
Returns the associated Atom.
getAtom(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Get the atom at position number in [0,..].
getAtom(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
Returns an Atom from this query bond.
getAtom() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RingIdentifierAtom
 
getAtom() - Method in class org.openscience.cdk.LonePair
Returns the associated Atom.
getAtom(int) - Method in class org.openscience.cdk.silent.AtomContainer
Get the atom at position number in [0,..].
getAtom(int) - Method in class org.openscience.cdk.silent.Bond
Returns an Atom from this bond.
getAtom() - Method in class org.openscience.cdk.silent.LonePair
Returns the associated Atom.
getAtom() - Method in class org.openscience.cdk.silent.SingleElectron
Returns the associated Atom.
getAtom() - Method in class org.openscience.cdk.SingleElectron
Returns the associated Atom.
getAtom() - Method in class org.openscience.cdk.smiles.InvPair
 
getAtom(int) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.TargetProperties
Deprecated.
 
getAtom(INode) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder
Deprecated.
Returns an atom associated with this node.
getAtom(INode) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQuery
Deprecated.
Returns an atom associated with this node.
getAtomArray(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
Constructs an array of Atom objects from an AtomContainer.
getAtomArray(List<IAtom>) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
Constructs an array of Atom objects from a List of Atom objects.
getAtomArray(IBond) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
Constructs an array of Atom objects from Bond.
getAtomAt(int) - Method in class org.openscience.cdk.Association
Returns an Atom from this Association.
getAtomById(IAtomContainer, String) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
Returns an atom in an atomcontainer identified by id
getAtomColor(IAtom) - Method in class org.openscience.cdk.renderer.color.CDK2DAtomColors
Returns the color for a certain atom type.
getAtomColor(IAtom, Color) - Method in class org.openscience.cdk.renderer.color.CDK2DAtomColors
Returns the color for a certain atom type, and uses the given default color if it fails to identify the atom type.
getAtomColor(IAtom) - Method in class org.openscience.cdk.renderer.color.CDKAtomColors
Deprecated.
Returns the CDK scheme color for the given atom's element.
getAtomColor(IAtom, Color) - Method in class org.openscience.cdk.renderer.color.CDKAtomColors
Deprecated.
Returns the CDK scheme color for the given atom's element, or defaults to the given color if no color is defined.
getAtomColor(IAtom) - Method in class org.openscience.cdk.renderer.color.CPKAtomColors
Deprecated.
Returns the font color for atom given atom.
getAtomColor(IAtom, Color) - Method in class org.openscience.cdk.renderer.color.CPKAtomColors
Deprecated.
Returns the font color for atom given atom.
getAtomColor(IAtom) - Method in interface org.openscience.cdk.renderer.color.IAtomColorer
Returns the color for a certain atom type.
getAtomColor(IAtom, Color) - Method in interface org.openscience.cdk.renderer.color.IAtomColorer
Returns the color for a certain atom type, and uses the given default color if it fails to identify the atom type.
getAtomColor(IAtom) - Method in class org.openscience.cdk.renderer.color.JmolColors
 
getAtomColor(IAtom, Color) - Method in class org.openscience.cdk.renderer.color.JmolColors
 
getAtomColor(IAtom) - Method in class org.openscience.cdk.renderer.color.PartialAtomicChargeColors
Returns the a color reflecting the given atom's partial charge.
getAtomColor(IAtom, Color) - Method in class org.openscience.cdk.renderer.color.PartialAtomicChargeColors
Returns the a color reflecting the given atom's partial charge, or defaults to the given color if no color is defined.
getAtomColor(IAtom) - Method in class org.openscience.cdk.renderer.color.RasmolColors
Returns the Rasmol color for the given atom's element.
getAtomColor(IAtom, Color) - Method in class org.openscience.cdk.renderer.color.RasmolColors
Returns the Rasmol color for the given atom's element, or defaults to the given color if no color is defined.
getAtomColor(IAtom) - Method in class org.openscience.cdk.renderer.color.UniColor
Returns the color for a certain atom type.
getAtomColor(IAtom, Color) - Method in class org.openscience.cdk.renderer.color.UniColor
Returns the color for a certain atom type, and uses the given default color if it fails to identify the atom type.
getAtomColor(IAtom, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator
Returns the drawing color of the given atom.
getAtomContainer(int) - Method in class org.openscience.cdk.AtomContainerSet
Returns the AtomContainer at position number in the container.
getAtomContainer(int) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
Returns the AtomContainer at position number in the container.
getAtomContainer(int) - Method in class org.openscience.cdk.debug.DebugSubstance
Returns the AtomContainer at position number in the container.
getAtomContainer() - Method in interface org.openscience.cdk.geometry.cip.ILigand
IAtomContainer of which this ligand is part.
getAtomContainer() - Method in class org.openscience.cdk.geometry.cip.Ligand
IAtomContainer of which this ligand is part.
getAtomContainer() - Method in class org.openscience.cdk.inchi.InChIToStructure
Returns generated molecule.
getAtomContainer(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
Returns the AtomContainer at position number in the container.
getAtomContainer() - Method in class org.openscience.cdk.io.iterator.event.EventCMLHandler
 
getAtomContainer() - Method in class org.openscience.cdk.io.iterator.event.EventCMLReader
 
getAtomContainer() - Method in interface org.openscience.cdk.io.iterator.event.IEventChemObjectReader
 
getAtomContainer() - Method in class org.openscience.cdk.signature.MoleculeFromSignatureBuilder
Gets the atom container.
getAtomContainer(int) - Method in class org.openscience.cdk.silent.AtomContainerSet
Returns the AtomContainer at position number in the container.
getAtomContainer(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
Method that actually does the work of convert the IMolecularFormula to IAtomContainer.
getAtomContainer(IMolecularFormula, IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
Method that actually does the work of convert the IMolecularFormula to IAtomContainer given a IAtomContainer.
getAtomContainer(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
Converts a formula string (like "C2H4") into an atom container with atoms but no bonds.
getAtomContainerCount() - Method in class org.openscience.cdk.AtomContainerSet
Returns the number of AtomContainers in this Container.
getAtomContainerCount() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
Returns the number of AtomContainers in this Container.
getAtomContainerCount() - Method in class org.openscience.cdk.debug.DebugSubstance
Returns the number of AtomContainers in this Container.
getAtomContainerCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
Returns the number of AtomContainers in this Container.
getAtomContainerCount() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
Return the total number of atom containers (count the root plus all substituents).
getAtomContainerCount() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
 
getAtomContainerCount() - Method in class org.openscience.cdk.silent.AtomContainerSet
Returns the number of AtomContainers in this Container.
getAtomContainerSet(IAtomContainer, IAtomContainer, IReactionScheme) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator
Extract the list of AtomContainers taking part in the IReactionScheme to originate a product given a reactant.
getAtomCount() - Method in class org.openscience.cdk.Association
Returns the number of Atoms in this Association.
getAtomCount() - Method in class org.openscience.cdk.AtomContainer
Returns the number of Atoms in this Container.
getAtomCount() - Method in class org.openscience.cdk.Bond
Returns the number of Atoms in this Bond.
getAtomCount() - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns the number of Atoms in this Container.
getAtomCount() - Method in class org.openscience.cdk.debug.DebugAtomContainer
Returns the number of Atoms in this Container.
getAtomCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns the number of Atoms in this Container.
getAtomCount() - Method in class org.openscience.cdk.debug.DebugBond
Returns the number of Atoms in this Bond.
getAtomCount() - Method in class org.openscience.cdk.debug.DebugCrystal
Returns the number of Atoms in this Container.
getAtomCount() - Method in class org.openscience.cdk.debug.DebugMonomer
Returns the number of Atoms in this Container.
getAtomCount() - Method in class org.openscience.cdk.debug.DebugPolymer
Returns the number of Atoms in this Container.
getAtomCount() - Method in class org.openscience.cdk.debug.DebugRing
Returns the number of Atoms in this Container.
getAtomCount() - Method in class org.openscience.cdk.debug.DebugStrand
Returns the number of Atoms in this Container.
getAtomCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Returns the number of Atoms in this Container.
getAtomCount() - Method in interface org.openscience.cdk.interfaces.IBond
Returns the number of Atoms in this Bond.
getAtomCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Returns the number of Atoms in this Container.
getAtomCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
Returns the number of Atoms in this Bond.
getAtomCount() - Method in class org.openscience.cdk.silent.AtomContainer
Returns the number of Atoms in this Container.
getAtomCount() - Method in class org.openscience.cdk.silent.Bond
Returns the number of Atoms in this Bond.
getAtomCount() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.TargetProperties
Deprecated.
 
getAtomCount(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
 
getAtomCount(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator
Get the total number of atoms inside an IChemFile.
getAtomCount(IChemModel) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
Get the total number of atoms inside an IChemModel.
getAtomCount(IChemSequence) - Static method in class org.openscience.cdk.tools.manipulator.ChemSequenceManipulator
Get the total number of atoms inside an IChemSequence.
getAtomCount(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
Checks a set of Nodes for the occurrence of each isotopes instance in the molecular formula.
getAtomCount(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
 
getAtomCount(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
 
getAtomCount(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
 
getAtomCount(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator
Return the total number of atoms over all the rings in the colllection.
getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugAtom
Returns the atomic number of this element.
getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugAtomType
Returns the atomic number of this element.
getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugElement
Returns the atomic number of this element.
getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
Returns the atomic number of this element.
getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugIsotope
Returns the atomic number of this element.
getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
Returns the atomic number of this element.
getAtomicNumber() - Method in class org.openscience.cdk.Element
Returns the atomic number of this element.
getAtomicNumber() - Method in interface org.openscience.cdk.interfaces.IElement
Returns the atomic number of this element.
getAtomicNumber() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
Returns the atomic number of this element.
getAtomicNumber() - Method in class org.openscience.cdk.silent.Element
Returns the atomic number of this element.
getAtomicNumber(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
Get the atomic number of the element.
getAtomicSoftnessCore(IAtomContainer, int) - Method in class org.openscience.cdk.charges.InductivePartialCharges
Gets the atomicSoftnessCore attribute of the InductivePartialCharges object.
getAtomIndices() - Method in class org.openscience.cdk.signature.Orbit
Gets all the atom indices as a list.
getAtomLayers(int[][]) - Static method in class org.openscience.cdk.graph.invariant.HuLuIndexTool
 
getAtomMatcher() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.NodeBuilder
Deprecated.
Returns Query Atom.
getAtomMatcher() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.INode
Deprecated.
Returns Query Atom.
getAtomNumber(IAtom) - Method in class org.openscience.cdk.AtomContainer
Returns the position of a given atom in the atoms array.
getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns the position of a given atom in the atoms array.
getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns the position of a given atom in the atoms array.
getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
Returns the position of a given atom in the atoms array.
getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
Returns the position of a given atom in the atoms array.
getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
Returns the position of a given atom in the atoms array.
getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
Returns the position of a given atom in the atoms array.
getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
Returns the position of a given atom in the atoms array.
getAtomNumber(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
getAtomNumber(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Returns the position of a given atom in the atoms array.
getAtomNumber(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
Returns the position of a given atom in the atoms array.
getAtomOverlapScore(IAtomContainer, Vector) - Method in class org.openscience.cdk.layout.OverlapResolver
Deprecated.
Calculates a score based on the overlap of atoms.
getAtomPlacer() - Method in class org.openscience.cdk.layout.RingPlacer
 
getAtoms() - Method in class org.openscience.cdk.Association
Returns the array of atoms making up this Association.
getAtoms() - Method in class org.openscience.cdk.sgroup.Sgroup
Access the atoms of this substructure group.
getAtoms() - Method in class org.openscience.cdk.smsd.ring.PathEdge
Deprecated.
 
getAtomType(String) - Method in class org.openscience.cdk.config.AtomTypeFactory
Get an AtomType with the given ID.
getAtomTypeFactory(IChemObjectBuilder) - Method in class org.openscience.cdk.tools.SaturationChecker
 
getAtomTypeFactory(IChemObjectBuilder) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
 
getAtomTypeMappings() - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingHandler
Returns a Map with atom type mappings.
getAtomTypeName() - Method in class org.openscience.cdk.AtomType
Gets the id attribute of the AtomType object.
getAtomTypeName() - Method in class org.openscience.cdk.debug.DebugAtom
Gets the id attribute of the AtomType object.
getAtomTypeName() - Method in class org.openscience.cdk.debug.DebugAtomType
Gets the id attribute of the AtomType object.
getAtomTypeName() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
Gets the id attribute of the AtomType object.
getAtomTypeName() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
Gets the id attribute of the AtomType object.
getAtomTypeName() - Method in interface org.openscience.cdk.interfaces.IAtomType
Gets the id attribute of the AtomType object.
getAtomTypeName() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
Gets the id attribute of the AtomType object.
getAtomTypeName() - Method in class org.openscience.cdk.silent.AtomType
Gets the id attribute of the AtomType object.
getAtomTypePatterns() - Method in class org.openscience.cdk.modeling.builder3d.MM2BasedAtomTypePattern
Gets the atomTypePatterns attribute of the MM2BasedAtomTypePattern object
getAtomTypePatterns() - Method in class org.openscience.cdk.modeling.builder3d.MMFF94BasedAtomTypePattern
Gets the atomTypePatterns attribute of the MM2BasedAtomTypePattern object
getAtomTypes(String) - Method in class org.openscience.cdk.config.AtomTypeFactory
Get an array of all atomTypes known to the AtomTypeFactory for the given element symbol and atomtype class.
getAtomTypes() - Method in class org.openscience.cdk.config.atomtypes.AtomTypeHandler
Returns a List with read IAtomType's.
getAtomTypes() - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeHandler
Returns a List with read IAtomType's.
getAtomTypes() - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
Gets the atomTypes attribute of the ForceFieldConfigurator object
getAtomTypes() - Method in class org.openscience.cdk.modeling.builder3d.MM2BasedParameterSetReader
 
getAtomTypes() - Method in class org.openscience.cdk.modeling.builder3d.MMFF94BasedParameterSetReader
 
getAtomVector(int) - Method in class org.openscience.cdk.Vibration
Gets a atom vector at index given.
getAtomVectorCount() - Method in class org.openscience.cdk.Vibration
Gets the number of atom vectors in the vibration.
getAtomVectors() - Method in class org.openscience.cdk.Vibration
Returns an Enumeration of the atom vectors of this vibration.
getAtomWeights(AtomContainer) - Static method in class org.openscience.cdk.graph.invariant.HuLuIndexTool
 
getAttachPointNum() - Method in interface org.openscience.cdk.interfaces.IPseudoAtom
Access the attachment point number.
getAttachPointNum() - Method in class org.openscience.cdk.PseudoAtom
Access the attachment point number.
getAttachPointNum() - Method in class org.openscience.cdk.silent.PseudoAtom
Access the attachment point number.
getAttributeKeys() - Method in class org.openscience.cdk.sgroup.Sgroup
Access all the attribute keys of this Sgroup.
getAutomorphismGroup(IAtomContainer) - Method in interface org.openscience.cdk.group.AtomContainerDiscretePartitionRefiner
Gets the automorphism group of the atom container.
getAutomorphismGroup(IAtomContainer, PermutationGroup) - Method in interface org.openscience.cdk.group.AtomContainerDiscretePartitionRefiner
Speed up the search for the automorphism group using the automorphisms in the supplied group.
getAutomorphismGroup(IAtomContainer, Partition) - Method in interface org.openscience.cdk.group.AtomContainerDiscretePartitionRefiner
Get the automorphism group of the molecule given an initial partition.
getAutomorphismGroup() - Method in interface org.openscience.cdk.group.DiscretePartitionRefiner
Get the automorphism group used to prune the search.
getAutomorphismPartition(IAtomContainer) - Method in interface org.openscience.cdk.group.AtomContainerDiscretePartitionRefiner
Get the automorphism partition (equivalence classes) of the atoms.
getAutomorphismPartition() - Method in interface org.openscience.cdk.group.DiscretePartitionRefiner
The automorphism partition is a partition of the elements of the group.
getAuxInfo() - Method in class org.openscience.cdk.inchi.InChIGenerator
Gets auxillary information.
getAvailableDictionaryClasses() - Method in class org.openscience.cdk.qsar.DescriptorEngine
Get the all the unique dictionary classes that the descriptors belong to.
getB() - Method in class org.openscience.cdk.Crystal
Gets the B unit cell axes in Cartesian coordinates as a three element double array.
getB() - Method in class org.openscience.cdk.debug.DebugCrystal
Gets the B unit cell axes in Cartesian coordinates as a three element double array.
getB() - Method in interface org.openscience.cdk.interfaces.ICrystal
Gets the B unit cell axes in carthesian coordinates as a three element double array.
getB() - Method in class org.openscience.cdk.silent.Crystal
Gets the B unit cell axes in Cartesian coordinates as a three element double array.
getBasicRings() - Method in class org.openscience.cdk.graph.SpanningTree
The basic rings of the spanning tree.
getBasis() - Method in class org.openscience.cdk.math.qm.Orbitals
Returns the basis set of this orbitals
getBegin() - Method in class org.openscience.cdk.Bond
Access the begin (or first) atom of the bond.
getBegin() - Method in class org.openscience.cdk.debug.DebugBond
Access the begin (or first) atom of the bond.
getBegin() - Method in interface org.openscience.cdk.interfaces.IBond
Access the begin (or first) atom of the bond.
getBegin() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
Access the begin (or first) atom of the bond.
getBegin() - Method in class org.openscience.cdk.silent.Bond
Access the begin (or first) atom of the bond.
getBeginColumn() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
Get token beginning column number.
getBeginColumn() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
Get token beginning column number.
getBeginLine() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
Get token beginning line number.
getBeginLine() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
Get token beginning line number.
getBest() - Method in interface org.openscience.cdk.group.DiscretePartitionRefiner
Get the best permutation found.
getBestAlignmentForLabel(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryTools
Determines the best alignment for the label of an atom in 2D space.
getBestAlignmentForLabel(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Determines the best alignment for the label of an atom in 2D space.
getBestAlignmentForLabelXY(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryTools
Determines the best alignment for the label of an atom in 2D space.
getBestAlignmentForLabelXY(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Determines the best alignment for the label of an atom in 2D space.
getBestCliqueSize() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.BKKCKCF
Deprecated.
 
getBibData() - Method in class org.openscience.cdk.tools.BremserOneSphereHOSECodePredictor
 
getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter
Calculates the circular fingerprint for the given IAtomContainer, and folds the result into a single bitset (see getSize()).
getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.EStateFingerprinter
Returns the bit fingerprint for the given IAtomContainer.
getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter
Generates a fingerprint of the default size for the given AtomContainer, using path and ring metrics.
getBitFingerprint(IAtomContainer, IRingSet, List<IRingSet>) - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter
Generates a fingerprint of the default size for the given AtomContainer, using path and ring metrics.
getBitFingerprint(IAtomContainer, AllRingsFinder) - Method in class org.openscience.cdk.fingerprint.Fingerprinter
Generates a fingerprint of the default size for the given AtomContainer.
getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.Fingerprinter
Generates a fingerprint of the default size for the given AtomContainer.
getBitFingerprint(IAtomContainer, int) - Method in class org.openscience.cdk.fingerprint.GraphOnlyFingerprinter
 
getBitFingerprint(IAtomContainer) - Method in interface org.openscience.cdk.fingerprint.IFingerprinter
Returns the bit fingerprint for the given IAtomContainer.
getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.LingoFingerprinter
 
getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.MACCSFingerprinter
Returns the bit fingerprint for the given IAtomContainer.
getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.PubchemFingerprinter
Calculate 881 bit Pubchem fingerprint for a molecule.
getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.ShortestPathFingerprinter
Generates a shortest path based BitSet fingerprint for the given AtomContainer.
getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.SignatureFingerprinter
 
getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.SubstructureFingerprinter
Returns the bit fingerprint for the given IAtomContainer.
getBitSet(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
Transforms an AtomContainer into a BitSet (which's size = number of bond in the atomContainer, all the bit are set to true).
getBitSet(IAtomContainer) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
Deprecated.
Transforms an AtomContainer into atom BitSet (which's size = number of bondA1 in the atomContainer, all the bit are set to true).
getBitSetFromFile(StringTokenizer) - Static method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D
 
getBond(int) - Method in class org.openscience.cdk.AtomContainer
Get the bond at position number in [0,..].
getBond(IAtom, IAtom) - Method in class org.openscience.cdk.AtomContainer
Returns the bond that connects the two given atoms.
getBond(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid
Get the bond at position number in [0,..].
getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns the bond that connects the two given atoms.
getBond(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer
Get the bond at position number in [0,..].
getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
Returns the bond that connects the two given atoms.
getBond(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Get the bond at position number in [0,..].
getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns the bond that connects the two given atoms.
getBond(int) - Method in class org.openscience.cdk.debug.DebugCrystal
Get the bond at position number in [0,..].
getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
Returns the bond that connects the two given atoms.
getBond(int) - Method in class org.openscience.cdk.debug.DebugMonomer
Get the bond at position number in [0,..].
getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
Returns the bond that connects the two given atoms.
getBond(int) - Method in class org.openscience.cdk.debug.DebugPolymer
Get the bond at position number in [0,..].
getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
Returns the bond that connects the two given atoms.
getBond(int) - Method in class org.openscience.cdk.debug.DebugRing
Get the bond at position number in [0,..].
getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugRing
Returns the bond that connects the two given atoms.
getBond(int) - Method in class org.openscience.cdk.debug.DebugStrand
Get the bond at position number in [0,..].
getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
Returns the bond that connects the two given atoms.
getBond(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Get the bond at position number in [0,..].
getBond(IAtom, IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Returns the bond that connectes the two given atoms.
getBond(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Get the bond at position number in [0,..].
getBond(IAtom, IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Returns the bond that connects the two given atoms.
getBond(int) - Method in class org.openscience.cdk.silent.AtomContainer
Get the bond at position number in [0,..].
getBond(IAtom, IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
Returns the bond that connects the two given atoms.
getBond(IAtom, IAtom) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.TargetProperties
Deprecated.
 
getBondAngleInteractionData(String, String, String, String) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94ParametersCall
Gets the bond-angle interaction parameter set.
getBondArray(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
Constructs an array of Bond objects from an AtomContainer.
getBondArray(List<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
Constructs an array of Atom objects from a List of Atom objects.
getBondCoordinates(IBond) - Static method in class org.openscience.cdk.geometry.GeometryTools
Writes the coordinates of the atoms participating the given bond into an array.
getBondCoordinates(IBond) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Writes the coordinates of the atoms participating the given bond into an array.
getBondCount() - Method in class org.openscience.cdk.AtomContainer
Returns the number of Bonds in this Container.
getBondCount() - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns the number of Bonds in this Container.
getBondCount() - Method in class org.openscience.cdk.debug.DebugAtomContainer
Returns the number of Bonds in this Container.
getBondCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns the number of Bonds in this Container.
getBondCount() - Method in class org.openscience.cdk.debug.DebugCrystal
Returns the number of Bonds in this Container.
getBondCount() - Method in class org.openscience.cdk.debug.DebugMonomer
Returns the number of Bonds in this Container.
getBondCount() - Method in class org.openscience.cdk.debug.DebugPolymer
Returns the number of Bonds in this Container.
getBondCount() - Method in class org.openscience.cdk.debug.DebugRing
Returns the number of Bonds in this Container.
getBondCount() - Method in class org.openscience.cdk.debug.DebugStrand
Returns the number of Bonds in this Container.
getBondCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Returns the number of Bonds in this Container.
getBondCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Returns the number of Bonds in this Container.
getBondCount() - Method in class org.openscience.cdk.silent.AtomContainer
Returns the number of Bonds in this Container.
getBondCount(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
 
getBondCount(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator
Get the total number of bonds inside an IChemFile.
getBondCount(IChemModel) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
Get the total number of bonds inside an IChemModel.
getBondCount(IChemSequence) - Static method in class org.openscience.cdk.tools.manipulator.ChemSequenceManipulator
Get the total number of bonds inside an IChemSequence.
getBondCount(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
 
getBondCount(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
 
getBondCount(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
 
getBondCount(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator
Return the total number of bonds over all the rings in the colllection.
getBondData(String, String, String) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94ParametersCall
Gets the bond parameter set.
getBondInSensitiveTimeOut() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
Deprecated.
get timeout in mins for bond insensitive searches
getBondInSensitiveTimeOut() - Method in class org.openscience.cdk.smsd.Isomorphism
Deprecated.
get timeout in mins for bond insensitive searches
getBondLength() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
Returns the bond length used for laying out the molecule.
getBondLength() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAngleBond
Get the angle between the three pharmacophore groups that make up the constraint.
getBondLength() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreBond
Get the distance between the two pharmacophore groups that make up the constraint.
getBondLengthAverage(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
An average of all 2D bond length values is produced.
getBondLengthAverage(IReaction) - Static method in class org.openscience.cdk.geometry.GeometryTools
 
getBondLengthAverage(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
An average of all 2D bond length values is produced.
getBondLengthAverage(IReaction) - Static method in class org.openscience.cdk.geometry.GeometryUtil
 
getBondLengthAverage3D(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
An average of all 3D bond length values is produced, using point3ds in atoms.
getBondLengthAverage3D(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
An average of all 3D bond length values is produced, using point3ds in atoms.
getBondLengthMedian(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
Calculate the median bond length of an atom container.
getBondLengthMedian(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Calculate the median bond length of an atom container.
getBondLengthRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>, boolean) - Static method in class org.openscience.cdk.geometry.GeometryTools
Return the RMSD of bonds length between the 2 aligned molecules.
getBondLengthRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>, boolean) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Return the RMSD of bonds length between the 2 aligned molecules.
getBondLengthValue(String, String) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
Gets the distanceValue attribute of the parameter set.
getBondMatcher() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.EdgeBuilder
Deprecated.
Returns bond matcher.
getBondMatcher() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IEdge
Deprecated.
Returns bond matcher.
getBondNumA() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.QueryProcessor
Deprecated.
 
getBondNumB() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.TargetProcessor
Deprecated.
 
getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.AtomContainer
Returns the position of the bond between two given atoms in the electronContainers array.
getBondNumber(IBond) - Method in class org.openscience.cdk.AtomContainer
Returns the position of a given bond in the electronContainers array.
getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns the position of the bond between two given atoms in the electronContainers array.
getBondNumber(IBond) - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns the position of a given bond in the electronContainers array.
getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns the position of the bond between two given atoms in the electronContainers array.
getBondNumber(IBond) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns the position of a given bond in the electronContainers array.
getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
Returns the position of the bond between two given atoms in the electronContainers array.
getBondNumber(IBond) - Method in class org.openscience.cdk.debug.DebugCrystal
Returns the position of a given bond in the electronContainers array.
getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
Returns the position of the bond between two given atoms in the electronContainers array.
getBondNumber(IBond) - Method in class org.openscience.cdk.debug.DebugMonomer
Returns the position of a given bond in the electronContainers array.
getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
Returns the position of the bond between two given atoms in the electronContainers array.
getBondNumber(IBond) - Method in class org.openscience.cdk.debug.DebugPolymer
Returns the position of a given bond in the electronContainers array.
getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugRing
Returns the position of the bond between two given atoms in the electronContainers array.
getBondNumber(IBond) - Method in class org.openscience.cdk.debug.DebugRing
Returns the position of a given bond in the electronContainers array.
getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
Returns the position of the bond between two given atoms in the electronContainers array.
getBondNumber(IBond) - Method in class org.openscience.cdk.debug.DebugStrand
Returns the position of a given bond in the electronContainers array.
getBondNumber(IAtom, IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
getBondNumber(IBond) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Returns the position of the bond between two given atoms in the electronContainers array.
getBondNumber(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Returns the position of a given bond in the electronContainers array.
getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
Returns the position of the bond between two given atoms in the electronContainers array.
getBondNumber(IBond) - Method in class org.openscience.cdk.silent.AtomContainer
Returns the position of a given bond in the electronContainers array.
getBondOrder() - Method in class org.openscience.cdk.smsd.helper.BondEnergy
Deprecated.
Returns the bond order for this bond type energy.
getBondOrderSum(IAtom) - Method in class org.openscience.cdk.AtomContainer
Deprecated.
Replaced by AtomContainerManipulator#getBondOrderSum(IAtomContainer, IAtom)
getBondOrderSum() - Method in class org.openscience.cdk.AtomType
Gets the bondOrderSum attribute of the AtomType object.
getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns the sum of the bond orders for a given Atom.
getBondOrderSum() - Method in class org.openscience.cdk.debug.DebugAtom
Gets the bondOrderSum attribute of the AtomType object.
getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
Returns the sum of the bond orders for a given Atom.
getBondOrderSum() - Method in class org.openscience.cdk.debug.DebugAtomType
Gets the bondOrderSum attribute of the AtomType object.
getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns the sum of the bond orders for a given Atom.
getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
Returns the sum of the bond orders for a given Atom.
getBondOrderSum() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
Gets the bondOrderSum attribute of the AtomType object.
getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
Returns the sum of the bond orders for a given Atom.
getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
Returns the sum of the bond orders for a given Atom.
getBondOrderSum() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
Gets the bondOrderSum attribute of the AtomType object.
getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
Returns the sum of the bond orders for a given Atom.
getBondOrderSum() - Method in class org.openscience.cdk.debug.DebugRing
Returns the sum of all bond orders in the ring.
getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
Returns the sum of the bond orders for a given Atom.
getBondOrderSum(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Returns the sum of the bond orders for a given Atom.
getBondOrderSum() - Method in interface org.openscience.cdk.interfaces.IAtomType
Gets the bondOrderSum attribute of the AtomType object.
getBondOrderSum() - Method in interface org.openscience.cdk.interfaces.IRing
Returns the sum of all bond orders in the ring.
getBondOrderSum() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
Gets the bondOrderSum attribute of the AtomType object.
getBondOrderSum(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Deprecated.
Replaced by AtomContainerManipulator#getBondOrderSum(IAtomContainer, IAtom)
getBondOrderSum() - Method in class org.openscience.cdk.Ring
Returns the sum of all bond orders in the ring.
getBondOrderSum(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
Deprecated.
Replaced by AtomContainerManipulator#getBondOrderSum(IAtomContainer, IAtom)
getBondOrderSum() - Method in class org.openscience.cdk.silent.AtomType
Gets the bondOrderSum attribute of the AtomType object.
getBondOrderSum() - Method in class org.openscience.cdk.silent.Ring
Returns the sum of all bond orders in the ring.
getBondOrderSum(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
Returns the sum of the bond order equivalents for a given IAtom.
getBondOverlapScore(IAtomContainer, Vector) - Method in class org.openscience.cdk.layout.OverlapResolver
Deprecated.
Calculates a score based on the intersection of bonds.
getBonds() - Method in interface org.openscience.cdk.interfaces.IDoubleBondStereochemistry
Returns an array of ligand bonds around the double bond.
getBonds() - Method in class org.openscience.cdk.sgroup.Sgroup
Access the bonds that belong to this substructure group.
getBonds() - Method in class org.openscience.cdk.stereo.DoubleBondStereochemistry
Returns an array of ligand bonds around the double bond.
getBondsAcyclicCount() - Method in class org.openscience.cdk.graph.SpanningTree
Number of acyclic bonds.
getBondsCyclicCount() - Method in class org.openscience.cdk.graph.SpanningTree
Number of cyclic bonds.
getBondSensitiveTimeOut() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
Deprecated.
get timeout in mins for bond sensitive searches
getBondSensitiveTimeOut() - Method in class org.openscience.cdk.smsd.Isomorphism
Deprecated.
get timeout in mins for bond sensitive searches
getBondSymbol(IBond) - Method in class org.openscience.cdk.fingerprint.Fingerprinter
Gets the bondSymbol attribute of the Fingerprinter class
getBondSymbol(IBond) - Method in class org.openscience.cdk.fingerprint.GraphOnlyFingerprinter
Gets the bondSymbol attribute of the Fingerprinter class.
getBondSymbol(IBond) - Method in class org.openscience.cdk.fingerprint.HybridizationFingerprinter
Gets the bond Symbol attribute of the Fingerprinter class.
getBounds(IRenderingElement) - Method in class org.openscience.cdk.renderer.AbstractRenderer
Given a rendering element, traverse the elements compute required bounds to full display all elements.
getBuilder() - Method in class org.openscience.cdk.ChemObject
 
getBuilder() - Method in class org.openscience.cdk.debug.DebugAdductFormula
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugAtom
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugAtomContainer
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugAtomType
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugBond
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugChemFile
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugChemModel
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugChemObject
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugChemSequence
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugCrystal
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugElectronContainer
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugElement
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugIsotope
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugLonePair
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugMapping
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugMolecularFormula
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugMonomer
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugPolymer
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugReaction
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugReactionScheme
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugReactionSet
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugRing
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugSingleElectron
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugStrand
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.debug.DebugSubstance
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.formula.AdductFormula
 
getBuilder() - Method in class org.openscience.cdk.formula.MolecularFormula
 
getBuilder() - Method in class org.openscience.cdk.formula.MolecularFormulaSet
 
getBuilder() - Method in interface org.openscience.cdk.interfaces.ICDKObject
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
 
getBuilder() - Method in class org.openscience.cdk.silent.AdductFormula
 
getBuilder() - Method in class org.openscience.cdk.silent.ChemObject
 
getBuilder() - Method in class org.openscience.cdk.silent.MolecularFormula
 
getBuilder() - Method in class org.openscience.cdk.silent.MolecularFormulaSet
 
getBuilder() - Method in class org.openscience.cdk.stereo.DoubleBondStereochemistry
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.stereo.ExtendedTetrahedral
Returns a IChemObjectBuilder for the data classes that extend this class.
getBuilder() - Method in class org.openscience.cdk.stereo.TetrahedralChirality
Returns a IChemObjectBuilder for the data classes that extend this class.
getC() - Method in class org.openscience.cdk.Crystal
Gets the C unit cell axes in Cartesian coordinates as a three element double array.
getC() - Method in class org.openscience.cdk.debug.DebugCrystal
Gets the C unit cell axes in Cartesian coordinates as a three element double array.
getC() - Method in interface org.openscience.cdk.interfaces.ICrystal
Gets the C unit cell axes in carthesian coordinates as a three element double array.
getC() - Method in class org.openscience.cdk.silent.Crystal
Gets the C unit cell axes in Cartesian coordinates as a three element double array.
getCachedDescriptorValue(IAtom) - Method in class org.openscience.cdk.qsar.AbstractAtomicDescriptor
Returns the cached DescriptorValue for the given IAtom.
getCachedDescriptorValue(IBond) - Method in class org.openscience.cdk.qsar.AbstractBondDescriptor
Returns the cached DescriptorValue for the given IBond.
getCanonicalMolecule(IAtomContainer) - Method in class org.openscience.cdk.smsd.labelling.CanonicalLabellingAdaptor
Deprecated.
getCanonicalMolecule(IAtomContainer) - Method in interface org.openscience.cdk.smsd.labelling.ICanonicalMoleculeLabeller
Deprecated.
 
getCanonicalMolecule(IAtomContainer) - Method in class org.openscience.cdk.smsd.labelling.MoleculeSignatureLabellingAdaptor
Deprecated.
getCanonicalPermutation(IAtomContainer) - Method in class org.openscience.cdk.smsd.labelling.CanonicalLabellingAdaptor
Deprecated.
getCanonicalPermutation(IAtomContainer) - Method in interface org.openscience.cdk.smsd.labelling.ICanonicalMoleculeLabeller
Deprecated.
 
getCanonicalPermutation(IAtomContainer) - Method in class org.openscience.cdk.smsd.labelling.MoleculeSignatureLabellingAdaptor
Deprecated.
getCanonicalReaction(IReaction) - Method in interface org.openscience.cdk.smsd.labelling.ICanonicalReactionLabeller
Deprecated.
Convert a reaction into a canonical form by canonizing each of the structures in the reaction in turn.
getCanonicalReaction(IReaction) - Method in class org.openscience.cdk.smsd.labelling.SignatureReactionCanoniser
Deprecated.
Convert a reaction into a canonical form by canonizing each of the structures in the reaction in turn.
getCanonicalReaction(IReaction) - Method in class org.openscience.cdk.smsd.labelling.SmilesReactionCanoniser
Deprecated.
Convert a reaction into a canonical form by canonizing each of the structures in the reaction in turn.
getCASId(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
Get the CAS ID for an element.
getcBondNeighborsA() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper
Deprecated.
 
getcBondNeighborsB() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper
Deprecated.
 
getCBondSetA() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper
Deprecated.
 
getCBondSetB() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper
Deprecated.
 
getCDKErrorCount() - Method in class org.openscience.cdk.validate.ValidationReport
Returns the number of CDK errors.
getCDKErrors() - Method in class org.openscience.cdk.validate.ValidationReport
Returns an array of ValidationTest indicating CDK problems.
getCEdgesSize() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
Deprecated.
 
getCEgdes() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
Deprecated.
 
getCell(int) - Method in class org.openscience.cdk.group.Partition
Gets the cell at this index.
getCenterOfMass() - Method in class org.openscience.cdk.geometry.alignment.KabschAlignment
Returns the center of mass for the first molecule or fragment used in the calculation.
getCentralAtom() - Method in interface org.openscience.cdk.geometry.cip.ILigand
The central IAtom to which this ligand is connected via one IBond.
getCentralAtom() - Method in class org.openscience.cdk.geometry.cip.Ligand
The central IAtom to which this ligand is connected via one IBond.
getChainID() - Method in class org.openscience.cdk.debug.DebugPDBAtom
get the Chain identifier of this atom.
getChainID() - Method in class org.openscience.cdk.debug.DebugPDBMonomer
Gets the Chain ID of this monomer.
getChainID() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
get the Chain identifier of this atom.
getChainID() - Method in interface org.openscience.cdk.interfaces.IPDBMonomer
Gets the Chain ID of this monomer.
getChainID() - Method in class org.openscience.cdk.protein.data.PDBAtom
get the Chain identifier of this atom.
getChainID() - Method in class org.openscience.cdk.protein.data.PDBMonomer
 
getChainID() - Method in class org.openscience.cdk.silent.PDBAtom
get the Chain identifier of this atom.
getChainID() - Method in class org.openscience.cdk.silent.PDBMonomer
 
getCharge() - Method in class org.openscience.cdk.Atom
Returns the partial charge of this atom.
getCharge() - Method in class org.openscience.cdk.debug.DebugAdductFormula
Returns the partial charge of this Adduct.
getCharge() - Method in class org.openscience.cdk.debug.DebugAtom
Returns the partial charge of this atom.
getCharge() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
Returns the partial charge of this atom.
getCharge() - Method in class org.openscience.cdk.debug.DebugMolecularFormula
Access the charge of this IMolecularFormula.
getCharge() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
Returns the partial charge of this atom.
getCharge() - Method in class org.openscience.cdk.formula.AdductFormula
Returns the partial charge of this Adduct.
getCharge() - Method in class org.openscience.cdk.formula.IsotopePattern
Get the charge in this pattern.
getCharge() - Method in class org.openscience.cdk.formula.MolecularFormula
Access the charge of this IMolecularFormula.
getCharge() - Method in interface org.openscience.cdk.interfaces.IAdductFormula
Returns the partial charge of this Adduct.
getCharge() - Method in interface org.openscience.cdk.interfaces.IAtom
Returns the partial charge of this atom.
getCharge() - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
Access the charge of this IMolecularFormula.
getCharge() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
Returns the partial charge of this atom.
getCharge() - Method in class org.openscience.cdk.silent.AdductFormula
Returns the partial charge of this Adduct.
getCharge() - Method in class org.openscience.cdk.silent.Atom
Returns the partial charge of this atom.
getCharge() - Method in class org.openscience.cdk.silent.MolecularFormula
Access the charge of this IMolecularFormula.
getChargeGroups() - Method in class org.openscience.cdk.libio.md.MDMolecule
 
getChemFile() - Method in class org.openscience.cdk.io.inchi.INChIHandler
 
getChemicalSeries(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
Get the chemical series for an element.
getChemModel(int) - Method in class org.openscience.cdk.ChemSequence
Returns the ChemModel at position number in the container.
getChemModel(int) - Method in class org.openscience.cdk.debug.DebugChemSequence
Returns the ChemModel at position number in the container.
getChemModel(int) - Method in interface org.openscience.cdk.interfaces.IChemSequence
Returns the ChemModel at position number in the container.
getChemModel(int) - Method in class org.openscience.cdk.silent.ChemSequence
Returns the ChemModel at position number in the container.
getChemModelCount() - Method in class org.openscience.cdk.ChemSequence
Returns the number of ChemModels in this Container.
getChemModelCount() - Method in class org.openscience.cdk.debug.DebugChemSequence
Returns the number of ChemModels in this Container.
getChemModelCount() - Method in interface org.openscience.cdk.interfaces.IChemSequence
Returns the number of ChemModels in this Container.
getChemModelCount() - Method in class org.openscience.cdk.silent.ChemSequence
Returns the number of ChemModels in this Container.
getChemObject(int) - Method in class org.openscience.cdk.debug.DebugMapping
Retrieves the first or second of the related IChemObjects.
getChemObject(int) - Method in interface org.openscience.cdk.interfaces.IMapping
Retrieve the first or second of the related IChemObjects.
getChemObject(int) - Method in class org.openscience.cdk.Mapping
Retrieves the first or second of the related IChemObjects.
getChemObject(int) - Method in class org.openscience.cdk.silent.Mapping
Retrieves the first or second of the related IChemObjects.
getChemObject() - Method in class org.openscience.cdk.validate.ValidationTest
 
getChemObjectReader() - Method in class org.openscience.cdk.io.random.RandomAccessReader
 
getChemSequence(int) - Method in class org.openscience.cdk.ChemFile
Returns the ChemSequence at position number in the container.
getChemSequence(int) - Method in class org.openscience.cdk.debug.DebugChemFile
Returns the ChemSequence at position number in the container.
getChemSequence(int) - Method in interface org.openscience.cdk.interfaces.IChemFile
Returns the ChemSequence at position number in the container.
getChemSequence(int) - Method in class org.openscience.cdk.silent.ChemFile
Returns the ChemSequence at position number in the container.
getChemSequenceCount() - Method in class org.openscience.cdk.ChemFile
Returns the number of ChemSequences in this Container.
getChemSequenceCount() - Method in class org.openscience.cdk.debug.DebugChemFile
Returns the number of ChemSequences in this Container.
getChemSequenceCount() - Method in interface org.openscience.cdk.interfaces.IChemFile
Returns the number of ChemSequences in this Container.
getChemSequenceCount() - Method in class org.openscience.cdk.silent.ChemFile
Returns the number of ChemSequences in this Container.
getChiCatHydrogen() - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
Gets chi_cat value for hydrogen, because H poses a special problem due to lack of possible second ionisation.
getChildren() - Method in class org.openscience.cdk.tools.diff.tree.AbstractDifferenceList
Returns an Iterable of IDifference for all childs of this IDifference.
getChildren() - Method in interface org.openscience.cdk.tools.diff.tree.IDifferenceList
Returns an Iterable of IDifference for all childs of this IDifference.
getChiralAtom() - Method in interface org.openscience.cdk.interfaces.ITetrahedralChirality
Atom that is the chirality center.
getChiralAtom() - Method in class org.openscience.cdk.stereo.TetrahedralChirality
Atom that is the chirality center.
getCID(XMLStreamReader) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
getCIPChirality(LigancyFourChirality) - Static method in class org.openscience.cdk.geometry.cip.CIPTool
Returns the R or S chirality according to the CIP rules, based on the given chirality information.
getCIPChirality(IAtomContainer, ITetrahedralChirality) - Static method in class org.openscience.cdk.geometry.cip.CIPTool
Returns the R or S chirality according to the CIP rules, based on the given chirality information.
getCIPChirality(IAtomContainer, IDoubleBondStereochemistry) - Static method in class org.openscience.cdk.geometry.cip.CIPTool
 
getClasses() - Method in class org.openscience.cdk.renderer.elements.MarkedElement
Access the classes of the element.
getClassName() - Method in class org.openscience.cdk.dict.Entry
 
getClassType() - Method in class org.openscience.cdk.fingerprint.model.Bayesian
Access to the fingerprint type.
getClipboardContent() - Method in class org.openscience.cdk.renderer.RendererModel
Returns the atoms and bonds on the Renderer2D clipboard.
getClosestAtom(int, int, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
Returns the atom of the given molecule that is closest to the given coordinates.
getClosestAtom(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryTools
Returns the atom of the given molecule that is closest to the given atom (excluding itself).
getClosestAtom(double, double, IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryTools
Returns the atom of the given molecule that is closest to the given coordinates and is not the atom.
getClosestAtom(double, double, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
Returns the atom of the given molecule that is closest to the given coordinates.
getClosestAtom(int, int, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Returns the atom of the given molecule that is closest to the given coordinates.
getClosestAtom(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Returns the atom of the given molecule that is closest to the given atom (excluding itself).
getClosestAtom(double, double, IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Returns the atom of the given molecule that is closest to the given coordinates and is not the atom.
getClosestAtom(double, double, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Returns the atom of the given molecule that is closest to the given coordinates.
getClosestBond(int, int, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
Returns the bond of the given molecule that is closest to the given coordinates.
getClosestBond(double, double, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
Returns the bond of the given molecule that is closest to the given coordinates.
getClosestBond(int, int, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Returns the bond of the given molecule that is closest to the given coordinates.
getClosestBond(double, double, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Returns the bond of the given molecule that is closest to the given coordinates.
getCoefficients() - Method in class org.openscience.cdk.math.qm.Orbitals
Get the coefficient matrix
getColorForBond(IBond, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
Determine the color of a bond, returning either the default color, the override color or whatever is in the color hash for that bond.
getColumn(int) - Method in class org.openscience.cdk.graph.invariant.GIMatrix
Returns the column-matrix at the given line index.
getColumn() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
Deprecated.
getColumn() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
Deprecated.
getColumns() - Method in class org.openscience.cdk.math.IMatrix
Returns the count of columns
getColumns() - Method in class org.openscience.cdk.math.Matrix
Returns the number of columns.
getCompGraphNodes() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
Deprecated.
 
getCompGraphNodesCZero() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
Deprecated.
 
getConfidenceLimit(String) - Method in class org.openscience.cdk.tools.BremserOneSphereHOSECodePredictor
 
getConnected(int) - Method in class org.openscience.cdk.signature.AtomSignature
 
getConnectedAtom(IAtom) - Method in class org.openscience.cdk.Bond
Returns the other atom in the bond, the atom is connected to the given atom.
getConnectedAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.IBond
Deprecated.
use the method IBond.getOther(IAtom)
getConnectedAtom(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
Returns the other atom in the bond, the atom is connected to the given atom.
getConnectedAtom(IAtom) - Method in class org.openscience.cdk.silent.Bond
Returns the other atom in the bond, the atom is connected to the given atom.
getConnectedAtomContainer() - Method in interface org.openscience.cdk.renderer.selection.IChemObjectSelection
Make an IAtomContainer where all the bonds only have atoms that are in the selection.
getConnectedAtoms(IAtom) - Method in class org.openscience.cdk.Bond
Returns all the atoms in the bond connected to the given atom.
getConnectedAtoms(IAtom) - Method in interface org.openscience.cdk.interfaces.IBond
Returns all the atoms in the bond connected to the given atom.
getConnectedAtoms(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
Returns all the atoms in the bond connected to the given atom.
getConnectedAtoms(IAtom) - Method in class org.openscience.cdk.silent.Bond
Returns all the atoms in the bond connected to the given atom.
getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.AtomContainer
Returns the number of atoms connected to the given atom.
getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns the number of atoms connected to the given atom.
getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
Returns the number of atoms connected to the given atom.
getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns the number of atoms connected to the given atom.
getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
Returns the number of atoms connected to the given atom.
getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
Returns the number of atoms connected to the given atom.
getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
Returns the number of atoms connected to the given atom.
getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
Returns the number of atoms connected to the given atom.
getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
Returns the number of atoms connected to the given atom.
getConnectedAtomsCount(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Returns the number of atoms connected to the given atom.
getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Returns the number of atoms connected to the given atom.
getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
Returns the number of atoms connected to the given atom.
getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.AtomContainer
Returns an ArrayList of all atoms connected to the given atom.
getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns an ArrayList of all atoms connected to the given atom.
getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
Returns an ArrayList of all atoms connected to the given atom.
getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns an ArrayList of all atoms connected to the given atom.
getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
Returns an ArrayList of all atoms connected to the given atom.
getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
Returns an ArrayList of all atoms connected to the given atom.
getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
Returns an ArrayList of all atoms connected to the given atom.
getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
Returns an ArrayList of all atoms connected to the given atom.
getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
Returns an ArrayList of all atoms connected to the given atom.
getConnectedAtomsList(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Returns an ArrayList of all atoms connected to the given atom.
getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Returns an ArrayList of all atoms connected to the given atom.
getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
Returns an ArrayList of all atoms connected to the given atom.
getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.AtomContainer
Returns the number of Bonds for a given Atom.
getConnectedBondsCount(int) - Method in class org.openscience.cdk.AtomContainer
Returns the number of connected atoms (degree) to the given atom.
getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns the number of Bonds for a given Atom.
getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
Returns the number of Bonds for a given Atom.
getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns the number of Bonds for a given Atom.
getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
Returns the number of Bonds for a given Atom.
getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
Returns the number of Bonds for a given Atom.
getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
Returns the number of Bonds for a given Atom.
getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
Returns the number of Bonds for a given Atom.
getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
Returns the number of Bonds for a given Atom.
getConnectedBondsCount(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Returns the number of Bonds for a given Atom.
getConnectedBondsCount(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Returns the number of connected atoms (degree) to the given atom.
getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Returns the number of Bonds for a given Atom.
getConnectedBondsCount(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Returns the number of connected atoms (degree) to the given atom.
getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
Returns the number of Bonds for a given Atom.
getConnectedBondsCount(int) - Method in class org.openscience.cdk.silent.AtomContainer
Returns the number of connected atoms (degree) to the given atom.
getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.AtomContainer
Returns an ArrayList of all Bonds connected to the given atom.
getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns an ArrayList of all Bonds connected to the given atom.
getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
Returns an ArrayList of all Bonds connected to the given atom.
getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns an ArrayList of all Bonds connected to the given atom.
getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
Returns an ArrayList of all Bonds connected to the given atom.
getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
Returns an ArrayList of all Bonds connected to the given atom.
getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
Returns an ArrayList of all Bonds connected to the given atom.
getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
Returns an ArrayList of all Bonds connected to the given atom.
getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
Returns an ArrayList of all Bonds connected to the given atom.
getConnectedBondsList(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Returns an ArrayList of all Bonds connected to the given atom.
getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Returns an ArrayList of all Bonds connected to the given atom.
getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
Returns an ArrayList of all Bonds connected to the given atom.
getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.AtomContainer
Returns an ArrayList of all electronContainers connected to the given atom.
getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns an ArrayList of all electronContainers connected to the given atom.
getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
Returns an ArrayList of all electronContainers connected to the given atom.
getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns an ArrayList of all electronContainers connected to the given atom.
getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
Returns an ArrayList of all electronContainers connected to the given atom.
getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
Returns an ArrayList of all electronContainers connected to the given atom.
getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
Returns an ArrayList of all electronContainers connected to the given atom.
getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
Returns an ArrayList of all electronContainers connected to the given atom.
getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
Returns an ArrayList of all electronContainers connected to the given atom.
getConnectedElectronContainersList(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Returns an ArrayList of all electronContainers connected to the given atom.
getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Returns an ArrayList of all electronContainers connected to the given atom.
getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
Returns an ArrayList of all electronContainers connected to the given atom.
getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.AtomContainer
Returns the number of LonePairs for a given Atom.
getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns the number of LonePairs for a given Atom.
getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
Returns the number of LonePairs for a given Atom.
getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns the number of LonePairs for a given Atom.
getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
Returns the number of LonePairs for a given Atom.
getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
Returns the number of LonePairs for a given Atom.
getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
Returns the number of LonePairs for a given Atom.
getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
Returns the number of LonePairs for a given Atom.
getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
Returns the number of LonePairs for a given Atom.
getConnectedLonePairsCount(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Returns the number of LonePairs for a given Atom.
getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Returns the number of LonePairs for a given Atom.
getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
Returns the number of LonePairs for a given Atom.
getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.AtomContainer
Returns the array of lone pairs connected to an atom.
getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns the array of lone pairs connected to an atom.
getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
Returns the array of lone pairs connected to an atom.
getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns the array of lone pairs connected to an atom.
getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
Returns the array of lone pairs connected to an atom.
getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
Returns the array of lone pairs connected to an atom.
getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
Returns the array of lone pairs connected to an atom.
getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
Returns the array of lone pairs connected to an atom.
getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
Returns the array of lone pairs connected to an atom.
getConnectedLonePairsList(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Returns the array of lone pairs connected to an atom.
getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Returns the array of lone pairs connected to an atom.
getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
Returns the array of lone pairs connected to an atom.
getConnectedRings(IRing) - Method in class org.openscience.cdk.debug.DebugRingSet
Returns all the rings in the RingSet that share one or more atoms with a given ring.
getConnectedRings(IRing) - Method in interface org.openscience.cdk.interfaces.IRingSet
Returns all the rings in the RingSet that share one or more atoms with a given ring.
getConnectedRings(IRing) - Method in class org.openscience.cdk.RingSet
Returns all the rings in the RingSet that share one or more atoms with a given ring.
getConnectedRings(IRing) - Method in class org.openscience.cdk.silent.RingSet
Returns all the rings in the RingSet that share one or more atoms with a given ring.
getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.AtomContainer
Returns the sum of the SingleElectron for a given Atom.
getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns the sum of the SingleElectron for a given Atom.
getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
Returns the sum of the SingleElectron for a given Atom.
getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns the sum of the SingleElectron for a given Atom.
getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
Returns the sum of the SingleElectron for a given Atom.
getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
Returns the sum of the SingleElectron for a given Atom.
getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
Returns the sum of the SingleElectron for a given Atom.
getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
Returns the sum of the SingleElectron for a given Atom.
getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
Returns the sum of the SingleElectron for a given Atom.
getConnectedSingleElectronsCount(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Returns the sum of the SingleElectron for a given Atom.
getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Returns the sum of the SingleElectron for a given Atom.
getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
Returns the sum of the SingleElectron for a given Atom.
getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.AtomContainer
Returns an array of all SingleElectron connected to the given atom.
getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns an array of all SingleElectron connected to the given atom.
getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
Returns an array of all SingleElectron connected to the given atom.
getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns an array of all SingleElectron connected to the given atom.
getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
Returns an array of all SingleElectron connected to the given atom.
getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
Returns an array of all SingleElectron connected to the given atom.
getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
Returns an array of all SingleElectron connected to the given atom.
getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
Returns an array of all SingleElectron connected to the given atom.
getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
Returns an array of all SingleElectron connected to the given atom.
getConnectedSingleElectronsList(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Returns an array of all SingleElectron connected to the given atom.
getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Returns an array of all SingleElectron connected to the given atom.
getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
Returns an array of all SingleElectron connected to the given atom.
getConnectivity(int, int) - Method in interface org.openscience.cdk.group.Refinable
Get the connectivity between two vertices as an integer, to allow for multigraphs : so a single edge is 1, a double edge 2, etc.
getContainer(IAtomContainer, IAtom) - Method in class org.openscience.cdk.tools.StructureResonanceGenerator
Get the container which the atom is found on resonance from a IAtomContainer.
getContainer(IAtomContainer, IBond) - Method in class org.openscience.cdk.tools.StructureResonanceGenerator
Get the container which the bond is found on resonance from a IAtomContainer.
getContainers(IAtomContainer) - Method in class org.openscience.cdk.tools.StructureResonanceGenerator
Get the container which is found resonance from a IAtomContainer.
getCoordinatesFromGridPoint(Point3d) - Method in class org.openscience.cdk.tools.GridGenerator
Method calculates coordinates from a given grid point.
getCoordinatesFromGridPoint(int) - Method in class org.openscience.cdk.tools.GridGenerator
Method calculates coordinates from a given grid array position.
getCount(int) - Method in interface org.openscience.cdk.fingerprint.ICountFingerprint
Returns the count value for the bin with the given index.
getCount(int) - Method in class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
 
getCount() - Method in class org.openscience.cdk.validate.ValidationReport
Returns the number of CDK errors.
getCountBasis() - Method in class org.openscience.cdk.math.qm.Orbitals
Set the count of bases
getCountElectrons() - Method in class org.openscience.cdk.math.qm.Orbitals
Gets the count of electrons, which occupies the orbitals
getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter
Calculates the circular fingerprint for the given IAtomContainer, and returns a datastructure that enumerates all of the fingerprints, and their counts (i.e.
getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.EStateFingerprinter
Returns the count fingerprint for the given IAtomContainer.
getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter
Returns the count fingerprint for the given IAtomContainer.
getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.Fingerprinter
 
getCountFingerprint(IAtomContainer) - Method in interface org.openscience.cdk.fingerprint.IFingerprinter
Returns the count fingerprint for the given IAtomContainer.
getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.LingoFingerprinter
 
getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.MACCSFingerprinter
Returns the count fingerprint for the given IAtomContainer.
getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.PubchemFingerprinter
Returns the count fingerprint for the given IAtomContainer.
getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.ShortestPathFingerprinter
 
getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.SignatureFingerprinter
 
getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.SubstructureFingerprinter
Returns the count fingerprint for the given IAtomContainer.
getCountForHash(int) - Method in interface org.openscience.cdk.fingerprint.ICountFingerprint
Get the number of times a certain hash exists in the fingerprint.
getCountForHash(int) - Method in class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
 
getCountOrbitals() - Method in class org.openscience.cdk.math.qm.Orbitals
Returns the count of orbitals
getCovalentRadius() - Method in class org.openscience.cdk.AtomType
Returns the covalent radius for this AtomType.
getCovalentRadius() - Method in class org.openscience.cdk.debug.DebugAtom
Returns the covalent radius for this AtomType.
getCovalentRadius() - Method in class org.openscience.cdk.debug.DebugAtomType
Returns the covalent radius for this AtomType.
getCovalentRadius() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
Returns the covalent radius for this AtomType.
getCovalentRadius() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
Returns the covalent radius for this AtomType.
getCovalentRadius() - Method in interface org.openscience.cdk.interfaces.IAtomType
Returns the covalent radius for this AtomType.
getCovalentRadius() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
Returns the covalent radius for this AtomType.
getCovalentRadius() - Method in class org.openscience.cdk.silent.AtomType
Returns the covalent radius for this AtomType.
getCovalentRadius(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
Get the covalent radius for an element.
getCreatormap() - Method in class org.openscience.cdk.io.RssWriter
 
getCrystal() - Method in class org.openscience.cdk.ChemModel
Gets the Crystal contained in this ChemModel.
getCrystal() - Method in class org.openscience.cdk.debug.DebugChemModel
Gets the Crystal contained in this ChemModel.
getCrystal() - Method in interface org.openscience.cdk.interfaces.IChemModel
Gets the Crystal contained in this ChemModel.
getCrystal() - Method in class org.openscience.cdk.silent.ChemModel
Gets the Crystal contained in this ChemModel.
getCTab1() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.QueryProcessor
Deprecated.
 
getCTab1() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.TargetProcessor
Deprecated.
 
getCTab2() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.QueryProcessor
Deprecated.
 
getCTab2() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.TargetProcessor
Deprecated.
 
getCTerminus() - Method in class org.openscience.cdk.AminoAcid
Retrieves the C-terminus atom.
getCTerminus() - Method in class org.openscience.cdk.debug.DebugAminoAcid
Retrieves the C-terminus atom.
getCTerminus() - Method in interface org.openscience.cdk.interfaces.IAminoAcid
Retrieves the C-terminus atom.
getCTerminus() - Method in class org.openscience.cdk.silent.AminoAcid
Retrieves the C-terminus atom.
getCurr() - Method in class org.openscience.cdk.smiles.InvPair
Get the current seed.
getCurrentMaxBondOrder(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker
Returns the currently maximum formable bond order for this atom.
getCurrentPermutation() - Method in class org.openscience.cdk.graph.Permutor
Get the permutation that is currently being used.
getCurrentPermutation() - Method in class org.openscience.cdk.smsd.labelling.Permutor
Deprecated.
Get the permutation that is currently being used.
getCurrentRecord() - Method in class org.openscience.cdk.io.random.RandomAccessReader
 
getCyclicFragmentsContainer() - Method in class org.openscience.cdk.graph.SpanningTree
Returns an IAtomContainer which contains all the atoms and bonds which are involved in ring systems.
getDatemap() - Method in class org.openscience.cdk.io.RssWriter
 
getDBE(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
Returns the number of double bond equivalents in this molecule.
getDeclaringClass() - Method in class org.openscience.cdk.DynamicFactory.BasicCreator
Access the implementation of this class.
getDeclaringClass() - Method in interface org.openscience.cdk.DynamicFactory.Creator
Access the implementation of this class.
getDEdgesSize() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
Deprecated.
 
getDefault() - Method in class org.openscience.cdk.renderer.generators.AtomNumberGenerator.AtomColorer
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.AtomNumberGenerator.AtomNumberTextColor
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.AtomNumberGenerator.ColorByType
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.AtomNumberGenerator.Offset
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.AtomNumberGenerator.WillDrawAtomNumbers
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.AtomColor
Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.AtomColorer
Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.AtomRadius
Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.ColorByType
Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.CompactAtom
Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.CompactShape
Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.KekuleStructure
Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.ShowEndCarbons
Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.ShowExplicitHydrogens
Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator.BondDistance
Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator.BondWidth
Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator.DefaultBondColor
Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator.TowardsRingCenterProportion
Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator.WedgeWidth
Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ArrowHeadWidth
Returns the default arrow head width.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.BackgroundColor
Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.BondLength
Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.FitToScreen
Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.FontName
Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ForegroundColor
Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.Margin
Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.Scale
Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ShowMoleculeTitle
Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ShowReactionTitle
Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ShowTooltip
Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.UseAntiAliasing
Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.UsedFontStyle
Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ZoomFactor
Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.BoundsGenerator.BoundsColor
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.ExtendedAtomGenerator.ShowAtomTypeNames
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.ExtendedAtomGenerator.ShowImplicitHydrogens
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.HighlightGenerator.HighlightPalette
Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.HighlightGenerator.HighlightRadius
Returns the default value.
getDefault() - Method in interface org.openscience.cdk.renderer.generators.IGeneratorParameter
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.MappingGenerator.AtomAtomMappingLineColor
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.MappingGenerator.MappingLineWidth
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.MappingGenerator.ShowAtomAtomMapping
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.ReactionSceneGenerator.ArrowHeadWidth
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.ReactionSceneGenerator.ShowReactionBoxes
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.RingGenerator.CDKStyleAromaticity
Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.RingGenerator.MaxDrawableAromaticRing
The maximum default ring size for which an aromatic ring should be drawn.
getDefault() - Method in class org.openscience.cdk.renderer.generators.RingGenerator.RingProportion
Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.RingGenerator.ShowAromaticity
Returns the default value.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.AnnotationColor
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.AnnotationDistance
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.AnnotationFontScale
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.AtomColor
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.BondSeparation
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.DashSection
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.FancyBoldWedges
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.FancyHashedWedges
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.HashSpacing
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.Highlighting
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.OuterGlowWidth
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.SgroupBracketDepth
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.SgroupFontScale
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.StrokeRatio
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.SymbolMarginRatio
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.Visibility
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.WaveSpacing
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.WedgeRatio
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.RendererModel.ColorHash
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.RendererModel.ExternalHighlightColor
Gets the default value for this parameter.
getDefault(Class<T>) - Method in class org.openscience.cdk.renderer.RendererModel
Returns the default value for the IGeneratorParameter for the active IRenderer.
getDefault() - Method in class org.openscience.cdk.renderer.RendererModel.MarkedOutput
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.RendererModel.Padding
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.RendererModel.SelectionColor
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.RendererModel.TitleColor
Gets the default value for this parameter.
getDefault() - Method in class org.openscience.cdk.renderer.RendererModel.TitleFontScale
Gets the default value for this parameter.
getDefaultSetting() - Method in class org.openscience.cdk.io.setting.IOSetting
 
getDefaultStretchBendData(int, int, int) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94ParametersCall
Gets the bond-angle interaction parameter set.
getDefinition() - Method in class org.openscience.cdk.dict.Entry
 
getDEgdes() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
Deprecated.
 
getDegree() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom
 
getDescription() - Method in class org.openscience.cdk.dict.Entry
 
getDescriptorClassNameByInterface(String, String[]) - Static method in class org.openscience.cdk.qsar.DescriptorEngine
Returns a list containing the classes that implement a specific interface.
getDescriptorClassNameByPackage(String, String[]) - Static method in class org.openscience.cdk.qsar.DescriptorEngine
Returns a list containing the classes found in the specified descriptor package.
getDescriptorClassNames() - Method in class org.openscience.cdk.qsar.DescriptorEngine
Returns a list containing the names of the classes implementing the descriptors.
getDescriptorInstances() - Method in class org.openscience.cdk.qsar.DescriptorEngine
Returns a List containing the instantiated descriptor classes.
getDescriptorMetadata() - Method in class org.openscience.cdk.dict.Entry
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor
Deprecated.
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInConjugatedPiSystemDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor
Deprecated.
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor
Returns an array of names for each descriptor value calculated.
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor
Returns an array of names for each descriptor value calculated.
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor
Returns an array of names for each descriptor value calculated.
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor
Deprecated.
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor
Returns the names of the descriptors made available by this class.
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor
 
getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.substance.OxygenAtomCountDescriptor
Returns an array of names for each descriptor value calculated.
getDescriptorNames() - Method in interface org.openscience.cdk.qsar.IDescriptor
Returns an array of names for each descriptor value calculated.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
 
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
 
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
 
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor
Returns the specific type of the FMF descriptor value.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor
Deprecated.
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor
Returns a type of return value calculated by this descriptor.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor
Returns a placeholder with the descriptor size and type.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in interface org.openscience.cdk.qsar.descriptors.substance.ISubstanceDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.substance.OxygenAtomCountDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorResultType() - Method in interface org.openscience.cdk.qsar.IMolecularDescriptor
Returns the specific type of the DescriptorResult object.
getDescriptorSpecifications() - Method in class org.openscience.cdk.qsar.DescriptorEngine
Returns the DescriptorSpecification objects for all available descriptors.
getDetails() - Method in class org.openscience.cdk.validate.ValidationTest
 
getDictionary(String) - Method in class org.openscience.cdk.dict.DictionaryDatabase
 
getDictionary() - Method in class org.openscience.cdk.dict.DictionaryHandler
 
getDictionaryClass(String) - Method in class org.openscience.cdk.qsar.DescriptorEngine
Returns the class(es) of the decsriptor as defined in the descriptor dictionary.
getDictionaryClass(IImplementationSpecification) - Method in class org.openscience.cdk.qsar.DescriptorEngine
Returns the class(es) of the descriptor as defined in the descriptor dictionary.
getDictionaryDefinition(String) - Method in class org.openscience.cdk.qsar.DescriptorEngine
Gets the definition of the descriptor.
getDictionaryDefinition(DescriptorSpecification) - Method in class org.openscience.cdk.qsar.DescriptorEngine
Gets the definition of the descriptor.
getDictionaryEntries(String) - Method in class org.openscience.cdk.dict.DictionaryDatabase
Returns a String[] with the id's of all entries in the specified database.
getDictionaryEntry(String) - Method in class org.openscience.cdk.dict.DictionaryDatabase
 
getDictionaryNames() - Method in class org.openscience.cdk.dict.DictionaryDatabase
Returns a String[] with the names of the known dictionaries.
getDictionaryTitle(String) - Method in class org.openscience.cdk.qsar.DescriptorEngine
Gets the label (title) of the descriptor.
getDictionaryTitle(DescriptorSpecification) - Method in class org.openscience.cdk.qsar.DescriptorEngine
Gets the label (title) of the descriptor.
getDictionaryType(String) - Method in class org.openscience.cdk.qsar.DescriptorEngine
Returns the type of the descriptor as defined in the descriptor dictionary.
getDictionaryType(IImplementationSpecification) - Method in class org.openscience.cdk.qsar.DescriptorEngine
Returns the type of the descriptor as defined in the descriptor dictionary.
getDim() - Method in class org.openscience.cdk.tools.GridGenerator
 
getDimValue(int) - Method in interface org.openscience.cdk.graph.rebond.Bspt.Tuple
 
getDimValue(int) - Method in class org.openscience.cdk.graph.rebond.Point
 
getDirection() - Method in class org.openscience.cdk.debug.DebugReaction
Returns the direction of the reaction.
getDirection() - Method in interface org.openscience.cdk.interfaces.IReaction
Returns the IReaction.Direction of the reaction.
getDirection() - Method in class org.openscience.cdk.Reaction
Returns the direction of the reaction.
getDirection() - Method in class org.openscience.cdk.silent.Reaction
Returns the direction of the reaction.
getDisplayMode() - Method in class org.openscience.cdk.renderer.GraphRendererModel
Get the display mode
getDrawCenter() - Method in class org.openscience.cdk.renderer.AbstractRenderer
Get the position on screen that the diagram will be drawn.
getDuration(long, long) - Static method in class org.openscience.cdk.tools.SwissArmyKnife
Deprecated.
Returns a string reporting the time passed between startTime and endTime, both given in milliseconds, in hours, minutes, seconds and milliseconds.
getDuration(long) - Static method in class org.openscience.cdk.tools.SwissArmyKnife
Deprecated.
Returns a String reporting the time passed during a given number of milliseconds.
getEAIDNumber(AtomContainer) - Static method in class org.openscience.cdk.graph.invariant.HuLuIndexTool
Calculates the extended adjacency matrix index.
getEdge(int) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder
Deprecated.
Returns an edge of the query mol at a given position.
getEdge(INode, INode) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder
Deprecated.
Returns an edge associated between two nodes.
getEdge(int) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQuery
Deprecated.
Returns an edge of the query mol at a given position.
getEdge(INode, INode) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQuery
Deprecated.
Returns an edge associated between two nodes.
getEdgeLabel(int, int) - Method in class org.openscience.cdk.signature.AtomSignature
 
getEdges() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.NodeBuilder
Deprecated.
Returns List of Edges.
getEdges() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.INode
Deprecated.
Returns List of Edges.
getElapsedTimeInHours() - Method in class org.openscience.cdk.smsd.tools.TimeManager
Deprecated.
Returns Elapsed Time In Hours
getElapsedTimeInMilliSeconds() - Method in class org.openscience.cdk.smsd.tools.TimeManager
Deprecated.
Returns Elapsed Time In Mill Seconds
getElapsedTimeInMinutes() - Method in class org.openscience.cdk.smsd.tools.TimeManager
Deprecated.
Returns Elapsed Time In Minutes
getElapsedTimeInSeconds() - Method in class org.openscience.cdk.smsd.tools.TimeManager
Deprecated.
Return Elapsed Time In Seconds
getElectronContainer(int) - Method in class org.openscience.cdk.AtomContainer
Returns the ElectronContainer at position number in the container.
getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns the ElectronContainer at position number in the container.
getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer
Returns the ElectronContainer at position number in the container.
getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns the ElectronContainer at position number in the container.
getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugCrystal
Returns the ElectronContainer at position number in the container.
getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugMonomer
Returns the ElectronContainer at position number in the container.
getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugPolymer
Returns the ElectronContainer at position number in the container.
getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugRing
Returns the ElectronContainer at position number in the container.
getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugStrand
Returns the ElectronContainer at position number in the container.
getElectronContainer(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Returns the ElectronContainer at position number in the container.
getElectronContainer(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Returns the ElectronContainer at position number in the container.
getElectronContainer(int) - Method in class org.openscience.cdk.silent.AtomContainer
Returns the ElectronContainer at position number in the container.
getElectronContainerArray(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
Constructs an array of Bond objects from an AtomContainer.
getElectronContainerArray(List<IElectronContainer>) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
Constructs an array of Atom objects from a List of Atom objects.
getElectronContainerCount() - Method in class org.openscience.cdk.AtomContainer
Returns the number of ElectronContainers in this Container.
getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns the number of ElectronContainers in this Container.
getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugAtomContainer
Returns the number of ElectronContainers in this Container.
getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns the number of ElectronContainers in this Container.
getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugCrystal
Returns the number of ElectronContainers in this Container.
getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugMonomer
Returns the number of ElectronContainers in this Container.
getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugPolymer
Returns the number of ElectronContainers in this Container.
getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugRing
Returns the number of ElectronContainers in this Container.
getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugStrand
Returns the number of ElectronContainers in this Container.
getElectronContainerCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Returns the number of ElectronContainers in this Container.
getElectronContainerCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Returns the number of ElectronContainers in this Container.
getElectronContainerCount() - Method in class org.openscience.cdk.silent.AtomContainer
Returns the number of ElectronContainers in this Container.
getElectronCount() - Method in class org.openscience.cdk.Association
Returns the number of electrons in a Association.
getElectronCount() - Method in class org.openscience.cdk.debug.DebugBond
Returns the number of electrons in this electron container.
getElectronCount() - Method in class org.openscience.cdk.debug.DebugElectronContainer
Returns the number of electrons in this electron container.
getElectronCount() - Method in class org.openscience.cdk.debug.DebugLonePair
Returns the number of electrons in a LonePair.
getElectronCount() - Method in class org.openscience.cdk.debug.DebugSingleElectron
Returns the number of electrons in this SingleElectron.
getElectronCount() - Method in class org.openscience.cdk.ElectronContainer
Returns the number of electrons in this electron container.
getElectronCount() - Method in interface org.openscience.cdk.interfaces.IElectronContainer
Returns the number of electrons in this electron container.
getElectronCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
Returns the number of electrons in this bond
getElectronCount() - Method in class org.openscience.cdk.LonePair
Returns the number of electrons in a LonePair.
getElectronCount() - Method in class org.openscience.cdk.silent.ElectronContainer
Returns the number of electrons in this electron container.
getElectronCount() - Method in class org.openscience.cdk.silent.LonePair
Returns the number of electrons in a LonePair.
getElectronCount() - Method in class org.openscience.cdk.silent.SingleElectron
Returns the number of electrons in this SingleElectron.
getElectronCount() - Method in class org.openscience.cdk.SingleElectron
Returns the number of electrons in this SingleElectron.
getElectronegativity(String) - Method in class org.openscience.cdk.tools.AtomicProperties
 
getElement(String) - Method in class org.openscience.cdk.config.IsotopeFactory
Returns an Element with a given element symbol.
getElement(int) - Method in class org.openscience.cdk.config.IsotopeFactory
Returns an element according to a given atomic number.
getElementCount(IMolecularFormula, IElement) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
Checks a set of Nodes for the occurrence of the isotopes in the molecular formula from a particular IElement.
getElementCount(IMolecularFormula, IIsotope) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
Occurrences of a given element from an isotope in a molecular formula.
getElementCount(IMolecularFormula, String) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
Occurrences of a given element in a molecular formula.
getElementCount() - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
Return the number of elements currently considered in the periodic table.
getElements(String) - Static method in class org.openscience.cdk.tools.HOSECodeAnalyser
 
getElementSymbol(int) - Method in class org.openscience.cdk.config.IsotopeFactory
Returns the symbol matching the element with the given atomic number.
getEnd() - Method in class org.openscience.cdk.Bond
Access the end (or second) atom of the bond.
getEnd() - Method in class org.openscience.cdk.debug.DebugBond
Access the end (or second) atom of the bond.
getEnd() - Method in interface org.openscience.cdk.interfaces.IBond
Access the end (or second) atom of the bond.
getEnd() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
Access the end (or second) atom of the bond.
getEnd() - Method in class org.openscience.cdk.silent.Bond
Access the end (or second) atom of the bond.
getEndChainID() - Method in class org.openscience.cdk.debug.DebugPDBStructure
get the ending Chain identifier of this structure.
getEndChainID() - Method in interface org.openscience.cdk.interfaces.IPDBStructure
get the ending Chain identifier of this structure.
getEndChainID() - Method in class org.openscience.cdk.protein.data.PDBStructure
get the ending Chain identifier of this structure.
getEndChainID() - Method in class org.openscience.cdk.silent.PDBStructure
get the ending Chain identifier of this structure.
getEndColumn() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
Get token end column number.
getEndColumn() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
Get token end column number.
getEndInsertionCode() - Method in class org.openscience.cdk.debug.DebugPDBStructure
get the ending Code for insertion of residues of this structure.
getEndInsertionCode() - Method in interface org.openscience.cdk.interfaces.IPDBStructure
get the ending Code for insertion of residues of this structure.
getEndInsertionCode() - Method in class org.openscience.cdk.protein.data.PDBStructure
get the ending Code for insertion of residues of this structure.
getEndInsertionCode() - Method in class org.openscience.cdk.silent.PDBStructure
get the ending Code for insertion of residues of this structure.
getEndLine() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
Get token end line number.
getEndLine() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
Get token end line number.
getEndSequenceNumber() - Method in class org.openscience.cdk.debug.DebugPDBStructure
get the ending sequence number of this structure.
getEndSequenceNumber() - Method in interface org.openscience.cdk.interfaces.IPDBStructure
get the ending sequence number of this structure.
getEndSequenceNumber() - Method in class org.openscience.cdk.protein.data.PDBStructure
get the ending sequence number of this structure.
getEndSequenceNumber() - Method in class org.openscience.cdk.silent.PDBStructure
get the ending sequence number of this structure.
getEnergies() - Method in class org.openscience.cdk.math.qm.ClosedShellJob
 
getEnergies() - Method in class org.openscience.cdk.math.qm.OneElectronJob
Returns the energies of the orbitals
getEnergies(IAtom, IAtom, IBond.Order) - Method in class org.openscience.cdk.smsd.tools.BondEnergies
Deprecated.
Returns bond energy for a bond type, given atoms and bond type
getEnergies(String, String, IBond.Order) - Method in class org.openscience.cdk.smsd.tools.BondEnergies
Deprecated.
Returns bond energy for a bond type, given atoms and bond type
getEnergies(IBond) - Method in class org.openscience.cdk.smsd.tools.BondEnergies
Deprecated.
Returns bond energy for a bond type, given atoms and bond type
getEnergy() - Method in class org.openscience.cdk.smsd.helper.BondEnergy
Deprecated.
Returns the energy for this bond type.
getEnergyScore(int) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
Deprecated.
Returns summation energy score of the disorder if the MCS is removed from the target and query graph.
getEnergyScore(int) - Method in class org.openscience.cdk.smsd.Isomorphism
Deprecated.
Returns summation energy score of the disorder if the MCS is removed from the target and query graph.
getEntries() - Method in class org.openscience.cdk.dict.Dictionary
 
getEntry(String) - Method in class org.openscience.cdk.dict.Dictionary
 
getEqual() - Method in class org.openscience.cdk.smsd.helper.BinaryTree
Deprecated.
Returns equal node
getEquivalenceClassesSizeVector() - Method in class org.openscience.cdk.ringsearch.SSSRFinder
Deprecated.
Returns a vector containing the size of the "interchangeability" equivalence classes.
getEquivalentClass(double[]) - Method in class org.openscience.cdk.graph.invariant.EquivalentClassPartitioner
Get the final equivalent class.
getError() - Method in class org.openscience.cdk.validate.ValidationTest
 
getErrorCount() - Method in class org.openscience.cdk.validate.ValidationReport
Returns the number of failed tests.
getErrors() - Method in class org.openscience.cdk.validate.ValidationReport
Returns an array of ValidationTest errors.
getEuclideanDistance() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
Deprecated.
Returns Euclidean Distance between query and target molecule.
getEuclideanDistance() - Method in class org.openscience.cdk.smsd.Isomorphism
Deprecated.
Returns Euclidean Distance between query and target molecule.
getExactMass() - Method in class org.openscience.cdk.debug.DebugAtom
Gets the ExactMass attribute of the Isotope object.
getExactMass() - Method in class org.openscience.cdk.debug.DebugAtomType
Gets the ExactMass attribute of the Isotope object.
getExactMass() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
The exact mass of an FragmentAtom is defined as the sum of exact masses of the IAtom's in the fragment.
getExactMass() - Method in class org.openscience.cdk.debug.DebugIsotope
Gets the ExactMass attribute of the Isotope object.
getExactMass() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
Gets the ExactMass attribute of the Isotope object.
getExactMass() - Method in class org.openscience.cdk.FragmentAtom
The exact mass of an FragmentAtom is defined as the sum of exact masses of the IAtom's in the fragment.
getExactMass() - Method in interface org.openscience.cdk.interfaces.IIsotope
Gets the ExactMass attribute of the Isotope object.
getExactMass() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
Gets the ExactMass attribute of the Isotope object.
getExactMass() - Method in class org.openscience.cdk.Isotope
Gets the ExactMass attribute of the Isotope object.
getExactMass() - Method in class org.openscience.cdk.silent.FragmentAtom
The exact mass of an FragmentAtom is defined as the sum of exact masses of the IAtom's in the fragment.
getExactMass() - Method in class org.openscience.cdk.silent.Isotope
Gets the ExactMass attribute of the Isotope object.
getExampleReactions() - Method in class org.openscience.cdk.dict.EntryReact
 
getException() - Method in class org.openscience.cdk.qsar.DescriptorValue
 
getExplicitHydrogenCount(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.normalize.SMSDNormalizer
Deprecated.
Returns The number of explicit hydrogens for a given IAtom.
getExplicitHydrogenCount(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator
Deprecated.
Returns The number of explicit hydrogens for a given IAtom.
getExtendedAdjacenyMatrix(AtomContainer) - Static method in class org.openscience.cdk.graph.invariant.HuLuIndexTool
 
getExtendGrid() - Method in class org.openscience.cdk.tools.GridGenerator
 
getExtension() - Method in class org.openscience.cdk.isomorphism.mcss.RNode
Gets the extension attribute of the RNode object.
getExtension() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode
Deprecated.
Gets the extension attribute of the RNode object
getExternalSelectedPart() - Method in class org.openscience.cdk.renderer.RendererModel
Get externally selected atoms.
getExternalSubset(String, String) - Method in class org.openscience.cdk.io.cml.CMLResolver
Not implemented: always returns null.
getFarthestAtom(Point3d, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
Gets the farthestAtom attribute of the AtomPlacer3D object.
getFfTypes() - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
gives a list of possible force field types
getFfTypes() - Method in class org.openscience.cdk.modeling.builder3d.ModelBuilder3D
Gives a list of possible force field types.
getFinalMapping() - Method in class org.openscience.cdk.smsd.helper.FinalMappings
Deprecated.
Returns the stored mappings
getFinalMapping() - Method in interface org.openscience.cdk.smsd.interfaces.IFinalMapping
Deprecated.
Returns the stored mappings
getFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.AbstractFingerprinter
Generate a binary fingerprint as a bit.
getFingerprint(IAtomContainer) - Method in interface org.openscience.cdk.fingerprint.IFingerprinter
Generate a binary fingerprint as a bit.
getFingerprintAsBytes() - Method in class org.openscience.cdk.fingerprint.PubchemFingerprinter
Returns the fingerprint generated for a molecule as a byte[].
getFinishedPercentage() - Method in class org.openscience.cdk.formula.MolecularFormulaGenerator
Returns a value between 0.0 and 1.0 indicating what portion of the search space has been examined so far by this MolecularFormulaGenerator.
getFirst() - Method in interface org.openscience.cdk.group.DiscretePartitionRefiner
Get the first permutation reached by the search.
getFirstAtom() - Method in class org.openscience.cdk.AtomContainer
Returns the atom at position 0 in the container.
getFirstAtom() - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns the atom at position 0 in the container.
getFirstAtom() - Method in class org.openscience.cdk.debug.DebugAtomContainer
Returns the atom at position 0 in the container.
getFirstAtom() - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns the atom at position 0 in the container.
getFirstAtom() - Method in class org.openscience.cdk.debug.DebugCrystal
Returns the atom at position 0 in the container.
getFirstAtom() - Method in class org.openscience.cdk.debug.DebugMonomer
Returns the atom at position 0 in the container.
getFirstAtom() - Method in class org.openscience.cdk.debug.DebugPolymer
Returns the atom at position 0 in the container.
getFirstAtom() - Method in class org.openscience.cdk.debug.DebugRing
Returns the atom at position 0 in the container.
getFirstAtom() - Method in class org.openscience.cdk.debug.DebugStrand
Returns the atom at position 0 in the container.
getFirstAtom() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
getFirstAtom() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Returns the atom at position 0 in the container.
getFirstAtom() - Method in class org.openscience.cdk.signature.Orbit
Gets the first atom index of the orbit.
getFirstAtom() - Method in class org.openscience.cdk.silent.AtomContainer
Returns the atom at position 0 in the container.
getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler
Deprecated.
Returns one of the best matches with atoms mapped.
getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler
Deprecated.
Returns one of the best matches with atoms mapped.
getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler
Deprecated.
Returns one of the best matches with atoms mapped.
getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler
Deprecated.
Returns one of the best matches with atoms mapped.
getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler
Deprecated.
Returns one of the best matches with atoms mapped.
getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler
Deprecated.
Returns one of the best matches with atoms mapped.
getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler
Deprecated.
Returns one of the best matches with atoms mapped.
getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
Deprecated.
Returns one of the best matches with atoms mapped.
getFirstAtomMapping() - Method in interface org.openscience.cdk.smsd.interfaces.IMCSBase
Deprecated.
Returns one of the best matches with atoms mapped.
getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.Isomorphism
Deprecated.
Returns one of the best matches with atoms mapped.
getFirstAttachmentPoint() - Method in class org.openscience.cdk.isomorphism.matchers.RGroup
 
getFirstBondMap() - Method in class org.openscience.cdk.smsd.Isomorphism
Deprecated.
 
getFirstGraphSize() - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
Returns the size of the first of the two compared graphs.
getFirstGraphSize() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
Deprecated.
Returns the size of the first of the two compared graphs.
getFirstInCell(int) - Method in class org.openscience.cdk.group.Partition
Gets the first element in the specified cell.
getFirstMap(IAtomContainer) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper
Deprecated.
Returns first solution map.
getFirstMap(TargetProperties) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper
Deprecated.
Returns first solution map.
getFirstMap(IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper
Deprecated.
Returns first solution map.
getFirstMap(TargetProperties) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper
Deprecated.
Returns first solution map.
getFirstMap(IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper
Deprecated.
Returns first solution map.
getFirstMap(TargetProperties) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper
Deprecated.
Returns first solution map.
getFirstMapping() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler
Deprecated.
Returns one of the best matches with atom indexes mapped.
getFirstMapping() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler
Deprecated.
Returns one of the best matches with atom indexes mapped.
getFirstMapping() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler
Deprecated.
Returns one of the best matches with atom indexes mapped.
getFirstMapping() - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler
Deprecated.
Returns one of the best matches with atom indexes mapped.
getFirstMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler
Deprecated.
Returns one of the best matches with atom indexes mapped.
getFirstMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler
Deprecated.
Returns one of the best matches with atom indexes mapped.
getFirstMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler
Deprecated.
Returns one of the best matches with atom indexes mapped.
getFirstMapping() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
Deprecated.
Returns one of the best matches with atom indexes mapped.
getFirstMapping() - Method in interface org.openscience.cdk.smsd.interfaces.IMCSBase
Deprecated.
Returns one of the best matches with atom indexes mapped.
getFirstMapping() - Method in class org.openscience.cdk.smsd.Isomorphism
Deprecated.
Returns one of the best matches with atom indexes mapped.
getFirstPoint() - Method in class org.openscience.cdk.sgroup.SgroupBracket
First point of the bracket (x1,y1).
getFlag(int) - Method in class org.openscience.cdk.ChemObject
Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugAtom
Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer
Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugAtomType
Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugBond
Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugChemFile
Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugChemModel
Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugChemObject
Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugChemSequence
Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugCrystal
Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugElectronContainer
Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugElement
Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugIsotope
Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugLonePair
Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugMapping
Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugMonomer
Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugPolymer
Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugReaction
Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugReactionScheme
Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugReactionSet
Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugRing
Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugSingleElectron
Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugStrand
Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.debug.DebugSubstance
Returns the value of a given flag.
getFlag(int) - Method in interface org.openscience.cdk.interfaces.IChemObject
Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
Returns the value of a given flag.
getFlag(int) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom
Deprecated.
getFlag(int) - Method in class org.openscience.cdk.silent.ChemObject
Returns the value of a given flag.
getFlags() - Method in class org.openscience.cdk.ChemObject
Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugAtom
Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugAtomContainer
Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugAtomType
Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugBond
Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugChemFile
Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugChemModel
Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugChemObject
Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugChemSequence
Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugCrystal
Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugElectronContainer
Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugElement
Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugIsotope
Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugLonePair
Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugMapping
Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugMonomer
Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugPolymer
Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugReaction
Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugReactionScheme
Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugReactionSet
Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugRing
Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugSingleElectron
Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugStrand
Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.debug.DebugSubstance
Returns the whole set of flags.
getFlags() - Method in interface org.openscience.cdk.interfaces.IChemObject
Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
Returns the whole set of flags.
getFlags() - Method in class org.openscience.cdk.silent.ChemObject
Returns the whole set of flags.
getFlagValue() - Method in class org.openscience.cdk.ChemObject
Access the internal value used to store the flags.
getFlagValue() - Method in interface org.openscience.cdk.interfaces.IChemObject
Access the internal value used to store the flags.
getFlagValue() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
Access the internal value used to store the flags.
getFlagValue() - Method in class org.openscience.cdk.silent.ChemObject
Access the internal value used to store the flags.
getFolding() - Method in class org.openscience.cdk.fingerprint.model.Bayesian
Access to the fingerprint folding extent.
getFont() - Method in class org.openscience.cdk.renderer.font.AWTFontManager
Get the current font.
getFontName() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
Get the font family name used in this font manager.
getFontSizeForZoom(double) - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
For a particular zoom, get the appropriate font size.
getFontStyle() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
Get the font style, defined in the IFontManager interface.
getForbidden() - Method in class org.openscience.cdk.isomorphism.mcss.RNode
Gets the forbidden attribute of the RNode object.
getForbidden() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode
Deprecated.
Gets the forbidden attribute of the RNode object
getFormalCharge() - Method in class org.openscience.cdk.AtomType
Returns the formal charge of this atom.
getFormalCharge() - Method in class org.openscience.cdk.debug.DebugAtom
Returns the formal charge of this atom.
getFormalCharge() - Method in class org.openscience.cdk.debug.DebugAtomType
Returns the formal charge of this atom.
getFormalCharge() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
Returns the formal charge of this atom.
getFormalCharge() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
Returns the formal charge of this atom.
getFormalCharge() - Method in interface org.openscience.cdk.interfaces.IAtomType
Returns the formal charge of this atom.
getFormalCharge() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
Returns the formal charge of this atom.
getFormalCharge() - Method in class org.openscience.cdk.silent.AtomType
Returns the formal charge of this atom.
getFormalNeighbourCount() - Method in class org.openscience.cdk.AtomType
Returns the formal neighbour count of this atom.
getFormalNeighbourCount() - Method in class org.openscience.cdk.debug.DebugAtom
Returns the formal neighbour count of this atom.
getFormalNeighbourCount() - Method in class org.openscience.cdk.debug.DebugAtomType
Returns the formal neighbour count of this atom.
getFormalNeighbourCount() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
Returns the formal neighbour count of this atom.
getFormalNeighbourCount() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
Returns the formal neighbour count of this atom.
getFormalNeighbourCount() - Method in interface org.openscience.cdk.interfaces.IAtomType
Returns the formal neighbour count of this atom.
getFormalNeighbourCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
Returns the formal neighbour count of this atom.
getFormalNeighbourCount() - Method in class org.openscience.cdk.silent.AtomType
Returns the formal neighbour count of this atom.
getFormat() - Method in class org.openscience.cdk.io.CDKSourceCodeWriter
 
getFormat() - Method in class org.openscience.cdk.io.CIFReader
 
getFormat() - Method in class org.openscience.cdk.io.CMLReader
 
getFormat() - Method in class org.openscience.cdk.io.CMLWriter
 
getFormat() - Method in class org.openscience.cdk.io.CrystClustReader
 
getFormat() - Method in class org.openscience.cdk.io.CrystClustWriter
 
getFormat() - Method in class org.openscience.cdk.io.CTXReader
 
getFormat() - Method in class org.openscience.cdk.io.GamessReader
 
getFormat() - Method in class org.openscience.cdk.io.Gaussian03Reader
 
getFormat() - Method in class org.openscience.cdk.io.Gaussian98Reader
 
getFormat() - Method in class org.openscience.cdk.io.GhemicalMMReader
 
getFormat() - Method in class org.openscience.cdk.io.HINReader
 
getFormat() - Method in class org.openscience.cdk.io.HINWriter
 
getFormat() - Method in interface org.openscience.cdk.io.IChemObjectIO
Returns the IResourceFormat class for this IO class.
getFormat() - Method in class org.openscience.cdk.io.INChIPlainTextReader
 
getFormat() - Method in class org.openscience.cdk.io.INChIReader
 
getFormat() - Method in class org.openscience.cdk.io.iterator.event.EventCMLReader
 
getFormat() - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundASNReader
 
getFormat() - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader
 
getFormat() - Method in class org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader
 
getFormat() - Method in class org.openscience.cdk.io.iterator.IteratingSDFReader
 
getFormat() - Method in class org.openscience.cdk.io.iterator.IteratingSMILESReader
Get the format for this reader.
getFormat() - Method in class org.openscience.cdk.io.MDLReader
Deprecated.
 
getFormat() - Method in class org.openscience.cdk.io.MDLRXNReader
 
getFormat() - Method in class org.openscience.cdk.io.MDLRXNV2000Reader
 
getFormat() - Method in class org.openscience.cdk.io.MDLRXNV3000Reader
 
getFormat() - Method in class org.openscience.cdk.io.MDLRXNWriter
 
getFormat() - Method in class org.openscience.cdk.io.MDLV2000Reader
 
getFormat() - Method in class org.openscience.cdk.io.MDLV2000Writer
 
getFormat() - Method in class org.openscience.cdk.io.MDLV3000Reader
 
getFormat() - Method in class org.openscience.cdk.io.MDLV3000Writer
Returns the IResourceFormat class for this IO class.
getFormat() - Method in class org.openscience.cdk.io.Mol2Reader
 
getFormat() - Method in class org.openscience.cdk.io.Mol2Writer
 
getFormat() - Method in class org.openscience.cdk.io.Mopac7Reader
 
getFormat() - Method in class org.openscience.cdk.io.MoSSOutputReader
Returns the IResourceFormat class for this IO class.
getFormat() - Method in class org.openscience.cdk.io.PCCompoundASNReader
 
getFormat() - Method in class org.openscience.cdk.io.PCCompoundXMLReader
 
getFormat() - Method in class org.openscience.cdk.io.PCSubstanceXMLReader
 
getFormat() - Method in class org.openscience.cdk.io.PDBReader
 
getFormat() - Method in class org.openscience.cdk.io.PDBWriter
 
getFormat() - Method in class org.openscience.cdk.io.PMPReader
 
getFormat() - Method in class org.openscience.cdk.io.program.GaussianInputWriter
 
getFormat() - Method in class org.openscience.cdk.io.program.Mopac7Writer
 
getFormat() - Method in class org.openscience.cdk.io.random.RandomAccessSDFReader
 
getFormat() - Method in class org.openscience.cdk.io.rdf.CDKOWLReader
Returns the IResourceFormat for this reader.
getFormat() - Method in class org.openscience.cdk.io.rdf.CDKOWLWriter
Returns the IResourceFormat for this writer.
getFormat() - Method in class org.openscience.cdk.io.RGroupQueryReader
 
getFormat() - Method in class org.openscience.cdk.io.RGroupQueryWriter
Returns output format.
getFormat() - Method in class org.openscience.cdk.io.RssWriter
 
getFormat() - Method in class org.openscience.cdk.io.SDFWriter
 
getFormat() - Method in class org.openscience.cdk.io.ShelXReader
 
getFormat() - Method in class org.openscience.cdk.io.ShelXWriter
 
getFormat() - Method in class org.openscience.cdk.io.SMILESReader
 
getFormat() - Method in class org.openscience.cdk.io.SMILESWriter
 
getFormat() - Method in class org.openscience.cdk.io.VASPReader
 
getFormat() - Method in class org.openscience.cdk.io.XYZReader
 
getFormat() - Method in class org.openscience.cdk.io.XYZWriter
 
getFormat() - Method in class org.openscience.cdk.io.ZMatrixReader
 
getFormatName() - Method in class org.openscience.cdk.io.formats.ABINITFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.Aces2Format
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.ADFFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.AlchemyFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.BGFFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.BSFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
 
getFormatName() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.CACheFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
 
getFormatName() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.CIFFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.CMLFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.CRK2DFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.CRK3DFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.CrystClustFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.CTXFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.DaltonFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.DMol3Format
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.DOCK5Format
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.FingerprintFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.GamessFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian03Format
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian90Format
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian92Format
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian94Format
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian95Format
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian98Format
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat
 
getFormatName() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.GROMOS96Format
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.HINFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.INChIFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat
Returns a one-lined format name of the format.
getFormatName() - Method in interface org.openscience.cdk.io.formats.IResourceFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.JaguarFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.JMEFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MacroModelFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MDLFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MDLV2000Format
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MDLV3000Format
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MMODFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.Mol2Format
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC7Format
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC93Format
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC97Format
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.MPQCFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.NWChemFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.PCModelFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.PDBFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.PDBMLFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.PMPFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.POVRayFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.PQSChemFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.QChemFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.RawCopyFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.SDFFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.ShelXFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.SMARTSFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.SMILESFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.SpartanFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.SVGFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.VASPFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.ViewmolFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.XEDFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.XYZFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.YasaraFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.ZindoFormat
Returns a one-lined format name of the format.
getFormatName() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat
Returns a one-lined format name of the format.
getFormats() - Method in class org.openscience.cdk.io.FormatFactory
Returns the list of recognizable formats.
getFormats() - Method in class org.openscience.cdk.io.ReaderFactory
 
getFormula() - Method in class org.openscience.cdk.formula.IsotopeContainer
Get the IMolecularFormula object of this container.
getFP(int) - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter
Returns the requested fingerprint.
getFPCount() - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter
Returns the number of fingerprints generated.
getFractionalPoint3d() - Method in class org.openscience.cdk.Atom
Returns a point specifying the location of this atom in a Crystal unit cell.
getFractionalPoint3d() - Method in class org.openscience.cdk.debug.DebugAtom
Returns a point specifying the location of this atom in a Crystal unit cell.
getFractionalPoint3d() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
Returns a point specifying the location of this atom in a Crystal unit cell.
getFractionalPoint3d() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
Returns a point specifying the location of this atom in a Crystal unit cell.
getFractionalPoint3d() - Method in interface org.openscience.cdk.interfaces.IAtom
Returns a point specifying the location of this atom in a Crystal unit cell.
getFractionalPoint3d() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
Returns a point specifying the location of this atom in a Crystal unit cell.
getFractionalPoint3d() - Method in class org.openscience.cdk.silent.Atom
Returns a point specifying the location of this atom in a Crystal unit cell.
getFragment() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
Returns the fully expended form of the IFragmentAtom.
getFragment() - Method in class org.openscience.cdk.FragmentAtom
 
getFragment() - Method in interface org.openscience.cdk.interfaces.IFragmentAtom
Returns the fully expended form of the IFragmentAtom.
getFragment() - Method in class org.openscience.cdk.silent.FragmentAtom
 
getFragments() - Method in class org.openscience.cdk.fragment.ExhaustiveFragmenter
Get the fragments generated as SMILES strings.
getFragments() - Method in interface org.openscience.cdk.fragment.IFragmenter
Get the fragments generated as SMILES strings.
getFragments() - Method in class org.openscience.cdk.fragment.MurckoFragmenter
This returns the frameworks and ring systems from a Murcko fragmentation.
getFragmentsAsContainers() - Method in class org.openscience.cdk.fragment.ExhaustiveFragmenter
Get the fragments generated as IAtomContainer objects..
getFragmentsAsContainers() - Method in interface org.openscience.cdk.fragment.IFragmenter
Get fragments generated as IAtomContainer objects.
getFragmentsAsContainers() - Method in class org.openscience.cdk.fragment.MurckoFragmenter
Get all frameworks and ring systems as IAtomContainer objects.
getFragmentSize(int) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
Deprecated.
Returns number of fragment generated in the solution space, if the MCS is removed from the target and query graph.
getFragmentSize(int) - Method in class org.openscience.cdk.smsd.Isomorphism
Deprecated.
Returns number of fragment generated in the solution space, if the MCS is removed from the target and query graph.
getFrameworks() - Method in class org.openscience.cdk.fragment.MurckoFragmenter
Get frameworks as SMILES strings.
getFrameworksAsContainers() - Method in class org.openscience.cdk.fragment.MurckoFragmenter
Get frameworks as IAtomContainer as objects.
getFunction(int) - Method in class org.openscience.cdk.renderer.GraphRendererModel
Get a function from this set
getFunctionalGroupSMARTS() - Static method in class org.openscience.cdk.fingerprint.StandardSubstructureSets
The functional groups.
getFunctionColor(int) - Method in class org.openscience.cdk.renderer.GraphRendererModel
Get a color from a function in this set
getFunctionsSize() - Method in class org.openscience.cdk.renderer.GraphRendererModel
Get the count of functions in this set
getGenerators() - Method in class org.openscience.cdk.renderer.AtomContainerRenderer
Returns a List of IGenerators for this renderer.
getGenerators() - Method in class org.openscience.cdk.renderer.ChemModelRenderer
Returns a List of IGenerators for this renderer.
getGenerators() - Method in interface org.openscience.cdk.renderer.IRenderer
Returns a List of IGenerators for this renderer.
getGenerators() - Method in class org.openscience.cdk.renderer.MoleculeSetRenderer
Returns a List of IGenerators for this renderer.
getGenerators() - Method in class org.openscience.cdk.renderer.ReactionRenderer
Returns a List of IGenerators for this renderer.
getGenerators() - Method in class org.openscience.cdk.renderer.ReactionSetRenderer
Returns a List of IGenerators for this renderer.
getGraph() - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
Returns the graph object of this RGraph.
getGraph() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
Deprecated.
Returns the graph object of this CDKRGraph.
getGraphics() - Method in class org.openscience.cdk.renderer.visitor.AWTDrawVisitor
Returns the Graphics2D for for this visitor.
getGrid() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
 
getGrid() - Method in class org.openscience.cdk.tools.GridGenerator
 
getGridArray() - Method in class org.openscience.cdk.tools.GridGenerator
 
getGridPointFrom3dCoordinates(Point3d) - Method in class org.openscience.cdk.tools.GridGenerator
Method calculates the nearest grid point from given coordinates.
getGroup() - Method in class org.openscience.cdk.isomorphism.matchers.RGroup
 
getGroup(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
Get the group of the element.
getHandedness(IAtom, IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.stereo.StereoTool
Gets the tetrahedral handedness of four atoms - three of which form the 'base' of the tetrahedron, and the other the apex.
getHash(int) - Method in interface org.openscience.cdk.fingerprint.ICountFingerprint
Returns the hash corresponding to the given index in the fingerprint.
getHash(int) - Method in class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
 
getHashMapBySingleCharCode() - Static method in class org.openscience.cdk.templates.AminoAcids
Returns a HashMap where the key is one of G, A, V, L, I, S, T, C, M, D, N, E, Q, R, K, H, F, Y, W and P.
getHashMapByThreeLetterCode() - Static method in class org.openscience.cdk.templates.AminoAcids
Returns a HashMap where the key is one of GLY, ALA, VAL, LEU, ILE, SER, THR, CYS, MET, ASP, ASN, GLU, GLN, ARG, LYS, HIS, PHE, TYR, TRP AND PRO.
getHeaviestRing(IRingSet, IBond) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator
We define the heaviest ring as the one with the highest number of double bonds.
getHeavyAtomRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>, boolean, boolean) - Static method in class org.openscience.cdk.geometry.GeometryTools
Return the RMSD of the heavy atoms between the 2 aligned molecules.
getHeavyAtomRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>, boolean, boolean) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Return the RMSD of the heavy atoms between the 2 aligned molecules.
getHeavyAtoms(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
Returns a set of nodes excluding all the hydrogens.
getHeavyElements(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
Returns a set of nodes excluding all the hydrogens.
getHeight() - Method in class org.openscience.cdk.signature.Orbit
Gets the height of the signature label.
getHetAtom() - Method in class org.openscience.cdk.debug.DebugPDBAtom
Determine whether this is a heteroatom or not.
getHetAtom() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
Determine whether this is a heteroatom or not.
getHetAtom() - Method in class org.openscience.cdk.protein.data.PDBAtom
 
getHetAtom() - Method in class org.openscience.cdk.silent.PDBAtom
 
getHighlightedAtom() - Method in class org.openscience.cdk.renderer.RendererModel
Returns the atom currently highlighted.
getHighlightedBond() - Method in class org.openscience.cdk.renderer.RendererModel
Returns the Bond currently highlighted.
getHillString(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
getHOSECode(IAtomContainer, IAtom, int) - Method in class org.openscience.cdk.tools.HOSECodeGenerator
Produces a HOSE code for Atom root in the IAtomContainer ac.
getHOSECode(IAtomContainer, IAtom, int, boolean) - Method in class org.openscience.cdk.tools.HOSECodeGenerator
Produces a HOSE code for Atom root in the IAtomContainer ac.
getHTML(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
Returns the string representation of the molecule formula based on Hill System with numbers wrapped in <sub></sub> tags.
getHTML(IMolecularFormula, boolean, boolean) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
Returns the string representation of the molecule formula based on Hill System with numbers wrapped in <sub></sub> tags and the isotope of each Element in <sup></sup> tags and the total charge of IMolecularFormula in <sup></sup> tags.
getHTML(IMolecularFormula, String[], boolean, boolean) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
Returns the string representation of the molecule formula with numbers wrapped in <sub></sub> tags and the isotope of each Element in <sup></sup> tags and the total showCharge of IMolecularFormula in <sup></sup> tags.
getHybridization() - Method in class org.openscience.cdk.AtomType
Returns the hybridization of this atom.
getHybridization() - Method in class org.openscience.cdk.debug.DebugAtom
Returns the hybridization of this atom.
getHybridization() - Method in class org.openscience.cdk.debug.DebugAtomType
Returns the hybridization of this atom.
getHybridization() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
Returns the hybridization of this atom.
getHybridization() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
Returns the hybridization of this atom.
getHybridization() - Method in interface org.openscience.cdk.interfaces.IAtomType
Returns the hybridization of this atom.
getHybridization() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
Returns the hybridization of this atom.
getHybridization() - Method in class org.openscience.cdk.silent.AtomType
Returns the hybridization of this atom.
getHydrogenCount(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.normalize.SMSDNormalizer
Deprecated.
The summed implicit + explicit hydrogens of the given IAtom.
getHydrogenCount(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator
Deprecated.
The summed implicit + explicit hydrogens of the given IAtom.
getiBondNeighborAtomsA() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper
Deprecated.
 
getiBondNeighborAtomsB() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper
Deprecated.
 
getIBondSetA() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper
Deprecated.
 
getIBondSetB() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper
Deprecated.
 
getICode() - Method in class org.openscience.cdk.debug.DebugPDBAtom
get Code for insertion of residues of this atom.
getICode() - Method in class org.openscience.cdk.debug.DebugPDBMonomer
Gets the ICode of this monomer.
getICode() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
get Code for insertion of residues of this atom.
getICode() - Method in interface org.openscience.cdk.interfaces.IPDBMonomer
Gets the ICode of this monomer.
getICode() - Method in class org.openscience.cdk.protein.data.PDBAtom
get Code for insertion of residues of this atom.
getICode() - Method in class org.openscience.cdk.protein.data.PDBMonomer
 
getICode() - Method in class org.openscience.cdk.silent.PDBAtom
get Code for insertion of residues of this atom.
getICode() - Method in class org.openscience.cdk.silent.PDBMonomer
 
getID() - Method in class org.openscience.cdk.ChemObject
Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugAtom
Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugAtomContainer
Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugAtomType
Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugBond
Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugChemFile
Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugChemModel
Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugChemObject
Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugChemSequence
Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugCrystal
Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugElectronContainer
Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugElement
Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugIsotope
Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugLonePair
Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugMapping
Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugMonomer
Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugPolymer
Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugReaction
Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugReactionScheme
Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugReactionSet
Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugRing
Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugSingleElectron
Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugStrand
Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.debug.DebugSubstance
Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.dict.Entry
 
getID() - Method in interface org.openscience.cdk.interfaces.IChemObject
Returns the identifier (ID) of this object.
getID() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
Returns the identifier (ID) of this object.
getId() - Method in class org.openscience.cdk.renderer.elements.MarkedElement
Access the id of the element.
getID() - Method in class org.openscience.cdk.silent.ChemObject
Returns the identifier (ID) of this object.
getId1() - Method in class org.openscience.cdk.isomorphism.mcss.RMap
Gets the id1 attribute of the RMap object.
getId1() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMap
Deprecated.
Gets the id1 attribute of the CDKRMap object
getId2() - Method in class org.openscience.cdk.isomorphism.mcss.RMap
Gets the id2 attribute of the RMap object.
getId2() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMap
Deprecated.
Gets the id2 attribute of the CDKRMap object
getIgnoreAromaticBonds() - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory
Deprecated.
GetImage() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
Get token literal value.
GetImage() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
Get token literal value.
getImaginaryPart() - Method in class org.openscience.cdk.math.Complex
Gets the imaginary part of this value
getIminus() - Method in class org.openscience.cdk.math.qm.AngularMomentum
Calculates the I- operator
getImplementationIdentifier() - Method in interface org.openscience.cdk.IImplementationSpecification
Identifier for this implementation which must include version information.
getImplementationIdentifier() - Method in class org.openscience.cdk.qsar.DescriptorSpecification
 
getImplementationIdentifier() - Method in class org.openscience.cdk.reaction.ReactionSpecification
 
getImplementationTitle() - Method in interface org.openscience.cdk.IImplementationSpecification
Human-readable name for the implementation for the algorithm specified by the reference.
getImplementationTitle() - Method in class org.openscience.cdk.qsar.DescriptorSpecification
 
getImplementationTitle() - Method in class org.openscience.cdk.reaction.ReactionSpecification
 
getImplementationVendor() - Method in interface org.openscience.cdk.IImplementationSpecification
Human-readable name for the vendor that holds copyright for this implementation.
getImplementationVendor() - Method in class org.openscience.cdk.qsar.DescriptorSpecification
 
getImplementationVendor() - Method in class org.openscience.cdk.reaction.ReactionSpecification
 
getImplicitHydrogenCount() - Method in class org.openscience.cdk.Atom
Returns the hydrogen count of this atom.
getImplicitHydrogenCount() - Method in class org.openscience.cdk.debug.DebugAtom
Returns the hydrogen count of this atom.
getImplicitHydrogenCount() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
Returns the hydrogen count of this atom.
getImplicitHydrogenCount() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
Returns the hydrogen count of this atom.
getImplicitHydrogenCount() - Method in interface org.openscience.cdk.interfaces.IAtom
Returns the implicit hydrogen count of this atom.
getImplicitHydrogenCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
Returns the hydrogen count of this atom.
getImplicitHydrogenCount(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.normalize.SMSDNormalizer
Deprecated.
Returns The number of Implicit Hydrogen Count for a given IAtom.
getImplicitHydrogenCount() - Method in class org.openscience.cdk.silent.Atom
Returns the hydrogen count of this atom.
getImplicitHydrogenCount(IAtom) - Static method in class org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator
Deprecated.
Returns The number of Implicit Hydrogen Count for a given IAtom.
getImplicitHydrogenCount(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
Counts the number of implicit hydrogens on the provided IAtomContainer.
getInchi() - Method in class org.openscience.cdk.inchi.InChIGenerator
Gets generated InChI string.
getInChIGenerator(IAtomContainer) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory
Gets an Standard InChI generator for a IAtomContainer.
getInChIGenerator(IAtomContainer, String) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory
Gets InChI generator for CDK IAtomContainer.
getInChIGenerator(IAtomContainer, List<INCHI_OPTION>) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory
Gets InChI generator for CDK IAtomContainer.
getInchiKey() - Method in class org.openscience.cdk.inchi.InChIGenerator
Gets generated InChIKey string.
getInchimap() - Method in class org.openscience.cdk.io.RssWriter
 
getInChIToStructure(String, IChemObjectBuilder) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory
Gets structure generator for an InChI string.
getInChIToStructure(String, IChemObjectBuilder, String) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory
Gets structure generator for an InChI string.
getInChIToStructure(String, IChemObjectBuilder, List<String>) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory
Gets structure generator for an InChI string.
getIndexFile(String) - Static method in class org.openscience.cdk.io.random.RandomAccessReader
Opens the file index file _cdk.index in a temporary folder, as specified by "java.io.tmpdir" property.
getIndexOfFirstNonDiscreteCell() - Method in class org.openscience.cdk.group.Partition
Gets the index of the first cell in the partition that is discrete.
getInitialLongestChain(IAtomContainer) - Static method in class org.openscience.cdk.layout.AtomPlacer
Search an aliphatic molecule for the longest chain.
getInitialPartition() - Method in interface org.openscience.cdk.group.Refinable
Get an initial partition of the vertices of the refinable - for example, by color.
getInstance(IChemObjectBuilder) - Static method in class org.openscience.cdk.atomtype.CDKAtomTypeMatcher
 
getInstance(IChemObjectBuilder, int) - Static method in class org.openscience.cdk.atomtype.CDKAtomTypeMatcher
 
getInstance(String) - Static method in class org.openscience.cdk.atomtype.mapper.AtomTypeMapper
Instantiates an atom type to atom type mapping, based on the given mapping file.
getInstance(String, InputStream) - Static method in class org.openscience.cdk.atomtype.mapper.AtomTypeMapper
Instantiates an atom type to atom type mapping, based on the given InputStream.
getInstance(IChemObjectBuilder) - Static method in class org.openscience.cdk.atomtype.SybylAtomTypeMatcher
Returns an instance of this atom typer.
getInstance(InputStream, String, IChemObjectBuilder) - Static method in class org.openscience.cdk.config.AtomTypeFactory
Method to create a default AtomTypeFactory, using the given InputStream.
getInstance(IChemObjectBuilder) - Static method in class org.openscience.cdk.config.AtomTypeFactory
Method to create a default AtomTypeFactory, using the structgen atom type list.
getInstance(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.config.AtomTypeFactory
Method to create a specialized AtomTypeFactory.
getInstance() - Static method in class org.openscience.cdk.config.Isotopes
Returns a singleton instance of this class.
getInstance(IChemObjectBuilder) - Static method in class org.openscience.cdk.config.XMLIsotopeFactory
Returns an IsotopeFactory instance.
getInstance() - Static method in class org.openscience.cdk.debug.DebugChemObjectBuilder
Access the singleton instance of this DebugChemObjectBuilder.
getInstance() - Static method in class org.openscience.cdk.DefaultChemObjectBuilder
Access the singleton instance of this DefaultChemObjectBuilder.
getInstance() - Static method in class org.openscience.cdk.inchi.InChIGeneratorFactory
Gives the one InChIGeneratorFactory instance, if needed also creates it.
getInstance() - Static method in class org.openscience.cdk.io.formats.ABINITFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.Aces2Format
 
getInstance() - Static method in class org.openscience.cdk.io.formats.ADFFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.AlchemyFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.BGFFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.BSFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.CacaoInternalFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.CACheFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.CDKOWLFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
 
getInstance() - Static method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
 
getInstance() - Static method in class org.openscience.cdk.io.formats.ChemDrawFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.ChemtoolFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.CIFFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.CMLFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.CMLRSSFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.CRK2DFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.CRK3DFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.CrystClustFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.CTXFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.DaltonFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.DMol3Format
 
getInstance() - Static method in class org.openscience.cdk.io.formats.DOCK5Format
 
getInstance() - Static method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.FingerprintFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.GamessFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.Gaussian03Format
 
getInstance() - Static method in class org.openscience.cdk.io.formats.Gaussian90Format
 
getInstance() - Static method in class org.openscience.cdk.io.formats.Gaussian92Format
 
getInstance() - Static method in class org.openscience.cdk.io.formats.Gaussian94Format
 
getInstance() - Static method in class org.openscience.cdk.io.formats.Gaussian95Format
 
getInstance() - Static method in class org.openscience.cdk.io.formats.Gaussian98Format
 
getInstance() - Static method in class org.openscience.cdk.io.formats.GaussianInputFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.GhemicalMMFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.GhemicalSPMFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.GROMOS96Format
 
getInstance() - Static method in class org.openscience.cdk.io.formats.HINFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.INChIFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.INChIPlainTextFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.JaguarFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.JMEFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.MacroModelFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.MDLFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.MDLRXNFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.MDLRXNV3000Format
 
getInstance() - Static method in class org.openscience.cdk.io.formats.MDLV2000Format
 
getInstance() - Static method in class org.openscience.cdk.io.formats.MDLV3000Format
 
getInstance() - Static method in class org.openscience.cdk.io.formats.MMODFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.Mol2Format
 
getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC2002Format
 
getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC2007Format
 
getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC2009Format
 
getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC2012Format
 
getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC7Format
 
getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC7InputFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC93Format
 
getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC97Format
 
getInstance() - Static method in class org.openscience.cdk.io.formats.MoSSOutputFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.MPQCFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.NWChemFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.PCModelFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.PDBFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.PDBMLFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.PMPFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.POVRayFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.PQSChemFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemASNFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.QChemFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.RawCopyFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.RGroupQueryFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.SDFFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.ShelXFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.SMARTSFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.SMILESFIXFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.SMILESFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.SpartanFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.SVGFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.SybylDescriptorFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.TinkerMM2Format
 
getInstance() - Static method in class org.openscience.cdk.io.formats.TinkerXYZFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.TurboMoleFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.UniChemXYZFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.VASPFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.ViewmolFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.XEDFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.XYZFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.YasaraFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.ZindoFormat
 
getInstance() - Static method in class org.openscience.cdk.io.formats.ZMatrixFormat
 
getInstance(TemplateHandler3D, String, IChemObjectBuilder) - Static method in class org.openscience.cdk.modeling.builder3d.ModelBuilder3D
 
getInstance(IChemObjectBuilder) - Static method in class org.openscience.cdk.modeling.builder3d.ModelBuilder3D
 
getInstance() - Static method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D
 
getInstance() - Static method in class org.openscience.cdk.silent.SilentChemObjectBuilder
Access the singleton instance of this SilentChemObjectBuilder.
getInstance() - Static method in class org.openscience.cdk.smsd.global.TimeOut
Deprecated.
Get Instance of the timeout.
getInstance() - Static method in class org.openscience.cdk.smsd.helper.FinalMappings
Deprecated.
Stores mapping solutions
getInstance() - Static method in class org.openscience.cdk.smsd.helper.LabelContainer
Deprecated.
Create ids from atom labels
getInstance() - Static method in class org.openscience.cdk.smsd.tools.BondEnergies
Deprecated.
Returns Singleton pattern instance for the Bond Energy class
getInstance() - Static method in class org.openscience.cdk.tools.AtomicProperties
 
getInstance(IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.CDKHydrogenAdder
 
getInstance(IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.CDKValencyChecker
 
getInt2DColumnSum(int[][]) - Static method in class org.openscience.cdk.graph.PathTools
Sums up the columns in a 2D int matrix.
getIntensity() - Method in class org.openscience.cdk.formula.IsotopeContainer
Get the intensity value of this container.
getInterfaces(Class<?>) - Method in class org.openscience.cdk.DynamicFactory.DefaultInterfaceProvider
Access the interfaces for a given class.
getInterfaces(Class<?>) - Method in interface org.openscience.cdk.DynamicFactory.InterfaceProvider
Access the interfaces for a given class.
getIntersection(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
Compares this AtomContainer with another given AtomContainer and returns the Intersection between them.
getIntLabel(int) - Method in class org.openscience.cdk.signature.AtomSignature
 
getIOSettings() - Method in class org.openscience.cdk.io.ChemObjectIO
Returns an array of IOSettings defined by this IChemObjectIO class.
getIOSettings() - Method in interface org.openscience.cdk.io.IChemObjectIO
Returns an array of IOSettings defined by this IChemObjectIO class.
getIOSettings() - Method in class org.openscience.cdk.io.random.DefaultRandomAccessChemObjectReader
 
getIplus() - Method in class org.openscience.cdk.math.qm.AngularMomentum
Calculates the I+ operator
getIsobutane(IChemObjectBuilder) - Static method in class org.openscience.cdk.templates.saturatedhydrocarbons.IsoAlkanes
 
getIsohexane(IChemObjectBuilder) - Static method in class org.openscience.cdk.templates.saturatedhydrocarbons.IsoAlkanes
 
getIsomorphAtomsMap(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
Returns the first isomorph 'atom mapping' found for g2 in g1.
getIsomorphAtomsMap(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
Deprecated.
Returns the first isomorph 'atom mapping' found for targetGraph in sourceGraph.
getIsomorphMap(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
Returns the first isomorph mapping found or null.
getIsomorphMap(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
Deprecated.
Returns the first isomorph mapping found or null.
getIsomorphMaps(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
Returns all the isomorph 'mappings' found between two atom containers.
getIsomorphMaps(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
Deprecated.
Returns all the isomorph 'mappings' found between two atom containers.
getIsopentane(IChemObjectBuilder) - Static method in class org.openscience.cdk.templates.saturatedhydrocarbons.IsoAlkanes
 
getIsotope(String, int) - Method in class org.openscience.cdk.config.IsotopeFactory
Get isotope based on element symbol and mass number.
getIsotope(String, double, double) - Method in class org.openscience.cdk.config.IsotopeFactory
Get an isotope based on the element symbol and exact mass.
getIsotope(String, int) - Method in class org.openscience.cdk.config.Isotopes
Get isotope based on element symbol and mass number.
getIsotope(String, double, double) - Method in class org.openscience.cdk.config.Isotopes
Get an isotope based on the element symbol and exact mass.
getIsotope(int) - Method in class org.openscience.cdk.formula.IsotopePattern
Returns the a isotopes given a specific position.
getIsotopeCount(IIsotope) - Method in class org.openscience.cdk.debug.DebugAdductFormula
Checks a set of Nodes for the occurrence of the isotope in the adduct formula from a particular isotope.
getIsotopeCount() - Method in class org.openscience.cdk.debug.DebugAdductFormula
Checks a set of Nodes for the number of different isotopes in the adduct formula.
getIsotopeCount(IIsotope) - Method in class org.openscience.cdk.debug.DebugMolecularFormula
Checks a set of Nodes for the occurrence of the isotope in the IMolecularFormula from a particular isotope.
getIsotopeCount() - Method in class org.openscience.cdk.debug.DebugMolecularFormula
Checks a set of Nodes for the number of different isotopes in the IMolecularFormula.
getIsotopeCount(IIsotope) - Method in class org.openscience.cdk.formula.AdductFormula
Checks a set of Nodes for the occurrence of the isotope in the adduct formula from a particular isotope.
getIsotopeCount() - Method in class org.openscience.cdk.formula.AdductFormula
Checks a set of Nodes for the number of different isotopes in the adduct formula.
getIsotopeCount(IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormula
Checks a set of Nodes for the occurrence of the isotope in the IMolecularFormula from a particular isotope.
getIsotopeCount() - Method in class org.openscience.cdk.formula.MolecularFormula
Checks a set of Nodes for the number of different isotopes in the IMolecularFormula.
getIsotopeCount() - Method in class org.openscience.cdk.formula.MolecularFormulaRange
Checks a set of Nodes for the number of different isotopes in the MolecularFormulaExpand.
getIsotopeCount(IIsotope) - Method in interface org.openscience.cdk.interfaces.IAdductFormula
Checks a set of Nodes for the occurrence of the isotope in the adduct formula from a particular isotope.
getIsotopeCount() - Method in interface org.openscience.cdk.interfaces.IAdductFormula
Checks a set of Nodes for the number of different isotopes in the adduct formula.
getIsotopeCount(IIsotope) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
Checks a set of Nodes for the occurrence of the isotope in the IMolecularFormula from a particular isotope.
getIsotopeCount() - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
Checks a set of Nodes for the number of different isotopes in the IMolecularFormula.
getIsotopeCount(IIsotope) - Method in class org.openscience.cdk.silent.AdductFormula
Checks a set of Nodes for the occurrence of the isotope in the adduct formula from a particular isotope.
getIsotopeCount() - Method in class org.openscience.cdk.silent.AdductFormula
Checks a set of Nodes for the number of different isotopes in the adduct formula.
getIsotopeCount(IIsotope) - Method in class org.openscience.cdk.silent.MolecularFormula
Checks a set of Nodes for the occurrence of the isotope in the IMolecularFormula from a particular isotope.
getIsotopeCount() - Method in class org.openscience.cdk.silent.MolecularFormula
Checks a set of Nodes for the number of different isotopes in the IMolecularFormula.
getIsotopeCountMax(IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormulaRange
Checks a set of Nodes for the maximal occurrence of the isotope in the MolecularFormulaExpand from a particular isotope.
getIsotopeCountMin(IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormulaRange
Checks a set of Nodes for the minimal occurrence of the isotope in the MolecularFormulaExpand from a particular isotope.
getIsotopes(String) - Method in class org.openscience.cdk.config.IsotopeFactory
Gets an array of all isotopes known to the IsotopeFactory for the given element symbol.
getIsotopes() - Method in class org.openscience.cdk.config.IsotopeFactory
Gets a array of all isotopes known to the IsotopeFactory.
getIsotopes(double, double) - Method in class org.openscience.cdk.config.IsotopeFactory
Gets an array of all isotopes matching the searched exact mass within a certain difference.
getIsotopes(String) - Method in class org.openscience.cdk.config.Isotopes
Gets an array of all isotopes known to the IsotopeFactory for the given element symbol.
getIsotopes() - Method in class org.openscience.cdk.config.Isotopes
Gets a array of all isotopes known to the IsotopeFactory.
getIsotopes(double, double) - Method in class org.openscience.cdk.config.Isotopes
Gets an array of all isotopes matching the searched exact mass within a certain difference.
getIsotopes() - Method in class org.openscience.cdk.config.isotopes.IsotopeHandler
Returns the isotopes read from the XML file.
getIsotopes() - Method in class org.openscience.cdk.formula.IsotopePattern
Returns the all isotopes that form this isotope pattern.
getIsotopes(IMolecularFormula) - Method in class org.openscience.cdk.formula.IsotopePatternGenerator
Get all combinatorial chemical isotopes given a structure.
getIsotopes(IMolecularFormula, IElement) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
Get a list of IIsotope from a given IElement which is contained molecular.
getIterator() - Method in class org.openscience.cdk.smsd.helper.FinalMappings
Deprecated.
Returns a mapping Iterator
getIterator() - Method in interface org.openscience.cdk.smsd.interfaces.IFinalMapping
Deprecated.
Returns a mapping Iterator
getIx() - Method in class org.openscience.cdk.math.qm.AngularMomentum
Calculates the Ix operator
getIy() - Method in class org.openscience.cdk.math.qm.AngularMomentum
Calculates the Iy operator
getIz() - Method in class org.openscience.cdk.math.qm.AngularMomentum
Calculates the Iz operator
getKey() - Method in enum org.openscience.cdk.sgroup.SgroupType
 
getLabel() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
Returns the label of this PseudoAtom.
getLabel() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
Returns the label of this PseudoAtom.
getLabel() - Method in class org.openscience.cdk.dict.Entry
 
getLabel() - Method in interface org.openscience.cdk.interfaces.IPseudoAtom
Returns the label of this PseudoAtom.
getLabel() - Method in class org.openscience.cdk.PseudoAtom
Returns the label of this PseudoAtom.
getLabel() - Method in class org.openscience.cdk.signature.Orbit
Gets the label of the orbit.
getLabel() - Method in class org.openscience.cdk.silent.PseudoAtom
Returns the label of this PseudoAtom.
getLabel(Integer) - Method in class org.openscience.cdk.smsd.helper.LabelContainer
Deprecated.
Returns Label of a given ID
getLabel() - Method in class org.openscience.cdk.Vibration
Gets the label identifying this vibration.
getLabelID(String) - Method in class org.openscience.cdk.smsd.helper.LabelContainer
Deprecated.
Returns label ID
getLargestRingSet(List<IRingSet>) - Method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D
Returns the largest (number of atoms) ring set in a molecule.
getLargestRingSet(List<IRingSet>) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator
Returns the largest (number of atoms) ring set in a molecule
getLast() - Method in class org.openscience.cdk.smiles.InvPair
 
getLastAtom() - Method in class org.openscience.cdk.AtomContainer
Returns the atom at the last position in the container.
getLastAtom() - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns the atom at the last position in the container.
getLastAtom() - Method in class org.openscience.cdk.debug.DebugAtomContainer
Returns the atom at the last position in the container.
getLastAtom() - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns the atom at the last position in the container.
getLastAtom() - Method in class org.openscience.cdk.debug.DebugCrystal
Returns the atom at the last position in the container.
getLastAtom() - Method in class org.openscience.cdk.debug.DebugMonomer
Returns the atom at the last position in the container.
getLastAtom() - Method in class org.openscience.cdk.debug.DebugPolymer
Returns the atom at the last position in the container.
getLastAtom() - Method in class org.openscience.cdk.debug.DebugRing
Returns the atom at the last position in the container.
getLastAtom() - Method in class org.openscience.cdk.debug.DebugStrand
Returns the atom at the last position in the container.
getLastAtom() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
getLastAtom() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Returns the atom at the last position in the container.
getLastAtom() - Method in class org.openscience.cdk.silent.AtomContainer
Returns the atom at the last position in the container.
getLatticeConstant() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
 
getLatticeConstant() - Method in class org.openscience.cdk.tools.GridGenerator
 
getLeft() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom
Deprecated.
getLeft() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond
 
getLeftTransversal(int) - Method in class org.openscience.cdk.group.PermutationGroup
Get the traversal Ui from the list of transversals.
getLength() - Method in class org.openscience.cdk.iupac.parser.AttachedGroup
Getter for property length.
getLength2D(IBond) - Static method in class org.openscience.cdk.geometry.GeometryTools
Returns the geometric length of this bond in 2D space.
getLength2D(IBond) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Returns the geometric length of this bond in 2D space.
getLevel() - Method in class org.openscience.cdk.io.setting.IOSetting
 
getLigandAtom() - Method in interface org.openscience.cdk.geometry.cip.ILigand
IAtom of the ligand that is connected to the central IAtom via one IBond.
getLigandAtom() - Method in class org.openscience.cdk.geometry.cip.Ligand
IAtom of the ligand that is connected to the chiral IAtom via one IBond.
getLigandLigands(ILigand) - Static method in class org.openscience.cdk.geometry.cip.CIPTool
Returns a CIP-expanded array of side chains of a ligand.
getLigands() - Method in interface org.openscience.cdk.interfaces.ITetrahedralChirality
Returns an array of ligand atoms around the chiral atom.
getLigands() - Method in class org.openscience.cdk.stereo.TetrahedralChirality
Returns an array of ligand atoms around the chiral atom.
getLimitedPathsOfLengthUpto(IAtomContainer, IAtom, int, int) - Static method in class org.openscience.cdk.graph.PathTools
Get all the paths starting from an atom of length 0 up to the specified length.
getLine(int) - Method in class org.openscience.cdk.graph.invariant.GIMatrix
Returns the line-matrix at the given line index.
getLine() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
Deprecated.
getLine() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
Deprecated.
getLinkageRadius() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
 
getLinkmap() - Method in class org.openscience.cdk.io.RssWriter
 
getListenerCount() - Method in class org.openscience.cdk.ChemObject
Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugAtom
Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugAtomContainer
Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugAtomType
Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugBond
Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugChemFile
Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugChemModel
Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugChemObject
Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugChemSequence
Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugCrystal
Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugElectronContainer
Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugElement
Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugIsotope
Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugLonePair
Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugMapping
Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugMonomer
Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugPolymer
Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugReaction
Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugReactionScheme
Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugReactionSet
Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugRing
Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugSingleElectron
Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugStrand
Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.debug.DebugSubstance
Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in interface org.openscience.cdk.interfaces.IChemObject
Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
Returns the number of ChemObjectListeners registered with this object.
getListenerCount() - Method in class org.openscience.cdk.silent.ChemObject
Returns the number of ChemObjectListeners registered with this object.
getListeners() - Method in class org.openscience.cdk.io.ChemObjectIO
Access all the listeners for this ChemObject Reader or Writer.
getListeners() - Method in interface org.openscience.cdk.io.IChemObjectIO
Access all the listeners for this ChemObject Reader or Writer.
getLocations() - Method in class org.openscience.cdk.iupac.parser.AttachedGroup
Getter for property locations.
getLog() - Method in class org.openscience.cdk.inchi.InChIGenerator
Gets generated log.
getLog() - Method in class org.openscience.cdk.inchi.InChIToStructure
Gets generated log.
getLoggingToolClass() - Static method in class org.openscience.cdk.tools.LoggingToolFactory
Gets the currently used ILoggingTool implementation.
getLonePair(int) - Method in class org.openscience.cdk.AtomContainer
Get the lone pair at position number in [0,..].
getLonePair(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid
Get the lone pair at position number in [0,..].
getLonePair(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer
Get the lone pair at position number in [0,..].
getLonePair(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Get the lone pair at position number in [0,..].
getLonePair(int) - Method in class org.openscience.cdk.debug.DebugCrystal
Get the lone pair at position number in [0,..].
getLonePair(int) - Method in class org.openscience.cdk.debug.DebugMonomer
Get the lone pair at position number in [0,..].
getLonePair(int) - Method in class org.openscience.cdk.debug.DebugPolymer
Get the lone pair at position number in [0,..].
getLonePair(int) - Method in class org.openscience.cdk.debug.DebugRing
Get the lone pair at position number in [0,..].
getLonePair(int) - Method in class org.openscience.cdk.debug.DebugStrand
Get the lone pair at position number in [0,..].
getLonePair(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Get the lone pair at position number in [0,..].
getLonePair(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Get the lone pair at position number in [0,..].
getLonePair(int) - Method in class org.openscience.cdk.silent.AtomContainer
Get the lone pair at position number in [0,..].
getLonePairCount() - Method in class org.openscience.cdk.AtomContainer
Returns the number of LonePairs in this Container.
getLonePairCount() - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns the number of LonePairs in this Container.
getLonePairCount() - Method in class org.openscience.cdk.debug.DebugAtomContainer
Returns the number of LonePairs in this Container.
getLonePairCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns the number of LonePairs in this Container.
getLonePairCount() - Method in class org.openscience.cdk.debug.DebugCrystal
Returns the number of LonePairs in this Container.
getLonePairCount() - Method in class org.openscience.cdk.debug.DebugMonomer
Returns the number of LonePairs in this Container.
getLonePairCount() - Method in class org.openscience.cdk.debug.DebugPolymer
Returns the number of LonePairs in this Container.
getLonePairCount() - Method in class org.openscience.cdk.debug.DebugRing
Returns the number of LonePairs in this Container.
getLonePairCount() - Method in class org.openscience.cdk.debug.DebugStrand
Returns the number of LonePairs in this Container.
getLonePairCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Returns the number of LonePairs in this Container.
getLonePairCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Returns the number of LonePairs in this Container.
getLonePairCount() - Method in class org.openscience.cdk.silent.AtomContainer
Returns the number of LonePairs in this Container.
getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.AtomContainer
Returns the position of a given lone pair in the lone pair array.
getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns the position of a given lone pair in the lone pair array.
getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns the position of a given lone pair in the lone pair array.
getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugCrystal
Returns the position of a given lone pair in the lone pair array.
getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugMonomer
Returns the position of a given lone pair in the lone pair array.
getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugPolymer
Returns the position of a given lone pair in the lone pair array.
getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugRing
Returns the position of a given lone pair in the lone pair array.
getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugStrand
Returns the position of a given lone pair in the lone pair array.
getLonePairNumber(ILonePair) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Returns the position of a given lone pair in the lone pair array.
getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.silent.AtomContainer
Returns the position of a given lone pair in the lone pair array.
getLongestUnplacedChain(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.layout.AtomPlacer
Search a molecule for the longest unplaced, aliphatic chain in it.
getLower() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryAngleBond
 
getLower() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryBond
 
getMajorIsotope(int) - Method in class org.openscience.cdk.config.IsotopeFactory
Returns the most abundant (major) isotope with a given atomic number.
getMajorIsotope(String) - Method in class org.openscience.cdk.config.IsotopeFactory
Returns the most abundant (major) isotope whose symbol equals element.
getMajorIsotope(int) - Method in class org.openscience.cdk.config.Isotopes
Returns the most abundant (major) isotope with a given atomic number.
getMajorIsotope(String) - Method in class org.openscience.cdk.config.Isotopes
Returns the most abundant (major) isotope whose symbol equals element.
getMajorIsotopeMass(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
Get the summed major isotopic mass of all elements from an MolecularFormula.
getMajorIsotopeMolecularFormula(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
Construct an instance of IMolecularFormula, initialized with a molecular formula string.
getMap() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IState
Deprecated.
Returns the current mapping of query atoms onto target atoms.
getMap() - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFState
Deprecated.
Returns the current mapping of query atoms onto target atoms.
getMappedAtomCount() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper
Deprecated.
 
getMappedAtomsOrg() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper
Deprecated.
 
getMappedChemObject(IReaction, IChemObject) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
get the IAtom which is mapped
getMappedSubstructures(IAtomContainer) - Method in class org.openscience.cdk.layout.TemplateHandler
Checks if one of the loaded templates is a substructure in the given Molecule and returns all matched substructures in a IAtomContainerSet.
getMapping() - Method in class org.openscience.cdk.atomtype.mapper.AtomTypeMapper
Returns the name of this mapping.
getMapping(int) - Method in interface org.openscience.cdk.interfaces.IReaction
Retrieves a mapping between the reactant and product side to this Reaction.
getMapping(int) - Method in class org.openscience.cdk.Reaction
Retrieves a mapping between the reactant and product side to this Reaction.
getMapping(int) - Method in class org.openscience.cdk.silent.Reaction
Retrieves a mapping between the reactant and product side to this Reaction.
getMappingCount() - Method in interface org.openscience.cdk.interfaces.IReaction
Get the number of mappings between the reactant and product side to this Reaction.
getMappingCount() - Method in class org.openscience.cdk.Reaction
Get the number of mappings between the reactant and product side to this Reaction.
getMappingCount() - Method in class org.openscience.cdk.silent.Reaction
Get the number of mappings between the reactant and product side to this Reaction.
getMappings() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregor
Deprecated.
Returns computed mappings.
getMappings() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
Deprecated.
Returns mapping solutions
getMaps(IAtomContainer) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper
Deprecated.
Returns all solution map.
getMaps(TargetProperties) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper
Deprecated.
Returns all solution map.
getMaps(IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper
Deprecated.
Returns all solution map.
getMaps(TargetProperties) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper
Deprecated.
Returns all solution map.
getMaps(IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper
Deprecated.
Returns all solution map.
getMaps(TargetProperties) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper
Deprecated.
Returns all solution map.
getMass() - Method in class org.openscience.cdk.formula.IsotopeContainer
Get the mass value of this container.
getMass(String) - Method in class org.openscience.cdk.tools.AtomicProperties
 
getMassNumber() - Method in class org.openscience.cdk.debug.DebugAtom
Returns the atomic mass of this element.
getMassNumber() - Method in class org.openscience.cdk.debug.DebugAtomType
Returns the atomic mass of this element.
getMassNumber() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
Returns the atomic mass of this element.
getMassNumber() - Method in class org.openscience.cdk.debug.DebugIsotope
Returns the atomic mass of this element.
getMassNumber() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
Returns the atomic mass of this element.
getMassNumber() - Method in interface org.openscience.cdk.interfaces.IIsotope
Returns the atomic mass of this element.
getMassNumber() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
Returns the atomic mass of this element.
getMassNumber() - Method in class org.openscience.cdk.Isotope
Returns the atomic mass of this element.
getMassNumber() - Method in class org.openscience.cdk.silent.Isotope
Returns the atomic mass of this element.
getMatchingAtoms() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom
Get the atoms of a target molecule that correspond to this group.
getMatchingAtoms() - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool
Get the atoms in the target molecule that match the query pattern.
getMatchingPharmacophoreAtoms() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher
Get the matching pharmacophore groups.
getMatchingPharmacophoreBonds() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher
Get the matching pharmacophore constraints.
getMatrix(IAtomContainer) - Static method in class org.openscience.cdk.graph.matrix.AdjacencyMatrix
Returns the adjacency matrix for the given AtomContainer.
getMatrix(IAtomContainer) - Static method in class org.openscience.cdk.graph.matrix.ConnectionMatrix
Returns the connection matrix representation of this AtomContainer.
getMatrix(IAtomContainer) - Static method in class org.openscience.cdk.graph.matrix.TopologicalMatrix
Returns the topological matrix for the given AtomContainer.
getMaxBondOrder() - Method in class org.openscience.cdk.AtomType
Gets the MaxBondOrder attribute of the AtomType object.
getMaxBondOrder() - Method in class org.openscience.cdk.debug.DebugAtom
Gets the MaxBondOrder attribute of the AtomType object.
getMaxBondOrder() - Method in class org.openscience.cdk.debug.DebugAtomType
Gets the MaxBondOrder attribute of the AtomType object.
getMaxBondOrder() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
Gets the MaxBondOrder attribute of the AtomType object.
getMaxBondOrder() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
Gets the MaxBondOrder attribute of the AtomType object.
getMaxBondOrder() - Method in interface org.openscience.cdk.interfaces.IAtomType
Gets the MaxBondOrder attribute of the AtomType object.
getMaxBondOrder() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
Gets the MaxBondOrder attribute of the AtomType object.
getMaxBondOrder() - Method in class org.openscience.cdk.silent.AtomType
Gets the MaxBondOrder attribute of the AtomType object.
getMaxCliqueSet() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.BKKCKCF
Deprecated.
 
getMaxGasteigerDamp() - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
Gets the maxGasteigerDamp attribute of the GasteigerMarsiliPartialCharges object.
getMaxGasteigerIters() - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
Gets the maxGasteigerIters attribute of the GasteigerMarsiliPartialCharges object.
getMaxGasteigerIters() - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges
Gets the maxGasteigerIters attribute of the GasteigerPEPEPartialCharges object.
getMaximalFormula(MolecularFormulaRange, IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaRangeManipulator
Returns the maximal occurrence of the IIsotope into IMolecularFormula from this MolelecularFormulaRange.
getMaximalStructures() - Method in class org.openscience.cdk.tools.StructureResonanceGenerator
Get the number maximal of resonance structures to be found.
getMaximum(List) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
Deprecated.
 
getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.AtomContainer
Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
getMaximumBondOrder(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
getMaximumBondOrder(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
 
getMaximumBondOrder(List<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
Returns the maximum bond order for a List of bonds.
getMaximumBondOrder(Iterator<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
Returns the maximum bond order for a List of bonds, given an iterator to the list.
getMaximumBondOrder(IBond, IBond) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
Returns the maximum bond order for the two bonds.
getMaximumBondOrder(IBond.Order, IBond.Order) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
Returns the maximum bond order for the two bond orders.
getMaxIterations() - Method in class org.openscience.cdk.charges.Electronegativity
get the maximum number of Iterations.
getMaxIterations() - Method in class org.openscience.cdk.charges.PiElectronegativity
get the maximum number of Iterations.
getMaxNoOfBonds(IAtom) - Method in class org.openscience.cdk.tools.AtomTypeAwareSaturationChecker
This method calculates the number of bonds that an IAtom can have.
getMaxOccurrenceElements(IMolecularFormulaSet) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaSetManipulator
Extract from a set of MolecularFormula the maximum occurrence of each element found and put the element and occurrence in a new IMolecularFormula.
getMaxResonStruc() - Method in class org.openscience.cdk.charges.Electronegativity
get the maximum number of resonance structures.
getMaxResonStruc() - Method in class org.openscience.cdk.charges.PiElectronegativity
get the maximum number of resonance structures.
getMaxResoStruc() - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges
Gets the maximum resonance structures to be searched.
getMaxX() - Method in class org.openscience.cdk.math.qm.FourierGridBasis
 
getMaxX() - Method in class org.openscience.cdk.math.qm.GaussiansBasis
Gets the dimension of the volume, which describes the base.
getMaxX() - Method in interface org.openscience.cdk.math.qm.IBasis
Gets the dimension of the volume, which describes the base.
getMaxx() - Method in class org.openscience.cdk.tools.GridGenerator
 
getMaxY() - Method in class org.openscience.cdk.math.qm.FourierGridBasis
 
getMaxY() - Method in class org.openscience.cdk.math.qm.GaussiansBasis
Gets the dimension of the volume, which describes the base.
getMaxY() - Method in interface org.openscience.cdk.math.qm.IBasis
Gets the dimension of the volume, which describes the base.
getMaxy() - Method in class org.openscience.cdk.tools.GridGenerator
 
getMaxZ() - Method in class org.openscience.cdk.math.qm.FourierGridBasis
 
getMaxZ() - Method in class org.openscience.cdk.math.qm.GaussiansBasis
Gets the dimension of the volume, which describes the base.
getMaxZ() - Method in interface org.openscience.cdk.math.qm.IBasis
Gets the dimension of the volume, which describes the base.
getMaxz() - Method in class org.openscience.cdk.tools.GridGenerator
 
getMCSSize() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregor
Deprecated.
Returns MCS size.
getMechanism() - Method in class org.openscience.cdk.dict.EntryReact
Get the mechanism of this reaction.
getMerge() - Method in class org.openscience.cdk.renderer.RendererModel
This is the central facility for handling "merges" of atoms.
getMessage() - Method in class org.openscience.cdk.inchi.InChIGenerator
Gets generated (error/warning) messages.
getMessage() - Method in class org.openscience.cdk.inchi.InChIToStructure
Gets generated (error/warning) messages.
getMessage() - Method in error org.openscience.cdk.iupac.parser.TokenMgrError
You can also modify the body of this method to customize your error messages.
getMessage() - Method in error org.openscience.cdk.smiles.smarts.parser.TokenMgrError
You can also modify the body of this method to customize your error messages.
getMIMEType() - Method in class org.openscience.cdk.io.formats.ABINITFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.Aces2Format
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.ADFFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.AlchemyFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.BGFFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.BSFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
 
getMIMEType() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.CACheFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
 
getMIMEType() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.CIFFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.CMLFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.CRK2DFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.CRK3DFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.CrystClustFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.CTXFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.DaltonFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.DMol3Format
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.DOCK5Format
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.FingerprintFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.GamessFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian03Format
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian90Format
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian92Format
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian94Format
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian95Format
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian98Format
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat
 
getMIMEType() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.GROMOS96Format
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.HINFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.INChIFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in interface org.openscience.cdk.io.formats.IResourceFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.JaguarFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.JMEFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MacroModelFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MDLFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MDLV2000Format
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MDLV3000Format
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MMODFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.Mol2Format
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC7Format
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC93Format
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC97Format
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.MPQCFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.NWChemFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.PCModelFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.PDBFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.PDBMLFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.PMPFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.POVRayFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.PQSChemFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.QChemFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.RawCopyFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.SDFFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.ShelXFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.SMARTSFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.SMILESFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.SpartanFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.SVGFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.VASPFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.ViewmolFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.XEDFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.XYZFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.YasaraFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.ZindoFormat
Returns the accepted MIME type for this format.
getMIMEType() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat
Returns the accepted MIME type for this format.
getMinimalFormula(MolecularFormulaRange, IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaRangeManipulator
Returns the minimal occurrence of the IIsotope into IMolecularFormula from this MolelecularFormulaRange.
getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.AtomContainer
Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
getMinimumBondOrder(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
getMinimumBondOrder(List<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
Returns the minimum bond order for a List of bonds.
getMinimumBondOrder(Iterator<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
Returns the minimum bond order for a List of bonds, given an iterator to the list.
getMinMax(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
Returns the minimum and maximum X and Y coordinates of the atoms in the AtomContainer.
getMinMax(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Returns the minimum and maximum X and Y coordinates of the atoms in the AtomContainer.
getMinOccurrenceElements(IMolecularFormulaSet) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaSetManipulator
Extract from a set of MolecularFormula the minimal occurrence of each element found and put the element and occurrence in a new IMolecularFormula.
getMinPSCluster() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
 
getMinPSPocket() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
 
getMinX() - Method in class org.openscience.cdk.math.qm.FourierGridBasis
 
getMinX() - Method in class org.openscience.cdk.math.qm.GaussiansBasis
Gets the dimension of the volume, which describes the base.
getMinX() - Method in interface org.openscience.cdk.math.qm.IBasis
Gets the dimension of the volume, which describes the base.
getMinx() - Method in class org.openscience.cdk.tools.GridGenerator
 
getMinY() - Method in class org.openscience.cdk.math.qm.FourierGridBasis
 
getMinY() - Method in class org.openscience.cdk.math.qm.GaussiansBasis
Gets the dimension of the volume, which describes the base.
getMinY() - Method in interface org.openscience.cdk.math.qm.IBasis
Gets the dimension of the volume, which describes the base.
getMiny() - Method in class org.openscience.cdk.tools.GridGenerator
 
getMinZ() - Method in class org.openscience.cdk.math.qm.FourierGridBasis
 
getMinZ() - Method in class org.openscience.cdk.math.qm.GaussiansBasis
Gets the dimension of the volume, which describes the base.
getMinZ() - Method in interface org.openscience.cdk.math.qm.IBasis
Gets the dimension of the volume, which describes the base.
getMinz() - Method in class org.openscience.cdk.tools.GridGenerator
 
getModelCenter() - Method in class org.openscience.cdk.renderer.AbstractRenderer
Get the center of the model.
getMolecularFormula(int) - Method in class org.openscience.cdk.debug.DebugAdductFormula
Returns the MolecularFormula at position number in the chemObject.
getMolecularFormula(int) - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet
Returns the MolecularFormula at position number in the chemObject.
getMolecularFormula(int) - Method in class org.openscience.cdk.formula.AdductFormula
Returns the MolecularFormula at position number in the chemObject.
getMolecularFormula(int) - Method in class org.openscience.cdk.formula.MolecularFormulaSet
Returns the MolecularFormula at position number in the chemObject.
getMolecularFormula(int) - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet
Returns the IMolecularFormula at position number in the chemObject.
getMolecularFormula(int) - Method in class org.openscience.cdk.silent.AdductFormula
Returns the MolecularFormula at position number in the chemObject.
getMolecularFormula(int) - Method in class org.openscience.cdk.silent.MolecularFormulaSet
Returns the MolecularFormula at position number in the chemObject.
getMolecularFormula(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
Construct an instance of IMolecularFormula, initialized with a molecular formula string.
getMolecularFormula(String, IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
add in a instance of IMolecularFormula the elements extracts form molecular formula string.
getMolecularFormula(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
Method that actually does the work of convert the atomContainer to IMolecularFormula.
getMolecularFormula(IAtomContainer, IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
Method that actually does the work of convert the atomContainer to IMolecularFormula given a IMolecularFormula.
getMolecularGraphDiameter(IAtomContainer) - Static method in class org.openscience.cdk.graph.PathTools
Returns the diameter of the molecular graph.
getMolecularGraphRadius(IAtomContainer) - Static method in class org.openscience.cdk.graph.PathTools
Returns the radius of the molecular graph.
getMolecule() - Method in class org.openscience.cdk.layout.AtomPlacer
Return the molecule the AtomPlacer currently works with
getMolecule() - Method in class org.openscience.cdk.layout.RingPlacer
 
getMolecule() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
Returns the molecule, usually used after a call of generateCoordinates()
getMolecule() - Method in class org.openscience.cdk.smsd.tools.MolHandler
Deprecated.
Returns the modified container
getMolecule() - Method in class org.openscience.cdk.structgen.RandomGenerator
Returns the molecule which reflects the current state of this stochastic structure generator.
getMoleculeGraph(IAtomContainer) - Static method in class org.openscience.cdk.graph.MoleculeGraphs
Creates a molecule graph for use with jgrapht.
getMoleculeSet() - Method in class org.openscience.cdk.ChemModel
Returns the MoleculeSet of this ChemModel.
getMoleculeSet() - Method in class org.openscience.cdk.debug.DebugChemModel
Returns the MoleculeSet of this ChemModel.
getMoleculeSet() - Method in interface org.openscience.cdk.interfaces.IChemModel
Returns the IAtomContainerSet of this ChemModel.
getMoleculeSet() - Method in class org.openscience.cdk.silent.ChemModel
Returns the MoleculeSet of this ChemModel.
getMonoIsotope() - Method in class org.openscience.cdk.formula.IsotopePattern
Returns the mono-isotope peak that form this isotope pattern.
getMonomer(String, String) - Method in class org.openscience.cdk.BioPolymer
Retrieves a Monomer object by specifying its name.
getMonomer(String) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Retrieves a Monomer object by specifying its name.
getMonomer(String, String) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Retrieves a Monomer object by specifying its name.
getMonomer(String) - Method in class org.openscience.cdk.debug.DebugPolymer
Retrieves a Monomer object by specifying its name.
getMonomer(String) - Method in class org.openscience.cdk.debug.DebugStrand
Retrieves a Monomer object by specifying its name.
getMonomer(String, String) - Method in interface org.openscience.cdk.interfaces.IBioPolymer
Retrieve a Monomer object by specifying its name.
getMonomer(String) - Method in interface org.openscience.cdk.interfaces.IPolymer
Retrieve a Monomer object by specifying its name.
getMonomer(String) - Method in interface org.openscience.cdk.interfaces.IStrand
Retrieve a Monomer object by specifying its name.
getMonomer(String) - Method in class org.openscience.cdk.Polymer
Retrieves a Monomer object by specifying its name.
getMonomer(String, String) - Method in class org.openscience.cdk.silent.BioPolymer
Retrieves a Monomer object by specifying its name.
getMonomer(String) - Method in class org.openscience.cdk.silent.Polymer
Retrieves a Monomer object by specifying its name.
getMonomer(String) - Method in class org.openscience.cdk.silent.Strand
Retrieves a Monomer object by specifying its name.
getMonomer(String) - Method in class org.openscience.cdk.Strand
Retrieves a Monomer object by specifying its name.
getMonomerCount() - Method in class org.openscience.cdk.BioPolymer
Returns the number of monomers present in BioPolymer.
getMonomerCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns the number of monomers present in BioPolymer.
getMonomerCount() - Method in class org.openscience.cdk.debug.DebugPolymer
Returns the number of monomers present in the Polymer.
getMonomerCount() - Method in class org.openscience.cdk.debug.DebugStrand
Returns the number of monomers present in the Strand.
getMonomerCount() - Method in interface org.openscience.cdk.interfaces.IBioPolymer
Return the number of monomers present in BioPolymer.
getMonomerCount() - Method in interface org.openscience.cdk.interfaces.IPolymer
Return the number of monomers present in the Polymer.
getMonomerCount() - Method in interface org.openscience.cdk.interfaces.IStrand
Return the number of monomers present in the Strand.
getMonomerCount() - Method in class org.openscience.cdk.Polymer
Returns the number of monomers present in the Polymer.
getMonomerCount() - Method in class org.openscience.cdk.silent.BioPolymer
Returns the number of monomers present in BioPolymer.
getMonomerCount() - Method in class org.openscience.cdk.silent.Polymer
Returns the number of monomers present in the Polymer.
getMonomerCount() - Method in class org.openscience.cdk.silent.Strand
Returns the number of monomers present in the Strand.
getMonomerCount() - Method in class org.openscience.cdk.Strand
Returns the number of monomers present in the Strand.
getMonomerName() - Method in class org.openscience.cdk.debug.DebugAminoAcid
Retrieves the monomer name.
getMonomerName() - Method in class org.openscience.cdk.debug.DebugMonomer
Retrieves the monomer name.
getMonomerName() - Method in interface org.openscience.cdk.interfaces.IMonomer
Retrieve the monomer name.
getMonomerName() - Method in class org.openscience.cdk.Monomer
Retrieves the monomer name.
getMonomerName() - Method in class org.openscience.cdk.silent.Monomer
Retrieves the monomer name.
getMonomerNames() - Method in class org.openscience.cdk.BioPolymer
Returns a collection of the names of all Monomers in this BioPolymer.
getMonomerNames() - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns a collection of the names of all Monomers in this BioPolymer.
getMonomerNames() - Method in class org.openscience.cdk.debug.DebugPolymer
Returns a collection of the names of all Monomers in this polymer.
getMonomerNames() - Method in class org.openscience.cdk.debug.DebugStrand
Returns a collection of the names of all Monomers in this polymer.
getMonomerNames() - Method in interface org.openscience.cdk.interfaces.IBioPolymer
Returns a collection of the names of all Monomers in this BioPolymer.
getMonomerNames() - Method in interface org.openscience.cdk.interfaces.IPolymer
Returns a collection of the names of all Monomers in this polymer.
getMonomerNames() - Method in interface org.openscience.cdk.interfaces.IStrand
Returns a collection of the names of all Monomers in this polymer.
getMonomerNames() - Method in class org.openscience.cdk.Polymer
Returns a collection of the names of all Monomers in this polymer.
getMonomerNames() - Method in class org.openscience.cdk.silent.BioPolymer
Returns a collection of the names of all Monomers in this BioPolymer.
getMonomerNames() - Method in class org.openscience.cdk.silent.Polymer
Returns a collection of the names of all Monomers in this polymer.
getMonomerNames() - Method in class org.openscience.cdk.silent.Strand
Returns a collection of the names of all Monomers in this polymer.
getMonomerNames() - Method in class org.openscience.cdk.Strand
Returns a collection of the names of all Monomers in this polymer.
getMonomerNamesInSequentialOrder() - Method in class org.openscience.cdk.protein.data.PDBPolymer
Returns the monomer names in the order in which they were added.
getMonomerNamesInSequentialOrder() - Method in class org.openscience.cdk.protein.data.PDBStrand
Returns the monomer names in the order in which they were added.
getMonomerNamesInSequentialOrder() - Method in class org.openscience.cdk.silent.PDBPolymer
Returns the monomer names in the order in which they were added.
getMonomers() - Method in class org.openscience.cdk.debug.DebugStrand
Returns a hashtable containing the monomers in the strand.
getMonomers() - Method in interface org.openscience.cdk.interfaces.IStrand
Returns the monomers in this strand.
getMonomers() - Method in class org.openscience.cdk.silent.Strand
Returns a hashtable containing the monomers in the strand.
getMonomers() - Method in class org.openscience.cdk.Strand
Returns a hashtable containing the monomers in the strand.
getMonomerType() - Method in class org.openscience.cdk.debug.DebugAminoAcid
Retrieves the monomer type.
getMonomerType() - Method in class org.openscience.cdk.debug.DebugMonomer
Retrieves the monomer type.
getMonomerType() - Method in interface org.openscience.cdk.interfaces.IMonomer
Retrieve the monomer type.
getMonomerType() - Method in class org.openscience.cdk.Monomer
Retrieves the monomer type.
getMonomerType() - Method in class org.openscience.cdk.silent.Monomer
Retrieves the monomer type.
getMorganNumbers(IAtomContainer) - Static method in class org.openscience.cdk.graph.invariant.MorganNumbersTools
Makes an array containing the morgan numbers of the atoms of atomContainer.
getMorganNumbersWithElementSymbol(IAtomContainer) - Static method in class org.openscience.cdk.graph.invariant.MorganNumbersTools
Makes an array containing the morgan numbers+element symbol of the atoms of atomContainer.
getMostComplexRing(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator
Returns the ring with the highest numbers of other rings attached to it.
getMultiMap() - Method in class org.openscience.cdk.io.RssWriter
 
getMultiplier(int) - Method in class org.openscience.cdk.AtomContainerSet
Returns the multiplier for the AtomContainer at position number in the container.
getMultiplier(IAtomContainer) - Method in class org.openscience.cdk.AtomContainerSet
Returns the multiplier of the given AtomContainer.
getMultiplier(int) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
Returns the multiplier for the AtomContainer at position number in the container.
getMultiplier(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
Returns the multiplier of the given AtomContainer.
getMultiplier(int) - Method in class org.openscience.cdk.debug.DebugSubstance
Returns the multiplier for the AtomContainer at position number in the container.
getMultiplier(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugSubstance
Returns the multiplier of the given AtomContainer.
getMultiplier(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
Returns the multiplier for the AtomContainer at position number in the container.
getMultiplier(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
Returns the multiplier of the given AtomContainer.
getMultiplier(int) - Method in class org.openscience.cdk.silent.AtomContainerSet
Returns the multiplier for the AtomContainer at position number in the container.
getMultiplier(IAtomContainer) - Method in class org.openscience.cdk.silent.AtomContainerSet
Returns the multiplier of the given AtomContainer.
getMultipliers() - Method in class org.openscience.cdk.AtomContainerSet
Returns an array of double with the stoichiometric coefficients of the products.
getMultipliers() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
Returns an array of double with the stoichiometric coefficients of the products.
getMultipliers() - Method in class org.openscience.cdk.debug.DebugSubstance
Returns an array of double with the stoichiometric coefficients of the products.
getMultipliers() - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
Returns an array of double with the stoichiometric coefficients of the products.
getMultipliers() - Method in class org.openscience.cdk.silent.AtomContainerSet
Returns an array of double with the stoichiometric coefficients of the products.
getName() - Method in class org.openscience.cdk.debug.DebugPDBAtom
get the Atom name of this atom.
getName() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
get the Atom name of this atom.
getName() - Method in interface org.openscience.cdk.interfaces.ISetting
Access the name of the setting.
getName() - Method in class org.openscience.cdk.io.setting.IOSetting
 
getName() - Method in class org.openscience.cdk.iupac.parser.AttachedGroup
Getter for property name.
getName() - Method in class org.openscience.cdk.libio.md.Residue
 
getName() - Method in class org.openscience.cdk.protein.data.PDBAtom
get the Atom name of this atom.
getName() - Method in class org.openscience.cdk.silent.PDBAtom
get the Atom name of this atom.
getName(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
Get the name of the element.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.ABINITFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.Aces2Format
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.ADFFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.AlchemyFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.BGFFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.BSFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
 
getNameExtensions() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.CACheFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
 
getNameExtensions() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.CIFFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.CMLFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.CRK2DFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.CRK3DFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.CrystClustFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.CTXFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.DaltonFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.DMol3Format
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.DOCK5Format
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.FingerprintFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.GamessFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian03Format
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian90Format
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian92Format
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian94Format
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian95Format
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian98Format
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat
 
getNameExtensions() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.GROMOS96Format
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.HINFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.INChIFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in interface org.openscience.cdk.io.formats.IResourceFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.JaguarFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.JMEFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MacroModelFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MDLFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MDLV2000Format
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MDLV3000Format
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MMODFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.Mol2Format
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC7Format
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC93Format
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC97Format
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.MPQCFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.NWChemFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.PCModelFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.PDBFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.PDBMLFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.PMPFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.POVRayFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.PQSChemFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.QChemFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.RawCopyFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.SDFFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.ShelXFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.SMARTSFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.SMILESFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.SpartanFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.SVGFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.VASPFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.ViewmolFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.XEDFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.XYZFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.YasaraFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.ZindoFormat
Returns an array of common resource name extensions.
getNameExtensions() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat
Returns an array of common resource name extensions.
getNames() - Static method in class org.openscience.cdk.config.fragments.EStateFragments
Get the fragment names.
getNames() - Method in class org.openscience.cdk.qsar.DescriptorValue
Returns an array of names for each descriptor value calculated.
getNativeRingRadius(IRing, double) - Method in class org.openscience.cdk.layout.RingPlacer
Returns the ring radius of a perfect polygons of size ring.getAtomCount() The ring radius is the distance of each atom to the ringcenter.
getNaturalAbundance() - Method in class org.openscience.cdk.debug.DebugAtom
Gets the NaturalAbundance attribute of the Isotope object.
getNaturalAbundance() - Method in class org.openscience.cdk.debug.DebugAtomType
Gets the NaturalAbundance attribute of the Isotope object.
getNaturalAbundance() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
Gets the NaturalAbundance attribute of the Isotope object.
getNaturalAbundance() - Method in class org.openscience.cdk.debug.DebugIsotope
Gets the NaturalAbundance attribute of the Isotope object.
getNaturalAbundance() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
Gets the NaturalAbundance attribute of the Isotope object.
getNaturalAbundance() - Method in interface org.openscience.cdk.interfaces.IIsotope
Gets the NaturalAbundance attribute of the Isotope object.
getNaturalAbundance() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
Gets the NaturalAbundance attribute of the Isotope object.
getNaturalAbundance() - Method in class org.openscience.cdk.Isotope
Gets the NaturalAbundance attribute of the Isotope object.
getNaturalAbundance() - Method in class org.openscience.cdk.silent.Isotope
Gets the NaturalAbundance attribute of the Isotope object.
getNaturalExactMass(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
Returns the molecular mass of the IAtomContainer.
getNaturalExactMass(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
Get the summed natural mass of all elements from an MolecularFormula.
getNaturalMass(IElement) - Method in class org.openscience.cdk.config.IsotopeFactory
Gets the natural mass of this element, defined as average of masses of isotopes, weighted by abundance.
getNeighborBondNumA() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper
Deprecated.
 
getNeighborBondNumA() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.QueryProcessor
Deprecated.
 
getNeighborBondNumB() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper
Deprecated.
 
getNeighborBondNumB() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.TargetProcessor
Deprecated.
 
getNeighbors(int) - Method in class org.openscience.cdk.geometry.surface.NeighborList
 
getNeighbors(IAtom) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.TargetProperties
Deprecated.
 
getNextBond(IBond, IAtom) - Method in class org.openscience.cdk.debug.DebugRing
Returns the next bond in order, relative to a given bond and atom.
getNextBond(IBond, IAtom) - Method in interface org.openscience.cdk.interfaces.IRing
Returns the next bond in order, relative to a given bond and atom.
getNextBond(IBond, IAtom) - Method in class org.openscience.cdk.Ring
Returns the next bond in order, relative to a given bond and atom.
getNextBond(IBond, IAtom) - Method in class org.openscience.cdk.silent.Ring
Returns the next bond in order, relative to a given bond and atom.
getNextBondVector(IAtom, IAtom, Point2d, boolean) - Method in class org.openscience.cdk.layout.AtomPlacer
Returns the next bond vector needed for drawing an extended linear chain of atoms.
getNextFormula() - Method in class org.openscience.cdk.formula.MolecularFormulaGenerator
Returns next generated formula or null in case no new formula was found (search is finished).
getNextPermutation() - Method in class org.openscience.cdk.graph.Permutor
Get the next permutation in the list.
getNextPermutation() - Method in class org.openscience.cdk.smsd.labelling.Permutor
Deprecated.
Get the next permutation in the list.
getNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
Gets the nextPlacedHeavyAtomWithAliphaticPlacedNeigbor from an atom container or molecule.
getNextPlacedHeavyAtomWithUnplacedRingNeighbour(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
Gets the nextPlacedHeavyAtomWithUnplacedRingNeighbour attribute of the AtomPlacer3D object.
getNextToken() - Method in class org.openscience.cdk.iupac.parser.NomParser
Deprecated.
Get the next Token.
getNextToken() - Method in class org.openscience.cdk.iupac.parser.NomParserTokenManager
Get the next Token.
getNextToken() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
Get the next Token.
getNextToken() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager
Get the next Token.
getNextUnplacedHeavyAtomWithAliphaticPlacedNeighbour(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
Gets the nextUnplacedHeavyAtomWithAliphaticPlacedNeighbour from an atom container or molecule.
getNode(int) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder
Deprecated.
Returns a node of the query mol at a given position.
getNode(IAtom) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder
Deprecated.
Return a node for a given atom else return null
getNode(int) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQuery
Deprecated.
Returns a node of the query mol at a given position.
getNodesInSphere(int) - Method in class org.openscience.cdk.tools.HOSECodeGenerator
 
getNormal(Point3d, Point3d, Point3d) - Static method in class org.openscience.cdk.stereo.StereoTool
Given three points (A, B, C), makes the vectors A-B and A-C, and makes the cross product of these two vectors; this has the effect of making a third vector at right angles to AB and AC.
getNormalizationFactor(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
Calculates the normalization factor in order to get an average bond length of 1.5.
getNormalizationFactor(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Calculates the normalization factor in order to get an average bond length of 1.5.
getNormalizedElectronegativity(String) - Method in class org.openscience.cdk.tools.AtomicProperties
 
getNormalizedMass(String) - Method in class org.openscience.cdk.tools.AtomicProperties
 
getNormalizedPolarizability(String) - Method in class org.openscience.cdk.tools.AtomicProperties
 
getNormalizedVdWVolume(String) - Method in class org.openscience.cdk.tools.AtomicProperties
 
getNoteComments() - Method in class org.openscience.cdk.fingerprint.model.Bayesian
Returns the optional comments, which is a list of arbitrary text strings.
getNoteOrigin() - Method in class org.openscience.cdk.fingerprint.model.Bayesian
Returns the optional description of the source for the model.
getNotEqual() - Method in class org.openscience.cdk.smsd.helper.BinaryTree
Deprecated.
Returns not equal node
getNoteTitle() - Method in class org.openscience.cdk.fingerprint.model.Bayesian
Returns the optional title used to describe the model.
getNotification() - Method in class org.openscience.cdk.ChemObject
 
getNotification() - Method in class org.openscience.cdk.debug.DebugChemObject
Returns the flag that indicates whether notification messages are sent around.
getNotification() - Method in interface org.openscience.cdk.interfaces.IChemObject
Returns the flag that indicates whether notification messages are sent around.
getNotification() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
 
getNotification() - Method in class org.openscience.cdk.renderer.RendererModel
Determines if the model sends around change notifications.
getNotification() - Method in class org.openscience.cdk.silent.ChemObject
 
getNS() - Method in class org.openscience.cdk.dict.Dictionary
 
getNTerminus() - Method in class org.openscience.cdk.AminoAcid
Retrieves the N-terminus atom.
getNTerminus() - Method in class org.openscience.cdk.debug.DebugAminoAcid
Retrieves the N-terminus atom.
getNTerminus() - Method in interface org.openscience.cdk.interfaces.IAminoAcid
Retrieves the N-terminus atom.
getNTerminus() - Method in class org.openscience.cdk.silent.AminoAcid
Retrieves the N-terminus atom.
getNumAtoms() - Method in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
 
getNumber() - Method in class org.openscience.cdk.libio.md.ChargeGroup
 
getNumber() - Method in class org.openscience.cdk.libio.md.Residue
 
getNumberOfFontSizes() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
Get the number of font sizes used.
getNumberOfIsotopes() - Method in class org.openscience.cdk.formula.IsotopePattern
Returns the number of isotopes in this pattern.
getNumberOfNeighbors(int) - Method in class org.openscience.cdk.geometry.surface.NeighborList
 
getNumberOfTriangles() - Method in class org.openscience.cdk.geometry.surface.Tessellate
 
getNumbers(IAtomContainer) - Static method in class org.openscience.cdk.graph.invariant.InChINumbersTools
Makes an array containing the InChI atom numbers of the non-hydrogen atoms in the atomContainer.
getOccupancy() - Method in class org.openscience.cdk.debug.DebugPDBAtom
get the Occupancy of this atom.
getOccupancy() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
get the Occupancy of this atom.
getOccupancy() - Method in class org.openscience.cdk.protein.data.PDBAtom
get the Occupancy of this atom.
getOccupancy() - Method in class org.openscience.cdk.silent.PDBAtom
get the Occupancy of this atom.
getOccurrence() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
Returns the occurrence value.
getOKCount() - Method in class org.openscience.cdk.validate.ValidationReport
Returns the number of tests without errors.
getOKs() - Method in class org.openscience.cdk.validate.ValidationReport
Returns an array of ValidationTest which did not find problems.
getOperator() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom
Deprecated.
getOperator() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond
 
getOptions() - Method in class org.openscience.cdk.io.setting.OptionIOSetting
Returns a Vector of Strings containing all possible options.
getOrbit(int) - Method in class org.openscience.cdk.group.Permutation
Get all the elements in the same orbit in the permutation (unsorted).
getOrder() - Method in class org.openscience.cdk.Bond
Returns the bond order of this bond.
getOrder() - Method in class org.openscience.cdk.debug.DebugBond
Returns the bond order of this bond.
getOrder() - Method in interface org.openscience.cdk.interfaces.IBond
Returns the bond order of this bond.
getOrder() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
Returns the query bond order of this query bond.
getOrder() - Method in class org.openscience.cdk.silent.Bond
Returns the bond order of this bond.
getOther(IAtom) - Method in class org.openscience.cdk.Bond
Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correct IBond.getConnectedAtoms(IAtom) should be used.
getOther(IAtom) - Method in class org.openscience.cdk.debug.DebugBond
Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correct IBond.getConnectedAtoms(IAtom) should be used.
getOther(IAtom) - Method in interface org.openscience.cdk.interfaces.IBond
Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correct IBond.getConnectedAtoms(IAtom) should be used.
getOther(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correct IBond.getConnectedAtoms(IAtom) should be used.
getOther(IAtom) - Method in class org.openscience.cdk.silent.Bond
Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correct IBond.getConnectedAtoms(IAtom) should be used.
getOtherBondAtom(IAtom, IBond) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
Returns the other atom of the bond.
getOverlaps(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
Returns all the maximal common substructure between two atom containers.
getOverlaps(IAtomContainer, IAtomContainer, boolean) - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlus
Deprecated.
 
getOverlaps(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
Deprecated.
Returns all the maximal common substructure between 2 atom containers.
getOverLaps(IAtomContainer, IAtomContainer, boolean) - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMapping
Deprecated.
Returns single mapping solutions.
getOverLaps(IQueryAtomContainer, IAtomContainer, boolean) - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMapping
Deprecated.
Returns single mapping solutions.
getOverlapScore(IAtomContainer, Vector, Vector) - Method in class org.openscience.cdk.layout.OverlapResolver
Deprecated.
Calculates a score based on the overlap of atoms and intersection of bonds.
getOxt() - Method in class org.openscience.cdk.debug.DebugPDBAtom
Returns true of this atom is a PDB OXT atom.
getOxt() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
Returns true of this atom is a PDB OXT atom.
getOxt() - Method in class org.openscience.cdk.protein.data.PDBAtom
 
getOxt() - Method in class org.openscience.cdk.silent.PDBAtom
 
getParameter(Class<T>) - Method in class org.openscience.cdk.renderer.RendererModel
Returns the IGeneratorParameter for the active IRenderer.
getParameterClass() - Method in class org.openscience.cdk.dict.EntryReact
Get the IParameterReact's of the reaction.
getParameterClass(Class<?>) - Method in interface org.openscience.cdk.reaction.IReactionProcess
Return the IParameterReact if it exists given the class.
getParameterClass(Class<?>) - Method in class org.openscience.cdk.reaction.ReactionEngine
Return the IParameterReact if it exists given the class.
getParameterList() - Method in interface org.openscience.cdk.reaction.IReactionProcess
Returns the current parameter values.
getParameterList() - Method in class org.openscience.cdk.reaction.ReactionEngine
Returns the current parameter values.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor
Gets the parameterNames attribute of the AtomDegreeDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor
Gets the parameterNames attribute of the VdWRadiusDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor
Gets the parameterNames attribute of the AtomHybridizationVSEPRDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor
Gets the parameterNames attribute of the VdWRadiusDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor
Gets the parameterNames attribute of the BondsToAtomDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor
Gets the parameterNames attribute of the VdWRadiusDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor
Gets the parameterNames attribute of the DistanceToAtomDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor
Gets the parameterNames attribute of the EffectiveAtomPolarizabilityDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor
Gets the parameterNames attribute of the InductiveAtomicHardnessDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor
Gets the parameterNames attribute of the InductiveAtomicSoftnessDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor
Gets the parameterNames attribute of the IPAtomicHOSEDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor
Deprecated.
Gets the parameterNames attribute of the IPAtomicLearningDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor
Gets the parameterNames attribute of the IsProtonInAromaticSystemDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInConjugatedPiSystemDescriptor
Gets the parameterNames attribute of the IsProtonInConjugatedPiSystemDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor
Gets the parameterNames attribute of the PartialPiChargeDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor
Gets the parameterNames attribute of the PartialSigmaChargeDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor
Gets the parameterNames attribute of the PartialTChargeMMFF94Descriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor
Gets the parameterNames attribute of the PartialTChargePEOEDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor
Gets the parameterNames attribute of the PeriodicTablePositionDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor
Gets the parameterNames attribute of the SigmaElectronegativityDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor
Gets the parameterNames attribute of the ProtonAffinityDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor
Gets the parameterNames attribute of the ProtonTotalPartialChargeDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R
Gets the parameterNames attribute of the RDFProtonDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR
Gets the parameterNames attribute of the RDFProtonDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR
Gets the parameterNames attribute of the RDFProtonDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol
Gets the parameterNames attribute of the RDFProtonDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR
Gets the parameterNames attribute of the RDFProtonDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor
Gets the parameterNames attribute of the SigmaElectronegativityDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor
Gets the parameterNames attribute of the StabilizationPlusChargeDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor
Gets the parameterNames attribute of the VdWRadiusDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor
Gets the parameterNames attribute of the PiContactDetectionDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptor
 
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor
Gets the parameterNames attribute of the BondPartialPiChargeDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor
Gets the parameterNames attribute of the BondPartialSigmaChargeDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor
Gets the parameterNames attribute of the BondPartialTChargeDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor
Gets the parameterNames attribute of the BondSigmaElectronegativityDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor
Deprecated.
Gets the parameterNames attribute of the IPBondLearningDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor
Returns the names of the parameters for this descriptor.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
 
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor
Gets the parameterNames attribute of the AromaticAtomsCountDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor
Gets the parameterNames attribute of the APolDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor
Gets the parameterNames attribute of the AromaticAtomsCountDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor
Gets the parameterNames attribute of the AromaticBondsCountDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor
Gets the parameterNames attribute of the AtomCountDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
 
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
 
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
 
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor
Returns the names of the parameters for this descriptor.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor
Gets the parameterNames attribute of the BCUTDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor
Gets the parameterNames attribute of the BondCountDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor
Gets the parameterNames attribute of the BPolDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor
Gets the parameterNames attribute of the GravitationalIndexDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
 
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
 
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
 
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
 
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor
Gets the parameterNames attribute of the CPSADescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor
Gets the parameterNames attribute of the EccentricConnectivityIndexDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor
Returns the names of the parameters for this descriptor.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor
Returns the names of the parameters for this descriptor.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor
Gets the parameterNames attribute of the FragmentComplexityDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor
Gets the parameterNames attribute of the GravitationalIndexDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor
Gets the parameterNames attribute of the HBondAcceptorCountDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor
Gets the parameterNames of the HBondDonorCountDescriptor.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor
Gets the parameterNames attribute of the HybridizationRatioDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor
Deprecated.
Gets the parameterNames attribute of the IPMolecularLearningDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor
Gets the parameterNames attribute of the KappaShapeIndicesDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor
Gets the parameterNames attribute of the descriptor.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor
Gets the parameterNames attribute of the LargestPiSystemDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor
Gets the parameterNames attribute of the LargestPiSystemDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor
Gets the parameterNames attribute of the PetitjeanNumberDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor
Gets the parameterNames attribute of the LongestAliphaticChainDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor
Gets the parameterNames attribute for this descriptor.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
Gets the parameterNames attribute of the WeightDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor
Gets the parameterNames attribute of the MomentOfInertiaDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor
Gets the parameterNames attribute of the PetitjeanNumberDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor
Gets the parameterNames attribute of the PetitjeanShapeIndexDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor
Gets the parameterNames attribute of the RotatableBondsCountDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor
Gets the parameterNames attribute of the RuleOfFiveDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor
Get parameters: empty, there are none.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor
Gets the parameterNames attribute of the TPSADescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor
Returns the names of the parameters for this descriptor.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor
Gets the parameterNames attribute of the VAdjMaDescriptor object
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor
Gets the parameterNames attribute of the WeightDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor
Gets the parameterNames attribute of the WeightedPathDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor
Gets the parameterNames attribute of the WHIMDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor
Gets the parameterNames attribute of the WienerNumbersDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor
Gets the parameterNames attribute of the XLogPDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor
Gets the parameterNames attribute of the ZagrebIndexDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor
Gets the parameterNames attribute of the TaeAminOAcidDescriptor object.
getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.substance.OxygenAtomCountDescriptor
Returns the names of the parameters for this descriptor.
getParameterNames() - Method in class org.openscience.cdk.qsar.DescriptorValue
 
getParameterNames() - Method in interface org.openscience.cdk.qsar.IDescriptor
Returns the names of the parameters for this descriptor.
getParameters() - Method in class org.openscience.cdk.dict.EntryReact
Get the parameters of the reaction.
getParameters() - Method in class org.openscience.cdk.fingerprint.AbstractFingerprinter
Base classes should override this method to report the parameters they are configured with.
getParameters() - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter
 
getParameters() - Method in class org.openscience.cdk.fingerprint.Fingerprinter
 
getParameters() - Method in class org.openscience.cdk.fingerprint.LingoFingerprinter
 
getParameters() - Method in class org.openscience.cdk.fingerprint.SignatureFingerprinter
 
getParameters() - Method in class org.openscience.cdk.formula.rules.ChargeRule
Gets the parameters attribute of the ChargeRule object.
getParameters() - Method in class org.openscience.cdk.formula.rules.ElementRule
Gets the parameters attribute of the ElementRule object.
getParameters() - Method in interface org.openscience.cdk.formula.rules.IRule
Returns the current parameter values.
getParameters() - Method in class org.openscience.cdk.formula.rules.IsotopePatternRule
Gets the parameters attribute of the IsotopePatternRule object.
getParameters() - Method in class org.openscience.cdk.formula.rules.MMElementRule
Gets the parameters attribute of the MMElementRule object.
getParameters() - Method in class org.openscience.cdk.formula.rules.NitrogenRule
Gets the parameters attribute of the NitrogenRule object.
getParameters() - Method in class org.openscience.cdk.formula.rules.RDBERule
Gets the parameters attribute of the RDBRule object.
getParameters() - Method in class org.openscience.cdk.formula.rules.ToleranceRangeRule
Gets the parameters attribute of the ToleranceRangeRule object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor
Gets the parameters attribute of the AtomDegreeDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor
Gets the parameters attribute of the VdWRadiusDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor
Gets the parameters attribute of the AtomHybridizationVSEPRDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor
Gets the parameters attribute of the VdWRadiusDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor
Gets the parameters attribute of the BondsToAtomDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor
Gets the parameters attribute of the VdWRadiusDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor
Gets the parameters attribute of the DistanceToAtomDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor
Gets the parameters attribute of the EffectiveAtomPolarizabilityDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor
Gets the parameters attribute of the InductiveAtomicHardnessDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor
Gets the parameters attribute of the InductiveAtomicSoftnessDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor
Gets the parameters attribute of the IPAtomicHOSEDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor
Deprecated.
Gets the parameters attribute of the IPAtomicLearningDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor
Gets the parameters attribute of the IsProtonInAromaticSystemDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInConjugatedPiSystemDescriptor
Gets the parameters attribute of the IsProtonInConjugatedPiSystemDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor
Gets the parameters attribute of the PartialPiChargeDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor
Gets the parameters attribute of the PartialSigmaChargeDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor
Gets the parameters attribute of the PartialTChargeMMFF94Descriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor
Gets the parameters attribute of the PartialTChargePEOEDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor
Gets the parameters attribute of the PeriodicTablePositionDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor
Gets the parameters attribute of the PiElectronegativityDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor
Gets the parameters attribute of the ProtonAffinityDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor
Gets the parameters attribute of the ProtonTotalPartialChargeDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R
Gets the parameters attribute of the RDFProtonDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR
Gets the parameters attribute of the RDFProtonDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR
Gets the parameters attribute of the RDFProtonDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol
Gets the parameters attribute of the RDFProtonDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR
Gets the parameters attribute of the RDFProtonDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor
Gets the parameters attribute of the SigmaElectronegativityDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor
Gets the parameters attribute of the StabilizationPlusChargeDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor
Gets the parameters attribute of the VdWRadiusDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor
Gets the parameters attribute of the PiContactDetectionDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptor
 
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor
Gets the parameters attribute of the BondPartialPiChargeDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor
Gets the parameters attribute of the BondPartialSigmaChargeDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor
Gets the parameters attribute of the BondPartialTChargeDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor
Gets the parameters attribute of the BondSigmaElectronegativityDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor
Deprecated.
Gets the parameters attribute of the IPBondLearningDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor
Returns the current parameter values.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
 
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor
Gets the parameters attribute of the AminoAcidsCountDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor
Gets the parameters attribute of the APolDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor
Gets the parameters attribute of the AromaticAtomsCountDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor
Gets the parameters attribute of the AromaticBondsCountDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor
Gets the parameters attribute of the AtomCountDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
 
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
 
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
 
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor
Returns the current parameter values.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor
Gets the parameters attribute of the BCUTDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor
Gets the parameters attribute of the BondCountDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor
Gets the parameters attribute of the BPolDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor
Gets the parameters attribute of the GravitationalIndexDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
 
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
 
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
 
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
 
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor
Gets the parameters attribute of the CPSADescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor
Gets the parameters attribute of the EccentricConnectivityIndexDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor
Returns the current parameter values.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor
Returns the current parameter values.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor
Gets the parameters attribute of the FragmentComplexityDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor
Gets the parameters attribute of the GravitationalIndexDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor
Gets the parameters attribute of the HBondAcceptorCountDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor
Gets the parameters of the HBondDonorCountDescriptor instance.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor
Gets the parameters attribute of the HybridizationRatioDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor
Deprecated.
Gets the parameters attribute of the IPMolecularLearningDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor
Gets the parameters attribute of the KappaShapeIndicesDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor
Gets the parameters attribute of the descriptor.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor
Gets the parameters attribute of the LargestChainDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor
Gets the parameters attribute of the LargestPiSystemDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor
Gets the parameters attribute of the PetitjeanNumberDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor
Gets the parameters attribute of the LongestAliphaticChainDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor
Gets the parameters attribute of the MannholdLogPDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
Gets the parameters attribute of the WeightDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor
Gets the parameters attribute of the MomentOfInertiaDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor
Gets the parameters attribute of the PetitjeanNumberDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor
Gets the parameters attribute of the PetitjeanShapeIndexDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor
Gets the parameters attribute of the RotatableBondsCountDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor
Gets the parameters attribute of the RuleOfFiveDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor
Get parameters: returns empty array, there are none.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor
Gets the parameters attribute of the TPSADescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor
Returns the current parameter values.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor
Gets the parameters attribute of the VAdjMaDescriptor object
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor
Gets the parameters attribute of the WeightDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor
Gets the parameters attribute of the WeightedPathDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor
Gets the parameters attribute of the WHIMDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor
Gets the parameters attribute of the WienerNumbersDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor
Gets the parameters attribute of the XLogPDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor
Gets the parameters attribute of the ZagrebIndexDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor
Gets the parameters attribute of the TaeAminoAcidDescriptor object.
getParameters() - Method in class org.openscience.cdk.qsar.descriptors.substance.OxygenAtomCountDescriptor
Returns the current parameter values.
getParameters() - Method in class org.openscience.cdk.qsar.DescriptorValue
 
getParameters() - Method in interface org.openscience.cdk.qsar.IDescriptor
Returns the current parameter values.
getParameters() - Method in class org.openscience.cdk.renderer.generators.AtomContainerBoundsGenerator
Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.AtomNumberGenerator
Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator
Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.BasicGenerator
Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator
Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.BoundsGenerator
Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.ExtendedAtomGenerator
Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.HighlightGenerator
Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in interface org.openscience.cdk.renderer.generators.IGenerator
Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.LonePairGenerator
Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.MappingGenerator
Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.ProductsBoxGenerator
Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.RadicalGenerator
Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.ReactantsBoxGenerator
Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.ReactionArrowGenerator
Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.ReactionBoxGenerator
Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.ReactionPlusGenerator
Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.ReactionSceneGenerator
Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.RingGenerator
Returns the list of IGeneratorParameter for this particular generator.
getParameters() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator
Returns the list of IGeneratorParameter for this particular generator.
getParameterSet() - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
Gets the parameterSet attribute of the ForceFieldConfigurator object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor
Gets the parameterType attribute of the AtomDegreeDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor
Gets the parameterType attribute of the VdWRadiusDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor
Gets the parameterType attribute of the AtomHybridizationVSEPRDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor
Gets the parameterType attribute of the VdWRadiusDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor
Gets the parameterType attribute of the BondsToAtomDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor
Gets the parameterType attribute of the VdWRadiusDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor
Gets the parameterType attribute of the DistanceToAtomDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor
Gets the parameterType attribute of the EffectiveAtomPolarizabilityDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor
Gets the parameterType attribute of the InductiveAtomicHardnessDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor
Gets the parameterType attribute of the InductiveAtomicSoftnessDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor
Gets the parameterType attribute of the IPAtomicHOSEDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor
Deprecated.
Gets the parameterType attribute of the IPAtomicLearningDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor
Gets the parameterType attribute of the IsProtonInAromaticSystemDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInConjugatedPiSystemDescriptor
Gets the parameterType attribute of the IsProtonInConjugatedPiSystemDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor
Gets the parameterType attribute of the PartialPiChargeDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor
Gets the parameterType attribute of the PartialSigmaChargeDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor
Gets the parameterType attribute of the PartialTChargeMMFF94Descriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor
Gets the parameterType attribute of the PartialTChargePEOEDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor
Gets the parameterType attribute of the PeriodicTablePositionDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor
Gets the parameterType attribute of the SigmaElectronegativityDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor
Gets the parameterType attribute of the ProtonAffinityDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor
Gets the parameterType attribute of the ProtonTotalPartialChargeDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R
Gets the parameterType attribute of the RDFProtonDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR
Gets the parameterType attribute of the RDFProtonDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR
Gets the parameterType attribute of the RDFProtonDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol
Gets the parameterType attribute of the RDFProtonDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR
Gets the parameterType attribute of the RDFProtonDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor
Gets the parameterType attribute of the SigmaElectronegativityDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor
Gets the parameterType attribute of the StabilizationPlusChargeDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor
Gets the parameterType attribute of the VdWRadiusDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor
Gets the parameterType attribute of the PiContactDetectionDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptor
 
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor
Gets the parameterType attribute of the BondPartialPiChargeDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor
Gets the parameterType attribute of the BondPartialSigmaChargeDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor
Gets the parameterType attribute of the BondPartialTChargeDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor
Gets the parameterType attribute of the BondSigmaElectronegativityDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor
Deprecated.
Gets the parameterType attribute of the IPBondLearningDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor
Returns a class matching that of the parameter with the given name.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
 
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor
Gets the parameterType attribute of the AromaticAtomsCountDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor
Gets the parameterType attribute of the APolDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor
Gets the parameterType attribute of the AromaticAtomsCountDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor
Gets the parameterType attribute of the AromaticBondsCountDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor
Gets the parameterType attribute of the AtomCountDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
 
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
 
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
 
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor
Returns a class matching that of the parameter with the given name.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor
Gets the parameterType attribute of the BCUTDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor
Gets the parameterType attribute of the BondCountDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor
Gets the parameterType attribute of the BPolDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor
Gets the parameterType attribute of the GravitationalIndexDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
 
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
 
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
 
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
 
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor
Gets the parameterType attribute of the CPSADescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor
Gets the parameterType attribute of the EccentricConnectivityIndexDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor
Returns a class matching that of the parameter with the given name.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor
Returns a class matching that of the parameter with the given name.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor
Gets the parameterType attribute of the FragmentComplexityDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor
Gets the parameterType attribute of the GravitationalIndexDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor
Gets the parameterType attribute of the HBondAcceptorCountDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor
Gets the parameterType of the HBondDonorCountDescriptor.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor
Gets the parameterType attribute of the HybridizationRatioDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor
Deprecated.
Gets the parameterType attribute of the IPMolecularLearningDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor
Gets the parameterType attribute of the KappaShapeIndicesDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor
Gets the parameterType attribute of the descriptor.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor
Gets the parameterType attribute of the LargestChainDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor
Gets the parameterType attribute of the LargestPiSystemDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor
Gets the parameterType attribute of the PetitjeanNumberDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor
Gets the parameterType attribute of the LongestAliphaticChainDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor
Gets the parameterType attribute for a given parameter name.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
Gets the parameterType attribute of the WeightDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor
Gets the parameterType attribute of the MomentOfInertiaDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor
Gets the parameterType attribute of the PetitjeanNumberDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor
Gets the parameterType attribute of the PetitjeanShapeIndexDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor
Gets the parameterType attribute of the RotatableBondsCountDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor
Gets the parameterType attribute of the RuleOfFiveDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor
Parameter types: there aren't any.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor
Gets the parameterType attribute of the TPSADescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor
Returns a class matching that of the parameter with the given name.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor
Gets the parameterType attribute of the VAdjMaDescriptor object
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor
Gets the parameterType attribute of the WeightDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor
Gets the parameterType attribute of the WeightedPathDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor
Gets the parameterType attribute of the WHIMDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor
Gets the parameterType attribute of the WienerNumbersDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor
Gets the parameterType attribute of the XLogPDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor
Gets the parameterType attribute of the ZagrebIndexDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor
Gets the parameterType attribute of the TaeAminoAcidDescriptor object.
getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.substance.OxygenAtomCountDescriptor
Returns a class matching that of the parameter with the given name.
getParameterType(String) - Method in interface org.openscience.cdk.qsar.IDescriptor
Returns a class matching that of the parameter with the given name.
getParameterValue() - Method in class org.openscience.cdk.dict.EntryReact
Get the parameter value of the reaction.
getParamterSet() - Method in class org.openscience.cdk.modeling.builder3d.MM2BasedParameterSetReader
 
getParamterSet() - Method in class org.openscience.cdk.modeling.builder3d.MMFF94BasedParameterSetReader
 
getParentMolecule() - Method in class org.openscience.cdk.libio.md.ChargeGroup
 
getParentMolecule() - Method in class org.openscience.cdk.libio.md.Residue
 
getParents() - Method in class org.openscience.cdk.sgroup.Sgroup
Access the parents of this Sgroup.
getPath(IAtomContainer, IAtom, IAtom) - Method in class org.openscience.cdk.graph.SpanningTree
Find a path connected a1 and a2 in the tree.
getPathsOfLength(IAtomContainer, IAtom, int) - Static method in class org.openscience.cdk.graph.PathTools
Get the paths starting from an atom of specified length.
getPathsOfLengthUpto(IAtomContainer, IAtom, int) - Static method in class org.openscience.cdk.graph.PathTools
Get all the paths starting from an atom of length 0 upto the specified length.
getPaulingElectronegativities(IAtomContainer, boolean) - Method in class org.openscience.cdk.charges.InductivePartialCharges
Gets the paulingElectronegativities attribute of the InductivePartialCharges object.
getPaulingElectronegativity(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
Get the Pauling electronegativity of an element.
getPeriod(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
Get the period of the element.
getPharmacophoreQuery() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher
Get the query pharmacophore.
getPhase(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
Get the phase of the element.
getPlacedAtoms(IAtomContainer) - Static method in class org.openscience.cdk.layout.AtomPlacer
Get all the placed atoms in an AtomContainer
getPlacedAtomsInAtomContainer(IAtom, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
Gets all placed neighbouring atoms of a atom.
getPlacedHeavyAtom(IAtomContainer, IAtom) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
Returns a placed atom connected to a given atom.
getPlacedHeavyAtom(IAtomContainer, IAtom, IAtom) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
Gets the first placed Heavy Atom around atomA which is not atomB.
getPlacedHeavyAtomInAtomContainer(IAtom, IAtom, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
Returns a placed neighbouring atom of a central atom atomA, which is not atomB.
getPlacedHeavyAtoms(IAtomContainer, IAtom) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
Gets the placed Heavy Atoms connected to an atom.
getPockets() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
 
getPocketSize() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
 
getPoint2d() - Method in class org.openscience.cdk.Atom
Returns a point specifying the location of this atom in a 2D space.
getPoint2d() - Method in class org.openscience.cdk.debug.DebugAtom
Returns a point specifying the location of this atom in a 2D space.
getPoint2d() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
Returns a point specifying the location of this atom in a 2D space.
getPoint2d() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
Returns a point specifying the location of this atom in a 2D space.
getPoint2d() - Method in interface org.openscience.cdk.interfaces.IAtom
Returns a point specifying the location of this atom in a 2D space.
getPoint2d() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
Returns a point specifying the location of this atom in a 2D space.
getPoint2d() - Method in class org.openscience.cdk.silent.Atom
Returns a point specifying the location of this atom in a 2D space.
getPoint3d() - Method in class org.openscience.cdk.Atom
Returns a point specifying the location of this atom in a 3D space.
getPoint3d() - Method in class org.openscience.cdk.debug.DebugAtom
Returns a point specifying the location of this atom in a 3D space.
getPoint3d() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
Returns a point specifying the location of this atom in a 3D space.
getPoint3d() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
Returns a point specifying the location of this atom in a 3D space.
getPoint3d() - Method in interface org.openscience.cdk.interfaces.IAtom
Returns a point specifying the location of this atom in a 3D space.
getPoint3d() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
Returns a point specifying the location of this atom in a 3D space.
getPoint3d() - Method in class org.openscience.cdk.silent.Atom
Returns a point specifying the location of this atom in a 3D space.
getPolarizabilitiyFactorForAtom(IAtomContainer, IAtom) - Method in class org.openscience.cdk.charges.Polarizability
Gets the polarizabilitiyFactorForAtom.
getPolarizability(String) - Method in class org.openscience.cdk.tools.AtomicProperties
 
getPosition(int) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
Gets the position of a base.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ABINITFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Aces2Format
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ADFFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.AlchemyFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.BGFFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.BSFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
 
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CACheFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
 
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CIFFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CMLFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CRK2DFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CRK3DFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CrystClustFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CTXFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.DaltonFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.DMol3Format
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.DOCK5Format
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.FingerprintFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.GamessFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian03Format
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian90Format
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian92Format
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian94Format
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian95Format
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian98Format
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat
 
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.GROMOS96Format
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.HINFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.INChIFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in interface org.openscience.cdk.io.formats.IResourceFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.JaguarFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.JMEFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MacroModelFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MDLFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MDLV2000Format
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MDLV3000Format
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MMODFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Mol2Format
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC7Format
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC93Format
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC97Format
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MPQCFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.NWChemFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PCModelFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PDBFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PDBMLFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PMPFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.POVRayFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PQSChemFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.QChemFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.RawCopyFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SDFFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ShelXFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SMARTSFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SMILESFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SpartanFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SVGFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.VASPFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ViewmolFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.XEDFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.XYZFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.YasaraFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ZindoFormat
Returns the preferred resource name extension.
getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat
Returns the preferred resource name extension.
getPrime() - Method in class org.openscience.cdk.smiles.InvPair
Get the current prime number.
getPrimeAt(int) - Static method in class org.openscience.cdk.math.Primes
Deprecated.
Returns the i-th prime number in the sequence of all prime numbers below 19700.
getProductCoefficient(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugReaction
Returns the stoichiometry coefficient of the given product.
getProductCoefficient(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IReaction
Returns the stoichiometry coefficient of the given product.
getProductCoefficient(IAtomContainer) - Method in class org.openscience.cdk.Reaction
Returns the stoichiometry coefficient of the given product.
getProductCoefficient(IAtomContainer) - Method in class org.openscience.cdk.silent.Reaction
Returns the stoichiometry coefficient of the given product.
getProductCoefficients() - Method in class org.openscience.cdk.debug.DebugReaction
Returns an array of double with the stoichiometric coefficients of the products.
getProductCoefficients() - Method in interface org.openscience.cdk.interfaces.IReaction
Returns an array of double with the stoichiometric coefficients of the products.
getProductCoefficients() - Method in class org.openscience.cdk.Reaction
Returns an array of double with the stoichiometric coefficients of the products.
getProductCoefficients() - Method in class org.openscience.cdk.silent.Reaction
Returns an array of double with the stoichiometric coefficients of the products.
getProductCount() - Method in class org.openscience.cdk.debug.DebugReaction
Returns the number of products in this reaction.
getProductCount() - Method in interface org.openscience.cdk.interfaces.IReaction
Returns the number of products in this reaction.
getProductCount() - Method in class org.openscience.cdk.Reaction
Returns the number of products in this reaction.
getProductCount() - Method in class org.openscience.cdk.silent.Reaction
Returns the number of products in this reaction.
getProductMolecule() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
Deprecated.
Returns modified target molecule on which mapping was performed.
getProductMolecule() - Method in class org.openscience.cdk.smsd.Isomorphism
Deprecated.
Returns modified target molecule on which mapping was performed.
getProducts() - Method in class org.openscience.cdk.debug.DebugReaction
Returns a MoleculeSet containing the products of this reaction.
getProducts() - Method in interface org.openscience.cdk.interfaces.IReaction
Returns a IAtomContaineSet containing the products of this reaction.
getProducts() - Method in class org.openscience.cdk.Reaction
Returns a MoleculeSet containing the products of this reaction.
getProducts() - Method in class org.openscience.cdk.silent.Reaction
Returns a MoleculeSet containing the products of this reaction.
getProperties() - Method in class org.openscience.cdk.ChemObject
Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugAtom
Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugAtomContainer
Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugAtomType
Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugBond
Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugChemFile
Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugChemModel
Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugChemObject
Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugChemSequence
Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugCrystal
Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugElectronContainer
Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugElement
Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugIsotope
Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugLonePair
Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugMapping
Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugMolecularFormula
Returns a Map with the IChemObject's properties.I should integrate into ChemObject.
getProperties() - Method in class org.openscience.cdk.debug.DebugMonomer
Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugPolymer
Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugReaction
Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugReactionScheme
Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugReactionSet
Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugRing
Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugSingleElectron
Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugStrand
Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.debug.DebugSubstance
Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.formula.MolecularFormula
Returns a Map with the IChemObject's properties.I should integrate into ChemObject.
getProperties() - Method in interface org.openscience.cdk.interfaces.IChemObject
Returns a Map with the IChemObject's properties.
getProperties() - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
Returns a Map with the IChemObject's properties.I should integrate into ChemObject.
getProperties() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.silent.ChemObject
Returns a Map with the IChemObject's properties.
getProperties() - Method in class org.openscience.cdk.silent.MolecularFormula
Returns a Map with the IChemObject's properties.I should integrate into ChemObject.
getProperty(Object) - Method in class org.openscience.cdk.ChemObject
Returns a property for the IChemObject.
getProperty(Object, Class<T>) - Method in class org.openscience.cdk.ChemObject
Access a property of the given description and cast the specified class.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugAtom
Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugAtomContainer
Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugAtomType
Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugBond
Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugChemFile
Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugChemModel
Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugChemObject
Returns a property for the IChemObject.
getProperty(Object, Class<T>) - Method in class org.openscience.cdk.debug.DebugChemObject
Access a property of the given description and cast the specified class.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugChemSequence
Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugCrystal
Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugElectronContainer
Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugElement
Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugIsotope
Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugLonePair
Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugMapping
Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugMolecularFormula
Returns a property for the IChemObject - the object is automatically cast to the required type.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugMonomer
Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugPolymer
Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugReaction
Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugReactionScheme
Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugReactionSet
Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugRing
Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugSingleElectron
Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugStrand
Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.debug.DebugSubstance
Returns a property for the IChemObject.
getProperty(Object) - Method in class org.openscience.cdk.formula.MolecularFormula
Returns a property for the IChemObject - the object is automatically cast to the required type.
getProperty(Object, Class<T>) - Method in class org.openscience.cdk.formula.MolecularFormula
Access a property of the given description and cast the specified class.
getProperty(Object) - Method in interface org.openscience.cdk.interfaces.IChemObject
Returns a property for the IChemObject - the object is automatically cast to the required type.
getProperty(Object, Class<T>) - Method in interface org.openscience.cdk.interfaces.IChemObject
Access a property of the given description and cast the specified class.
getProperty(Object) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
Returns a property for the IChemObject - the object is automatically cast to the required type.
getProperty(Object, Class<T>) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
Access a property of the given description and cast the specified class.
getProperty(Object) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
Returns a property for the IChemObject.
getProperty(Object, Class<T>) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
Access a property of the given description and cast the specified class.
getProperty(Object) - Method in class org.openscience.cdk.silent.ChemObject
Returns a property for the IChemObject.
getProperty(Object, Class<T>) - Method in class org.openscience.cdk.silent.ChemObject
Access a property of the given description and cast the specified class.
getProperty(Object) - Method in class org.openscience.cdk.silent.MolecularFormula
Returns a property for the IChemObject - the object is automatically cast to the required type.
getProperty(Object, Class<T>) - Method in class org.openscience.cdk.silent.MolecularFormula
Access a property of the given description and cast the specified class.
getProtein() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
 
getProteinInterior() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
 
getQSARs(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.tools.IonizationPotentialTool
Deprecated.
Get the results of 7 qsar descriptors been applied.
getQSARs(IAtomContainer, IBond) - Static method in class org.openscience.cdk.tools.IonizationPotentialTool
Deprecated.
Get the results of 7 qsar descriptors been applied.
getQueryNode() - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.Match
Deprecated.
Return query node
getQuestion() - Method in class org.openscience.cdk.io.setting.IOSetting
 
getRandom() - Static method in class org.openscience.cdk.math.RandomNumbersTool
Returns the instance of Random used by this class.
getRandomNextPermutation() - Method in class org.openscience.cdk.graph.Permutor
Randomly skip ahead in the list of permutations.
getRandomNextPermutation() - Method in class org.openscience.cdk.smsd.labelling.Permutor
Deprecated.
Randomly skip ahead in the list of permutations.
getRandomSeed() - Static method in class org.openscience.cdk.math.RandomNumbersTool
Returns the seed being used by this random number generator.
getRange(IMolecularFormulaSet) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaRangeManipulator
Extract from a set of MolecularFormula the range of each each element found and put the element and occurrence in a new MolecularFormulaRange.
getRank() - Method in class org.openscience.cdk.graph.Permutor
Get the current rank.
getRank() - Method in class org.openscience.cdk.smsd.labelling.Permutor
Deprecated.
 
getRAtom() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
 
getRawContent() - Method in class org.openscience.cdk.dict.Entry
 
getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter
Invalid: it is not appropriate to convert the integer hash codes into strings.
getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.EStateFingerprinter
Returns the raw representation of the fingerprint for the given IAtomContainer.
getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter
Returns the raw representation of the fingerprint for the given IAtomContainer.
getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.Fingerprinter
Returns the raw representation of the fingerprint for the given IAtomContainer.
getRawFingerprint(IAtomContainer) - Method in interface org.openscience.cdk.fingerprint.IFingerprinter
Returns the raw representation of the fingerprint for the given IAtomContainer.
getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.LingoFingerprinter
 
getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.MACCSFingerprinter
Returns the raw representation of the fingerprint for the given IAtomContainer.
getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.PubchemFingerprinter
Returns the raw representation of the fingerprint for the given IAtomContainer.
getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.ShortestPathFingerprinter
Returns the raw representation of the fingerprint for the given IAtomContainer.
getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.SignatureFingerprinter
 
getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.SubstructureFingerprinter
Returns the raw representation of the fingerprint for the given IAtomContainer.
getRDBEValue(IMolecularFormula) - Method in class org.openscience.cdk.formula.rules.RDBERule
Method to extract the Ring Double Bond Equivalents (RDB) value.
getReactantCoefficient(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugReaction
Returns the stoichiometry coefficient of the given reactant.
getReactantCoefficient(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IReaction
Returns the stoichiometry coefficient of the given reactant.
getReactantCoefficient(IAtomContainer) - Method in class org.openscience.cdk.Reaction
Returns the stoichiometry coefficient of the given reactant.
getReactantCoefficient(IAtomContainer) - Method in class org.openscience.cdk.silent.Reaction
Returns the stoichiometry coefficient of the given reactant.
getReactantCoefficients() - Method in class org.openscience.cdk.debug.DebugReaction
Returns an array of double with the stoichiometric coefficients of the reactants.
getReactantCoefficients() - Method in interface org.openscience.cdk.interfaces.IReaction
Returns an array of double with the stoichiometric coefficients of the reactants.
getReactantCoefficients() - Method in class org.openscience.cdk.Reaction
Returns an array of double with the stoichiometric coefficients of the reactants.
getReactantCoefficients() - Method in class org.openscience.cdk.silent.Reaction
Returns an array of double with the stoichiometric coefficients of the reactants.
getReactantCount() - Method in class org.openscience.cdk.debug.DebugReaction
Returns the number of reactants in this reaction.
getReactantCount() - Method in interface org.openscience.cdk.interfaces.IReaction
Returns the number of reactants in this reaction.
getReactantCount() - Method in class org.openscience.cdk.Reaction
Returns the number of reactants in this reaction.
getReactantCount() - Method in class org.openscience.cdk.silent.Reaction
Returns the number of reactants in this reaction.
getReactantMolecule() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
Deprecated.
Returns modified query molecule on which mapping was performed.
getReactantMolecule() - Method in class org.openscience.cdk.smsd.Isomorphism
Deprecated.
Returns modified query molecule on which mapping was performed.
getReactants() - Method in class org.openscience.cdk.debug.DebugReaction
Returns a MoleculeSet containing the reactants in this reaction.
getReactants() - Method in interface org.openscience.cdk.interfaces.IReaction
Returns a IAtomContaineSet containing the reactants in this reaction.
getReactants() - Method in class org.openscience.cdk.Reaction
Returns a MoleculeSet containing the reactants in this reaction.
getReactants() - Method in class org.openscience.cdk.silent.Reaction
Returns a MoleculeSet containing the reactants in this reaction.
getReaction(int) - Method in class org.openscience.cdk.debug.DebugReactionSet
Returns the Reaction at position number in the container.
getReaction(int) - Method in interface org.openscience.cdk.interfaces.IReactionSet
Returns the Reaction at position number in the container.
getReaction(int) - Method in class org.openscience.cdk.reaction.ReactionChain
Get the reaction of this chain reaction object at the position.
getReaction(int) - Method in class org.openscience.cdk.ReactionSet
Returns the Reaction at position number in the container.
getReaction(int) - Method in class org.openscience.cdk.silent.ReactionSet
Returns the Reaction at position number in the container.
getReactionByAtomContainerID(IReactionSet, String) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
Gets a reaction from a ReactionSet by ID of any product or reactant.
getReactionByReactionID(IReactionSet, String) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
Gets a reaction from a ReactionSet by ID.
getReactionCount() - Method in class org.openscience.cdk.debug.DebugReactionSet
Returns the number of Reactions in this Container.
getReactionCount() - Method in interface org.openscience.cdk.interfaces.IReactionSet
Returns the number of Reactions in this Container.
getReactionCount() - Method in class org.openscience.cdk.ReactionSet
Returns the number of Reactions in this Container.
getReactionCount() - Method in class org.openscience.cdk.silent.ReactionSet
Returns the number of Reactions in this Container.
getReactionMetadata() - Method in class org.openscience.cdk.dict.EntryReact
 
getReactions() - Method in class org.openscience.cdk.tools.StructureResonanceGenerator
Get the reactions that must be presents in the generation of the resonance.
getReactionSchemeCount() - Method in class org.openscience.cdk.debug.DebugReactionScheme
Returns the number of ReactionScheme in this Scheme.
getReactionSchemeCount() - Method in interface org.openscience.cdk.interfaces.IReactionScheme
Returns the number of ReactionScheme in this Scheme.
getReactionSchemeCount() - Method in class org.openscience.cdk.ReactionScheme
Returns the number of ReactionScheme in this Scheme.
getReactionSchemeCount() - Method in class org.openscience.cdk.silent.ReactionScheme
Returns the number of ReactionScheme in this Scheme.
getReactionSet() - Method in class org.openscience.cdk.ChemModel
Gets the ReactionSet contained in this ChemModel.
getReactionSet() - Method in class org.openscience.cdk.debug.DebugChemModel
Gets the ReactionSet contained in this ChemModel.
getReactionSet() - Method in interface org.openscience.cdk.interfaces.IChemModel
Gets the ReactionSet contained in this ChemModel.
getReactionSet() - Method in class org.openscience.cdk.silent.ChemModel
Gets the ReactionSet contained in this ChemModel.
getReactionStep(IReaction) - Method in class org.openscience.cdk.reaction.ReactionChain
Get the position of the reaction into this chain reaction object.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.ABINITFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.Aces2Format
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.ADFFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.AlchemyFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.BGFFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.BSFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
 
getReaderClassName() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.CACheFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
 
getReaderClassName() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.CIFFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.CMLFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.CRK2DFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.CRK3DFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.CrystClustFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.CTXFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.DaltonFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.DMol3Format
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.DOCK5Format
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.FingerprintFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.GamessFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian03Format
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian90Format
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian92Format
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian94Format
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian95Format
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian98Format
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat
 
getReaderClassName() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.GROMOS96Format
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.HINFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in interface org.openscience.cdk.io.formats.IChemFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.INChIFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.JaguarFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.JMEFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MacroModelFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MDLFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MDLV2000Format
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MDLV3000Format
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MMODFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.Mol2Format
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC7Format
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC93Format
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC97Format
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.MPQCFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.NWChemFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.PCModelFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.PDBFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.PDBMLFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.PMPFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.PQSChemFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.QChemFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.RawCopyFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.SDFFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.ShelXFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.SMARTSFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.SMILESFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.SpartanFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.VASPFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.ViewmolFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.XEDFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.XYZFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.YasaraFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.ZindoFormat
Returns the class name of the CDK Reader for this format.
getReaderClassName() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat
Returns the class name of the CDK Reader for this format.
getRealPart() - Method in class org.openscience.cdk.math.Complex
Gets the real part of this complex value
getRecord() - Method in class org.openscience.cdk.debug.DebugPDBAtom
get one entire line from the PDB entry file which describe the IPDBAtom.
getRecord() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
Get one entire line from the PDB entry file which describe the IPDBAtom.
getRecord() - Method in class org.openscience.cdk.protein.data.PDBAtom
get one entire line from the PDB entry file which describe the IPDBAtom.
getRecord() - Method in class org.openscience.cdk.silent.PDBAtom
get one entire line from the PDB entry file which describe the IPDBAtom.
getRectangle2D(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
Returns the 2D rectangle spanning the space occupied by the atom container.
getReference() - Method in class org.openscience.cdk.dict.DictRef
 
getRelevantAtomContainer(IAtomContainerSet, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
 
getRelevantAtomContainer(IAtomContainerSet, IBond) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
 
getRelevantAtomContainer(IChemModel, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
This badly named methods tries to determine which AtomContainer in the ChemModel is best suited to contain added Atom's and Bond's.
getRelevantAtomContainer(IChemModel, IBond) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
Retrieves the first IAtomContainer containing a given IBond from an IChemModel.
getRelevantAtomContainer(IAtomContainerSet, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
 
getRelevantAtomContainer(IAtomContainerSet, IBond) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
 
getRelevantAtomContainer(IReaction, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
 
getRelevantAtomContainer(IReaction, IBond) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
 
getRelevantAtomContainer(IReactionSet, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
 
getRelevantAtomContainer(IReactionSet, IBond) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
 
getRelevantReaction(IChemModel, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
Retrieves the first IReaction containing a given IAtom from an IChemModel.
getRelevantReaction(IReactionSet, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
 
getRelevantReaction(IReactionSet, IBond) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
 
getRelevantReactions(IReactionSet, IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
Get all Reactions object containing a Molecule from a set of Reactions.
getRelevantReactionsAsProduct(IReactionSet, IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
Get all Reactions object containing a Molecule as a Product from a set of Reactions.
getRelevantReactionsAsReactant(IReactionSet, IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
Get all Reactions object containing a Molecule as a Reactant from a set of Reactions.
getRemoveHydrogenFlag() - Method in class org.openscience.cdk.smsd.tools.MolHandler
Deprecated.
Returns true if hydrogens were made implicit else return false
getRenderer2DModel() - Method in class org.openscience.cdk.renderer.AbstractRenderer
Get the RendererModel used by this renderer, which provides access to the various parameters used to generate and draw the diagram.
getRenderer2DModel() - Method in interface org.openscience.cdk.renderer.IRenderer
Returns the drawing model, giving access to drawing parameters.
getRendererModel() - Method in class org.openscience.cdk.renderer.visitor.AWTDrawVisitor
Returns the current RendererModel.
getRenderingParameters() - Method in class org.openscience.cdk.renderer.RendererModel
Returns all IGeneratorParameters for the current RendererModel.
getRepresentations() - Method in class org.openscience.cdk.dict.EntryReact
Get the Representation of the reaction.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.CDKSourceCodeWriter
 
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ABINITFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Aces2Format
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ADFFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.AlchemyFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.BGFFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.BSFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
 
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CACheFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
 
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CIFFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CMLFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CRK2DFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CRK3DFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CrystClustFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CTXFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.DaltonFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.DMol3Format
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.DOCK5Format
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.FingerprintFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.GamessFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian03Format
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian90Format
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian92Format
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian94Format
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian95Format
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian98Format
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.GROMOS96Format
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.HINFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in interface org.openscience.cdk.io.formats.IChemFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.INChIFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.JaguarFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.JMEFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MacroModelFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLV2000Format
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLV3000Format
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MMODFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Mol2Format
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC7Format
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC93Format
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC97Format
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MPQCFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.NWChemFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PCModelFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PDBFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PDBMLFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PMPFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PQSChemFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.QChemFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.RawCopyFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SDFFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ShelXFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SMARTSFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SMILESFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SpartanFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.VASPFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ViewmolFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.XEDFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.XYZFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.YasaraFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ZindoFormat
Returns an integer indicating the data features that this format requires.
getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat
Returns an integer indicating the data features that this format requires.
getRequiredRGroupNumber() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
 
getResidues() - Method in class org.openscience.cdk.libio.md.MDMolecule
 
getResName() - Method in class org.openscience.cdk.debug.DebugPDBAtom
get the Residue name of this atom.
getResName() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
get the Residue name of this atom.
getResName() - Method in class org.openscience.cdk.protein.data.PDBAtom
get the Residue name of this atom.
getResName() - Method in class org.openscience.cdk.silent.PDBAtom
get the Residue name of this atom.
getResSeq() - Method in class org.openscience.cdk.debug.DebugPDBAtom
get the Residue sequence number of this atom.
getResSeq() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
get the Residue sequence number of this atom.
getResSeq() - Method in interface org.openscience.cdk.interfaces.IPDBMonomer
Gets the sequence identifier of this monomer.
getResSeq() - Method in class org.openscience.cdk.protein.data.PDBAtom
get the Residue sequence number of this atom.
getResSeq() - Method in class org.openscience.cdk.protein.data.PDBMonomer
 
getResSeq() - Method in class org.openscience.cdk.silent.PDBAtom
get the Residue sequence number of this atom.
getResSeq() - Method in class org.openscience.cdk.silent.PDBMonomer
 
getRestrictions() - Method in class org.openscience.cdk.formula.MassToFormulaTool
Deprecated.
Get the restrictions that must be presents in the molecular formula.
getReturnStatus() - Method in class org.openscience.cdk.inchi.InChIGenerator
Gets return status from InChI process.
getReturnStatus() - Method in class org.openscience.cdk.inchi.InChIToStructure
Gets return status from InChI process.
getRGroupDefinitions() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
Getter for the R-group definitions (substituents).
getRGroupDefinitions() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
 
getRGroupNumber() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
 
getRgroupQueryAtoms(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
Returns all R# type atoms (pseudo atoms) found in the root structure for a certain provided RGgroup number.
getRGroups() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
 
getRight() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom
Deprecated.
getRight() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond
 
getRingBond() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RingIdentifierAtom
 
getRings(IBond) - Method in class org.openscience.cdk.debug.DebugRingSet
Returns a vector of all rings that this bond is part of.
getRings(IAtom) - Method in class org.openscience.cdk.debug.DebugRingSet
Returns a vector of all rings that this atom is part of.
getRings(IBond) - Method in interface org.openscience.cdk.interfaces.IRingSet
Returns a vector of all rings that this bond is part of.
getRings(IAtom) - Method in interface org.openscience.cdk.interfaces.IRingSet
Returns a vector of all rings that this atom is part of.
getRings(IBond) - Method in class org.openscience.cdk.RingSet
Returns a vector of all rings that this bond is part of.
getRings(IAtom) - Method in class org.openscience.cdk.RingSet
Returns a vector of all rings that this atom is part of.
getRings(IBond) - Method in class org.openscience.cdk.silent.RingSet
Returns a vector of all rings that this bond is part of.
getRings(IAtom) - Method in class org.openscience.cdk.silent.RingSet
Returns a vector of all rings that this atom is part of.
getRingSet() - Method in class org.openscience.cdk.ChemModel
Returns the RingSet of this ChemModel.
getRingSet() - Method in class org.openscience.cdk.debug.DebugChemModel
Returns the RingSet of this ChemModel.
getRingSet() - Method in interface org.openscience.cdk.interfaces.IChemModel
Returns the RingSet of this ChemModel.
getRingSet(IAtomContainer) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
Determine the ring set for this atom container.
getRingSet() - Method in class org.openscience.cdk.silent.ChemModel
Returns the RingSet of this ChemModel.
getRingSet(IAtomContainer) - Method in class org.openscience.cdk.smsd.ring.HanserRingFinder
Deprecated.
Returns Ring set based on Hanser Ring Finding method
getRingSet(IAtomContainer) - Method in interface org.openscience.cdk.smsd.ring.RingFinder
Deprecated.
Returns CDK object Ring set based on Hanser Ring Finding method
getRingSize() - Method in class org.openscience.cdk.debug.DebugRing
Returns the number of atoms\edges in this ring.
getRingSize() - Method in interface org.openscience.cdk.interfaces.IRing
Returns the number of atoms/bonds in this ring.
getRingSize() - Method in class org.openscience.cdk.Ring
Returns the number of atoms\edges in this ring.
getRingSize() - Method in class org.openscience.cdk.silent.Ring
Returns the number of atoms\edges in this ring.
getRingSystems() - Method in class org.openscience.cdk.fragment.MurckoFragmenter
Get the ring system fragments as SMILES strings.
getRingSystemsAsContainers() - Method in class org.openscience.cdk.fragment.MurckoFragmenter
Get rings systems as IAtomContainer objects.
getRMap() - Method in class org.openscience.cdk.isomorphism.mcss.RNode
Gets the rMap attribute of the RNode object.
getRMap() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode
Deprecated.
Gets the rMap attribute of the RNode object
getrMap() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode
Deprecated.
Returns resolution Map
getRMSD() - Method in class org.openscience.cdk.geometry.alignment.KabschAlignment
Returns the RMSD from the alignment.
getROCAUC() - Method in class org.openscience.cdk.fingerprint.model.Bayesian
Returns the integral of the area-under-the-curve of the receiver-operator-characteristic.
getROCType() - Method in class org.openscience.cdk.fingerprint.model.Bayesian
Returns a string description of the method used to create the ROC curve (e.g.
getRocX() - Method in class org.openscience.cdk.fingerprint.model.Bayesian
Returns X-values that can be used to plot the ROC-curve.
getRocY() - Method in class org.openscience.cdk.fingerprint.model.Bayesian
Returns Y-values that can be used to plot the ROC-curve.
getRoot(int) - Method in class org.openscience.cdk.group.DisjointSetForest
Travel up the tree that this element is in, until the root of the set is found, and return that root.
getRoot(Node) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
 
getRootAttachmentPoints() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
Getter for root attachment points = bonds that connect R pseudo-atoms to the scaffold.
getRootAttachmentPoints() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
 
getRootStructure() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
Getter for the root structure of this R-Group.
getRootStructure() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
 
getRotationMatrix() - Method in class org.openscience.cdk.geometry.alignment.KabschAlignment
Returns the rotation matrix (u).
getRows() - Method in class org.openscience.cdk.math.IMatrix
Returns the count of rows
getRows() - Method in class org.openscience.cdk.math.Matrix
Returns the number of rows.
getRSolvent() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
 
getRules() - Method in class org.openscience.cdk.formula.MolecularFormulaChecker
Get the IRules to be applied to validate the IMolecularFormula.
getScaleFactor(IAtomContainer, double) - Static method in class org.openscience.cdk.geometry.GeometryTools
Determines the scale factor for displaying a structure loaded from disk in a frame.
getScaleFactor(IAtomContainer, double) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Determines the scale factor for displaying a structure loaded from disk in a frame.
getSearchDepth() - Method in class org.openscience.cdk.fingerprint.Fingerprinter
 
getSecondAttachmentPoint() - Method in class org.openscience.cdk.isomorphism.matchers.RGroup
 
getSecondGraphSize() - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
Returns the size of the second of the two compared graphs.
getSecondGraphSize() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
Deprecated.
Returns the size of the second of the two compared graphs.
getSecondPoint() - Method in class org.openscience.cdk.sgroup.SgroupBracket
Second point of the bracket (x2,y2).
getSegID() - Method in class org.openscience.cdk.debug.DebugPDBAtom
get the Segment identifier, left-justified of this atom.
getSegID() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
get the Segment identifier, left-justified of this atom.
getSegID() - Method in class org.openscience.cdk.protein.data.PDBAtom
get the Segment identifier, left-justified of this atom.
getSegID() - Method in class org.openscience.cdk.silent.PDBAtom
get the Segment identifier, left-justified of this atom.
getSelection() - Method in class org.openscience.cdk.renderer.RendererModel
Returns an IChemObjectSelection with the currently selected IChemObjects.
getSerial() - Method in class org.openscience.cdk.debug.DebugPDBAtom
get the Atom serial number of this atom.
getSerial() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
get the Atom serial number of this atom.
getSerial() - Method in class org.openscience.cdk.protein.data.PDBAtom
get the Atom serial number of this atom.
getSerial() - Method in class org.openscience.cdk.silent.PDBAtom
get the Atom serial number of this atom.
getSetbits() - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
 
getSetbits() - Method in interface org.openscience.cdk.fingerprint.IBitFingerprint
Returns a listing of the bits in the fingerprint that are set to true.
getSetbits() - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
 
getSetNumA() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper
Deprecated.
 
getSets() - Method in class org.openscience.cdk.group.DisjointSetForest
Retrieve the sets as 2D-array of ints.
getSetting(String) - Method in class org.openscience.cdk.io.ChemObjectIO
Access a named setting managed by this reader/writer.
getSetting(String, Class<S>) - Method in class org.openscience.cdk.io.ChemObjectIO
Access a named setting managed by this reader/writer.
getSetting(String) - Method in interface org.openscience.cdk.io.IChemObjectIO
Access a named setting managed by this reader/writer.
getSetting(String, Class<S>) - Method in interface org.openscience.cdk.io.IChemObjectIO
Access a named setting managed by this reader/writer.
getSetting() - Method in class org.openscience.cdk.io.setting.IOSetting
Sets the setting for a certain question.
getSettings() - Method in class org.openscience.cdk.io.ChemObjectIO
Access a collection of IOSettings for this reader/writer.
getSettings() - Method in interface org.openscience.cdk.io.IChemObjectIO
Access a collection of IOSettings for this reader/writer.
getSettings() - Method in class org.openscience.cdk.io.setting.SettingManager
Access a collection of all settings in the manager.
getSettingValue() - Method in class org.openscience.cdk.io.setting.IntegerIOSetting
 
getShortestPath(IAtomContainer, IAtom, IAtom) - Static method in class org.openscience.cdk.graph.PathTools
Deprecated.
This implementation recalculates all shortest paths from the start atom for each method call and does not indicate if there are equally short paths from the start to the end. Replaced by ShortestPaths.atomsTo(IAtom)
getSID(XMLStreamReader) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
 
getSingleBondEquivalentSum(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
Returns the sum of bond orders, where a single bond counts as one single bond equivalent, a double as two, etc.
getSingleBondEquivalentSum(List<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
Get the single bond equivalent (SBE) of a list of bonds.
getSingleBondEquivalentSum(Iterator<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
Get the single bond equivalent (SBE) of a list of bonds, given an iterator to the list.
getSingleElectron(int) - Method in class org.openscience.cdk.AtomContainer
Get the single electron at position number in [0,..].
getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid
Get the single electron at position number in [0,..].
getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer
Get the single electron at position number in [0,..].
getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Get the single electron at position number in [0,..].
getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugCrystal
Get the single electron at position number in [0,..].
getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugMonomer
Get the single electron at position number in [0,..].
getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugPolymer
Get the single electron at position number in [0,..].
getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugRing
Get the single electron at position number in [0,..].
getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugStrand
Get the single electron at position number in [0,..].
getSingleElectron(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Get the single electron at position number in [0,..].
getSingleElectron(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Get the single electron at position number in [0,..].
getSingleElectron(int) - Method in class org.openscience.cdk.silent.AtomContainer
Get the single electron at position number in [0,..].
getSingleElectronCount() - Method in class org.openscience.cdk.AtomContainer
Returns the number of the single electrons in this container.
getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns the number of the single electrons in this container.
getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugAtomContainer
Returns the number of the single electrons in this container.
getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns the number of the single electrons in this container.
getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugCrystal
Returns the number of the single electrons in this container.
getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugMonomer
Returns the number of the single electrons in this container.
getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugPolymer
Returns the number of the single electrons in this container.
getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugRing
Returns the number of the single electrons in this container.
getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugStrand
Returns the number of the single electrons in this container.
getSingleElectronCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Returns the number of the single electrons in this container.
getSingleElectronCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Returns the number of the single electrons in this container,
getSingleElectronCount() - Method in class org.openscience.cdk.silent.AtomContainer
Returns the number of the single electrons in this container,
getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.AtomContainer
Returns the position of a given single electron in the single electron array.
getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAminoAcid
Returns the position of a given single electron in the single electron array.
getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns the position of a given single electron in the single electron array.
getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugCrystal
Returns the position of a given single electron in the single electron array.
getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugMonomer
Returns the position of a given single electron in the single electron array.
getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugPolymer
Returns the position of a given single electron in the single electron array.
getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugRing
Returns the position of a given single electron in the single electron array.
getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugStrand
Returns the position of a given single electron in the single electron array.
getSingleElectronNumber(ISingleElectron) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Returns the position of a given single electron in the single electron array.
getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.silent.AtomContainer
Returns the position of a given single electron in the single electron array.
getSingleElectrons() - Method in enum org.openscience.cdk.io.MDLV2000Writer.SPIN_MULTIPLICITY
The number of single electrons that correspond to the spin multiplicity.
getSize() - Method in class org.openscience.cdk.config.AtomTypeFactory
Returns the number of atom types in this list.
getSize() - Method in class org.openscience.cdk.config.IsotopeFactory
Returns the number of isotopes defined by this class.
getSize() - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter
Returns the extent of the folded fingerprints.
getSize() - Method in class org.openscience.cdk.fingerprint.EStateFingerprinter
Returns the size (or length) of the fingerprint.
getSize() - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter
Returns the size (or length) of the fingerprint.
getSize() - Method in class org.openscience.cdk.fingerprint.Fingerprinter
 
getSize() - Method in interface org.openscience.cdk.fingerprint.IFingerprinter
Returns the size (or length) of the fingerprint.
getSize() - Method in class org.openscience.cdk.fingerprint.LingoFingerprinter
 
getSize() - Method in class org.openscience.cdk.fingerprint.MACCSFingerprinter
Returns the size (or length) of the fingerprint.
getSize() - Method in class org.openscience.cdk.fingerprint.PubchemFingerprinter
Get the size of the fingerprint.
getSize() - Method in class org.openscience.cdk.fingerprint.ShortestPathFingerprinter
 
getSize() - Method in class org.openscience.cdk.fingerprint.SignatureFingerprinter
 
getSize() - Method in class org.openscience.cdk.fingerprint.SubstructureFingerprinter
Returns the size (or length) of the fingerprint.
getSize() - Method in class org.openscience.cdk.group.PermutationGroup
Get the number of elements in each permutation in the group.
getSize() - Method in class org.openscience.cdk.math.IVector
Return the size from this vector
getSize() - Method in class org.openscience.cdk.math.qm.FourierGridBasis
 
getSize() - Method in class org.openscience.cdk.math.qm.GaussiansBasis
Gets the number of base vectors.
getSize() - Method in interface org.openscience.cdk.math.qm.IBasis
Gets the number of base vectors
getSize() - Method in class org.openscience.cdk.math.Vector
Returns the size of this vector
getSize() - Method in class org.openscience.cdk.smsd.helper.FinalMappings
Deprecated.
Returns number of stored mappings
getSize() - Method in class org.openscience.cdk.smsd.helper.LabelContainer
Deprecated.
Returns label count
getSize() - Method in interface org.openscience.cdk.smsd.interfaces.IFinalMapping
Deprecated.
Returns number of stored mappings
getSmarts() - Static method in class org.openscience.cdk.config.fragments.EStateFragments
Get the SMARTS patterns.
getSmarts() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom
Get the SMARTS for the group.
getSmarts() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryAtom
Get the SMARTS pattern for this pharmacophore group.
getSmarts() - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool
Returns the current SMARTS pattern being used.
getSolutions() - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
Returns the list of solutions.
getSolutions() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
Deprecated.
Returns the list of solutions.
getSolvantValue() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
 
getSortedEnergy() - Method in class org.openscience.cdk.smsd.filters.ChemicalFilters
Deprecated.
Return sorted energy in ascending order.
getSortedFragment() - Method in class org.openscience.cdk.smsd.filters.ChemicalFilters
Deprecated.
Return sorted fragment in ascending order of the size.
getSource() - Method in interface org.openscience.cdk.interfaces.IChemObjectChangeEvent
IChemObject that fired the event.
getSource() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
Deprecated.
Returns source molecule
getSource() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.EdgeBuilder
Deprecated.
Returns source Node.
getSource() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IEdge
Deprecated.
Returns source Node.
getSource() - Method in class org.openscience.cdk.smsd.ring.PathEdge
Deprecated.
 
getSpaceGroup() - Method in class org.openscience.cdk.Crystal
Gets the space group of this crystal.
getSpaceGroup() - Method in class org.openscience.cdk.debug.DebugCrystal
Gets the space group of this crystal.
getSpaceGroup() - Method in interface org.openscience.cdk.interfaces.ICrystal
Gets the space group of this crystal.
getSpaceGroup() - Method in class org.openscience.cdk.silent.Crystal
Gets the space group of this crystal.
getSpanningTree() - Method in class org.openscience.cdk.graph.SpanningTree
Access the computed spanning tree of the input molecule.
getSpanningTreeSize() - Method in class org.openscience.cdk.graph.SpanningTree
Size of the spanning tree specified as the number of edges in the tree.
getSpatproduct(Vector3d, Vector3d, Vector3d) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
Gets the spatproduct of three vectors.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor
 
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor
Gets the specification attribute of the AtomHybridizationDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor
Gets the specification attribute of the AtomHybridizationVSEPRDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor
Gets the specification attribute of the AtomValenceDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor
Gets the specification attribute of the BondsToAtomDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor
Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor
Gets the specification attribute of the DistanceToAtomDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor
Gets the specification attribute of the EffectiveAtomPolarizabilityDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor
Gets the specification attribute of the InductiveAtomicHardnessDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor
Gets the specification attribute of the InductiveAtomicSoftnessDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor
Gets the specification attribute of the IPAtomicHOSEDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor
Deprecated.
Gets the specification attribute of the IPAtomicLearningDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor
Gets the specification attribute of the IsProtonInAromaticSystemDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInConjugatedPiSystemDescriptor
Gets the specification attribute of the IsProtonInConjugatedPiSystemDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor
Gets the specification attribute of the PartialPiChargeDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor
Gets the specification attribute of the PartialSigmaChargeDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor
Gets the specification attribute of the PartialTChargeMMFF94Descriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor
Gets the specification attribute of the PartialTChargePEOEDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor
Gets the specification attribute of the PeriodicTablePositionDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor
Gets the specification attribute of the PiElectronegativityDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor
Gets the specification attribute of the ProtonAffinityDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor
Gets the specification attribute of the ProtonTotalPartialChargeDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R
Gets the specification attribute of the RDFProtonDescriptor_G3R object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR
Gets the specification attribute of the RDFProtonDescriptor_GDR object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR
Gets the specification attribute of the RDFProtonDescriptor_GHR object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol
Gets the specification attribute of the RDFProtonDescriptor_GHR_topol object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR
Gets the specification attribute of the RDFProtonDescriptor_GSR object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor
Gets the specification attribute of the SigmaElectronegativityDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor
Gets the specification attribute of the StabilizationPlusChargeDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor
Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor
Gets the specification attribute of the PiContactDetectionDescriptor object.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptor
 
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor
Gets the specification attribute of the BondPartialPiChargeDescriptor object.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor
Gets the specification attribute of the BondPartialSigmaChargeDescriptor object.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor
Gets the specification attribute of the BondPartialTChargeDescriptor object.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor
Gets the specification attribute of the BondSigmaElectronegativityDescriptor object.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor
Deprecated.
Gets the specification attribute of the IPBondLearningDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor
Returns a IImplementationSpecification which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
 
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor
Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor
Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor
Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor
Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor
Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
 
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
 
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
 
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor
Returns a IImplementationSpecification which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor
 
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor
Gets the specification attribute of the BondCountDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor
 
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor
 
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
 
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
 
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
 
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
 
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor
 
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor
 
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor
Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor
Returns a IImplementationSpecification which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor
Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor
 
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor
Gets the specification attribute of the HBondAcceptorCountDescriptor object.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor
Gets the specification attribute of the HBondDonorCountDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor
Returns a DescriptorSpecification which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor
Deprecated.
Gets the specification attribute of the IPMolecularLearningDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor
Gets the specification attribute of the KappaShapeIndicesDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor
Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor
Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor
Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor
Gets the specification attribute of the PetitjeanNumberDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor
Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor
Gets the specification attribute of the MannholdLogPDescriptor object.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor
 
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor
Gets the specification attribute of the PetitjeanNumberDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor
 
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor
Gets the specification attribute of the RotatableBondsCountDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor
Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor
Fetch descriptor specification.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor
Gets the specification attribute of the TPSADescriptor object.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor
Returns a IImplementationSpecification which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor
Gets the specification attribute of the VAdjMaDescriptor object
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor
Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor
 
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor
 
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor
Returns a Map which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor
Gets the specification attribute of the XLogPDescriptor object.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor
Gets the specification attribute of the ZagrebIndexDescriptor object.
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor
 
getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.substance.OxygenAtomCountDescriptor
Returns a IImplementationSpecification which specifies which descriptor is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.qsar.DescriptorValue
 
getSpecification() - Method in interface org.openscience.cdk.qsar.IDescriptor
Returns a IImplementationSpecification which specifies which descriptor is implemented by this class.
getSpecification() - Method in interface org.openscience.cdk.reaction.IReactionProcess
Returns a Map which specifies which reaction is implemented by this class.
getSpecification() - Method in class org.openscience.cdk.reaction.type.AdductionProtonLPReaction
Gets the specification attribute of the AdductionProtonLPReaction object.
getSpecification() - Method in class org.openscience.cdk.reaction.type.AdductionProtonPBReaction
Gets the specification attribute of the AdductionProtonPBReaction object.
getSpecification() - Method in class org.openscience.cdk.reaction.type.AdductionSodiumLPReaction
Gets the specification attribute of the AdductionSodiumLPReaction object.
getSpecification() - Method in class org.openscience.cdk.reaction.type.CarbonylEliminationReaction
Gets the specification attribute of the CarbonylEliminationReaction object.
getSpecification() - Method in class org.openscience.cdk.reaction.type.ElectronImpactNBEReaction
Gets the specification attribute of the ElectronImpactNBEReaction object.
getSpecification() - Method in class org.openscience.cdk.reaction.type.ElectronImpactPDBReaction
Gets the specification attribute of the ElectronImpactPDBReaction object.
getSpecification() - Method in class org.openscience.cdk.reaction.type.ElectronImpactSDBReaction
Gets the specification attribute of the ElectronImpactSDBReaction object.
getSpecification() - Method in class org.openscience.cdk.reaction.type.HeterolyticCleavagePBReaction
Gets the specification attribute of the HeterolyticCleavagePBReaction object.
getSpecification() - Method in class org.openscience.cdk.reaction.type.HeterolyticCleavageSBReaction
Gets the specification attribute of the HeterolyticCleavageSBReaction object.
getSpecification() - Method in class org.openscience.cdk.reaction.type.HomolyticCleavageReaction
Gets the specification attribute of the HomolyticCleavageReaction object.
getSpecification() - Method in class org.openscience.cdk.reaction.type.HyperconjugationReaction
Gets the specification attribute of the HyperconjugationReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.PiBondingMovementReaction
Gets the specification attribute of the PiBondingMovementReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalChargeSiteInitiationHReaction
Gets the specification attribute of the RadicalChargeSiteInitiationHReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalChargeSiteInitiationReaction
Gets the specification attribute of the RadicalChargeSiteInitiationReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrAlphaReaction
Gets the specification attribute of the RadicalSiteHrAlphaReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrBetaReaction
Gets the specification attribute of the RadicalSiteHrBetaReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrDeltaReaction
Gets the specification attribute of the RadicalSiteHrDeltaReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrGammaReaction
Gets the specification attribute of the RadicalSiteHrGammaReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteInitiationHReaction
Gets the specification attribute of the RadicalSiteInitiationHReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteInitiationReaction
Gets the specification attribute of the RadicalSiteInitiationReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrAlphaReaction
Gets the specification attribute of the RadicalSiteRrAlphaReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrBetaReaction
Gets the specification attribute of the RadicalSiteRrBetaReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrDeltaReaction
Gets the specification attribute of the RadicalSiteRrDeltaReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrGammaReaction
Gets the specification attribute of the RadicalSiteRrGammaReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.RearrangementAnionReaction
Gets the specification attribute of the RearrangementAnionReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.RearrangementCationReaction
Gets the specification attribute of the RearrangementCationReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.RearrangementLonePairReaction
Gets the specification attribute of the RearrangementLonePairReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.RearrangementRadicalReaction
Gets the specification attribute of the RearrangementRadicalReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.SharingAnionReaction
Gets the specification attribute of the SharingAnionReaction object.
getSpecification() - Method in class org.openscience.cdk.reaction.type.SharingChargeDBReaction
Gets the specification attribute of the SharingChargeDBReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.SharingChargeSBReaction
Gets the specification attribute of the SharingChargeSBReaction object
getSpecification() - Method in class org.openscience.cdk.reaction.type.SharingLonePairReaction
Gets the specification attribute of the SharingLonePairReaction object.
getSpecification() - Method in class org.openscience.cdk.reaction.type.TautomerizationReaction
Gets the specification attribute of the TautomerizationReaction object.
getSpecificationReference() - Method in interface org.openscience.cdk.IImplementationSpecification
Pointer to a dictionary or ontology describing a unique algorithm.
getSpecificationReference() - Method in class org.openscience.cdk.qsar.DescriptorSpecification
 
getSpecificationReference() - Method in class org.openscience.cdk.reaction.ReactionSpecification
 
getSpheres(IAtomContainer, IAtom, int, boolean) - Method in class org.openscience.cdk.tools.HOSECodeGenerator
This method is intended to be used to get the atoms around an atom in spheres.
getSpinVector(double, double) - Method in class org.openscience.cdk.math.qm.AngularMomentum
Calculates a spin vector by a direction specified by theta and phi
getSquarePlanarShape(IAtom, IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.stereo.StereoTool
Given four atoms (assumed to be in the same plane), returns the arrangement of those atoms in that plane.
getSSSRWeightVector() - Method in class org.openscience.cdk.ringsearch.SSSRFinder
Deprecated.
Returns a vector containing the lengths of the rings in a SSSR.
getStartChainID() - Method in class org.openscience.cdk.debug.DebugPDBStructure
get start Chain identifier of this structure.
getStartChainID() - Method in interface org.openscience.cdk.interfaces.IPDBStructure
get start Chain identifier of this structure.
getStartChainID() - Method in class org.openscience.cdk.protein.data.PDBStructure
get start Chain identifier of this structure.
getStartChainID() - Method in class org.openscience.cdk.silent.PDBStructure
get start Chain identifier of this structure.
getStartInsertionCode() - Method in class org.openscience.cdk.debug.DebugPDBStructure
get start Code for insertion of residues of this structure.
getStartInsertionCode() - Method in interface org.openscience.cdk.interfaces.IPDBStructure
get start Code for insertion of residues of this structure.
getStartInsertionCode() - Method in class org.openscience.cdk.protein.data.PDBStructure
get start Code for insertion of residues of this structure.
getStartInsertionCode() - Method in class org.openscience.cdk.silent.PDBStructure
get start Code for insertion of residues of this structure.
getStartSequenceNumber() - Method in class org.openscience.cdk.debug.DebugPDBStructure
get the start sequence number of this structure.
getStartSequenceNumber() - Method in interface org.openscience.cdk.interfaces.IPDBStructure
get the start sequence number of this structure.
getStartSequenceNumber() - Method in class org.openscience.cdk.protein.data.PDBStructure
get the start sequence number of this structure.
getStartSequenceNumber() - Method in class org.openscience.cdk.silent.PDBStructure
get the start sequence number of this structure.
getStepSize() - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
Get the StepSize attribute of the GasteigerMarsiliPartialCharges object.
getStepSize() - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges
Get the StepSize attribute of the GasteigerMarsiliPartialCharges object.
getStereo() - Method in class org.openscience.cdk.Bond
Returns the stereo descriptor for this bond.
getStereo() - Method in class org.openscience.cdk.debug.DebugBond
Returns the stereo descriptor for this bond.
getStereo() - Method in interface org.openscience.cdk.interfaces.IBond
Returns the stereo descriptor for this bond.
getStereo() - Method in interface org.openscience.cdk.interfaces.IDoubleBondStereochemistry
Defines the stereochemistry around the double bond.
getStereo() - Method in interface org.openscience.cdk.interfaces.ITetrahedralChirality
Defines the stereochemistry around the chiral atom.
getStereo() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
Returns the stereo descriptor for this query bond.
getStereo() - Method in class org.openscience.cdk.silent.Bond
Returns the stereo descriptor for this bond.
getStereo() - Method in class org.openscience.cdk.stereo.DoubleBondStereochemistry
Defines the stereochemistry around the double bond.
getStereo(IAtom, IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.stereo.StereoTool
Take four atoms, and return Stereo.CLOCKWISE or Stereo.ANTI_CLOCKWISE.
getStereo() - Method in class org.openscience.cdk.stereo.TetrahedralChirality
Defines the stereochemistry around the chiral atom.
getStereoBond() - Method in interface org.openscience.cdk.interfaces.IDoubleBondStereochemistry
IBond that is the stereo center.
getStereoBond() - Method in class org.openscience.cdk.stereo.DoubleBondStereochemistry
IBond that is the stereo center.
getStereoMatches() - Method in class org.openscience.cdk.smsd.filters.ChemicalFilters
Deprecated.
Return Stereo matches in descending order.
getStereoParity() - Method in class org.openscience.cdk.Atom
Returns the stereo parity of this atom.
getStereoParity() - Method in class org.openscience.cdk.debug.DebugAtom
Returns the stereo parity of this atom.
getStereoParity() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
Returns the stereo parity of this atom.
getStereoParity() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
Returns the stereo parity of this atom.
getStereoParity() - Method in interface org.openscience.cdk.interfaces.IAtom
Deprecated.
use IStereoElements for storing stereochemistry
getStereoParity() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
Returns the stereo parity of this atom.
getStereoParity() - Method in class org.openscience.cdk.silent.Atom
Returns the stereo parity of this atom.
getStereoScore(int) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
Deprecated.
Returns a number which denotes the quality of the mcs.
getStereoScore(int) - Method in class org.openscience.cdk.smsd.Isomorphism
Deprecated.
Returns a number which denotes the quality of the mcs.
getStrand(String) - Method in class org.openscience.cdk.BioPolymer
Retrieves a Monomer object by specifying its name.
getStrand(String) - Method in class org.openscience.cdk.debug.DebugBioPolymer
Retrieves a Monomer object by specifying its name.
getStrand(String) - Method in interface org.openscience.cdk.interfaces.IBioPolymer
Retrieve a Monomer object by specifying its name.
getStrand(String) - Method in class org.openscience.cdk.silent.BioPolymer
Retrieves a Monomer object by specifying its name.
getStrandCount() - Method in class org.openscience.cdk.BioPolymer
Returns the number of strands present in the BioPolymer.
getStrandCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns the number of strands present in the BioPolymer.
getStrandCount() - Method in interface org.openscience.cdk.interfaces.IBioPolymer
Return the number of strands present in the BioPolymer.
getStrandCount() - Method in class org.openscience.cdk.silent.BioPolymer
Returns the number of strands present in the BioPolymer.
getStrandName() - Method in class org.openscience.cdk.debug.DebugStrand
Retrieves the strand name.
getStrandName() - Method in interface org.openscience.cdk.interfaces.IStrand
Retrieve the strand name.
getStrandName() - Method in class org.openscience.cdk.silent.Strand
Retrieves the strand name.
getStrandName() - Method in class org.openscience.cdk.Strand
Retrieves the strand name.
getStrandNames() - Method in class org.openscience.cdk.BioPolymer
Returns a collection of the names of all Strands in this BioPolymer.
getStrandNames() - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns a collection of the names of all Strands in this BioPolymer.
getStrandNames() - Method in interface org.openscience.cdk.interfaces.IBioPolymer
Returns a collection of the names of all Strands in this BioPolymer.
getStrandNames() - Method in class org.openscience.cdk.silent.BioPolymer
Returns a collection of the names of all Strands in this BioPolymer.
getStrands() - Method in class org.openscience.cdk.BioPolymer
 
getStrands() - Method in class org.openscience.cdk.debug.DebugBioPolymer
Returns a Map containing the strands in the Polymer.
getStrands() - Method in interface org.openscience.cdk.interfaces.IBioPolymer
Returns a Map containing the strands in the Polymer.
getStrands() - Method in class org.openscience.cdk.silent.BioPolymer
 
getStrandType() - Method in class org.openscience.cdk.debug.DebugStrand
Retrieves the strand type.
getStrandType() - Method in interface org.openscience.cdk.interfaces.IStrand
Retrieve the strand type.
getStrandType() - Method in class org.openscience.cdk.silent.Strand
Retrieves the strand type.
getStrandType() - Method in class org.openscience.cdk.Strand
Retrieves the strand type.
getString(IMolecularFormula, String[], boolean) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
Returns the string representation of the molecule formula.
getString(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
Returns the string representation of the molecule formula.
getString(IMolecularFormula, boolean) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
Returns the string representation of the molecule formula.
getStrokeMap() - Method in class org.openscience.cdk.renderer.visitor.AWTDrawVisitor
Returns the current stroke map.
getStructures() - Method in class org.openscience.cdk.debug.DebugPDBPolymer
Returns a Collection containing the PDBStructure in the PDBPolymer.
getStructures() - Method in interface org.openscience.cdk.interfaces.IPDBPolymer
Returns a Collection containing the PDBStructure in the PDBPolymer.
getStructures() - Method in class org.openscience.cdk.protein.data.PDBPolymer
 
getStructures() - Method in class org.openscience.cdk.silent.PDBPolymer
 
getStructures(IAtomContainer) - Method in class org.openscience.cdk.tools.StructureResonanceGenerator
Get the resonance structures from an IAtomContainer.
getStructureType() - Method in class org.openscience.cdk.debug.DebugPDBStructure
get Structure Type of this structure.
getStructureType() - Method in interface org.openscience.cdk.interfaces.IPDBStructure
get Structure Type of this structure.
getStructureType() - Method in class org.openscience.cdk.protein.data.PDBStructure
get Structure Type of this structure.
getStructureType() - Method in class org.openscience.cdk.silent.PDBStructure
get Structure Type of this structure.
getSubgraph() - Method in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
 
getSubgraphAtomsMap(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
Returns the first subgraph 'atom mapping' found for g2 in g1, where g2 must be a substructure of g1.
getSubgraphAtomsMap(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
Deprecated.
Returns the first subgraph 'atom mapping' found for targetGraph in sourceGraph.
getSubgraphAtomsMaps(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
Returns all subgraph 'atom mappings' found for g2 in g1, where g2 must be a substructure of g1.
getSubgraphAtomsMaps(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
Deprecated.
Returns all subgraph 'atom mappings' found for targetGraph in sourceGraph.
getSubgraphMap(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
Returns the first subgraph 'bond mapping' found for g2 in g1.
getSubgraphMap(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
Deprecated.
Returns the first subgraph 'bondA1 mapping' found for targetGraph in sourceGraph.
getSubgraphMaps(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
Returns all the subgraph 'bond mappings' found for g2 in g1.
getSubgraphMaps(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
Deprecated.
Returns all the subgraph 'bondA1 mappings' found for targetGraph in sourceGraph.
getSubscript() - Method in class org.openscience.cdk.sgroup.Sgroup
Access the subscript value.
getSubstituents() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
Return all the substituent atom containers, in other words the atom containers defined in this RGroupQuery except for the root structure.
getSubstituents() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
 
getSubstructure(int) - Method in class org.openscience.cdk.fingerprint.SubstructureFingerprinter
Retrieves the SMARTS representation of a substructure for a given bit in the fingerprint.
GetSuffix(int) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
Get the suffix.
GetSuffix(int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
Get the suffix.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.CDKSourceCodeWriter
 
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ABINITFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Aces2Format
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ADFFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.AlchemyFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.BGFFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.BSFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
 
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CACheFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
 
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CIFFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CMLFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CRK2DFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CRK3DFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CrystClustFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CTXFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.DaltonFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.DMol3Format
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.DOCK5Format
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.FingerprintFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.GamessFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian03Format
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian90Format
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian92Format
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian94Format
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian95Format
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian98Format
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.GROMOS96Format
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.HINFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in interface org.openscience.cdk.io.formats.IChemFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.INChIFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.JaguarFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.JMEFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MacroModelFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLV2000Format
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLV3000Format
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MMODFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Mol2Format
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC7Format
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC93Format
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC97Format
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MPQCFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.NWChemFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PCModelFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PDBFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PDBMLFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PMPFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PQSChemFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.QChemFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.RawCopyFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SDFFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ShelXFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SMARTSFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SMILESFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SpartanFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.VASPFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ViewmolFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.XEDFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.XYZFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.YasaraFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ZindoFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat
Returns an integer indicating the data features that this format supports.
getSupportedDataFeatures(IAtomContainer) - Static method in class org.openscience.cdk.tools.DataFeaturesTool
Determines the features present in the given IAtomContainer.
getSurfaceArea(int) - Method in class org.openscience.cdk.geometry.surface.NumericalSurface
Get the surface area for the specified atom.
getSurfacePoints(int) - Method in class org.openscience.cdk.geometry.surface.NumericalSurface
Get an array of the points on the accessible surface of a specific atom.
getSwitchingAtom() - Method in class org.openscience.cdk.libio.md.ChargeGroup
 
getSymbol() - Method in class org.openscience.cdk.debug.DebugAtom
Returns the element symbol of this element.
getSymbol() - Method in class org.openscience.cdk.debug.DebugAtomType
Returns the element symbol of this element.
getSymbol() - Method in class org.openscience.cdk.debug.DebugElement
Returns the element symbol of this element.
getSymbol() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
Returns the element symbol of this element.
getSymbol() - Method in class org.openscience.cdk.debug.DebugIsotope
Returns the element symbol of this element.
getSymbol() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
Returns the element symbol of this element.
getSymbol() - Method in class org.openscience.cdk.Element
Returns the element symbol of this element.
getSymbol() - Method in interface org.openscience.cdk.interfaces.IElement
Returns the element symbol of this element.
getSymbol() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
Returns the element symbol of this element.
getSymbol() - Method in class org.openscience.cdk.silent.Element
Returns the element symbol of this element.
getSymbol(int) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
Get the symbol for the specified atomic number.
getSymbolFirstAtom() - Method in class org.openscience.cdk.smsd.helper.BondEnergy
Deprecated.
Returns the element symbol of the first atom.
getSymbolSecondAtom() - Method in class org.openscience.cdk.smsd.helper.BondEnergy
Deprecated.
Returns the element symbol of the second atom.
getSymbolSet() - Method in class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom
Retrieve the Set of symbols
getSymbolSet() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom
Retrieve the Set of symbols
getTabSize(int) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
 
getTabSize(int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
 
getTanimotoAtomSimilarity() - Method in class org.openscience.cdk.smsd.Isomorphism
Deprecated.
 
getTanimotoBondSimilarity() - Method in class org.openscience.cdk.smsd.Isomorphism
Deprecated.
 
getTanimotoSimilarity() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
Deprecated.
Returns Tanimoto similarity between query and target molecules (Score is between 0-min and 1-max).
getTanimotoSimilarity() - Method in class org.openscience.cdk.smsd.Isomorphism
Deprecated.
Returns Tanimoto similarity between query and target molecules (Score is between 0-min and 1-max).
getTarget() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
Deprecated.
Returns target molecule
getTarget() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.EdgeBuilder
Deprecated.
Returns target Node.
getTarget() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IEdge
Deprecated.
Returns target Node.
getTarget() - Method in class org.openscience.cdk.smsd.ring.PathEdge
Deprecated.
 
getTargetAtom() - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.Match
Deprecated.
Return Target Atom
getTargetQueryBondMappings() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher
Return a list of HashMap's that allows one to get the query constraint for a given pharmacophore bond.
getTautomers(IAtomContainer) - Method in class org.openscience.cdk.tautomers.InChITautomerGenerator
Public method to get tautomers for an input molecule, based on the InChI which will be calculated by JNI-InChI.
getTautomers(IAtomContainer, String) - Method in class org.openscience.cdk.tautomers.InChITautomerGenerator
getTempFactor() - Method in class org.openscience.cdk.debug.DebugPDBAtom
get the Temperature factor of this atom.
getTempFactor() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
get the Temperature factor of this atom.
getTempFactor() - Method in class org.openscience.cdk.protein.data.PDBAtom
get the Temperature factor of this atom.
getTempFactor() - Method in class org.openscience.cdk.silent.PDBAtom
get the Temperature factor of this atom.
getTemplateAt(int) - Method in class org.openscience.cdk.layout.TemplateHandler
Gets the templateAt attribute of the TemplateHandler object
getTemplateAt(int) - Method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D
Gets the templateAt attribute of the TemplateHandler object.
getTemplateCount() - Method in class org.openscience.cdk.layout.TemplateHandler
Gets the templateCount attribute of the TemplateHandler object
getTemplateCount() - Method in class org.openscience.cdk.modeling.builder3d.ModelBuilder3D
Returns the number of loaded templates.
getTemplateCount() - Method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D
Gets the templateCount attribute of the TemplateHandler object.
getTemplateHandler() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
Deprecated.
always null, substructure templates are not used anymore
getTessAsPoint3ds() - Method in class org.openscience.cdk.geometry.surface.Tessellate
 
getTessAsTriangles() - Method in class org.openscience.cdk.geometry.surface.Tessellate
 
getTextBasePoint(String, double, double, Graphics2D) - Method in class org.openscience.cdk.renderer.visitor.AbstractAWTDrawVisitor
Calculates the base point where text should be rendered, as text in Java is typically placed using the left-lower corner point in screen coordinates.
getTextBounds(String, double, double, Graphics2D) - Method in class org.openscience.cdk.renderer.visitor.AbstractAWTDrawVisitor
Calculates the boundaries of a text string in screen coordinates.
getTextBounds(String, Graphics2D) - Method in class org.openscience.cdk.renderer.visitor.AbstractAWTDrawVisitor
Obtain the exact bounding box of the text in the provided graphics environment.
getTimeManager() - Static method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlus
Deprecated.
 
getTimeManager() - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
Deprecated.
 
getTimeManager() - Static method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper
Deprecated.
 
getTimeManager() - Static method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper
Deprecated.
 
getTimeout() - Method in class org.openscience.cdk.ringsearch.AllRingsFinder
Deprecated.
timeout not used
getTimeout() - Static method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlus
Deprecated.
 
getTimeout() - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
Deprecated.
 
getTimeout() - Static method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper
Deprecated.
 
getTimeout() - Static method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper
Deprecated.
 
getTimeOut() - Method in class org.openscience.cdk.smsd.global.TimeOut
Deprecated.
Return cutoff value for time out.
getTitle() - Method in class org.openscience.cdk.ConformerContainer
Get the title of the conformers.
getTitle() - Method in class org.openscience.cdk.renderer.GraphRendererModel
Get the main title
getTitlemap() - Method in class org.openscience.cdk.io.RssWriter
 
getToken(int) - Method in class org.openscience.cdk.iupac.parser.NomParser
Deprecated.
Get the specific Token.
getToken(int) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
Get the specific Token.
getTolerance() - Method in class org.openscience.cdk.formula.IsotopePatternSimilarity
Get the tolerance of the mass accuracy.
getToolTipText(IAtom) - Method in class org.openscience.cdk.renderer.RendererModel
Gets the toolTipText for atom certain atom.
getToolTipTextMap() - Method in class org.openscience.cdk.renderer.RendererModel
Gets the toolTipTextMap.
getTopoEquivClassbyHuXu(IAtomContainer) - Method in class org.openscience.cdk.graph.invariant.EquivalentClassPartitioner
Get the topological equivalent class of the molecule.
getTorsionAngle(Point3d, Point3d, Point3d, Point3d) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
Calculates the torsionAngle of a-b-c-d.
getTorsionData(String, String, String, String, String) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94ParametersCall
Gets the bond parameter set.
getTotalCharge(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
Get the summed charge of all atoms in an AtomContainer
getTotalCharge(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
 
getTotalCharge(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
 
getTotalExactMass(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
Get the summed exact mass of all atoms in an AtomContainer.
getTotalExactMass(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
Get the summed exact mass of all isotopes from an MolecularFormula.
getTotalFormalCharge(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
Get the total formal charge on a molecule.
getTotalFormalCharge(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
 
getTotalFormalCharge(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
 
getTotalHydrogenCount(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
Counts the number of hydrogens on the provided IAtomContainer.
getTotalHydrogenCount(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
 
getTotalHydrogenCount(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
 
getTotalMassNumber(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
Get the summed mass number of all isotopes from an MolecularFormula.
getTotalNaturalAbundance(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
Get the summed natural abundance of all atoms in an AtomContainer
getTotalNaturalAbundance(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
Get the summed natural abundance of all isotopes from an MolecularFormula.
getTotalNegativeFormalCharge(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
Get the total formal negative charge on a molecule.
getTotalPositiveFormalCharge(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
Get the total positive formal charge on a molecule.
getTotalSurfaceArea() - Method in class org.openscience.cdk.geometry.surface.NumericalSurface
Get the total surface area for the AtomContainer.
getTrainingActives() - Method in class org.openscience.cdk.fingerprint.model.Bayesian
Returns the number of actives in the training set that was used to create the model.
getTrainingSize() - Method in class org.openscience.cdk.fingerprint.model.Bayesian
Returns the size of the training set, i.e.
getType() - Method in class org.openscience.cdk.dict.DictRef
 
getType() - Method in class org.openscience.cdk.isomorphism.matchers.CTFileQueryBond
Getter for type
getType() - Method in class org.openscience.cdk.sgroup.Sgroup
Access the type of the Sgroup.
getUncommon(IAtomContainer, IAtomContainer, boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler
Deprecated.
 
getUncommon(IAtomContainer, IAtomContainer, boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler
Deprecated.
 
getUniqueMatchingAtoms() - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool
Get the atoms in the target molecule that match the query pattern.
getUniqueMatchingPharmacophoreAtoms() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher
Get the uniue matching pharmacophore groups.
getUnplacedRingHeavyAtom(IAtomContainer, IAtom) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
Gets the unplacedRingHeavyAtom attribute of the AtomPlacer3D object.
getUnsetAtomsInAtomContainer(IAtom, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
Gets the unsetAtomsInAtomContainer attribute of the AtomTetrahedralLigandPlacer3D object.
getUpper() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryAngleBond
 
getUpper() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryBond
 
getUseTemplates() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
Deprecated.
always false, substructure templates are not used anymore
getUSmilesNumbers(IAtomContainer) - Static method in class org.openscience.cdk.graph.invariant.InChINumbersTools
Obtain the InChI numbers for the input container to be used to order atoms in Universal SMILES [O’Boyle, Noel, Towards a Universal SMILES representation - A standard method to generate canonical SMILES based on the InChI, Journal of Cheminformatics, 2012, 4:?-?, doi:10.1186/1758-2946-4-22].
getValence(IAtom) - Static method in class org.openscience.cdk.qsar.AtomValenceTool
 
getValency() - Method in class org.openscience.cdk.AtomType
Gets the the exact electron valency of the AtomType object.
getValency() - Method in class org.openscience.cdk.debug.DebugAtom
Gets the the exact electron valency of the AtomType object.
getValency() - Method in class org.openscience.cdk.debug.DebugAtomType
Gets the the exact electron valency of the AtomType object.
getValency() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
Gets the the exact electron valency of the AtomType object.
getValency() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
Gets the the exact electron valency of the AtomType object.
getValency() - Method in interface org.openscience.cdk.interfaces.IAtomType
Gets the the exact electron valency of the AtomType object.
getValency() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
Gets the the exact electron valency of the AtomType object.
getValency() - Method in class org.openscience.cdk.silent.AtomType
Gets the the exact electron valency of the AtomType object.
getValue() - Method in enum org.openscience.cdk.io.MDLV2000Writer.SPIN_MULTIPLICITY
Radical value for the spin multiplicity in the properties block.
getValue() - Method in class org.openscience.cdk.iupac.parser.Token
An optional attribute value of the Token.
getValue(double, double, double) - Method in interface org.openscience.cdk.math.IFunction
Return the function value at (x,y,z)
getValue(int, double, double, double) - Method in class org.openscience.cdk.math.qm.FourierGridBasis
 
getValue(int, double, double, double) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
Calculates the function value an (x,y,z).
getValue(int, double, double, double) - Method in interface org.openscience.cdk.math.qm.IBasis
Calculates the function value an (x,y,z).
getValue(int, double, double, double) - Method in class org.openscience.cdk.math.qm.Orbitals
Get the function value of a orbital at the position (x,y,z)
getValue() - Method in class org.openscience.cdk.qsar.DescriptorValue
 
getValue() - Method in interface org.openscience.cdk.reaction.type.parameters.IParameterReact
Get the value of the parameter.
getValue() - Method in class org.openscience.cdk.reaction.type.parameters.ParameterReact
Get the value of the parameter.
getValue() - Method in interface org.openscience.cdk.renderer.generators.IGeneratorParameter
Gets the value for this parameter.
getValue() - Method in class org.openscience.cdk.renderer.generators.parameter.AbstractGeneratorParameter
Gets the value for this parameter.
getValue(SgroupKey) - Method in class org.openscience.cdk.sgroup.Sgroup
Access an attribute for the Sgroup.
getValue() - Method in class org.openscience.cdk.smiles.smarts.parser.Token
An optional attribute value of the Token.
getValue() - Method in class org.openscience.cdk.smsd.helper.BinaryTree
Deprecated.
Return value of the node
getValueAt(int, int) - Method in class org.openscience.cdk.graph.invariant.GIMatrix
Returns the value of the given element.
getValues() - Method in class org.openscience.cdk.group.Permutation
Get all the values as an array.
getValues(Matrix) - Method in interface org.openscience.cdk.math.IFunction
Return the function value The rows of the matrix x are the Parameters like x,y,z and the columns are the values which must calculated.
getValues(int, Matrix) - Method in class org.openscience.cdk.math.qm.FourierGridBasis
 
getValues(int, Matrix) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
Calculates the function values.
getValues(int, Matrix) - Method in interface org.openscience.cdk.math.qm.IBasis
Calculates the function values.
getValues(int, Matrix) - Method in class org.openscience.cdk.math.qm.Orbitals
Get the function value of a orbital
getVanDerWaalsFile() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
 
getVdwRadius(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
Get the Van der Waals radius for the element in question.
getVdWVolume(String) - Method in class org.openscience.cdk.tools.AtomicProperties
 
getVectorFromColumn(int) - Method in class org.openscience.cdk.math.IMatrix
Creates a vector with the content of a column from this matrix
getVectorFromColumn(int) - Method in class org.openscience.cdk.math.Matrix
Creates a Vector with the content of a column from this Matrix.
getVectorFromDiagonal() - Method in class org.openscience.cdk.math.IMatrix
Creates a vector with the content of the diagonal elements from this matrix
getVectorFromDiagonal() - Method in class org.openscience.cdk.math.Matrix
Creates a Vector with the content of the diagonal elements from this Matrix.
getVectorFromRow(int) - Method in class org.openscience.cdk.math.IMatrix
Creates a vector with the content of a row from this matrix
getVectorFromRow(int) - Method in class org.openscience.cdk.math.Matrix
Creates a Vector with the content of a row from this Matrix.
getVersion() - Static method in class org.openscience.cdk.CDK
Returns the version of this CDK library.
getVersionDescription() - Method in class org.openscience.cdk.fingerprint.AbstractFingerprinter
 
getVersionDescription() - Method in interface org.openscience.cdk.fingerprint.IFingerprinter
Generate a fingerprint type version description in chemfp's FPS format.
getVertexCount() - Method in interface org.openscience.cdk.group.Refinable
Get the number of vertices in the graph to be refined.
getVertexCount() - Method in class org.openscience.cdk.signature.MoleculeSignature
 
getVertexCountAtDistance(IAtomContainer, int) - Static method in class org.openscience.cdk.graph.PathTools
Returns the number of vertices that are a distance 'd' apart.
getVertexSymbol(int) - Method in class org.openscience.cdk.signature.AtomSignature
 
getVisitedAtoms() - Method in interface org.openscience.cdk.geometry.cip.ILigand
Returns a list of visitedAtoms.
getVisitedAtoms() - Method in class org.openscience.cdk.geometry.cip.Ligand
Returns a list of visitedAtoms.
getWarningCount() - Method in class org.openscience.cdk.validate.ValidationReport
Returns the number of tests which gave warnings.
getWarningFlags() - Method in class org.openscience.cdk.inchi.InChIToStructure
Returns warning flags, see INCHIDIFF in inchicmp.h.
getWarnings() - Method in class org.openscience.cdk.validate.ValidationReport
Returns an array of ValidationTest warnings.
getWidthForBond(IBond, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
Determine the width of a bond, returning either the width defined in the model, or the override width.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.ABINITFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.Aces2Format
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.ADFFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.AlchemyFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.BGFFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.BSFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
 
getWriterClassName() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.CACheFormat
 
getWriterClassName() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
 
getWriterClassName() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat
 
getWriterClassName() - Method in class org.openscience.cdk.io.formats.CIFFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.CMLFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.CRK2DFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.CRK3DFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.CrystClustFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.CTXFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.DaltonFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.DMol3Format
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.DOCK5Format
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.FingerprintFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.GamessFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.Gaussian03Format
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.Gaussian90Format
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.Gaussian92Format
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.Gaussian94Format
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.Gaussian95Format
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.Gaussian98Format
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat
 
getWriterClassName() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.GROMOS96Format
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.HINFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in interface org.openscience.cdk.io.formats.IChemFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.INChIFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.JaguarFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.JMEFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MacroModelFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MDLFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MDLV2000Format
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MDLV3000Format
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MMODFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.Mol2Format
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC7Format
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC93Format
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC97Format
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.MPQCFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.NWChemFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.PCModelFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.PDBFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.PDBMLFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.PMPFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.PQSChemFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.QChemFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.RawCopyFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.SDFFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.ShelXFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.SMARTSFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.SMILESFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.SpartanFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.VASPFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.ViewmolFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.XEDFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.XYZFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.YasaraFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.ZindoFormat
Returns the class name of the CDK Writer for this format.
getWriterClassName() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat
Returns the class name of the CDK Writer for this format.
getXMax() - Method in class org.openscience.cdk.renderer.GraphRendererModel
Sets the function area, which will painted
getXMin() - Method in class org.openscience.cdk.renderer.GraphRendererModel
Gets the function area, which will painted
getXTitle() - Method in class org.openscience.cdk.renderer.GraphRendererModel
Get the title of the x axis
getYMax() - Method in class org.openscience.cdk.renderer.GraphRendererModel
Sets the function area, which will painted
getYMin() - Method in class org.openscience.cdk.renderer.GraphRendererModel
Sets the function area, which will painted
getYTitle() - Method in class org.openscience.cdk.renderer.GraphRendererModel
Get the title of the y axis
getZ() - Method in class org.openscience.cdk.Crystal
Gets the number of asymmetric parts in the unit cell.
getZ() - Method in class org.openscience.cdk.debug.DebugCrystal
Gets the number of asymmetric parts in the unit cell.
getZ() - Method in interface org.openscience.cdk.interfaces.ICrystal
Gets the number of asymmetric parts in the unit cell.
getZ() - Method in class org.openscience.cdk.silent.Crystal
Gets the number of asymmetric parts in the unit cell.
GhemicalMMFormat - Class in org.openscience.cdk.io.formats
See here.
GhemicalMMFormat() - Constructor for class org.openscience.cdk.io.formats.GhemicalMMFormat
 
GhemicalMMReader - Class in org.openscience.cdk.io
Reads Ghemical ( http://www.uku.fi/~thassine/ghemical/) molecular mechanics (*.mm1gp) files.
GhemicalMMReader(Reader) - Constructor for class org.openscience.cdk.io.GhemicalMMReader
 
GhemicalMMReader(InputStream) - Constructor for class org.openscience.cdk.io.GhemicalMMReader
 
GhemicalMMReader() - Constructor for class org.openscience.cdk.io.GhemicalMMReader
 
GhemicalSPMFormat - Class in org.openscience.cdk.io.formats
 
GhemicalSPMFormat() - Constructor for class org.openscience.cdk.io.formats.GhemicalSPMFormat
 
GIF_FMT - Static variable in class org.openscience.cdk.depict.Depiction
Graphics Interchange Format (GIF) format key.
GIMatrix - Class in org.openscience.cdk.graph.invariant
This class is intended to provide the user an efficient way of implementing matrix of double number and using normal operations (linear operations, addition, subtraction, multiplication, inversion, concatenation) on them.
GIMatrix(int[][]) - Constructor for class org.openscience.cdk.graph.invariant.GIMatrix
Class constructor.
GIMatrix(double[][]) - Constructor for class org.openscience.cdk.graph.invariant.GIMatrix
Class constructor.
GIMatrix(int, int) - Constructor for class org.openscience.cdk.graph.invariant.GIMatrix
Class constructor.
GIMatrix(GIMatrix) - Constructor for class org.openscience.cdk.graph.invariant.GIMatrix
Class constructor.
GIMatrix(GIMatrix[][]) - Constructor for class org.openscience.cdk.graph.invariant.GIMatrix
Class constructor.
giveAngle(IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.geometry.BondTools
Calls giveAngleBothMethods with bool = true.
giveAngleBothMethods(IAtom, IAtom, IAtom, boolean) - Static method in class org.openscience.cdk.geometry.BondTools
Gives the angle between two lines starting at atom from and going to to1 and to2.
giveAngleBothMethods(Point2d, Point2d, Point2d, boolean) - Static method in class org.openscience.cdk.geometry.BondTools
 
giveAngleFromMiddle(IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.geometry.BondTools
Calls giveAngleBothMethods with bool = false.
GOLD - Static variable in enum org.openscience.cdk.config.Elements
 
GOLD - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
graph - Variable in class org.openscience.cdk.stereo.StereoElementFactory
Adjacency list graph representation.
GraphOnlyFingerprinter - Class in org.openscience.cdk.fingerprint
Specialized version of the Fingerprinter which does not take bond orders into account.
GraphOnlyFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.GraphOnlyFingerprinter
Creates a fingerprint generator of length defaultSize and with a search depth of defaultSearchDepth.
GraphOnlyFingerprinter(int) - Constructor for class org.openscience.cdk.fingerprint.GraphOnlyFingerprinter
 
GraphOnlyFingerprinter(int, int) - Constructor for class org.openscience.cdk.fingerprint.GraphOnlyFingerprinter
 
GraphRendererModel - Class in org.openscience.cdk.renderer
This class handles a set of function for the GraphRenderer
GraphRendererModel() - Constructor for class org.openscience.cdk.renderer.GraphRendererModel
 
GraphUtil - Class in org.openscience.cdk.graph
Collection of static utilities for manipulating adjacency list representations stored as a int[][].
GraphUtil.EdgeToBondMap - Class in org.openscience.cdk.graph
Utility for storing IBonds indexed by vertex end points.
GravitationalIndexDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
IDescriptor characterizing the mass distribution of the molecule.
GravitationalIndexDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor
 
GridGenerator - Class in org.openscience.cdk.tools
Generates a grid of points in 3D space within given boundaries.
GridGenerator() - Constructor for class org.openscience.cdk.tools.GridGenerator
 
GridGenerator(double, double) - Constructor for class org.openscience.cdk.tools.GridGenerator
 
GridGenerator(double, double, double) - Constructor for class org.openscience.cdk.tools.GridGenerator
 
GridGenerator(double[], double, boolean) - Constructor for class org.openscience.cdk.tools.GridGenerator
 
gridToGridArray(double[][][]) - Method in class org.openscience.cdk.tools.GridGenerator
Method transforms the grid to an array.
gridToPmesh(String) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
Method writes the grid to pmesh format.
GROMOS96Format - Class in org.openscience.cdk.io.formats
See here.
GROMOS96Format() - Constructor for class org.openscience.cdk.io.formats.GROMOS96Format
 
group() - Method in enum org.openscience.cdk.config.Elements
Return the group in the periodic table this element belongs to.
GroupExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
 
groupOneMetals() - Method in class org.openscience.cdk.iupac.parser.NomParser
Deprecated.
 
groupTwoMetals() - Method in class org.openscience.cdk.iupac.parser.NomParser
Deprecated.
 
growArraySize - Variable in class org.openscience.cdk.AtomContainer
Amount by which the bond and atom arrays grow when elements are added and the arrays are not large enough for that.
growArraySize - Variable in class org.openscience.cdk.AtomContainerSet
Amount by which the AtomContainers array grows when elements are added and the array is not large enough for that.
growArraySize - Variable in class org.openscience.cdk.ChemFile
Amount by which the chemsequence array grows when elements are added and the array is not large enough for that.
growArraySize - Variable in class org.openscience.cdk.ChemSequence
Amount by which the chemModels array grows when elements are added and the array is not large enough for that.
growArraySize - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Amount by which the bond and atom arrays grow when elements are added and the arrays are not large enough for that.
growArraySize - Variable in class org.openscience.cdk.Reaction
 
growArraySize - Variable in class org.openscience.cdk.silent.AtomContainer
Amount by which the bond and atom arrays grow when elements are added and the arrays are not large enough for that.
growArraySize - Variable in class org.openscience.cdk.silent.AtomContainerSet
Amount by which the AtomContainers array grows when elements are added and the array is not large enough for that.
growArraySize - Variable in class org.openscience.cdk.silent.ChemFile
Amount by which the chemsequence array grows when elements are added and the array is not large enough for that.
growArraySize - Variable in class org.openscience.cdk.silent.ChemSequence
Amount by which the chemModels array grows when elements are added and the array is not large enough for that.
growArraySize - Variable in class org.openscience.cdk.silent.Reaction
 
growAtomContainerArray() - Method in class org.openscience.cdk.AtomContainerSet
Grows the atomContainer array by a given size.
growAtomContainerArray() - Method in class org.openscience.cdk.silent.AtomContainerSet
Grows the atomContainer array by a given size.
growChemModelArray() - Method in class org.openscience.cdk.ChemSequence
Grows the chemModel array by a given size.
growChemModelArray() - Method in class org.openscience.cdk.silent.ChemSequence
Grows the chemModel array by a given size.
growChemSequenceArray() - Method in class org.openscience.cdk.ChemFile
Grows the ChemSequence array by a given size.
growChemSequenceArray() - Method in class org.openscience.cdk.silent.ChemFile
Grows the ChemSequence array by a given size.
guessFormat(Reader) - Method in class org.openscience.cdk.io.FormatFactory
Creates a String of the Class name of the IChemObject reader for this file format.
guessFormat(InputStream) - Method in class org.openscience.cdk.io.FormatFactory
 

H

h - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
H - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
H_AND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
HAFNIUM - Static variable in enum org.openscience.cdk.config.Elements
 
HAFNIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
handleError(String) - Method in class org.openscience.cdk.io.DefaultChemObjectReader
Redirects an error message to the IChemObjectReaderErrorHandler.
handleError(String, Exception) - Method in class org.openscience.cdk.io.DefaultChemObjectReader
Redirects an error message to the IChemObjectReaderErrorHandler.
handleError(String, int, int, int) - Method in class org.openscience.cdk.io.DefaultChemObjectReader
Redirects an error message to the IChemObjectReaderErrorHandler.
handleError(String, int, int, int, Exception) - Method in class org.openscience.cdk.io.DefaultChemObjectReader
Redirects an error message to the IChemObjectReaderErrorHandler.
handleError(String) - Method in interface org.openscience.cdk.io.IChemObjectReader
Redirects an error message to the IChemObjectReaderErrorHandler.
handleError(String, Exception) - Method in interface org.openscience.cdk.io.IChemObjectReader
Redirects an error message to the IChemObjectReaderErrorHandler.
handleError(String, int, int, int) - Method in interface org.openscience.cdk.io.IChemObjectReader
Redirects an error message to the IChemObjectReaderErrorHandler.
handleError(String, int, int, int, Exception) - Method in interface org.openscience.cdk.io.IChemObjectReader
Redirects an error message to the IChemObjectReaderErrorHandler.
handleError(String) - Method in interface org.openscience.cdk.io.IChemObjectReaderErrorHandler
Method that should react on an error message send by an IChemObjectReader.
handleError(String, Exception) - Method in interface org.openscience.cdk.io.IChemObjectReaderErrorHandler
Method that should react on an error message send by an IChemObjectReader.
handleError(String, int, int, int) - Method in interface org.openscience.cdk.io.IChemObjectReaderErrorHandler
Method that should react on an error message send by an IChemObjectReader.
handleError(String, int, int, int, Exception) - Method in interface org.openscience.cdk.io.IChemObjectReaderErrorHandler
Method that should react on an error message send by an IChemObjectReader.
handleError(String) - Method in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader
Redirects an error message to the IChemObjectReaderErrorHandler.
handleError(String, Exception) - Method in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader
Redirects an error message to the IChemObjectReaderErrorHandler.
handleError(String, int, int, int) - Method in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader
Redirects an error message to the IChemObjectReaderErrorHandler.
handleError(String, int, int, int, Exception) - Method in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader
Redirects an error message to the IChemObjectReaderErrorHandler.
HanserRingFinder - Class in org.openscience.cdk.smsd.ring
Deprecated.
Use CDK AllRingsFinder. A more recent version of SMSD is available at http://github.com/asad/smsd.
HanserRingFinder() - Constructor for class org.openscience.cdk.smsd.ring.HanserRingFinder
Deprecated.
 
has(String) - Method in class org.openscience.cdk.io.setting.SettingManager
Determines whether the manager currently holds a setting of the provided name.
has2DCoordinates(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
Determines if all this IAtomContainer's atoms contain 2D coordinates.
has2DCoordinates(IAtom) - Static method in class org.openscience.cdk.geometry.GeometryTools
Determines if this Atom contains 2D coordinates.
has2DCoordinates(IBond) - Static method in class org.openscience.cdk.geometry.GeometryTools
Determines if this Bond contains 2D coordinates.
has2DCoordinates(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Determines if all this IAtomContainer's atoms contain 2D coordinates.
has2DCoordinates(IAtom) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Determines if this Atom contains 2D coordinates.
has2DCoordinates(IBond) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Determines if this Bond contains 2D coordinates.
has2DCoordinatesNew(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
has2DCoordinatesNew(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
has3DCoordinates(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
Determines if all this IAtomContainer's atoms contain 3D coordinates.
has3DCoordinates(IChemModel) - Static method in class org.openscience.cdk.geometry.GeometryTools
Determines if this model contains 3D coordinates for all atoms.
has3DCoordinates(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Determines if all this IAtomContainer's atoms contain 3D coordinates.
has3DCoordinates(IChemModel) - Static method in class org.openscience.cdk.geometry.GeometryUtil
Determines if this model contains 3D coordinates for all atoms.
HAS_2D_COORDINATES - Static variable in class org.openscience.cdk.tools.DataFeatures
 
HAS_3D_COORDINATES - Static variable in class org.openscience.cdk.tools.DataFeatures
 
HAS_ATOM_ELEMENT_SYMBOL - Static variable in class org.openscience.cdk.tools.DataFeatures
 
HAS_ATOM_FORMAL_CHARGES - Static variable in class org.openscience.cdk.tools.DataFeatures
 
HAS_ATOM_HYBRIDIZATIONS - Static variable in class org.openscience.cdk.tools.DataFeatures
FIXME: NOT YET IN BODF !!!
HAS_ATOM_ISOTOPE_NUMBERS - Static variable in class org.openscience.cdk.tools.DataFeatures
 
HAS_ATOM_MASS_NUMBERS - Static variable in class org.openscience.cdk.tools.DataFeatures
 
HAS_ATOM_PARTIAL_CHARGES - Static variable in class org.openscience.cdk.tools.DataFeatures
 
HAS_DIETZ_REPRESENTATION - Static variable in class org.openscience.cdk.tools.DataFeatures
 
HAS_FRACTIONAL_CRYSTAL_COORDINATES - Static variable in class org.openscience.cdk.tools.DataFeatures
 
HAS_GRAPH_REPRESENTATION - Static variable in class org.openscience.cdk.tools.DataFeatures
 
HAS_REACTIONS - Static variable in class org.openscience.cdk.tools.DataFeatures
FIXME: NOT YET IN BODF !!!
HAS_UNITCELL_PARAMETERS - Static variable in class org.openscience.cdk.tools.DataFeatures
FIXME: NOT YET IN BODF !!!
HASATOM - Static variable in class org.openscience.cdk.libio.jena.CDK
 
HASATOMICNUMBER - Static variable in class org.openscience.cdk.libio.jena.CDK
 
HASATOMTYPENAME - Static variable in class org.openscience.cdk.libio.jena.CDK
 
HASBOND - Static variable in class org.openscience.cdk.libio.jena.CDK
 
hasCoordinates(IAtom) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator
Checks an atom to see if it has 2D coordinates.
hasCrystalCoordinates(IAtomContainer) - Static method in class org.openscience.cdk.geometry.CrystalGeometryTools
Determines if this model contains fractional (crystal) coordinates.
hasDictionary(String) - Method in class org.openscience.cdk.dict.DictionaryDatabase
Returns true if the database contains the dictionary.
HASELECTRONCOUNT - Static variable in class org.openscience.cdk.libio.jena.CDK
 
hasElementSymbols(IAtomContainer) - Static method in class org.openscience.cdk.tools.features.MoleculeFeaturesTool
 
hasEntry(String) - Method in class org.openscience.cdk.dict.Dictionary
 
hasEntry(String, String) - Method in class org.openscience.cdk.dict.DictionaryDatabase
Returns true if the given dictionary contains the given entry.
HASEXACTMASS - Static variable in class org.openscience.cdk.libio.jena.CDK
 
HASFORMALCHARGE - Static variable in class org.openscience.cdk.libio.jena.CDK
 
hasFormalCharges(IAtomContainer) - Static method in class org.openscience.cdk.tools.features.MoleculeFeaturesTool
 
hasGraphRepresentation(IAtomContainer) - Static method in class org.openscience.cdk.tools.features.MoleculeFeaturesTool
Checks whether all bonds have exactly two atoms.
hasHash(int) - Method in interface org.openscience.cdk.fingerprint.ICountFingerprint
Whether the fingerprint contains the given hash.
hasHash(int) - Method in class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
 
hashCode() - Method in class org.openscience.cdk.DynamicFactory.ConstructorKey
hashCode() - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
 
hashCode - Variable in class org.openscience.cdk.fingerprint.CircularFingerprinter.FP
 
hashCode() - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
 
hashCode() - Method in class org.openscience.cdk.group.Partition
hashCode() - Method in class org.openscience.cdk.group.Permutation
hashCode() - Method in class org.openscience.cdk.io.formats.AbstractResourceFormat
 
hashCode() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
 
hashCode() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom
 
hashCode() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycle
Deprecated.
 
hashCode() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMap
Deprecated.
Returns a hash code for object comparison.
HashGeneratorMaker - Class in org.openscience.cdk.hash
Fluent API for creating hash generators.
HashGeneratorMaker() - Constructor for class org.openscience.cdk.hash.HashGeneratorMaker
 
HASHYBRIDIZATION - Static variable in class org.openscience.cdk.libio.jena.CDK
 
HASLABEL - Static variable in class org.openscience.cdk.libio.jena.CDK
 
hasLabel(String) - Method in class org.openscience.cdk.signature.Orbit
Checks to see if the orbit has this string as a label.
hasMap(IAtomContainer) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper
Deprecated.
checks if a map exits for a molecule.
hasMap(TargetProperties) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper
Deprecated.
checks if a map exits for a molecule.
hasMap(IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper
Deprecated.
checks if a map exits for a molecule.
hasMap(TargetProperties) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper
Deprecated.
checks if a map exits for a molecule.
hasMap(IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper
Deprecated.
checks if a map exits for a molecule.
hasMap(TargetProperties) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper
Deprecated.
checks if a map exits for a molecule.
HASMASSNUMBER - Static variable in class org.openscience.cdk.libio.jena.CDK
 
HASMAXBONDORDER - Static variable in class org.openscience.cdk.libio.jena.CDK
 
hasMoreElements() - Method in class org.openscience.cdk.formula.rules.RDBERule.Combinations
 
HASNATURALABUNDANCE - Static variable in class org.openscience.cdk.libio.jena.CDK
 
hasNext() - Method in class org.openscience.cdk.graph.MinimalPathIterator
 
hasNext() - Method in class org.openscience.cdk.graph.Permutor
 
hasNext() - Method in class org.openscience.cdk.io.iterator.IteratingMDLConformerReader
 
hasNext() - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundASNReader
 
hasNext() - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader
 
hasNext() - Method in class org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader
 
hasNext() - Method in class org.openscience.cdk.io.iterator.IteratingSDFReader
Returns true if another IAtomContainer can be read.
hasNext() - Method in class org.openscience.cdk.io.iterator.IteratingSMILESReader
Checks whether there is another molecule to read.
hasNext() - Method in class org.openscience.cdk.io.random.RandomAccessReader
 
hasNext() - Method in class org.openscience.cdk.smsd.labelling.Permutor
Deprecated.
 
hasNextCandidate() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IState
Deprecated.
Returns true if another candidate match can be found or false otherwise.
hasNextCandidate() - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFState
Deprecated.
Returns true if another candidate match can be found or false otherwise.
HASORDER - Static variable in class org.openscience.cdk.libio.jena.CDK
 
hasParameter(Class<T>) - Method in class org.openscience.cdk.renderer.RendererModel
Returns true if the passed IGeneratorParameters has been registered.
hasPartialCharges(IAtomContainer) - Static method in class org.openscience.cdk.tools.features.MoleculeFeaturesTool
 
hasPerfectConfiguration(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker
 
hasPrevious() - Method in class org.openscience.cdk.io.random.RandomAccessReader
 
hasSetting(String) - Method in class org.openscience.cdk.io.ChemObjectIO
Determine whether this reader/writer has a setting of the provided name.
hasSetting(String) - Method in interface org.openscience.cdk.io.IChemObjectIO
Determine whether this reader/writer has a setting of the provided name.
HASSIUM - Static variable in enum org.openscience.cdk.config.Elements
 
HASSIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
hasSymbol(String) - Method in class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom
Check whether a symbol is already registered
hasSymbol(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom
Check whether a symbol is already registered
hasUnsetNeighbour(IAtom, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
 
HBondAcceptorCountDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
This descriptor calculates the number of hydrogen bond acceptors using a slightly simplified version of the PHACIR atom types.
HBondAcceptorCountDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor
Constructor for the HBondAcceptorCountDescriptor object
HBondDonorCountDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
This descriptor calculates the number of hydrogen bond donors using a slightly simplified version of the PHACIR atom types.
HBondDonorCountDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor
Constructor for the HBondDonorCountDescriptor object
hCounts - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
 
HE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
HEADER_DATE_FORMAT - Static variable in class org.openscience.cdk.io.MDLV3000Writer
 
headerOptions - Variable in class org.openscience.cdk.io.random.RandomAccessReader
 
height() - Method in class org.openscience.cdk.graph.invariant.GIMatrix
Returns the number of lines of the matrix.
height() - Method in class org.openscience.cdk.renderer.elements.Bounds
Specifies the height of the bounding box.
height - Variable in class org.openscience.cdk.renderer.elements.RectangleElement
The height of the rectangle.
HELIUM - Static variable in enum org.openscience.cdk.config.Elements
 
HELIX - Static variable in class org.openscience.cdk.protein.data.PDBStructure
 
HELIX - Static variable in class org.openscience.cdk.silent.PDBStructure
 
HEN - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
HENICOS - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
HEPT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
HeterolyticCleavageMechanism - Class in org.openscience.cdk.reaction.mechanism
This mechanism displaces the chemical bond to an Atom.
HeterolyticCleavageMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.HeterolyticCleavageMechanism
 
HeterolyticCleavagePBReaction - Class in org.openscience.cdk.reaction.type
IReactionProcess which a bond is broken displacing the electron to one of the atoms.
HeterolyticCleavagePBReaction() - Constructor for class org.openscience.cdk.reaction.type.HeterolyticCleavagePBReaction
Constructor of the HeterolyticCleavagePBReaction object.
HeterolyticCleavageSBReaction - Class in org.openscience.cdk.reaction.type
IReactionProcess which a bond is broken displacing the electron to one of the atoms.
HeterolyticCleavageSBReaction() - Constructor for class org.openscience.cdk.reaction.type.HeterolyticCleavageSBReaction
Constructor of the HeterolyticCleavageSBReaction object.
HEX - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
HF - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
HG - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
HIDDEN - Static variable in class org.openscience.cdk.renderer.generators.standard.StandardGenerator
Marks atoms and bonds as being hidden from the actual depiction.
HIDDEN_FULLY - Static variable in class org.openscience.cdk.renderer.generators.standard.StandardGenerator
 
HIGHLIGHT_COLOR - Static variable in class org.openscience.cdk.renderer.generators.standard.StandardGenerator
Defines that a chem object should be highlighted in a depiction.
HighlightGenerator - Class in org.openscience.cdk.renderer.generators
Generate an under/overlaid highlight in structure depictions.
HighlightGenerator() - Constructor for class org.openscience.cdk.renderer.generators.HighlightGenerator
 
HighlightGenerator.HighlightPalette - Class in org.openscience.cdk.renderer.generators
Defines the color palette used to provide the highlight colors.
HighlightGenerator.HighlightPalette() - Constructor for class org.openscience.cdk.renderer.generators.HighlightGenerator.HighlightPalette
 
HighlightGenerator.HighlightRadius - Class in org.openscience.cdk.renderer.generators
Magic number with unknown units that defines the radius around an atom, e.g.
HighlightGenerator.HighlightRadius() - Constructor for class org.openscience.cdk.renderer.generators.HighlightGenerator.HighlightRadius
 
HighlightGenerator.Palette - Interface in org.openscience.cdk.renderer.generators
Defines a color palette, the palette should provide a color the specified identifier (id).
highThresh - Variable in class org.openscience.cdk.fingerprint.model.Bayesian
 
HINFormat - Class in org.openscience.cdk.io.formats
See here.
HINFormat() - Constructor for class org.openscience.cdk.io.formats.HINFormat
 
HINReader - Class in org.openscience.cdk.io
Reads an object from HIN formated input.
HINReader(Reader) - Constructor for class org.openscience.cdk.io.HINReader
Construct a new reader from a Reader type object
HINReader(InputStream) - Constructor for class org.openscience.cdk.io.HINReader
 
HINReader() - Constructor for class org.openscience.cdk.io.HINReader
 
HINWriter - Class in org.openscience.cdk.io
Writer that outputs in the HIN format.
HINWriter(Writer) - Constructor for class org.openscience.cdk.io.HINWriter
Constructor.
HINWriter(OutputStream) - Constructor for class org.openscience.cdk.io.HINWriter
 
HINWriter() - Constructor for class org.openscience.cdk.io.HINWriter
 
HO - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
HOLMIUM - Static variable in enum org.openscience.cdk.config.Elements
 
HOLMIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
HomolyticCleavageMechanism - Class in org.openscience.cdk.reaction.mechanism
This mechanism breaks the chemical bond between atoms.
HomolyticCleavageMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.HomolyticCleavageMechanism
 
HomolyticCleavageReaction - Class in org.openscience.cdk.reaction.type
IReactionProcess which breaks the bond homogeneously leading to radical ions.
HomolyticCleavageReaction() - Constructor for class org.openscience.cdk.reaction.type.HomolyticCleavageReaction
Constructor of the HomolyticCleavageReaction object.
HOSECode - Variable in class org.openscience.cdk.tools.HOSECodeGenerator
The HOSECode string that we assemble
HOSECodeAnalyser - Class in org.openscience.cdk.tools
Analyses a molecular formula given in String format and builds an AtomContainer with the Atoms in the molecular formula.
HOSECodeAnalyser() - Constructor for class org.openscience.cdk.tools.HOSECodeAnalyser
 
HOSECodeGenerator - Class in org.openscience.cdk.tools
Generates HOSE codes [Bremser, W., HOSE - A Novel Substructure Code, Analytica Chimica Acta, 1978, 103:355-365].
HOSECodeGenerator() - Constructor for class org.openscience.cdk.tools.HOSECodeGenerator
Constructor for the HOSECodeGenerator.
HuLuIndexTool - Class in org.openscience.cdk.graph.invariant
Collection of methods for the calculation of topological indices of a molecular graph.
HuLuIndexTool() - Constructor for class org.openscience.cdk.graph.invariant.HuLuIndexTool
 
HX - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
HYBRID_PLANAR3 - Static variable in class org.openscience.cdk.libio.jena.CDK
 
HYBRID_S - Static variable in class org.openscience.cdk.libio.jena.CDK
 
HYBRID_SP1 - Static variable in class org.openscience.cdk.libio.jena.CDK
 
HYBRID_SP2 - Static variable in class org.openscience.cdk.libio.jena.CDK
 
HYBRID_SP3 - Static variable in class org.openscience.cdk.libio.jena.CDK
 
HYBRID_SP3D1 - Static variable in class org.openscience.cdk.libio.jena.CDK
 
HYBRID_SP3D2 - Static variable in class org.openscience.cdk.libio.jena.CDK
 
HYBRID_SP3D3 - Static variable in class org.openscience.cdk.libio.jena.CDK
 
HYBRID_SP3D4 - Static variable in class org.openscience.cdk.libio.jena.CDK
 
HYBRID_SP3D5 - Static variable in class org.openscience.cdk.libio.jena.CDK
 
hybridization - Variable in class org.openscience.cdk.AtomType
The hybridization state of this atom with CDKConstants.HYBRIDIZATION_UNSET as default.
hybridization - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom
The hybridization state of this atom with CDKConstants.HYBRIDIZATION_UNSET as default.
hybridization - Variable in class org.openscience.cdk.silent.AtomType
The hybridization state of this atom with CDKConstants.HYBRIDIZATION_UNSET as default.
HYBRIDIZATION_SP1 - Static variable in class org.openscience.cdk.CDKConstants
A geometry of neighboring atoms when an s orbital is hybridized with one p orbital.
HYBRIDIZATION_SP2 - Static variable in class org.openscience.cdk.CDKConstants
A geometry of neighboring atoms when an s orbital is hybridized with two p orbitals.
HYBRIDIZATION_SP3 - Static variable in class org.openscience.cdk.CDKConstants
A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals.
HYBRIDIZATION_SP3D1 - Static variable in class org.openscience.cdk.CDKConstants
A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals with one d orbital.
HYBRIDIZATION_SP3D2 - Static variable in class org.openscience.cdk.CDKConstants
A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals with two d orbitals.
HYBRIDIZATION_SP3D3 - Static variable in class org.openscience.cdk.CDKConstants
A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals with three d orbitals.
HYBRIDIZATION_SP3D4 - Static variable in class org.openscience.cdk.CDKConstants
A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals with four d orbitals.
HYBRIDIZATION_SP3D5 - Static variable in class org.openscience.cdk.CDKConstants
A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals with five d orbitals.
HYBRIDIZATION_UNSET - Static variable in class org.openscience.cdk.CDKConstants
A undefined hybridization.
HybridizationFingerprinter - Class in org.openscience.cdk.fingerprint
Generates a fingerprint for a given IAtomContainer.
HybridizationFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.HybridizationFingerprinter
Creates a fingerprint generator of length DEFAULT_SIZE and with a search depth of DEFAULT_SEARCH_DEPTH.
HybridizationFingerprinter(int) - Constructor for class org.openscience.cdk.fingerprint.HybridizationFingerprinter
 
HybridizationFingerprinter(int, int) - Constructor for class org.openscience.cdk.fingerprint.HybridizationFingerprinter
Constructs a fingerprint generator that creates fingerprints of the given size, using a generation algorithm with the given search depth.
HybridizationNumber() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
 
HybridizationNumberAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
This matcher checks the hybridization state of an atom.
HybridizationNumberAtom(int, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.HybridizationNumberAtom
Creates a new instance
HybridizationRatioDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
IMolecularDescriptor that reports the fraction of sp3 carbons to sp2 carbons.
HybridizationRatioDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor
Constructor for the HybridizationRatioDescriptor object.
HYDROGEN - Static variable in enum org.openscience.cdk.config.Elements
 
HYDROGEN - Static variable in class org.openscience.cdk.geometry.cip.CIPTool
IAtom index to indicate an implicit hydrogen, not present in the chemical graph.
HydrogenAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
This matches Hydrogen atoms.
HydrogenAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.HydrogenAtom
Creates a new instance.
hydrogenCount - Variable in class org.openscience.cdk.Atom
The number of implicitly bound hydrogen atoms for this atom.
hydrogenCount - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom
The number of implicitly bound hydrogen atoms for this atom.
hydrogenCount - Variable in class org.openscience.cdk.renderer.elements.AtomSymbolElement
The hydrogen count.
hydrogenCount - Variable in class org.openscience.cdk.silent.Atom
The number of implicitly bound hydrogen atoms for this atom.
HydrogenPlacer - Class in org.openscience.cdk.layout
This is a wrapper class for some existing methods in AtomPlacer.
HydrogenPlacer() - Constructor for class org.openscience.cdk.layout.HydrogenPlacer
 
HYDROXY - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
HyperconjugationReaction - Class in org.openscience.cdk.reaction.type
HyperconjugationReaction is the stabilizing interaction that results from the interaction of the electrons in a s-bond (for our case only C-H) with an adjacent empty (or partially filled) p-orbital.
HyperconjugationReaction() - Constructor for class org.openscience.cdk.reaction.type.HyperconjugationReaction
Constructor of the HyperconjugationReaction object

I

I - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
IAdductFormula - Interface in org.openscience.cdk.interfaces
Class defining an adduct object in a MolecularFormula.
IAminoAcid - Interface in org.openscience.cdk.interfaces
A AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.
IAtom - Interface in org.openscience.cdk.interfaces
Represents the idea of an chemical atom.
IAtomColorer - Interface in org.openscience.cdk.renderer.color
Interface to a class for coloring atoms.
IAtomContainer - Interface in org.openscience.cdk.interfaces
Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.
IAtomContainerSet - Interface in org.openscience.cdk.interfaces
A set of AtomContainers.
IAtomicDescriptor - Interface in org.openscience.cdk.qsar
Classes that implement this interface are QSAR descriptor calculators.
IAtomPairDescriptor - Interface in org.openscience.cdk.qsar
Classes that implement this interface are QSAR descriptor calculators.
IAtomType - Interface in org.openscience.cdk.interfaces
The base class for atom types.
IAtomType.Hybridization - Enum in org.openscience.cdk.interfaces
An enum for the different hybridization states.
IAtomTypeConfigurator - Interface in org.openscience.cdk.config
Interface that allows reading atom type configuration data from some source.
IAtomTypeGuesser - Interface in org.openscience.cdk.atomtype
Classes that implement this interface are atom type guessers.
IAtomTypeMatcher - Interface in org.openscience.cdk.atomtype
Classes that implement this interface are atom type matchers.
IBasis - Interface in org.openscience.cdk.math.qm
A basis set must implement this class.
IBioPolymer - Interface in org.openscience.cdk.interfaces
A BioPolymer is a subclass of a Polymer which is supposed to store additional informations about the Polymer which are connected to BioPolymers.
IBitFingerprint - Interface in org.openscience.cdk.fingerprint
Interface for bit fingerprint representations.
IBond - Interface in org.openscience.cdk.interfaces
Implements the concept of a covalent bond between two or more atoms.
IBond.Order - Enum in org.openscience.cdk.interfaces
A list of permissible bond orders.
IBond.Stereo - Enum in org.openscience.cdk.interfaces
Enumeration of possible stereo types of two-atom bonds.
IBondDescriptor - Interface in org.openscience.cdk.qsar
Classes that implement this interface are QSAR descriptor calculators.
ICanonicalMoleculeLabeller - Interface in org.openscience.cdk.smsd.labelling
Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
ICanonicalReactionLabeller - Interface in org.openscience.cdk.smsd.labelling
Deprecated.
This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
ICDKChangeListener - Interface in org.openscience.cdk.event
A ChangeListener for the CDK, to be independent from the Swing package.
ICDKObject - Interface in org.openscience.cdk.interfaces
The base class for all data objects in this CDK.
ICDKSelectionChangeListener - Interface in org.openscience.cdk.event
A ChangeListener for the CDK, to be independent from the Swing package.
IChargeCalculator - Interface in org.openscience.cdk.charges
Interface for classes that calculate (partial) charges centered on atom nuclei.
IChemFile - Interface in org.openscience.cdk.interfaces
An IChemObject containing a number of ChemSequences.
IChemFormat - Interface in org.openscience.cdk.io.formats
This class is the interface that all ChemFormat's should implement.
IChemFormatMatcher - Interface in org.openscience.cdk.io.formats
This interface is used for classes that are able to match a certain chemical file format.
IChemFormatMatcher.MatchResult - Class in org.openscience.cdk.io.formats
Simple class holds whether a format matcher matched, when it matched and what the format was.
IChemFormatMatcher.MatchResult(boolean, IChemFormat, int) - Constructor for class org.openscience.cdk.io.formats.IChemFormatMatcher.MatchResult
 
IChemModel - Interface in org.openscience.cdk.interfaces
An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.
IChemObject - Interface in org.openscience.cdk.interfaces
The base class for all chemical objects in this cdk.
IChemObjectBuilder - Interface in org.openscience.cdk.interfaces
A helper class to instantiate a ICDKObject instance for a specific implementation.
IChemObjectChangeEvent - Interface in org.openscience.cdk.interfaces
Event fired by CDK IChemObject classes to their registered listeners in case something changed within them.
IChemObjectIO - Interface in org.openscience.cdk.io
This class is the interface that all IO readers should implement.
IChemObjectIOListener - Interface in org.openscience.cdk.io.listener
Allows monitoring of progress of file reader activities.
IChemObjectListener - Interface in org.openscience.cdk.interfaces
Classes implementing this interface must implement this method such that they react appropriately to changes in the object they are interested in.
IChemObjectReader - Interface in org.openscience.cdk.io
This interface specifies the common functionality all IO readers should provide.
IChemObjectReader.Mode - Enum in org.openscience.cdk.io
 
IChemObjectReaderErrorHandler - Interface in org.openscience.cdk.io
Interface for classes aimed to handle IChemObjectReader errors.
IChemObjectSelection - Interface in org.openscience.cdk.renderer.selection
A selection of some atoms and bonds from an IAtomContainer or IChemModel.
IChemObjectWriter - Interface in org.openscience.cdk.io
This class is the interface that all IO writers should implement.
IChemSequence - Interface in org.openscience.cdk.interfaces
A sequence of ChemModels, which can, for example, be used to store the course of a reaction.
ICMLConvention - Interface in org.openscience.cdk.io.cml
This interface describes the procedures classes must implement to be plugable into the CMLHandler.
ICMLCustomizer - Interface in org.openscience.cdk.libio.cml
Interface for classes that allow the Convertor to be customized for certain features.
ICMLModule - Interface in org.openscience.cdk.io.cml
This interface describes the procedures classes must implement to be plugable into the CMLHandler.
ICountFingerprint - Interface in org.openscience.cdk.fingerprint
Interface for count fingerprint representations.
ICrystal - Interface in org.openscience.cdk.interfaces
Class representing a molecular crystal.
ID - Static variable in class org.openscience.cdk.templates.AminoAcids
 
ID_KEY - Static variable in class org.openscience.cdk.renderer.elements.MarkedElement
 
ID_MAP - Static variable in class org.openscience.cdk.renderer.generators.HighlightGenerator
Property key.
IDCreator - Class in org.openscience.cdk.tools
Class that provides methods to give unique IDs to ChemObjects.
IDCreator() - Constructor for class org.openscience.cdk.tools.IDCreator
 
IDeduceBondOrderTool - Interface in org.openscience.cdk.tools
A common interface for tools that deduce bond orders from connectivity and optionally additional information, like number of implicit or explicit hydrogens, or hybridization states.
IDENTIFIER - Static variable in class org.openscience.cdk.libio.jena.CDK
 
identifyMatchedParts(List<List<CDKRMap>>, IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
Deprecated.
 
identifySingleAtomsMatchedParts(List<CDKRMap>, IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
Deprecated.
 
identity(int) - Static method in class org.openscience.cdk.graph.invariant.GIMatrix
Returns the identity matrix.
IDescriptor - Interface in org.openscience.cdk.qsar
Classes that implement this interface are QSAR descriptor calculators.
IDescriptorResult - Interface in org.openscience.cdk.qsar.result
Object that provides access to the calculated descriptor value.
IDifference - Interface in org.openscience.cdk.tools.diff.tree
Object that describes the difference between two Objects.
IDifferenceList - Interface in org.openscience.cdk.tools.diff.tree
IDifference between two Objects which contains one or more child IDifference objects.
IDoubleBondStereochemistry - Interface in org.openscience.cdk.interfaces
Stereochemistry specification for double bond stereochemistry.
IDoubleBondStereochemistry.Conformation - Enum in org.openscience.cdk.interfaces
Enumeration that defines the two possible values for this stereochemistry type.
IDrawVisitor - Interface in org.openscience.cdk.renderer.visitor
An IDrawVisitor is an IRenderingVisitor that can be customized and knows about fonts and other rendering parameters.
IEdge - Interface in org.openscience.cdk.smsd.algorithm.vflib.interfaces
Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
IElectronContainer - Interface in org.openscience.cdk.interfaces
Base class for entities containing electrons, like bonds, orbitals, lone-pairs.
IElectronicPropertyCalculator - Interface in org.openscience.cdk.charges
Interface for classes that calculate (partial) charges centered on atom nuclei.
IElement - Interface in org.openscience.cdk.interfaces
Implements the idea of an element in the periodic table.
IEventChemObjectReader - Interface in org.openscience.cdk.io.iterator.event
Interface for an iterating molecule reader.
IFinalMapping - Interface in org.openscience.cdk.smsd.interfaces
Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
IFingerprinter - Interface in org.openscience.cdk.fingerprint
Interface for fingerprint calculators.
IFontManager - Interface in org.openscience.cdk.renderer.font
An interface for managing the drawing of fonts at different zoom levels.
IFontManager.FontStyle - Enum in org.openscience.cdk.renderer.font
Style of the font to use to draw text.
IFragmentAtom - Interface in org.openscience.cdk.interfaces
Class to represent an IPseudoAtom which embeds an IAtomContainer.
IFragmenter - Interface in org.openscience.cdk.fragment
An interface for classes implementing fragmentation algorithms.
IFunction - Interface in org.openscience.cdk.math
A class, which has a function value should implement this interface.
IGenerator<T extends IChemObject> - Interface in org.openscience.cdk.renderer.generators
An IGenerator converts chemical entities into parts of the chemical drawing expressed as IRenderingElements.
IGeneratorParameter<T> - Interface in org.openscience.cdk.renderer.generators
Parameter from some rendering of the 2D diagram.
ignoringAtomTypes() - Method in class org.openscience.cdk.group.PartitionRefinement.AtomRefinerBuilder
 
ignoringBondOrders() - Method in class org.openscience.cdk.group.PartitionRefinement.AtomRefinerBuilder
 
ignoringBondOrders() - Method in class org.openscience.cdk.group.PartitionRefinement.BondRefinerBuilder
 
IGraphMatrix - Interface in org.openscience.cdk.graph.matrix
Interface describing a molecular graph matrix calculator.
IImplementationSpecification - Interface in org.openscience.cdk
Interface that is used to describe the specification of a certain implementation of an algorithm.
IIsotope - Interface in org.openscience.cdk.interfaces
Used to store and retrieve data of a particular isotope.
IIteratingChemObjectReader<T extends IChemObject> - Interface in org.openscience.cdk.io.iterator
Interface for an iterating molecule reader.
ILigand - Interface in org.openscience.cdk.geometry.cip
Concept of a ligand in CIP terms, reflecting a side chain of a central atom that can have precedence over another.
ILoggingTool - Interface in org.openscience.cdk.tools
Useful for logging messages.
ILonePair - Interface in org.openscience.cdk.interfaces
A LonePair is an orbital primarily located with one Atom, containing two electrons.
imag - Variable in class org.openscience.cdk.math.Complex
The imaginary part of this value
image - Variable in class org.openscience.cdk.iupac.parser.Token
The string image of the token.
image - Variable in class org.openscience.cdk.smiles.smarts.parser.Token
The string image of the token.
imagmatrix - Variable in class org.openscience.cdk.math.IMatrix
the imaginary part of the content
imagvector - Variable in class org.openscience.cdk.math.IVector
The imaginary part of this vector
IMapper - Interface in org.openscience.cdk.smsd.algorithm.vflib.interfaces
Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
IMapping - Interface in org.openscience.cdk.interfaces
Represents a mapping of two atoms.
IMatrix - Class in org.openscience.cdk.math
This class contains a complex matrix.
IMatrix(int, int) - Constructor for class org.openscience.cdk.math.IMatrix
Creates a complex matrix
IMatrix(Matrix) - Constructor for class org.openscience.cdk.math.IMatrix
Creates a complex copy of a matrix
IMCSBase - Interface in org.openscience.cdk.smsd.interfaces
Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
IMolecularDescriptor - Interface in org.openscience.cdk.qsar
Classes that implement this interface are QSAR descriptor calculators for IAtomContainer objects.
IMolecularFormula - Interface in org.openscience.cdk.interfaces
Class defining a molecular formula object.
IMolecularFormulaSet - Interface in org.openscience.cdk.interfaces
Class defining a molecular formula object.
IMonomer - Interface in org.openscience.cdk.interfaces
A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.
IMouseEventRelay - Interface in org.openscience.cdk.controller
Widget toolkit-independent interface to relay for mouse events.
implementorsOf(Class<T>) - Method in class org.openscience.cdk.DynamicFactory
Access the registered implementations for a given interface.
ImplicitHCount() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
 
ImplicitHCountAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
This matcher checks the number of implicit hydrogens of the Atom.
ImplicitHCountAtom(int, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.ImplicitHCountAtom
Creates a new instance
ImplicitHighAndBond() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
 
ImplicitHighAndExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
 
ImplicitHydrogenLigand - Class in org.openscience.cdk.geometry.cip
Subclass of Ligand to which no further recursion must be applied.
ImplicitHydrogenLigand(IAtomContainer, VisitedAtoms, IAtom) - Constructor for class org.openscience.cdk.geometry.cip.ImplicitHydrogenLigand
 
IN - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
inBuf - Variable in class org.openscience.cdk.iupac.parser.SimpleCharStream
 
inBuf - Variable in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
 
INCHI - Static variable in class org.openscience.cdk.CDKConstants
The IUPAC International Chemical Identifier.
inchi - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
 
INChIContentProcessorTool - Class in org.openscience.cdk.io.inchi
Tool to help process INChI 1.12beta content.
INChIContentProcessorTool() - Constructor for class org.openscience.cdk.io.inchi.INChIContentProcessorTool
 
INChIFormat - Class in org.openscience.cdk.io.formats
See here.
INChIFormat() - Constructor for class org.openscience.cdk.io.formats.INChIFormat
 
InChIGenerator - Class in org.openscience.cdk.inchi
This class generates the IUPAC International Chemical Identifier (InChI) for a CDK IAtomContainer.
InChIGenerator(IAtomContainer, boolean) - Constructor for class org.openscience.cdk.inchi.InChIGenerator
Constructor.
InChIGenerator(IAtomContainer, String, boolean) - Constructor for class org.openscience.cdk.inchi.InChIGenerator
Constructor.
InChIGenerator(IAtomContainer, List<INCHI_OPTION>, boolean) - Constructor for class org.openscience.cdk.inchi.InChIGenerator
Constructor.
InChIGeneratorFactory - Class in org.openscience.cdk.inchi
Factory providing access to InChIGenerator and InChIToStructure.
INChIHandler - Class in org.openscience.cdk.io.inchi
SAX2 implementation for INChI XML fragment parsing.
INChIHandler() - Constructor for class org.openscience.cdk.io.inchi.INChIHandler
Constructor for the IChIHandler.
InChILabelling - Static variable in class org.openscience.cdk.smiles.SmiFlavor
Output SMILES in a canonical order using the InChI labelling algorithm.
InChINumbersTools - Class in org.openscience.cdk.graph.invariant
Tool for calculating atom numbers using the InChI algorithm.
InChINumbersTools() - Constructor for class org.openscience.cdk.graph.invariant.InChINumbersTools
 
INChIPlainTextFormat - Class in org.openscience.cdk.io.formats
 
INChIPlainTextFormat() - Constructor for class org.openscience.cdk.io.formats.INChIPlainTextFormat
 
INChIPlainTextReader - Class in org.openscience.cdk.io
Reads the content of a IUPAC/NIST Chemical Identifier (INChI) plain text document.
INChIPlainTextReader(Reader) - Constructor for class org.openscience.cdk.io.INChIPlainTextReader
Construct a INChI reader from a Reader object.
INChIPlainTextReader(InputStream) - Constructor for class org.openscience.cdk.io.INChIPlainTextReader
 
INChIPlainTextReader() - Constructor for class org.openscience.cdk.io.INChIPlainTextReader
 
INChIReader - Class in org.openscience.cdk.io
Reads the content of a IUPAC/NIST Chemical Identifier (INChI) document.
INChIReader(InputStream) - Constructor for class org.openscience.cdk.io.INChIReader
Construct a INChI reader from a InputStream object.
INChIReader() - Constructor for class org.openscience.cdk.io.INChIReader
 
InChITautomerGenerator - Class in org.openscience.cdk.tautomers
Creates tautomers for a given input molecule, based on the mobile H atoms listed in the InChI.
InChITautomerGenerator(int) - Constructor for class org.openscience.cdk.tautomers.InChITautomerGenerator
Create a tautomer generator specifygin whether to enable, keto-enol (-KET) and 1,5-shifts (-15T).
InChITautomerGenerator() - Constructor for class org.openscience.cdk.tautomers.InChITautomerGenerator
Create a tautomer generator, keto-enol (-KET) and 1,5-shifts (-15T) are disabled.
InChIToStructure - Class in org.openscience.cdk.inchi
This class generates a CDK IAtomContainer from an InChI string.
InChIToStructure(String, IChemObjectBuilder) - Constructor for class org.openscience.cdk.inchi.InChIToStructure
Constructor.
InChIToStructure(String, IChemObjectBuilder, String) - Constructor for class org.openscience.cdk.inchi.InChIToStructure
Constructor.
InChIToStructure(String, IChemObjectBuilder, List<String>) - Constructor for class org.openscience.cdk.inchi.InChIToStructure
Constructor.
IncorrectUseOfCDKCoreClassError - Error in org.openscience.cdk.exception
Error that is thrown by debug implementations of the core CDK classes.
IncorrectUseOfCDKCoreClassError(String) - Constructor for error org.openscience.cdk.exception.IncorrectUseOfCDKCoreClassError
 
increaseBondOrder(IBond.Order) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
Returns the IBond.Order one higher.
increaseBondOrder(IBond) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
Increment the bond order of this bond.
increaseFontSize() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
Move the font size pointer up.
index - Variable in class org.openscience.cdk.io.random.RandomAccessReader
 
indexCreated - Variable in class org.openscience.cdk.io.random.RandomAccessReader
 
indexOf(IAtom) - Method in class org.openscience.cdk.AtomContainer
Access the storage index of an atom.
indexOf(IBond) - Method in class org.openscience.cdk.AtomContainer
Access the storage index of a bond.
indexOf(ISingleElectron) - Method in class org.openscience.cdk.AtomContainer
Access the storage index of a single electron (radical).
indexOf(ILonePair) - Method in class org.openscience.cdk.AtomContainer
Access the storage index of a long pair.
indexOf(Object) - Method in class org.openscience.cdk.ConformerContainer
Returns the lowest index at which the specific IAtomContainer appears in the list or -1 if is not found.
indexOf(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
Access the storage index of an atom.
indexOf(IBond) - Method in class org.openscience.cdk.debug.DebugAtomContainer
Access the storage index of a bond.
indexOf(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAtomContainer
Access the storage index of a single electron (radical).
indexOf(ILonePair) - Method in class org.openscience.cdk.debug.DebugAtomContainer
Access the storage index of a long pair.
indexOf(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Access the storage index of an atom.
indexOf(IBond) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Access the storage index of a bond.
indexOf(ISingleElectron) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Access the storage index of a single electron (radical).
indexOf(ILonePair) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Access the storage index of a long pair.
indexOf(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
 
indexOf(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
 
indexOf(ISingleElectron) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
 
indexOf(ILonePair) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
 
indexOf(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
Access the storage index of an atom.
indexOf(IBond) - Method in class org.openscience.cdk.silent.AtomContainer
Access the storage index of a bond.
indexOf(ISingleElectron) - Method in class org.openscience.cdk.silent.AtomContainer
Access the storage index of a single electron (radical).
indexOf(ILonePair) - Method in class org.openscience.cdk.silent.AtomContainer
Access the storage index of a long pair.
IndexOutOfBoundsException - Exception in org.openscience.cdk.graph.invariant.exception
 
IndexOutOfBoundsException() - Constructor for exception org.openscience.cdk.graph.invariant.exception.IndexOutOfBoundsException
 
indexVersion - Variable in class org.openscience.cdk.io.random.RandomAccessReader
 
INDIUM - Static variable in enum org.openscience.cdk.config.Elements
 
INDIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
InductiveAtomicHardnessDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
Inductive atomic hardness of an atom in a polyatomic system can be defined as the "resistance" to a change of the atomic charge.
InductiveAtomicHardnessDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor
Constructor for the InductiveAtomicHardnessDescriptor object
InductiveAtomicSoftnessDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
Inductive atomic softness of an atom in a polyatomic system can be defined as charge delocalizing ability.
InductiveAtomicSoftnessDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor
Constructor for the InductiveAtomicSoftnessDescriptor object
InductivePartialCharges - Class in org.openscience.cdk.charges
The calculation of the inductive partial atomic charges and equalization of effective electronegativities is based on [Cherkasov, A., Inductive Electronegativity Scale. Iterative Calculation of Inductive Partial Charges, J. Chem. Inf. Comput. Sci., 2003, 43:2039-2047].
InductivePartialCharges() - Constructor for class org.openscience.cdk.charges.InductivePartialCharges
Constructor for the InductivePartialCharges object.
info(Object) - Method in interface org.openscience.cdk.tools.ILoggingTool
Shows INFO output for the Object.
info(Object, Object...) - Method in interface org.openscience.cdk.tools.ILoggingTool
Shows INFO output for the given Object's.
info(Object) - Method in class org.openscience.cdk.tools.LoggingTool
Shows INFO output for the Object.
info(Object, Object...) - Method in class org.openscience.cdk.tools.LoggingTool
Shows INFO output for the given Object's.
info(Object) - Method in class org.openscience.cdk.tools.SystemOutLoggingTool
Shows INFO output for the Object.
info(Object, Object...) - Method in class org.openscience.cdk.tools.SystemOutLoggingTool
Shows INFO output for the given Object's.
inHash - Variable in class org.openscience.cdk.fingerprint.model.Bayesian
 
inherit(ICMLModule) - Method in class org.openscience.cdk.io.cml.CMLCoreModule
 
inherit(ICMLModule) - Method in interface org.openscience.cdk.io.cml.ICMLModule
 
init(IAtomContainer, IAtomContainer, boolean, boolean) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
Deprecated.
initialize query and target molecules.
init(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
Deprecated.
initialize query and target molecules.
init(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.Isomorphism
Deprecated.
 
init(IAtomContainer, IAtomContainer, boolean, boolean) - Method in class org.openscience.cdk.smsd.Isomorphism
Deprecated.
initialize query and target molecules.
init(String, String, boolean, boolean) - Method in class org.openscience.cdk.smsd.Isomorphism
Deprecated.
Initialize the query and targetAtomCount mol via mol files
initialise(IChemObjectBuilder) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor
 
initialise(IChemObjectBuilder) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor
 
initialise(IChemObjectBuilder) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor
 
initialise(IChemObjectBuilder) - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor
 
initialise(IChemObjectBuilder) - Method in class org.openscience.cdk.qsar.descriptors.substance.OxygenAtomCountDescriptor
Initialise the descriptor with the specified chem object builder.
initialise(IChemObjectBuilder) - Method in interface org.openscience.cdk.qsar.IDescriptor
Initialise the descriptor with the specified chem object builder.
initialize(Map<String, List>) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94ParametersCall
Initialize the AtomOrder class.
initializeGrid(double) - Method in class org.openscience.cdk.tools.GridGenerator
Method initialise the given grid points with a value.
initializeGrid(double[][][], double) - Method in class org.openscience.cdk.tools.GridGenerator
Method initialise the given grid points with a value.
initializeSpecifications(List<IDescriptor>) - Method in class org.openscience.cdk.qsar.DescriptorEngine
 
initiate(IAtomContainerSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in interface org.openscience.cdk.reaction.IReactionMechanism
Initiates the process for the given mechanism.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in interface org.openscience.cdk.reaction.IReactionProcess
Initiates the process for the given Reaction.
initiate(IAtomContainerSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.AdductionLPMechanism
Initiates the process for the given mechanism.
initiate(IAtomContainerSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.AdductionPBMechanism
Initiates the process for the given mechanism.
initiate(IAtomContainerSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.HeterolyticCleavageMechanism
Initiates the process for the given mechanism.
initiate(IAtomContainerSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.HomolyticCleavageMechanism
Initiates the process for the given mechanism.
initiate(IAtomContainerSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.RadicalSiteIonizationMechanism
Initiates the process for the given mechanism.
initiate(IAtomContainerSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.RadicalSiteRearrangementMechanism
Initiates the process for the given mechanism.
initiate(IAtomContainerSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.RearrangementChargeMechanism
Initiates the process for the given mechanism.
initiate(IAtomContainerSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.RemovingSEofBMechanism
Initiates the process for the given mechanism.
initiate(IAtomContainerSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.RemovingSEofNBMechanism
Initiates the process for the given mechanism.
initiate(IAtomContainerSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.SharingElectronMechanism
Initiates the process for the given mechanism.
initiate(IAtomContainerSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.TautomerizationMechanism
Initiates the process for the given mechanism.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.AdductionProtonLPReaction
Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.AdductionProtonPBReaction
Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.AdductionSodiumLPReaction
Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.CarbonylEliminationReaction
Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.ElectronImpactNBEReaction
Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.ElectronImpactPDBReaction
Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.ElectronImpactSDBReaction
Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.HeterolyticCleavagePBReaction
Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.HeterolyticCleavageSBReaction
Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.HomolyticCleavageReaction
Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.HyperconjugationReaction
Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.PiBondingMovementReaction
Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.RadicalChargeSiteInitiationHReaction
Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.RadicalChargeSiteInitiationReaction
Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrAlphaReaction
Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrBetaReaction
Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrDeltaReaction
Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrGammaReaction
Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteInitiationHReaction
Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteInitiationReaction
Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrAlphaReaction
Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrBetaReaction
Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrDeltaReaction
Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrGammaReaction
Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.RearrangementAnionReaction
Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.RearrangementCationReaction
Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.RearrangementLonePairReaction
Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.RearrangementRadicalReaction
Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.SharingAnionReaction
Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.SharingChargeDBReaction
Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.SharingChargeSBReaction
Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.SharingLonePairReaction
Initiate process.
initiate(IAtomContainerSet, IAtomContainerSet) - Method in class org.openscience.cdk.reaction.type.TautomerizationReaction
Initiate process.
initilize(Map) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
Initialize the atomPlacer class.
inLower() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
Test to see if the lower virtual pointer is in use.
INode - Interface in org.openscience.cdk.smsd.algorithm.vflib.interfaces
Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
inOrder() - Method in class org.openscience.cdk.group.Partition
Check whether the cells are ordered such that for cells i and j, first(j) > first(i) and last(j) > last(i).
input - Variable in class org.openscience.cdk.inchi.InChIGenerator
 
input - Variable in class org.openscience.cdk.inchi.InChIToStructure
 
input_stream - Variable in class org.openscience.cdk.iupac.parser.NomParserTokenManager
 
input_stream - Variable in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager
 
inputBuffer - Variable in class org.openscience.cdk.io.VASPReader
 
inputStream - Variable in class org.openscience.cdk.iupac.parser.SimpleCharStream
 
inputStream - Variable in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
 
inRange() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
Check that the font pointer is in the range (0, numberOfFonts - 1).
inSameAromaticRing(IAtomContainer, IAtom, IAtom, IRingSet) - Static method in class org.openscience.cdk.atomtype.EStateAtomTypeMatcher
 
inSameCell(int, int) - Method in class org.openscience.cdk.group.Partition
Check that two elements are in the same cell of the partition.
insertCell(int, SortedSet<Integer>) - Method in class org.openscience.cdk.group.Partition
Insert a cell into the partition at the specified index.
instantiateDescriptors(List<String>) - Method in class org.openscience.cdk.qsar.DescriptorEngine
 
IntArrayCountFingerprint - Class in org.openscience.cdk.fingerprint
 
IntArrayCountFingerprint() - Constructor for class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
 
IntArrayCountFingerprint(Map<String, Integer>) - Constructor for class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
 
IntArrayCountFingerprint(Map<String, Integer>, boolean) - Constructor for class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
Create an IntArrayCountFingerprint from a rawFingerprint and if behaveAsBitFingerprint make it only return 0 or 1 as count thus behaving like a bit finger print.
IntArrayFingerprint - Class in org.openscience.cdk.fingerprint
 
IntArrayFingerprint(Map<String, Integer>) - Constructor for class org.openscience.cdk.fingerprint.IntArrayFingerprint
 
IntArrayFingerprint(int[]) - Constructor for class org.openscience.cdk.fingerprint.IntArrayFingerprint
 
IntArrayFingerprint() - Constructor for class org.openscience.cdk.fingerprint.IntArrayFingerprint
 
IntArrayFingerprint(IBitFingerprint) - Constructor for class org.openscience.cdk.fingerprint.IntArrayFingerprint
 
IntegerArrayResult - Class in org.openscience.cdk.qsar.result
 
IntegerArrayResult() - Constructor for class org.openscience.cdk.qsar.result.IntegerArrayResult
 
IntegerArrayResult(int) - Constructor for class org.openscience.cdk.qsar.result.IntegerArrayResult
 
IntegerArrayResultType - Class in org.openscience.cdk.qsar.result
IDescriptorResult type for booleans.
IntegerArrayResultType(int) - Constructor for class org.openscience.cdk.qsar.result.IntegerArrayResultType
 
IntegerDifference - Class in org.openscience.cdk.tools.diff.tree
IDifference between two Integer.
IntegerIOSetting - Class in org.openscience.cdk.io.setting
An class for a reader setting which must be of type String.
IntegerIOSetting(String, IOSetting.Importance, String, String) - Constructor for class org.openscience.cdk.io.setting.IntegerIOSetting
 
IntegerResult - Class in org.openscience.cdk.qsar.result
Object that provides access to the calculated descriptor value.
IntegerResult(int) - Constructor for class org.openscience.cdk.qsar.result.IntegerResult
 
IntegerResultType - Class in org.openscience.cdk.qsar.result
IDescriptorResult type for booleans.
IntegerResultType() - Constructor for class org.openscience.cdk.qsar.result.IntegerResultType
 
interpretProjections(Projection...) - Method in class org.openscience.cdk.stereo.StereoElementFactory
Indicate that stereochemistry drawn as a certain projection should be interpreted.
intf() - Method in class org.openscience.cdk.DynamicFactory.ConstructorKey
Access the interface this key indexes.
Intractable - Exception in org.openscience.cdk.exception
Indicates a computation did not complete within some predefined bound.
Intractable(String) - Constructor for exception org.openscience.cdk.exception.Intractable
Create a new exception with the specified message.
intValue() - Method in class org.openscience.cdk.qsar.result.IntegerResult
 
inUpper() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
Test to see if the upper virtual pointer is in use.
InvalidSmilesException - Exception in org.openscience.cdk.exception
Exception thrown when an error is occurred during SMILES parsing.
InvalidSmilesException(String) - Constructor for exception org.openscience.cdk.exception.InvalidSmilesException
Constructs a new exception with a custom message.
InvalidSmilesException(String, Exception) - Constructor for exception org.openscience.cdk.exception.InvalidSmilesException
Constructs a new exception with a custom message and a stacktrace.
INVARIANCE_PAIR - Static variable in class org.openscience.cdk.smiles.InvPair
The description used to set the invariance numbers in the atom's property
Invariant - Interface in org.openscience.cdk.group
Marker interface for invariants.
inverse() - Method in class org.openscience.cdk.graph.invariant.GIMatrix
Returns the transpose of this matrix.
InverseSymbolSetQueryAtom - Class in org.openscience.cdk.isomorphism.matchers
A QueryAtom that matches all symbols but those in this container.
InverseSymbolSetQueryAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom
Constructor for the InverseSymbolSetQueryAtom object
invert() - Method in class org.openscience.cdk.group.Permutation
Invert the permutation, so that for all i : inv[p[i]] = i.
invert() - Method in enum org.openscience.cdk.interfaces.IDoubleBondStereochemistry.Conformation
Invert this conformation, inv(together) = opposite, inv(opposite) = together.
invert() - Method in enum org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo
Invert this conformation, inv(clockwise) = anti_clockwise, inv(anti_clockwise) = clockwise.
invertLine(int, int) - Method in class org.openscience.cdk.graph.invariant.GIMatrix
Returns the resulting matrix of an elementary linear operation that consists of inverting two lines.
invisibleCarbon(IAtom, IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator
Checks an atom to see if it is an 'invisible carbon' - that is, it is: a) a carbon atom and b) this carbon should not be shown.
invisibleHydrogen(IAtom, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator
Checks an atom to see if it is an 'invisible hydrogen' - that is, it is a) an (explicit) hydrogen, and b) explicit hydrogens are set to off.
InvPair - Class in org.openscience.cdk.smiles
This is used to hold the invariance numbers for the canonical labeling of IAtomContainers.
InvPair() - Constructor for class org.openscience.cdk.smiles.InvPair
 
InvPair(long, IAtom) - Constructor for class org.openscience.cdk.smiles.InvPair
 
invRange - Variable in class org.openscience.cdk.fingerprint.model.Bayesian
 
IODINE - Static variable in enum org.openscience.cdk.config.Elements
 
IODO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
IonizationPotentialTool - Class in org.openscience.cdk.tools
Deprecated.
Results depend on the order of atoms in bonds, resolving this would require retraining the models which are not available.
IonizationPotentialTool() - Constructor for class org.openscience.cdk.tools.IonizationPotentialTool
Deprecated.
 
IOSetting - Class in org.openscience.cdk.io.setting
An interface for reader settings.
IOSetting(String, IOSetting.Importance, String, String) - Constructor for class org.openscience.cdk.io.setting.IOSetting
The default constructor that sets this field.
IOSetting.Importance - Enum in org.openscience.cdk.io.setting
 
IParameterReact - Interface in org.openscience.cdk.reaction.type.parameters
Interface for classes that generate parameters used in reactions.
IPAtomicHOSEDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
This class returns the ionization potential of an atom containing lone pair electrons.
IPAtomicHOSEDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor
Constructor for the IPAtomicHOSEDescriptor object.
IPAtomicLearningDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
Deprecated.
IPAtomicLearningDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor
Deprecated.
Constructor for the IPAtomicLearningDescriptor object.
IPBondLearningDescriptor - Class in org.openscience.cdk.qsar.descriptors.bond
Deprecated.
IPBondLearningDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor
Deprecated.
Constructor for the IPBondLearningDescriptor object
IPDBAtom - Interface in org.openscience.cdk.interfaces
A PDBAtom is a subclass of a Atom which is supposed to store additional informations about the Atom.
IPDBMonomer - Interface in org.openscience.cdk.interfaces
Represents the idea of an protein monomer as found in PDB files.
IPDBPolymer - Interface in org.openscience.cdk.interfaces
A PDBPolymer is a subclass of a BioPolymer which is supposed to store additional informations about the BioPolymer which are connected to BioPolymers.
IPDBStructure - Interface in org.openscience.cdk.interfaces
Represents the idea of an chemical structure.
IPMolecularLearningDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
Deprecated.
IPMolecularLearningDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor
Deprecated.
Constructor for the IPMolecularLearningDescriptor object
IPolymer - Interface in org.openscience.cdk.interfaces
Subclass of Molecule to store Polymer specific attributes that a Polymer has.
IPseudoAtom - Interface in org.openscience.cdk.interfaces
Represents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc.
IQuery - Interface in org.openscience.cdk.smsd.algorithm.vflib.interfaces
Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
IQueryAtom - Interface in org.openscience.cdk.isomorphism.matchers
Defines the ability to be matched against IAtom's.
IQueryAtomContainer - Interface in org.openscience.cdk.isomorphism.matchers
General concept of a IAtomContainer aimed at doing molecular subgraph queries using the UniversalIsomorphismTester.
IQueryBond - Interface in org.openscience.cdk.isomorphism.matchers
Defines the abililty to be matched against IBond's.
IQueryCompiler - Interface in org.openscience.cdk.smsd.algorithm.vflib.interfaces
Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
IR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
RegularExpression Id.
IRandomAccessChemObjectReader<T> - Interface in org.openscience.cdk.io.random
Extension of ListIterator.
IRDFWeightFunction - Interface in org.openscience.cdk.geometry
Weight function used in the RDFCalculator.
IReaction - Interface in org.openscience.cdk.interfaces
Represents the idea of a chemical reaction.
IReaction.Direction - Enum in org.openscience.cdk.interfaces
Permissible reaction directions.
IReactionMechanism - Interface in org.openscience.cdk.reaction
Classes that implement this interface are reaction mechanisms.
IReactionProcess - Interface in org.openscience.cdk.reaction
Classes that implement this interface are Reactions types.
IReactionScheme - Interface in org.openscience.cdk.interfaces
Classes that implement this interface of a scheme.
IReactionSet - Interface in org.openscience.cdk.interfaces
A set of reactions, for example those taking part in a reaction.
IReaderListener - Interface in org.openscience.cdk.io.listener
Allows monitoring of progress of file reader activities.
IRenderer<T extends IChemObject> - Interface in org.openscience.cdk.renderer
Interface that all 2D renderers implement.
IRenderingElement - Interface in org.openscience.cdk.renderer.elements
Widget toolkit-independent, abstract definition of something to be drawn.
IRenderingVisitor - Interface in org.openscience.cdk.renderer.elements
An IRenderingVisitor is responsible of converting an abstract chemical drawing into a widget set specific drawing.
IResourceFormat - Interface in org.openscience.cdk.io.formats
This class is the interface that all ResourceFormat's should implement.
IRGroupQuery - Interface in org.openscience.cdk.isomorphism.matchers
Interface definition for Rgroup query classes.
IRIDIUM - Static variable in enum org.openscience.cdk.config.Elements
 
IRIDIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
IRing - Interface in org.openscience.cdk.interfaces
Class representing a ring structure in a molecule.
IRingSet - Interface in org.openscience.cdk.interfaces
Maintains a set of Ring objects.
IRON - Static variable in enum org.openscience.cdk.config.Elements
 
IRON - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
RegularExpression Id.
IRule - Interface in org.openscience.cdk.formula.rules
Interface which groups all method that validate a IMolecularFormula.
IS_HYDROGENBOND_ACCEPTOR - Static variable in class org.openscience.cdk.CDKConstants
Sets to true if the atom is an hydrogen bond acceptor.
IS_HYDROGENBOND_DONOR - Static variable in class org.openscience.cdk.CDKConstants
Sets to true if the atom is an hydrogen bond donor.
IS_TYPEABLE - Static variable in class org.openscience.cdk.CDKConstants
Flag is set if an atom could be typed.
ISALIPHATIC - Static variable in class org.openscience.cdk.CDKConstants
Flag that is set if a chemobject is part of an aliphatic chain.
isAntisymmetric() - Method in class org.openscience.cdk.graph.invariant.GIMatrix
Verifies if the matrix is antisymmetric, that is if the matrix is equal to the opposite of it's transpose.
isAromatic(IRing, IAtomContainer) - Static method in class org.openscience.cdk.aromaticity.AromaticityCalculator
Deprecated.
Tests the ring in the molecule for aromaticity.
isAromatic() - Method in class org.openscience.cdk.Atom
Access whether this atom has been marked as aromatic.
isAromatic() - Method in class org.openscience.cdk.Bond
Access whether this bond has been marked as aromatic.
ISAROMATIC - Static variable in class org.openscience.cdk.CDKConstants
Flag is set if chemobject is part of an aromatic system.
isAromatic() - Method in interface org.openscience.cdk.interfaces.IAtom
Access whether this atom has been marked as aromatic.
isAromatic() - Method in interface org.openscience.cdk.interfaces.IBond
Access whether this bond has been marked as aromatic.
isAromatic() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
Access whether this atom has been marked as aromatic.
isAromatic() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
Access whether this bond has been marked as aromatic.
isAromatic() - Method in class org.openscience.cdk.silent.Atom
Access whether this atom has been marked as aromatic.
isAromatic() - Method in class org.openscience.cdk.silent.Bond
Access whether this bond has been marked as aromatic.
isAssignable(DynamicFactory.ConstructorKey) - Method in class org.openscience.cdk.DynamicFactory.ConstructorKey
Checks whether this key is assignable to the candidate.
isAtomMatch(AtomMatcher, AtomMatcher, IAtomContainer, IBond, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultMatcher
Deprecated.
 
isAtomMatch(String, String, String, String) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
Deprecated.
 
isBondMatch(BondMatcher, IAtomContainer, IBond, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultMatcher
Deprecated.
 
isBondMatchFlag() - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultBondMatcher
Deprecated.
 
isBondMatchFlag() - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultMCSPlusAtomMatcher
Deprecated.
 
isBondMatchFlag() - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultRGraphAtomMatcher
Deprecated.
 
isBondMatchFlag() - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFAtomMatcher
Deprecated.
 
isBondMatchFlag() - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFBondMatcher
Deprecated.
 
isBondMatchFlag() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler
Deprecated.
 
isBondMatchFlag() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler
Deprecated.
 
isBondMatchFlag() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler
Deprecated.
 
isCachedAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.qsar.AbstractAtomicDescriptor
Returns true if the cached IDescriptorResult's are for the given IAtomContainer.
isCachedAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.qsar.AbstractBondDescriptor
Returns true if the cached IDescriptorResult's are for the given IAtomContainer.
isCanonical(IAtomContainer) - Method in interface org.openscience.cdk.group.AtomContainerDiscretePartitionRefiner
Checks if the atom container is canonical.
isCisTrans(IAtom, IAtom, IAtom, IAtom, IAtomContainer) - Static method in class org.openscience.cdk.geometry.BondTools
Says if two atoms are in cis or trans position around a double bond.
isClockwise() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom
 
isColinear(Point3d, Point3d, Point3d) - Static method in class org.openscience.cdk.stereo.StereoTool
Checks the three supplied points to see if they fall on the same line.
ISCONJUGATED - Static variable in class org.openscience.cdk.CDKConstants
Flag is set if chemobject is part of a conjugated system.
isConnected(IAtomContainer) - Static method in class org.openscience.cdk.graph.ConnectivityChecker
Check whether a set of atoms in an IAtomContainer is connected.
isConnected(int, int) - Method in class org.openscience.cdk.signature.SignatureQuotientGraph
 
isConnectedTo(IBond) - Method in class org.openscience.cdk.Bond
Checks whether a bond is connected to another one.
isConnectedTo(IBond) - Method in class org.openscience.cdk.debug.DebugBond
Checks whether a bond is connected to another one.
isConnectedTo(IBond) - Method in interface org.openscience.cdk.interfaces.IBond
Checks whether a bond is connected to another one.
isConnectedTo(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
Checks whether a query bond is connected to another one.
isConnectedTo(IBond) - Method in class org.openscience.cdk.silent.Bond
Checks whether a bond is connected to another one.
isCycle() - Method in class org.openscience.cdk.smsd.ring.PathEdge
Deprecated.
 
isDead() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IState
Deprecated.
Returns true if no match will come from this IState.
isDead() - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFState
Deprecated.
Returns true if no match will come from this IState.
isDebugEnabled() - Method in interface org.openscience.cdk.tools.ILoggingTool
Use this method for computational demanding debug info.
isDebugEnabled() - Method in class org.openscience.cdk.tools.LoggingTool
Use this method for computational demanding debug info.
isDebugEnabled() - Method in class org.openscience.cdk.tools.SystemOutLoggingTool
Use this method for computational demanding debug info.
isDiagonal() - Method in class org.openscience.cdk.graph.invariant.GIMatrix
Verifies whether or not the matrix is diagonal.
isDisconnected() - Method in class org.openscience.cdk.graph.SpanningTree
Is the molecule disconnected and has more then one component.
isDiscrete() - Method in class org.openscience.cdk.group.Partition
Checks that all the cells are singletons - that is, they only have one element.
isDiscreteCell(int) - Method in class org.openscience.cdk.group.Partition
Check to see if the cell at cellIndex is discrete - that is, it only has one element.
isElement(String) - Method in class org.openscience.cdk.config.IsotopeFactory
Checks whether the given element exists.
isEmpty() - Method in class org.openscience.cdk.AtomContainer
Indicates whether this container is empty.
isEmpty() - Method in class org.openscience.cdk.AtomContainerSet
Returns true if this IAtomContainerSet is empty.
isEmpty() - Method in class org.openscience.cdk.ChemModel
Returns true if this ChemModel is empty.
isEmpty() - Method in class org.openscience.cdk.ConformerContainer
Checks whether any conformers are stored or not.
isEmpty() - Method in class org.openscience.cdk.debug.DebugAtomContainer
Indicates whether this container is empty.
isEmpty() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
Returns true if this IAtomContainerSet is empty.
isEmpty() - Method in class org.openscience.cdk.debug.DebugChemModel
Returns true if this ChemModel is empty.
isEmpty() - Method in class org.openscience.cdk.debug.DebugCrystal
Indicates whether this container is empty.
isEmpty() - Method in class org.openscience.cdk.debug.DebugReactionSet
Returns true if this IReactionSet is empty.
isEmpty() - Method in class org.openscience.cdk.debug.DebugSubstance
Returns true if this IAtomContainerSet is empty.
isEmpty() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
Indicates whether this container is empty.
isEmpty() - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
Returns true if this IAtomContainerSet is empty.
isEmpty() - Method in interface org.openscience.cdk.interfaces.IChemModel
Returns true if this ChemModel is empty.
isEmpty() - Method in interface org.openscience.cdk.interfaces.IReactionSet
Returns true if this IReactionSet is empty.
isEmpty() - Method in interface org.openscience.cdk.interfaces.IRingSet
Returns true if this IRingSet has no atoms.
isEmpty() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
Indicates whether this container is empty.
isEmpty() - Method in class org.openscience.cdk.ReactionSet
Returns true if this IReactionSet is empty.
isEmpty() - Method in class org.openscience.cdk.renderer.elements.Bounds
The bounds are empty and contain no elements.
isEmpty() - Method in class org.openscience.cdk.signature.Orbit
Checks to see if the orbit is empty.
isEmpty() - Method in class org.openscience.cdk.silent.AtomContainer
Indicates whether this container is empty.
isEmpty() - Method in class org.openscience.cdk.silent.AtomContainerSet
Returns true if this IAtomContainerSet is empty.
isEmpty() - Method in class org.openscience.cdk.silent.ChemModel
Returns true if this ChemModel is empty.
isEmpty() - Method in class org.openscience.cdk.silent.ReactionSet
Returns true if this IReactionSet is empty.
isEnabled(String) - Method in class org.openscience.cdk.depict.Abbreviations
Check whether an abbreviation is enabled.
ISequenceSubRule<ILigand> - Interface in org.openscience.cdk.geometry.cip.rules
Sequence sub rule used in the CIP method to decide which of the two ligands takes precedence [Cahn, R.S. and Ingold, C. and Prelog, V., Specification of Molecular Chirality, Angew. Chem. Int. Ed., 1966, 5:385-415].
ISetting - Interface in org.openscience.cdk.interfaces
A simple setting that can be managed by the SettingManager.
isExpanded() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
Helper method to indicate that the method should be drawn fully, and not just the abbreviated form.
isExpanded() - Method in class org.openscience.cdk.FragmentAtom
 
isExpanded() - Method in interface org.openscience.cdk.interfaces.IFragmentAtom
Helper method to indicate that the method should be drawn fully, and not just the abbreviated form.
isExpanded() - Method in class org.openscience.cdk.silent.FragmentAtom
 
isFilled() - Method in interface org.openscience.cdk.renderer.selection.IChemObjectSelection
The opposite of a method like "isEmpty".
isFinished() - Method in interface org.openscience.cdk.group.PermutationGroup.Backtracker
Check to see if the backtracker is finished.
isFurtherMappingPossible(IAtomContainer, IAtomContainer, int, int, List<Integer>, List<Integer>, List<String>, List<String>, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
Deprecated.
 
isGoal() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IState
Deprecated.
Returns true if all atoms in the query molecule have been mapped.
isGoal() - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFState
Deprecated.
Returns true if all atoms in the query molecule have been mapped.
isHigherOrder(IBond.Order, IBond.Order) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
Returns true if the first bond has a higher bond order than the second bond.
isHydrogen(IAtom) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator
Determines if the atom is a hydrogen.
isIdentity() - Method in class org.openscience.cdk.group.Permutation
Check to see if this permutation is the identity permutation.
ISimpleChemObjectReader - Interface in org.openscience.cdk.io
This class is the interface that all IO readers should implement.
isIndexCreated() - Method in class org.openscience.cdk.io.random.RandomAccessReader
 
ISingleElectron - Interface in org.openscience.cdk.interfaces
A Single Electron is an orbital which is occupied by only one electron.
isInRing() - Method in class org.openscience.cdk.Atom
Access whether this atom has been flagged as in a ring.
isInRing() - Method in class org.openscience.cdk.Bond
Access whether this bond has been flagged as in a ring.
ISINRING - Static variable in class org.openscience.cdk.CDKConstants
Flag that is set when the chemobject is part of a ring.
isInRing() - Method in interface org.openscience.cdk.interfaces.IAtom
Access whether this atom has been flagged as in a ring.
isInRing() - Method in interface org.openscience.cdk.interfaces.IBond
Access whether this bond has been flagged as in a ring.
isInRing() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
Access whether this atom has been flagged as in a ring.
isInRing() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
Access whether this bond has been flagged as in a ring.
isInRing() - Method in class org.openscience.cdk.silent.Atom
Access whether this atom has been flagged as in a ring.
isInRing() - Method in class org.openscience.cdk.silent.Bond
Access whether this bond has been flagged as in a ring.
isInterrupted() - Method in class org.openscience.cdk.smiles.DeduceBondSystemTool
Deprecated.
Returns if the next or running calculation should be interrupted.
isInterrupted() - Method in class org.openscience.cdk.smiles.FixBondOrdersTool
Deprecated.
Returns if the next or running calculation should be interrupted.
isInvertible() - Method in class org.openscience.cdk.graph.invariant.GIMatrix
Verifies if the matrix is invertible or not by asking for its determinant.
isIsomorph(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
Tests if g1 and g2 are isomorph.
isIsomorph(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
Deprecated.
Tests if sourceGraph and targetGraph are isomorph.
isIsomorphic(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.IsomorphismTester
Checks whether a given molecule is isomorphic with the one that has been assigned to this IsomorphismTester at construction time.
isIsomorphic(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.IsomorphismTester
Checks whether a given molecule is isomorphic with the one that has been assigned to this IsomorphismTester at construction time.
isLeft(IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.geometry.BondTools
Says if an atom is on the left side of a another atom seen from a certain atom or not.
isLowerOrder(IBond.Order, IBond.Order) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
Returns true if the first bond has a lower bond order than the second bond.
isMappingCheckFlag() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper
Deprecated.
 
isMatchBond() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
Deprecated.
 
isMatchBonds() - Method in class org.openscience.cdk.smsd.Isomorphism
Deprecated.
 
isMatchFeasible(IAtomContainer, IBond, IAtomContainer, IBond, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
Deprecated.
 
isMatchFeasible(Match) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IState
Deprecated.
Returns true if the given match will work with the current map, or false otherwise.
isMatchFeasible(Match) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFState
Deprecated.
Returns true if the given match will work with the current map, or false otherwise.
isNewMatrix() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregor
Deprecated.
Checks if its a new Matrix.
ISNOTINRING - Static variable in class org.openscience.cdk.CDKConstants
Flag that is set when the chemobject is part of a ring.
IsoAlkanes - Class in org.openscience.cdk.templates.saturatedhydrocarbons
This class contains methods for generating simple organic alkanes.
IsoAlkanes() - Constructor for class org.openscience.cdk.templates.saturatedhydrocarbons.IsoAlkanes
 
isOctahedral(IAtom, IAtom, IAtom, IAtom, IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.stereo.StereoTool
Checks these 7 atoms to see if they are at the points of an octahedron.
isOK(IAtomContainer) - Method in class org.openscience.cdk.smiles.DeduceBondSystemTool
Deprecated.
Determines if, according to the algorithms implemented in this class, the given AtomContainer has properly distributed double bonds.
isolated() - Method in interface org.openscience.cdk.ringsearch.CyclicVertexSearch
Construct the sets of vertices which belong to isolated cycles.
isolated() - Method in class org.openscience.cdk.ringsearch.RingSearch
Construct the sets of vertices which belong to isolated rings.
isolatedRingFragments() - Method in class org.openscience.cdk.ringsearch.RingSearch
Construct a list of IAtomContainers each of which only contains a single isolated ring.
Isomeric - Static variable in class org.openscience.cdk.smiles.SmiFlavor
Output non-canonical SMILES with stereochemistry, atomic masses.
isomeric() - Static method in class org.openscience.cdk.smiles.SmilesGenerator
Convenience method for creating an isomeric generator.
Isomorphism - Class in org.openscience.cdk.smsd
Deprecated.
A more recent version of SMSD is available at http://github.com/asad/smsd
Isomorphism(Algorithm, boolean) - Constructor for class org.openscience.cdk.smsd.Isomorphism
Deprecated.
This is the algorithm factory and entry port for all the MCS algorithm in the Isomorphism supported algorithm Algorithm types:
  • 0: Default,
  • 1: MCSPlus,
  • 2: VFLibMCS,
  • 3: CDKMCS,
  • 4: SubStructure
  • IsomorphismTester - Class in org.openscience.cdk.isomorphism
    A too simplistic implementation of an isomorphism test for chemical graphs.
    IsomorphismTester() - Constructor for class org.openscience.cdk.isomorphism.IsomorphismTester
    Constructor for the IsomorphismTester object
    IsomorphismTester(IAtomContainer) - Constructor for class org.openscience.cdk.isomorphism.IsomorphismTester
    Constructor for the IsomorphismTester object
    isotope - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
     
    Isotope - Class in org.openscience.cdk
    Used to store and retrieve data of a particular isotope.
    Isotope(String) - Constructor for class org.openscience.cdk.Isotope
    Constructor for the Isotope object.
    Isotope(int, String, int, double, double) - Constructor for class org.openscience.cdk.Isotope
    Constructor for the Isotope object.
    Isotope(int, String, double, double) - Constructor for class org.openscience.cdk.Isotope
    Constructor for the Isotope object.
    Isotope(String, int) - Constructor for class org.openscience.cdk.Isotope
    Constructor for the Isotope object.
    Isotope(IElement) - Constructor for class org.openscience.cdk.Isotope
    Constructs an empty by copying the symbol, atomic number, flags, and identifier from the given IElement.
    ISOTOPE - Static variable in class org.openscience.cdk.libio.jena.CDK
     
    Isotope - Class in org.openscience.cdk.silent
    Used to store and retrieve data of a particular isotope.
    Isotope(String) - Constructor for class org.openscience.cdk.silent.Isotope
    Constructor for the Isotope object.
    Isotope(int, String, int, double, double) - Constructor for class org.openscience.cdk.silent.Isotope
    Constructor for the Isotope object.
    Isotope(int, String, double, double) - Constructor for class org.openscience.cdk.silent.Isotope
    Constructor for the Isotope object.
    Isotope(String, int) - Constructor for class org.openscience.cdk.silent.Isotope
    Constructor for the Isotope object.
    Isotope(IElement) - Constructor for class org.openscience.cdk.silent.Isotope
    Constructs an empty by copying the symbol, atomic number, flags, and identifier from the given IElement.
    IsotopeContainer - Class in org.openscience.cdk.formula
    This class defines a isotope container.
    IsotopeContainer() - Constructor for class org.openscience.cdk.formula.IsotopeContainer
    Constructor of the IsotopeContainer object.
    IsotopeContainer(IMolecularFormula, double) - Constructor for class org.openscience.cdk.formula.IsotopeContainer
    Constructor of the IsotopeContainer object setting a IMolecularFormula object and intensity value.
    IsotopeContainer(double, double) - Constructor for class org.openscience.cdk.formula.IsotopeContainer
    Constructor of the IsotopeContainer object setting a mass and intensity value.
    IsotopeDiff - Class in org.openscience.cdk.tools.diff
    Compares two IIsotope classes.
    IsotopeFactory - Class in org.openscience.cdk.config
    Used to store and return data of a particular isotope.
    IsotopeFactory() - Constructor for class org.openscience.cdk.config.IsotopeFactory
     
    IsotopeHandler - Class in org.openscience.cdk.config.isotopes
    Reads an isotope list in CML2 format.
    IsotopeHandler(IChemObjectBuilder) - Constructor for class org.openscience.cdk.config.isotopes.IsotopeHandler
    Constructs an IsotopeHandler used by the IsotopeReader.
    IsotopePattern - Class in org.openscience.cdk.formula
    This class defines the properties of a deisotoped pattern distribution.
    IsotopePattern() - Constructor for class org.openscience.cdk.formula.IsotopePattern
    Constructor of the IsotopePattern object.
    IsotopePatternGenerator - Class in org.openscience.cdk.formula
    Generates all Combinatorial chemical isotopes given a structure.
    IsotopePatternGenerator() - Constructor for class org.openscience.cdk.formula.IsotopePatternGenerator
    Constructor for the IsotopeGenerator.
    IsotopePatternGenerator(double) - Constructor for class org.openscience.cdk.formula.IsotopePatternGenerator
    Constructor for the IsotopeGenerator.
    IsotopePatternManipulator - Class in org.openscience.cdk.formula
    Class to manipulate IsotopePattern objects.
    IsotopePatternManipulator() - Constructor for class org.openscience.cdk.formula.IsotopePatternManipulator
     
    IsotopePatternRule - Class in org.openscience.cdk.formula.rules
    This class validate if the Isotope Pattern from a given IMolecularFormula correspond with other to compare.
    IsotopePatternRule() - Constructor for class org.openscience.cdk.formula.rules.IsotopePatternRule
    Constructor for the IsotopePatternRule object.
    IsotopePatternSimilarity - Class in org.openscience.cdk.formula
    This class gives a score hit of similarity between two different isotope abundance pattern.
    IsotopePatternSimilarity() - Constructor for class org.openscience.cdk.formula.IsotopePatternSimilarity
    Constructor for the IsotopePatternSimilarity object.
    IsotopeReader - Class in org.openscience.cdk.config.isotopes
    Reader that instantiates an XML parser and customized handler to process the isotope information in the CML2 isotope data file.
    IsotopeReader(InputStream, IChemObjectBuilder) - Constructor for class org.openscience.cdk.config.isotopes.IsotopeReader
    Instantiates a new reader that parses the XML from the given input.
    isotopes - Variable in class org.openscience.cdk.config.IsotopeFactory
     
    Isotopes - Class in org.openscience.cdk.config
    List of isotopes.
    isotopes() - Method in class org.openscience.cdk.debug.DebugAdductFormula
    Returns an Iterator for looping over all isotopes in this adduct formula.
    isotopes() - Method in class org.openscience.cdk.debug.DebugMolecularFormula
    Returns an Iterator for looping over all isotopes in this IMolecularFormula.
    isotopes() - Method in class org.openscience.cdk.formula.AdductFormula
    Returns an Iterator for looping over all isotopes in this adduct formula.
    isotopes() - Method in class org.openscience.cdk.formula.MolecularFormula
    Returns an Iterator for looping over all isotopes in this IMolecularFormula.
    isotopes() - Method in class org.openscience.cdk.formula.MolecularFormulaRange
    Returns an Iterator for looping over all isotopes in this MolecularFormulaExpand.
    isotopes() - Method in interface org.openscience.cdk.interfaces.IAdductFormula
    Returns an Iterator for looping over all isotopes in this adduct formula.
    isotopes() - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
    Returns an Iterable for looping over all isotopes in this IMolecularFormula.
    isotopes() - Method in class org.openscience.cdk.silent.AdductFormula
    Returns an Iterator for looping over all isotopes in this adduct formula.
    isotopes() - Method in class org.openscience.cdk.silent.MolecularFormula
    Returns an Iterator for looping over all isotopes in this IMolecularFormula.
    isotopic() - Method in class org.openscience.cdk.hash.HashGeneratorMaker
    Discriminate isotopes.
    ISOTROPIC_SHIELDING - Static variable in class org.openscience.cdk.CDKConstants
    The Isotropic Shielding, usually calculated by a quantum chemistry program like Gaussian.
    isOverSaturated(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker
    Checks if the current atom has exceeded its bond order sum value.
    ISPLACED - Static variable in class org.openscience.cdk.CDKConstants
    Flag that is set if the chemobject is placed (somewhere).
    isPrecedingPathTo(int) - Method in class org.openscience.cdk.graph.ShortestPaths
    Returns whether the first shortest path from the start to a given end vertex which only passed through vertices smaller then start.
    isPreservingAromaticity() - Method in class org.openscience.cdk.smiles.SmilesParser
    Deprecated.
    IsProtonInAromaticSystemDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
    This descriptor returns 1 if the protons is directly bonded to an aromatic system, it returns 2 if the distance between aromatic system and proton is 2 bonds, and it return 0 for other positions.
    IsProtonInAromaticSystemDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor
    Constructor for the IsProtonInAromaticSystemDescriptor object
    IsProtonInConjugatedPiSystemDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
    This class evaluates if a proton is joined to a conjugated system.
    IsProtonInConjugatedPiSystemDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInConjugatedPiSystemDescriptor
    Constructor for the IsProtonInConjugatedPiSystemDescriptor object
    isReady() - Method in class org.openscience.cdk.io.MDLV3000Reader
     
    isRecordEnd(String) - Method in class org.openscience.cdk.io.random.RandomAccessReader
     
    isRecordEnd(String) - Method in class org.openscience.cdk.io.random.RandomAccessSDFReader
     
    isRestH() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
     
    isSameRing(IRingSet, IAtom, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator
    Checks if atom1 and atom2 share membership in the same ring or ring system.
    isSameRMap(CDKRMap, CDKRMap) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
    Deprecated.
     
    isSaturated(IAtomContainer) - Method in class org.openscience.cdk.tools.AtomTypeAwareSaturationChecker
    isSaturated(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.AtomTypeAwareSaturationChecker
    isSaturated(IAtomContainer) - Method in class org.openscience.cdk.tools.CDKValencyChecker
     
    isSaturated(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.CDKValencyChecker
     
    isSaturated(IAtomContainer) - Method in interface org.openscience.cdk.tools.IValencyChecker
     
    isSaturated(IAtom, IAtomContainer) - Method in interface org.openscience.cdk.tools.IValencyChecker
     
    isSaturated(IAtomContainer) - Method in class org.openscience.cdk.tools.LonePairElectronChecker
    Determines of all atoms on the AtomContainer have the right number the lone pair electrons.
    isSaturated(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.LonePairElectronChecker
    Checks if an Atom is saturated their lone pair electrons by comparing it with known AtomTypes.
    isSaturated(IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker
    Determines of all atoms on the AtomContainer are saturated.
    isSaturated(IBond, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker
    Returns whether a bond is saturated.
    isSaturated(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker
    Checks whether an Atom is saturated by comparing it with known AtomTypes.
    isSaturated(IBond, IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
    Returns whether a bond is saturated.
    isSaturated(IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
    Determines of all atoms on the AtomContainer are saturated.
    isSaturated(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
    Checks whether an Atom is saturated by comparing it with known AtomTypes.
    isSet() - Method in class org.openscience.cdk.io.setting.BooleanIOSetting
     
    isSetParameter() - Method in interface org.openscience.cdk.reaction.type.parameters.IParameterReact
    Get if this parameter needs to take account.
    isSetParameter() - Method in class org.openscience.cdk.reaction.type.parameters.ParameterReact
    Get if this parameter needs to take account.
    isSquare() - Method in class org.openscience.cdk.graph.invariant.GIMatrix
    Verifies if the matrix is square, that is if it has an equal number of lines and columns.
    isSquarePlanar(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.BondTools
    Says if an atom as a center of a square planar chirality.
    isSquarePlanar(IAtom, IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.stereo.StereoTool
    Checks these four atoms for square planarity.
    isStereo(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.BondTools
    Says if an atom as a center of any valid stereo configuration or not.
    isStereocenter(int) - Method in class org.openscience.cdk.stereo.Stereocenters
    Is the atom be a stereocenter (i.e.
    isStereoMisMatch() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
    Deprecated.
    Returns true if mols have different stereo chemistry else false if no stereo mismatch.
    isStereoMisMatch() - Method in class org.openscience.cdk.smsd.Isomorphism
    Deprecated.
    Returns true if mols have different stereo chemistry else false if no stereo mismatch.
    isSubgraph(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
    Tests if g2 a subgraph of g1.
    isSubgraph(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
    Deprecated.
    Tests if targetGraph atom subgraph of sourceGraph.
    isSubgraph(List<CDKRMap>, List<CDKRMap>) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
    Deprecated.
     
    isSubgraph(boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler
    Deprecated.
    Initialise the Subgraph search algorithm.
    isSubgraph(boolean) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler
    Deprecated.
     
    isSubgraph(boolean) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler
    Deprecated.
     
    isSubgraph() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
    Deprecated.
    Checks if query is a subgraph of the target.
    isSubgraph(boolean) - Method in class org.openscience.cdk.smsd.interfaces.AbstractSubGraph
    Deprecated.
    Initialise the Subgraph search algorithm.
    isSubgraph() - Method in class org.openscience.cdk.smsd.Isomorphism
    Deprecated.
    Checks if query is a subgraph of the target.
    isSubset(BitSet, BitSet) - Static method in class org.openscience.cdk.fingerprint.FingerprinterTool
    Checks whether all the positive bits in BitSet bs2 occur in BitSet bs1.
    isSymmetric() - Method in class org.openscience.cdk.graph.invariant.GIMatrix
    Verifies if the matrix is symmetric, that is if the matrix is equal to it's transpose.
    IState - Interface in org.openscience.cdk.smsd.algorithm.vflib.interfaces
    Deprecated.
    SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    IStereoElement - Interface in org.openscience.cdk.interfaces
    Represents the concept of a stereo element in the molecule.
    isTetrahedral(IAtomContainer, IAtom, boolean) - Static method in class org.openscience.cdk.geometry.BondTools
    Says if an atom as a center of a tetrahedral chirality.
    isTheSame(IIsotope, IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormula
    Compare to IIsotope.
    isTheSame(IIsotope, IIsotope) - Method in class org.openscience.cdk.silent.MolecularFormula
    Compare to IIsotope.
    isTimeOut() - Static method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlus
    Deprecated.
     
    isTimeOut() - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
    Deprecated.
     
    isTimeOut() - Static method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper
    Deprecated.
     
    isTimeOut() - Static method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper
    Deprecated.
     
    isTimeOut() - Method in class org.openscience.cdk.smsd.Isomorphism
    Deprecated.
     
    isTimeoutFlag() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
    Deprecated.
    Returns true if a time out occurred else false
    isTimeOutFlag() - Method in class org.openscience.cdk.smsd.global.TimeOut
    Deprecated.
    Return true if its a timeout else return false.
    IStrand - Interface in org.openscience.cdk.interfaces
    A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms.
    isTriangularInferior() - Method in class org.openscience.cdk.graph.invariant.GIMatrix
    Verifies if the matrix is triangular inferior or not.
    isTriangularSuperior() - Method in class org.openscience.cdk.graph.invariant.GIMatrix
    Verifies if the matrix is triangular superior or not.
    isTrigonalBipyramidal(IAtom, IAtom, IAtom, IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.stereo.StereoTool
    Checks these 6 atoms to see if they form a trigonal-bipyramidal shape.
    isTrigonalBipyramidalOrOctahedral(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.BondTools
    Says if an atom as a center of a trigonal-bipyramidal or actahedral chirality.
    IStructureGenerationListener - Interface in org.openscience.cdk.structgen
     
    ISubstance - Interface in org.openscience.cdk.interfaces
    A chemical substance that consists of one or more chemical structures.
    ISubstanceDescriptor - Interface in org.openscience.cdk.qsar.descriptors.substance
    Classes that implement this interface are QSAR substance calculators.
    isUniform() - Method in class org.openscience.cdk.DynamicFactory.ConstructorKey
    Indicates whether this key has multiple parameters and they are of uniform type.
    isUnsaturated(IBond, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker
    Returns whether a bond is unsaturated.
    isUnsaturated(IBond, IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
    Returns whether a bond is unsaturated.
    isUnspecified() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom
     
    isValid(IMolecularFormula) - Method in class org.openscience.cdk.formula.MolecularFormulaChecker
    Validate if a IMolecularFormula is valid.
    isValid(String) - Static method in class org.openscience.cdk.index.CASNumber
    Checks whether the registry number is valid.
    isValidDoubleBondConfiguration(IAtomContainer, IBond) - Static method in class org.openscience.cdk.geometry.BondTools
    Tells if a certain bond is center of a valid double bond configuration.
    isValidOccurrenceSyntax(String) - Static method in class org.openscience.cdk.isomorphism.matchers.RGroupList
    Validates the occurrence value.
    isValidRgroupQueryLabel(String) - Static method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
    Validates a Pseudo atom's label to be valid RGroup query label (R1..R32).
    isValidSum(IMolecularFormula) - Method in class org.openscience.cdk.formula.MolecularFormulaChecker
    Validate if a IMolecularFormula is valid.
    isVisited(IAtom) - Method in interface org.openscience.cdk.geometry.cip.ILigand
    Returns a true if the atom has been visited before.
    isVisited(IAtom) - Method in class org.openscience.cdk.geometry.cip.Ligand
    Returns a true if the atom has been visited before.
    isVisited(IAtom) - Method in class org.openscience.cdk.geometry.cip.VisitedAtoms
    Returns true if the given atom already has been visited.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.ABINITFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.Aces2Format
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.ADFFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.AlchemyFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.BGFFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.BSFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
     
    isXMLBased() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.CACheFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
     
    isXMLBased() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.CIFFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.CMLFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.CRK2DFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.CRK3DFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.CrystClustFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.CTXFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.DaltonFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.DMol3Format
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.DOCK5Format
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.FingerprintFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.GamessFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.Gaussian03Format
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.Gaussian90Format
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.Gaussian92Format
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.Gaussian94Format
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.Gaussian95Format
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.Gaussian98Format
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.GROMOS96Format
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.HINFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.INChIFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in interface org.openscience.cdk.io.formats.IResourceFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.JaguarFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.JMEFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.MacroModelFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.MDLFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.MDLV2000Format
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.MDLV3000Format
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.MMODFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.Mol2Format
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.MOPAC7Format
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.MOPAC93Format
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.MOPAC97Format
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.MPQCFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.NWChemFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.PCModelFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.PDBFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.PDBMLFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.PMPFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.POVRayFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.PQSChemFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.QChemFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.RawCopyFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.SDFFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.ShelXFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.SMARTSFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.SMILESFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.SpartanFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.SVGFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.VASPFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.ViewmolFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.XEDFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.XYZFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.YasaraFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.ZindoFormat
    Indicates if the format is an XML-based language.
    isXMLBased() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat
    Indicates if the format is an XML-based language.
    ITALIC_DISPLAY_PREFIX - Static variable in class org.openscience.cdk.renderer.generators.standard.StandardGenerator
    A special markup for annotation labels that hints the generator to renderer the annotation label in italic.
    IteratingMDLConformerReader - Class in org.openscience.cdk.io.iterator
    Iterate over conformers of a collection of molecules stored in SDF format.
    IteratingMDLConformerReader(Reader, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingMDLConformerReader
     
    IteratingMDLConformerReader(InputStream, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingMDLConformerReader
     
    IteratingPCCompoundASNReader - Class in org.openscience.cdk.io.iterator
    Iterating PubChem PCCompound ASN reader.
    IteratingPCCompoundASNReader(Reader, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingPCCompoundASNReader
    Constructs a new IteratingPCCompoundASNReader that can read Molecule from a given Reader.
    IteratingPCCompoundASNReader(InputStream, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingPCCompoundASNReader
    Constructs a new IteratingPCCompoundASNReader that can read Molecule from a given InputStream and IChemObjectBuilder.
    IteratingPCCompoundXMLReader - Class in org.openscience.cdk.io.iterator
    Iterating PubChem PCCompound ASN.1 XML reader.
    IteratingPCCompoundXMLReader(Reader, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader
    Constructs a new IteratingPCCompoundXMLReader that can read Molecule from a given Reader and IChemObjectBuilder.
    IteratingPCCompoundXMLReader(InputStream, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader
    Constructs a new IteratingPCCompoundXLReader that can read Molecule from a given InputStream and IChemObjectBuilder.
    IteratingPCSubstancesXMLReader - Class in org.openscience.cdk.io.iterator
    Iterating PubChem PC-Substances ASN.1 XML reader.
    IteratingPCSubstancesXMLReader(Reader, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader
    Constructs a new IteratingPCSubstancesXMLReader that can read Molecule from a given Reader and IChemObjectBuilder.
    IteratingPCSubstancesXMLReader(InputStream, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader
    Constructs a new IteratingPCSubstancesXMLReader that can read Molecule from a given InputStream and IChemObjectBuilder.
    IteratingSDFReader - Class in org.openscience.cdk.io.iterator
    Iterating MDL SDF reader.
    IteratingSDFReader(Reader, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingSDFReader
    Constructs a new IteratingMDLReader that can read Molecule from a given Reader.
    IteratingSDFReader(InputStream, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingSDFReader
    Constructs a new IteratingMDLReader that can read Molecule from a given InputStream.
    IteratingSDFReader(InputStream, IChemObjectBuilder, boolean) - Constructor for class org.openscience.cdk.io.iterator.IteratingSDFReader
    Constructs a new IteratingMDLReader that can read Molecule from a given a InputStream.
    IteratingSDFReader(Reader, IChemObjectBuilder, boolean) - Constructor for class org.openscience.cdk.io.iterator.IteratingSDFReader
    Constructs a new IteratingMDLReader that can read Molecule from a given a Reader.
    IteratingSMILESReader - Class in org.openscience.cdk.io.iterator
    Iterating SMILES file reader.
    IteratingSMILESReader(Reader, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingSMILESReader
    Constructs a new IteratingSMILESReader that can read Molecule from a given Reader.
    IteratingSMILESReader(InputStream, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingSMILESReader
    Constructs a new IteratingSMILESReader that can read Molecule from a given InputStream and IChemObjectBuilder.
    iteration - Variable in class org.openscience.cdk.fingerprint.CircularFingerprinter.FP
     
    iterator() - Method in class org.openscience.cdk.ConformerContainer
    Gets an iterator over the conformers.
    iterator() - Method in class org.openscience.cdk.debug.DebugAdductFormula
    Returns an Iterator for looping over all IMolecularFormula in this adduct formula.
    iterator() - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet
    Returns an Iterator for looping over all IMolecularFormula in this MolecularFormulaSet.
    iterator() - Method in class org.openscience.cdk.depict.Abbreviations
    Iterate over loaded abbreviations.
    iterator() - Method in class org.openscience.cdk.formula.AdductFormula
    Returns an Iterator for looping over all IMolecularFormula in this adduct formula.
    iterator() - Method in class org.openscience.cdk.formula.MolecularFormulaSet
    Returns an Iterator for looping over all IMolecularFormula in this MolecularFormulaSet.
    iterator() - Method in class org.openscience.cdk.isomorphism.Mappings
    iterator() - Method in class org.openscience.cdk.renderer.elements.ElementGroup
    iterator() - Method in class org.openscience.cdk.signature.Orbit
    iterator() - Method in class org.openscience.cdk.silent.AdductFormula
    Returns an Iterator for looping over all IMolecularFormula in this adduct formula.
    iterator() - Method in class org.openscience.cdk.silent.MolecularFormulaSet
    Returns an Iterator for looping over all IMolecularFormula in this MolecularFormulaSet.
    ITetrahedralChirality - Interface in org.openscience.cdk.interfaces
    Stereochemistry specification for quadrivalent atoms.
    ITetrahedralChirality.Stereo - Enum in org.openscience.cdk.interfaces
    Enumeration that defines the two possible chiralities for this stereochemistry type.
    iupacRecommendations() - Static method in class org.openscience.cdk.renderer.SymbolVisibility
    Displays a symbol based on the preferred representation from the IUPAC guidelines (GR-2.1.2) [Jonathan Brecher, Graphical representation standards for chemical structure diagrams (IUPAC Recommendations 2008), Pure Appl. Chem, 2008, 80:277–410].
    iupacRecommendationsWithoutTerminalCarbon() - Static method in class org.openscience.cdk.renderer.SymbolVisibility
    Displays a symbol based on the acceptable representation from the IUPAC guidelines (GR-2.1.2) [Jonathan Brecher, Graphical representation standards for chemical structure diagrams (IUPAC Recommendations 2008), Pure Appl. Chem, 2008, 80:277–410].
    IValencyChecker - Interface in org.openscience.cdk.tools
    A common interface for SaturationChecker and ValencyChecker.
    IValidator - Interface in org.openscience.cdk.validate
    Interface that Validators need to implement to be used in validation.
    IVector - Class in org.openscience.cdk.math
     
    IVector(int) - Constructor for class org.openscience.cdk.math.IVector
    Constructs a vector with "size"-elements
    IViewEventRelay - Interface in org.openscience.cdk.controller
     
    IWriterListener - Interface in org.openscience.cdk.io.listener
    Allows monitoring of progress of writing activities.

    J

    JaguarFormat - Class in org.openscience.cdk.io.formats
    See here.
    JaguarFormat() - Constructor for class org.openscience.cdk.io.formats.JaguarFormat
     
    jcpAngles - Static variable in class org.openscience.cdk.layout.RingPlacer
    Suggested ring start angles for JChempaint, different due to Y inversion of canvas.
    jj_nt - Variable in class org.openscience.cdk.iupac.parser.NomParser
    Deprecated.
    Next token.
    jj_nt - Variable in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
    Next token.
    jjFillToken() - Method in class org.openscience.cdk.iupac.parser.NomParserTokenManager
     
    jjFillToken() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager
     
    jjnewLexState - Static variable in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager
    Lex State array.
    jjstrLiteralImages - Static variable in class org.openscience.cdk.iupac.parser.NomParserTokenManager
    Token literal values.
    jjstrLiteralImages - Static variable in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager
    Token literal values.
    jjtAccept(SMARTSParserVisitor, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.Node
    Accept the visitor.
    jjtAddChild(Node, int) - Method in interface org.openscience.cdk.smiles.smarts.parser.Node
    This method tells the node to add its argument to the node's list of children.
    JJTALIPHATIC - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTANYATOM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTAROMATIC - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTATOM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTATOMICMASS - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTATOMICNUMBER - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTCHARGE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTCHIRALITY - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    jjtClose() - Method in interface org.openscience.cdk.smiles.smarts.parser.Node
    This method is called after all the child nodes have been added.
    JJTELEMENT - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTEXPLICITATOM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTEXPLICITCONNECTIVITY - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTEXPLICITHIGHANDBOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTEXPLICITHIGHANDEXPRESSION - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    jjtGetChild(int) - Method in interface org.openscience.cdk.smiles.smarts.parser.Node
    This method returns a child node.
    jjtGetNumChildren() - Method in interface org.openscience.cdk.smiles.smarts.parser.Node
    Return the number of children the node has.
    jjtGetParent() - Method in interface org.openscience.cdk.smiles.smarts.parser.Node
     
    JJTGROUP - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTHYBRDIZATIONNUMBER - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTIMPLICITHCOUNT - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTIMPLICITHIGHANDBOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTIMPLICITHIGHANDEXPRESSION - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTLOWANDBOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTLOWANDEXPRESSION - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    jjtNodeName - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTNONCHHEAVYATOM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTNOTBOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTNOTEXPRESSION - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    jjtOpen() - Method in interface org.openscience.cdk.smiles.smarts.parser.Node
    This method is called after the node has been made the current node.
    JJTORBOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTOREXPRESSION - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTPERIODICGROUPNUMBER - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTREACTION - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTRECURSIVESMARTSEXPRESSION - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    jjtree - Variable in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
     
    jjtRemoveChild(int) - Method in interface org.openscience.cdk.smiles.smarts.parser.Node
    Removes a child from this node
    JJTRINGCONNECTIVITY - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTRINGIDENTIFIER - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTRINGMEMBERSHIP - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    jjtSetParent(Node) - Method in interface org.openscience.cdk.smiles.smarts.parser.Node
    This pair of methods are used to inform the node of its parent.
    JJTSIMPLEBOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTSMALLESTRINGSIZE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTSMARTS - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTSMARTSParserState - Class in org.openscience.cdk.smiles.smarts.parser
     
    JJTSMARTSParserState() - Constructor for class org.openscience.cdk.smiles.smarts.parser.JJTSMARTSParserState
     
    JJTSTART - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTTOTALCONNECTIVITY - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTTOTALHCOUNT - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTVALENCE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JJTVOID - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
     
    JMEFormat - Class in org.openscience.cdk.io.formats
     
    JMEFormat() - Constructor for class org.openscience.cdk.io.formats.JMEFormat
     
    JMOLANIMATIONConvention - Class in org.openscience.cdk.io.cml
     
    JMOLANIMATIONConvention(IChemFile) - Constructor for class org.openscience.cdk.io.cml.JMOLANIMATIONConvention
     
    JMOLANIMATIONConvention(ICMLModule) - Constructor for class org.openscience.cdk.io.cml.JMOLANIMATIONConvention
     
    JmolColors - Class in org.openscience.cdk.renderer.color
    Default Jmol colors.
    JmolColors() - Constructor for class org.openscience.cdk.renderer.color.JmolColors
     
    JniInChIInputAdapter - Class in org.openscience.cdk.inchi
     
    JniInChIInputAdapter(String) - Constructor for class org.openscience.cdk.inchi.JniInChIInputAdapter
     
    JniInChIInputAdapter(List<INCHI_OPTION>) - Constructor for class org.openscience.cdk.inchi.JniInChIInputAdapter
     
    JPG_FMT - Static variable in class org.openscience.cdk.depict.Depiction
    Joint Photographic Experts Group (JPG) format key.

    K

    K - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    KabschAlignment - Class in org.openscience.cdk.geometry.alignment
    Aligns two structures to minimize the RMSD using the Kabsch algorithm.
    KabschAlignment(IAtom[], IAtom[]) - Constructor for class org.openscience.cdk.geometry.alignment.KabschAlignment
    Sets up variables for the alignment algorithm.
    KabschAlignment(IAtom[], IAtom[], double[]) - Constructor for class org.openscience.cdk.geometry.alignment.KabschAlignment
    Sets up variables for the alignment algorithm.
    KabschAlignment(IAtomContainer, IAtomContainer) - Constructor for class org.openscience.cdk.geometry.alignment.KabschAlignment
    Sets up variables for the alignment algorithm.
    KabschAlignment(IAtomContainer, IAtomContainer, double[]) - Constructor for class org.openscience.cdk.geometry.alignment.KabschAlignment
    Sets up variables for the alignment algorithm.
    KappaShapeIndicesDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
    Kier and Hall kappa molecular shape indices compare the molecular graph with minimal and maximal molecular graphs; a description is given at: http://www.chemcomp.com/Journal_of_CCG/Features/descr.htm#KH : "they are intended to capture different aspects of molecular shape.
    KappaShapeIndicesDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor
    Constructor for the KappaShapeIndicesDescriptor object
    kekulise(boolean) - Method in class org.openscience.cdk.smiles.SmilesParser
    Indicated whether structures should be automatically kekulised if they are provided as aromatic.
    kekuliseAromaticRings(IAtomContainer) - Method in class org.openscience.cdk.smiles.FixBondOrdersTool
    Deprecated.
    kekuliseAromaticRings - function to add double/single bond order information for molecules having rings containing all atoms marked SP2 or Planar3 hybridisation.
    Kekulization - Class in org.openscience.cdk.aromaticity
    Assign a Kekulé representation to the aromatic systems of a compound.
    Kekulization() - Constructor for class org.openscience.cdk.aromaticity.Kekulization
     
    kekulize(IAtomContainer) - Static method in class org.openscience.cdk.aromaticity.Kekulization
    Assign a Kekulé representation to the aromatic systems of a compound.
    KETO_ENOL - Static variable in class org.openscience.cdk.tautomers.InChITautomerGenerator
    Generate InChI with -KET (keto-enol tautomers) option.
    key(Class<?>, Class<?>...) - Static method in class org.openscience.cdk.DynamicFactory
    Creates a constructor key for use in accessing constructors.
    KEY - Static variable in class org.openscience.cdk.isomorphism.ComponentGrouping
    Key indicates where the grouping should be store in the query properties.
    KierHallSmartsDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
    A fragment count descriptor that uses e-state fragments.
    KierHallSmartsDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor
     
    kind - Variable in class org.openscience.cdk.iupac.parser.Token
    An integer that describes the kind of this token.
    kind - Variable in class org.openscience.cdk.smiles.smarts.parser.Token
    An integer that describes the kind of this token.
    KlekotaRothFingerprinter - Class in org.openscience.cdk.fingerprint
    SMARTS based substructure fingerprint based on Chemical substructures that enrich for biological activity [Klekota, Justin and Roth, Frederick P., Chemical substructures that enrich for biological activity, Bioinformatics, 2008, 24:2518-2525, doi:10.1093/bioinformatics/btn479].
    KlekotaRothFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.KlekotaRothFingerprinter
     
    KR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    KRYPTON - Static variable in enum org.openscience.cdk.config.Elements
     

    L

    L_AND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    L_BRACKET - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    L_PAREN - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    LA - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    label(IAtomContainer) - Static method in class org.openscience.cdk.geometry.cip.CIPTool
    Convenience method for labelling all stereo elements.
    label(IAtomContainer, int[][]) - Static method in class org.openscience.cdk.graph.invariant.Canon
    Compute the canonical labels for the provided structure.
    label(IAtomContainer, int[][], long[]) - Static method in class org.openscience.cdk.graph.invariant.Canon
    Compute the canonical labels for the provided structure.
    LabelContainer - Class in org.openscience.cdk.smsd.helper
    Deprecated.
    SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    LabelContainer() - Constructor for class org.openscience.cdk.smsd.helper.LabelContainer
    Deprecated.
     
    labelReaction(IReaction, ICanonicalMoleculeLabeller) - Method in class org.openscience.cdk.smsd.labelling.AbstractReactionLabeller
    Deprecated.
     
    LANTHANUM - Static variable in enum org.openscience.cdk.config.Elements
     
    LANTHANUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    LARGE_FIRST - Static variable in class org.openscience.cdk.silent.RingSet
    Flag to denote that the set is order with the largest ring first?
    LARGE_FIRST - Static variable in class org.openscience.cdk.tools.manipulator.RingSizeComparator
    Flag to denote that the set is order with the largest ring first
    LargestChainDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
    Class that returns the number of atoms in the largest chain.
    LargestChainDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor
    Constructor for the LargestChain object.
    LargestPiSystemDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
    Class that returns the number of atoms in the largest pi system.
    LargestPiSystemDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor
    Constructor for the LargestPiSystemDescriptor object.
    last() - Method in interface org.openscience.cdk.io.random.IRandomAccessChemObjectReader
     
    last() - Method in class org.openscience.cdk.io.random.RandomAccessReader
     
    lastIndexOf(Object) - Method in class org.openscience.cdk.ConformerContainer
    Returns the highest index at which the specific IAtomContainer appears in the list or -1 if is not found.
    LAWRENCIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    LAWRENCIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    LEAD - Static variable in enum org.openscience.cdk.config.Elements
     
    LEAD - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    length() - Method in class org.openscience.cdk.io.cml.CMLModuleStack
     
    length() - Method in class org.openscience.cdk.math.Vector
    Return the length from this vector
    length() - Method in class org.openscience.cdk.qsar.result.BooleanResultType
     
    length() - Method in class org.openscience.cdk.qsar.result.DoubleArrayResult
     
    length() - Method in class org.openscience.cdk.qsar.result.DoubleArrayResultType
     
    length() - Method in class org.openscience.cdk.qsar.result.DoubleResult
     
    length() - Method in class org.openscience.cdk.qsar.result.DoubleResultType
     
    length() - Method in interface org.openscience.cdk.qsar.result.IDescriptorResult
    Returns the length of this descriptor.
    length() - Method in class org.openscience.cdk.qsar.result.IntegerArrayResult
     
    length() - Method in class org.openscience.cdk.qsar.result.IntegerArrayResultType
     
    length() - Method in class org.openscience.cdk.qsar.result.IntegerResult
     
    length() - Method in class org.openscience.cdk.qsar.result.IntegerResultType
     
    LengthOverBreadthDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
    Evaluates length over breadth descriptors.
    LengthOverBreadthDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor
    Constructor for the LengthOverBreadthDescriptor object.
    level - Variable in class org.openscience.cdk.io.setting.IOSetting
     
    LexicalError(boolean, int, int, int, String, char) - Static method in error org.openscience.cdk.iupac.parser.TokenMgrError
    Returns a detailed message for the Error when it is thrown by the token manager to indicate a lexical error.
    LexicalError(boolean, int, int, int, String, char) - Static method in error org.openscience.cdk.smiles.smarts.parser.TokenMgrError
    Returns a detailed message for the Error when it is thrown by the token manager to indicate a lexical error.
    lexStateNames - Static variable in class org.openscience.cdk.iupac.parser.NomParserTokenManager
    Lexer state names.
    lexStateNames - Static variable in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager
    Lexer state names.
    LI - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    Ligand - Class in org.openscience.cdk.geometry.cip
    Concept of a ligand in CIP terms, reflecting a side chain of a central atom that can have precedence over another.
    Ligand(IAtomContainer, VisitedAtoms, IAtom, IAtom) - Constructor for class org.openscience.cdk.geometry.cip.Ligand
     
    limit(int) - Method in class org.openscience.cdk.isomorphism.Mappings
    Limit the number of mappings - only this number of mappings will be generate.
    line - Variable in class org.openscience.cdk.iupac.parser.SimpleCharStream
     
    line - Variable in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
     
    LineElement - Class in org.openscience.cdk.renderer.elements
    A line between two points.
    LineElement(double, double, double, double, double, Color) - Constructor for class org.openscience.cdk.renderer.elements.LineElement
    Make a line element.
    LineElement.LineType - Enum in org.openscience.cdk.renderer.elements
    The type of the line.
    LineTo - Class in org.openscience.cdk.renderer.elements.path
    A line element in the path.
    LineTo(Point2d) - Constructor for class org.openscience.cdk.renderer.elements.path.LineTo
    Make a line to this point.
    LineTo(double[]) - Constructor for class org.openscience.cdk.renderer.elements.path.LineTo
    Make a line path element.
    LineTo(double, double) - Constructor for class org.openscience.cdk.renderer.elements.path.LineTo
    Make a line path element.
    lineTo(Point2d) - Method in class org.openscience.cdk.renderer.elements.path.PathBuilder
    Make a line in the path, from the last point to the given point.
    LingoFingerprinter - Class in org.openscience.cdk.fingerprint
    An implementation of the LINGO fingerprint [Vidal, D. and Thormann, M. and Pons, M., LINGO, an Efficient Holographic Text Based Method To Calculate Biophysical Properties and Intermolecular Similarities, J. Chem. Inf. Model., 2005, 45:386-393, doi:10.1021/ci0496797].
    LingoFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.LingoFingerprinter
    Initialize the fingerprinter with a default substring length of 4.
    LingoFingerprinter(int) - Constructor for class org.openscience.cdk.fingerprint.LingoFingerprinter
    Initialize the fingerprinter.
    LingoSimilarity - Class in org.openscience.cdk.similarity
    A class to evaluate the similarity between two LINGO's as described in [Vidal, D. and Thormann, M. and Pons, M., LINGO, an Efficient Holographic Text Based Method To Calculate Biophysical Properties and Intermolecular Similarities, J. Chem. Inf. Model., 2005, 45:386-393, doi:10.1021/ci0496797].
    listDictionaries() - Method in class org.openscience.cdk.dict.DictionaryDatabase
    Returns true if the database contains the dictionary.
    listDifferences(BitSet, BitSet) - Static method in class org.openscience.cdk.fingerprint.FingerprinterTool
    This lists all bits set in bs2 and not in bs2 (other way round not considered) in a list and to logger.
    listFormats() - Method in class org.openscience.cdk.depict.Depiction
    List the available formats that can be rendered.
    listIterator() - Method in class org.openscience.cdk.ConformerContainer
     
    listIterator(int) - Method in class org.openscience.cdk.ConformerContainer
     
    listNumbers(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.layout.AtomPlacer
    Returns a string with the numbers of all atoms in an AtomContainer relative to a given molecule.
    listNumbers(IAtomContainer, List<IAtom>) - Static method in class org.openscience.cdk.layout.AtomPlacer
    Returns a string with the numbers of all atoms in a Vector relative to a given molecule.
    listPlaced(IAtomContainer) - Method in class org.openscience.cdk.layout.AtomPlacer
    Returns a string with the numbers of all placed atoms in an AtomContainer
    LITHIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    LITHIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    LITHO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    LIVERMORIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    loadFromFile(String) - Method in class org.openscience.cdk.depict.Abbreviations
    Load a set of abbreviations from a classpath resource or file in SMILES format.
    loadIndex(File) - Method in class org.openscience.cdk.io.random.RandomAccessReader
     
    loadMolecule(String) - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
     
    loadTemplates(IChemObjectBuilder) - Method in class org.openscience.cdk.layout.TemplateHandler
    Loads all existing templates into memory.
    logger - Static variable in class org.openscience.cdk.config.IsotopeFactory
     
    logger - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
     
    logger - Static variable in class org.openscience.cdk.io.iterator.event.EventCMLHandler
     
    logger - Static variable in class org.openscience.cdk.io.random.RandomAccessReader
     
    logger - Static variable in class org.openscience.cdk.tools.SmilesValencyChecker
     
    LoggingTool - Class in org.openscience.cdk.tools
    Useful for logging messages.
    LoggingTool() - Constructor for class org.openscience.cdk.tools.LoggingTool
    Constructs a LoggingTool which produces log lines without any special indication which class the message originates from.
    LoggingTool(Object) - Constructor for class org.openscience.cdk.tools.LoggingTool
    Constructs a LoggingTool which produces log lines indicating them to be for the Class of the Object.
    LoggingTool(Class<?>) - Constructor for class org.openscience.cdk.tools.LoggingTool
    Constructs a LoggingTool which produces log lines indicating them to be for the given Class.
    LoggingToolFactory - Class in org.openscience.cdk.tools
    Factory used to instantiate a ILoggingTool.
    LoggingToolFactory() - Constructor for class org.openscience.cdk.tools.LoggingToolFactory
     
    LogicalOperatorAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
    This class matches a logical operator that connects two query atoms.
    LogicalOperatorAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom
     
    LogicalOperatorBond - Class in org.openscience.cdk.isomorphism.matchers.smarts
    This class matches a logical operator that connects two query bonds.
    LogicalOperatorBond(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond
     
    LONE_PAIR_COUNT - Static variable in class org.openscience.cdk.CDKConstants
    Used as property key for indicating the HOSE code for a certain atom type.
    LonePair - Class in org.openscience.cdk
    A LonePair is an orbital primarily located with one Atom, containing two electrons.
    LonePair() - Constructor for class org.openscience.cdk.LonePair
    Constructs an unconnected lone pair.
    LonePair(IAtom) - Constructor for class org.openscience.cdk.LonePair
    Constructs an lone pair on an Atom.
    LonePair - Class in org.openscience.cdk.silent
    A LonePair is an orbital primarily located with one Atom, containing two electrons.
    LonePair() - Constructor for class org.openscience.cdk.silent.LonePair
    Constructs an unconnected lone pair.
    LonePair(IAtom) - Constructor for class org.openscience.cdk.silent.LonePair
    Constructs an lone pair on an Atom.
    lonePairCount - Variable in class org.openscience.cdk.AtomContainer
    Number of lone pairs contained by this object.
    lonePairCount - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
    Number of lone pairs contained by this object.
    lonePairCount - Variable in class org.openscience.cdk.silent.AtomContainer
    Number of lone pairs contained by this object.
    LonePairDiff - Class in org.openscience.cdk.tools.diff
    Compares two ILonePair classes.
    LonePairElectronChecker - Class in org.openscience.cdk.tools
    Provides methods for checking whether an atoms lone pair electrons are saturated with respect to a particular atom type.
    LonePairElectronChecker() - Constructor for class org.openscience.cdk.tools.LonePairElectronChecker
     
    LonePairGenerator - Class in org.openscience.cdk.renderer.generators
    Generate the symbols for lone pairs.
    LonePairGenerator() - Constructor for class org.openscience.cdk.renderer.generators.LonePairGenerator
     
    lonePairs - Variable in class org.openscience.cdk.AtomContainer
    Internal array of lone pairs.
    lonePairs() - Method in class org.openscience.cdk.AtomContainer
    Returns an Iterable for looping over all lone pairs in this container.
    lonePairs() - Method in class org.openscience.cdk.debug.DebugAminoAcid
    Returns an Iterable for looping over all lone pairs in this container.
    lonePairs() - Method in class org.openscience.cdk.debug.DebugAtomContainer
    Returns an Iterable for looping over all lone pairs in this container.
    lonePairs() - Method in class org.openscience.cdk.debug.DebugBioPolymer
    Returns an Iterable for looping over all lone pairs in this container.
    lonePairs() - Method in class org.openscience.cdk.debug.DebugCrystal
    Returns an Iterable for looping over all lone pairs in this container.
    lonePairs() - Method in class org.openscience.cdk.debug.DebugMonomer
    Returns an Iterable for looping over all lone pairs in this container.
    lonePairs() - Method in class org.openscience.cdk.debug.DebugPolymer
    Returns an Iterable for looping over all lone pairs in this container.
    lonePairs() - Method in class org.openscience.cdk.debug.DebugRing
    Returns an Iterable for looping over all lone pairs in this container.
    lonePairs() - Method in class org.openscience.cdk.debug.DebugStrand
    Returns an Iterable for looping over all lone pairs in this container.
    lonePairs() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
    Returns an Iterable for looping over all lone pairs in this container.
    lonePairs - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
    Internal array of lone pairs.
    lonePairs() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
    Returns an Iterable for looping over all lone pairs in this container.
    lonePairs - Variable in class org.openscience.cdk.silent.AtomContainer
    Internal array of lone pairs.
    lonePairs() - Method in class org.openscience.cdk.silent.AtomContainer
    Returns an Iterable for looping over all lone pairs in this container.
    LongestAliphaticChainDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
    Class that returns the number of atoms in the longest aliphatic chain.
    LongestAliphaticChainDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor
    Constructor for the LongestAliphaticChainDescriptor object.
    LowAndBond() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
     
    LowAndExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
     
    lowThresh - Variable in class org.openscience.cdk.fingerprint.model.Bayesian
     
    LR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    LU - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    LUTETIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    LUTETIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.

    M

    MACCSFingerprinter - Class in org.openscience.cdk.fingerprint
    This fingerprinter generates 166 bit MACCS keys.
    MACCSFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.MACCSFingerprinter
     
    MACCSFingerprinter(IChemObjectBuilder) - Constructor for class org.openscience.cdk.fingerprint.MACCSFingerprinter
     
    MacroModelFormat - Class in org.openscience.cdk.io.formats
     
    MacroModelFormat() - Constructor for class org.openscience.cdk.io.formats.MacroModelFormat
     
    mag() - Method in class org.openscience.cdk.math.Quaternion
     
    mag_sq() - Method in class org.openscience.cdk.math.Quaternion
     
    MAGNESIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    MAGNESIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    main(String[]) - Static method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor
     
    mainChainConstruct() - Method in class org.openscience.cdk.iupac.parser.NomParser
    Deprecated.
    Main chains are compulsary and consist of an optional "cyclo", a length prefix and a posfix denoting functional groups.
    mainChainPrefix() - Method in class org.openscience.cdk.iupac.parser.NomParser
    Deprecated.
    Deal with the main chain's length.
    mainChainSuffix() - Method in class org.openscience.cdk.iupac.parser.NomParser
    Deprecated.
    Figure out the functional group by the main chain's suffix.
    majorIsotopes - Variable in class org.openscience.cdk.config.IsotopeFactory
     
    make123Triazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
    Returns 1,2,3-triazole without explicit hydrogens.
    make124Triazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
    Returns 1,2,4-triazole without explicit hydrogens.
    make4x3CondensedRings() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
     
    makeAdenine() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
     
    makeAlkane(int) - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
    Generate an Alkane (chain of carbons with no hydrogens) of a given length.
    makeAlphaPinene() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
     
    makeAtomContainer(IAtom, List<IBond>, IAtom) - Static method in class org.openscience.cdk.fragment.FragmentUtils
     
    makeAtomsMapOfBondsMap(List<RMap>, IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
    This makes a map of matching atoms out of a map of matching bonds as produced by the get(Subgraph|Ismorphism)Map methods.
    makeAtomsMapOfBondsMap(List<CDKRMap>, IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
    Deprecated.
    This makes atom map of matching atoms out of atom map of matching bonds as produced by the get(Subgraph|Ismorphism)Map methods.
    makeAtomsMapsOfBondsMaps(List<List<RMap>>, IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
    This makes maps of matching atoms out of a maps of matching bonds as produced by the get(Subgraph|Ismorphism)Maps methods.
    makeAtomsMapsOfBondsMaps(List<List<CDKRMap>>, IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
    Deprecated.
    This makes maps of matching atoms out of atom maps of matching bonds as produced by the get(Subgraph|Ismorphism)Maps methods.
    makeAzulene() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
    Returns azulene without explicit hydrogens.
    makeBenzene() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
     
    makeBicycloRings() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
     
    makeBiphenyl() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
    Returns biphenyl without explicit hydrogens.
    makeBitFingerprint(Map<String, Integer>) - Static method in class org.openscience.cdk.fingerprint.FingerprinterTool
    Convert a mapping of features and their counts to a 1024-bit binary fingerprint.
    makeBitFingerprint(Map<String, Integer>, int) - Static method in class org.openscience.cdk.fingerprint.FingerprinterTool
    Convert a mapping of features and their counts to a binary fingerprint.
    makeBitFingerprint(Map<String, Integer>, int, int) - Static method in class org.openscience.cdk.fingerprint.FingerprinterTool
    Convert a mapping of features and their counts to a binary fingerprint.
    makeBondMapOfAtomMap(IAtomContainer, IAtomContainer, Map<IAtom, IAtom>) - Static method in class org.openscience.cdk.smsd.Isomorphism
    Deprecated.
    Returns bond map between source and target molecules based on the atoms
    makeBondMapsOfAtomMaps(IAtomContainer, IAtomContainer, List<Map<IAtom, IAtom>>) - Static method in class org.openscience.cdk.smsd.Isomorphism
    Deprecated.
    Returns bond maps between source and target molecules based on the atoms
    makeBranchedAliphatic() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
     
    makeBremserCompliant(String) - Method in class org.openscience.cdk.tools.HOSECodeGenerator
     
    makeCanonicalSmileFromRingSystems(String, String) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor
     
    makeCountFingerprint(Map<String, Integer>) - Static method in class org.openscience.cdk.fingerprint.FingerprinterTool
    Wrap a mapping of features and their counts to a continuous (count based) fingerprint.
    makeCyclobutadiene() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
    Returns cyclobutadiene without explicit hydrogens.
    makeCyclobutane() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
    Returns cyclobutane without explicit hydrogens.
    makeCyclohexane() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
    Returns cyclohexane without explicit hydrogens.
    makeCyclohexene() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
    Returns cyclohexene without explicit hydrogens.
    makeCyclopentane() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
    Returns cyclopentane without explicit hydrogens.
    makeDeepCopy(IAtomContainer) - Static method in class org.openscience.cdk.normalize.SMSDNormalizer
    Deprecated.
    Returns deep copy of the molecule
    makeDeepCopy(IAtomContainer) - Static method in class org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator
    Deprecated.
    Retrurns deep copy of the molecule
    makeDiamantane() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
     
    makeEdge(int, int, String, String, String) - Method in class org.openscience.cdk.signature.MoleculeFromSignatureBuilder
     
    makeEthylCyclohexane() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
     
    makeEthylPropylPhenantren() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
     
    makeFingerprintFromRingSystems(String, String, boolean, boolean) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor
     
    makeFingerprintsFromSdf(boolean, boolean, Map<String, Integer>, BufferedReader, int) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor
     
    makeFonts() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
    Make widget-specific fonts.
    makeFonts() - Method in class org.openscience.cdk.renderer.font.AWTFontManager
    Make widget-specific fonts.
    makeFusedRings() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
     
    makeGraph() - Method in class org.openscience.cdk.signature.MoleculeFromSignatureBuilder
     
    makeImidazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
    Returns imidazole without explicit hydrogens.
    makeIndex() - Method in class org.openscience.cdk.io.random.RandomAccessReader
    The index file RandomAccessReader.getIndexFile(String) is loaded, if already exists, or created a new.
    makeIndole() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
    Returns indole without explicit hydrogens.
    makeIsothiazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
    Returns isothiazole without explicit hydrogens.
    makeIsoxazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
    Returns Isoxazole without explicit hydrogens.
    makeLabel(int) - Static method in class org.openscience.cdk.isomorphism.matchers.RGroup
    Makes a label/title to be used for a substituent.
    makeMethylDecaline() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
     
    makeOxadiazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
    Returns oxadiazole without explicit hydrogens.
    makeOxazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
    Returns Oxazole without explicit hydrogens.
    makePhenylAmine() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
     
    makePhenylEthylBenzene() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
     
    makePiperidine() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
     
    makePropylCycloPropane() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
     
    makePyrazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
    Returns pyrazole without explicit hydrogens.
    makePyridazine() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
    Returns pyridazine without explicit hydrogens.
    makePyridine() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
    Returns pyridine without explicit hydrogens.
    makePyridineOxide() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
    Returns pyridine oxide without explicit hydrogens.
    makePyrimidine() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
    Returns pyrimidine without explicit hydrogens.
    makePyrrole() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
    Returns pyrrole without explicit hydrogens.
    makePyrroleAnion() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
    Returns pyrrole anion without explicit hydrogens.
    makeQuinone() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
     
    makeReferencesExplicit(IChemObject) - Static method in class org.openscience.cdk.dict.CDKDictionaryReferences
     
    makeSingleRing() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
     
    makeSpiroRings() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
     
    makeSteran() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
     
    makeStereocenter(Point3d, IBond, Point3d, Point3d, Point3d[]) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
    set Atoms in respect to stereoinformation.
    makeSymN(int) - Static method in class org.openscience.cdk.group.PermutationGroup
    Make the symmetric group Sym(N) for N.
    makeTetrahydropyran() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
     
    makeTetrazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
    Returns tetrazole without explicit hydrogens.
    makeThiadiazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
    Returns thiadiazole without explicit hydrogens.
    makeThiazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
    Returns thiazole without explicit hydrogens.
    makeTriazine() - Static method in class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
    Returns triazine without explicit hydrogens.
    makeUnion(int, int) - Method in class org.openscience.cdk.group.DisjointSetForest
    Union these two elements - in other words, put them in the same set.
    makeUpDownBonds(IAtomContainer) - Static method in class org.openscience.cdk.geometry.BondTools
     
    makeVertex(String) - Method in class org.openscience.cdk.signature.MoleculeFromSignatureBuilder
     
    MANGANESE - Static variable in enum org.openscience.cdk.config.Elements
     
    MANGANESE - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    MannholdLogPDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
    Prediction of logP based on the number of carbon and hetero atoms.
    MannholdLogPDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor
     
    map(Map<IAtom, IAtom>, Map<IBond, IBond>) - Method in interface org.openscience.cdk.interfaces.IDoubleBondStereochemistry
    Map the atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping.
    map(Map<IAtom, IAtom>, Map<IBond, IBond>) - Method in interface org.openscience.cdk.interfaces.IStereoElement
    Map the atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping.
    map(Map<IAtom, IAtom>, Map<IBond, IBond>) - Method in interface org.openscience.cdk.interfaces.ITetrahedralChirality
    Map the atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping.
    map(Function<int[], T>) - Method in class org.openscience.cdk.isomorphism.Mappings
    Map the mappings to another type.
    map - Variable in class org.openscience.cdk.Reaction
     
    map - Variable in class org.openscience.cdk.silent.Reaction
     
    map(Map<IAtom, IAtom>, Map<IBond, IBond>) - Method in class org.openscience.cdk.stereo.DoubleBondStereochemistry
     
    map(Map<IAtom, IAtom>, Map<IBond, IBond>) - Method in class org.openscience.cdk.stereo.ExtendedTetrahedral
    Map the atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping.
    map(Map<IAtom, IAtom>, Map<IBond, IBond>) - Method in class org.openscience.cdk.stereo.TetrahedralChirality
    Map the atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping.
    mapAtomsOfAlignedStructures(IAtomContainer, IAtomContainer, double, Map<Integer, Integer>) - Static method in class org.openscience.cdk.geometry.GeometryTools
    Returns a Map with the AtomNumbers, the first number corresponds to the first (or the largest AtomContainer) atomcontainer.
    mapAtomsOfAlignedStructures(IAtomContainer, IAtomContainer, double, Map<Integer, Integer>) - Static method in class org.openscience.cdk.geometry.GeometryUtil
    Returns a Map with the AtomNumbers, the first number corresponds to the first (or the largest AtomContainer) atomcontainer.
    mapAtomsOfAlignedStructures(IAtomContainer, IAtomContainer, Map<Integer, Integer>) - Static method in class org.openscience.cdk.isomorphism.AtomMappingTools
    Returns a Map with the AtomNumbers, the first number corresponds to the first (or the largest AtomContainer) atomContainer.
    mapAtomType(String) - Method in class org.openscience.cdk.atomtype.mapper.AtomTypeMapper
    Maps an atom type from one scheme to another, as specified in the input used when creating this AtomTypeMapper instance.
    MAPPED - Static variable in class org.openscience.cdk.CDKConstants
    Flag is set if a chemobject is mapped to another chemobject.
    Mapping - Class in org.openscience.cdk
    A Mapping is an relation between two ChemObjects in a non-chemical entity.
    Mapping(IChemObject, IChemObject) - Constructor for class org.openscience.cdk.Mapping
    Constructs an unconnected lone pair.
    Mapping - Class in org.openscience.cdk.silent
    A Mapping is an relation between two ChemObjects in a non-chemical entity.
    Mapping(IChemObject, IChemObject) - Constructor for class org.openscience.cdk.silent.Mapping
    Constructs an unconnected lone pair.
    mappingCount - Variable in class org.openscience.cdk.Reaction
     
    mappingCount - Variable in class org.openscience.cdk.silent.Reaction
     
    MappingGenerator - Class in org.openscience.cdk.renderer.generators
    IGenerator that will show how atoms map between the reactant and product side.
    MappingGenerator() - Constructor for class org.openscience.cdk.renderer.generators.MappingGenerator
     
    MappingGenerator.AtomAtomMappingLineColor - Class in org.openscience.cdk.renderer.generators
    The width on screen of an atom-atom mapping line.
    MappingGenerator.AtomAtomMappingLineColor() - Constructor for class org.openscience.cdk.renderer.generators.MappingGenerator.AtomAtomMappingLineColor
     
    MappingGenerator.MappingLineWidth - Class in org.openscience.cdk.renderer.generators
    The width on screen of an atom-atom mapping line.
    MappingGenerator.MappingLineWidth() - Constructor for class org.openscience.cdk.renderer.generators.MappingGenerator.MappingLineWidth
     
    MappingGenerator.ShowAtomAtomMapping - Class in org.openscience.cdk.renderer.generators
    Boolean by which atom-atom mapping depiction can be temporarily disabled.
    MappingGenerator.ShowAtomAtomMapping() - Constructor for class org.openscience.cdk.renderer.generators.MappingGenerator.ShowAtomAtomMapping
     
    mappings() - Method in interface org.openscience.cdk.interfaces.IReaction
    Returns the mappings between the reactant and the product side.
    Mappings - Class in org.openscience.cdk.isomorphism
    A fluent interface for handling (sub)-graph mappings from a query to a target structure.
    mappings() - Method in class org.openscience.cdk.Reaction
    Returns the mappings between the reactant and the product side.
    mappings() - Method in class org.openscience.cdk.silent.Reaction
    Returns the mappings between the reactant and the product side.
    mapTemplateExact(IAtomContainer) - Method in class org.openscience.cdk.layout.TemplateHandler
    Checks if one of the loaded templates is isomorph to the given Molecule.
    mapTemplates(IAtomContainer) - Method in class org.openscience.cdk.layout.TemplateHandler
    Checks if one of the loaded templates is a substructure in the given Molecule.
    mapTemplates(IAtomContainer, double) - Method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D
    mapTemplates(IAtomContainer, int) - Method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D
    Checks if one of the loaded templates is a substructure in the given Molecule.
    markAromaticRings(IRing) - Static method in class org.openscience.cdk.tools.manipulator.RingManipulator
    Marks the ring aromatic if all atoms and all bonds are aromatic.
    markAromaticRings(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator
    Iterates over the rings in the ring set, and marks the ring aromatic if all atoms and all bonds are aromatic.
    MarkedElement - Class in org.openscience.cdk.renderer.elements
    A marked element adds meta-data (id and tags) to a CDK rendering element (or group of elements).
    markNotPlaced(IAtomContainer) - Static method in class org.openscience.cdk.layout.AtomPlacer
    Marks all the atoms in the given AtomContainer as not placed
    markPlaced(IAtomContainer) - Static method in class org.openscience.cdk.layout.AtomPlacer
    Marks all the atoms in the given AtomContainer as placed
    markPlaced(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
    Mark all atoms in chain as placed.
    markRingAtomsAndBonds(IAtomContainer) - Static method in class org.openscience.cdk.graph.Cycles
    Find and mark all cyclic atoms and bonds in the provided molecule.
    markRingAtomsAndBonds(IAtomContainer, int[][], GraphUtil.EdgeToBondMap) - Static method in class org.openscience.cdk.graph.Cycles
    Find and mark all cyclic atoms and bonds in the provided molecule.
    markup(IRenderingElement, String...) - Static method in class org.openscience.cdk.renderer.elements.MarkedElement
    Markup a rendering element with the specified classes.
    markupAtom(IRenderingElement, IAtom) - Static method in class org.openscience.cdk.renderer.elements.MarkedElement
    Markup a atom with the class 'atom' and optionally the ids/classes from it's properties.
    markupBond(IRenderingElement, IBond) - Static method in class org.openscience.cdk.renderer.elements.MarkedElement
    Markup a bond with the class 'bond' and optionally the ids/classes from it's properties.
    markupMol(IRenderingElement, IAtomContainer) - Static method in class org.openscience.cdk.renderer.elements.MarkedElement
    Markup a molecule with the class 'mol' and optionally the ids/classes from it's properties.
    markWithError(IChemObject) - Static method in class org.openscience.cdk.validate.ProblemMarker
     
    markWithWarning(IChemObject) - Static method in class org.openscience.cdk.validate.ProblemMarker
     
    MASS_ELECTRON - Static variable in class org.openscience.cdk.PhysicalConstants
    Mass of an electron.
    MASS_PROTON - Static variable in class org.openscience.cdk.PhysicalConstants
    Mass of a proton.
    MassAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
    This class matches an atom based on the atomic mass.
    MassAtom(int, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.MassAtom
    Creates a new instance
    MassToFormulaTool - Class in org.openscience.cdk.formula
    Deprecated.
    Please use MolecularFormulaGenerator
    MassToFormulaTool(IChemObjectBuilder) - Constructor for class org.openscience.cdk.formula.MassToFormulaTool
    Deprecated.
    Construct an instance of MassToFormulaTool.
    match(int, int) - Method in class org.openscience.cdk.graph.Matching
    Add the edge '{u,v}' to the matched edge set.
    match(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.Pattern
    Find a matching of this pattern in the target.
    match(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.Ullmann
     
    match(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.VentoFoggia
    Find a matching of this pattern in the target.
    match(IAtomContainer) - Method in class org.openscience.cdk.smiles.smarts.SmartsPattern
    Find a matching of this pattern in the target.
    Match - Class in org.openscience.cdk.smsd.algorithm.vflib.map
    Deprecated.
    SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    Match(INode, IAtom) - Constructor for class org.openscience.cdk.smsd.algorithm.vflib.map.Match
    Deprecated.
    Constructor
    matchAll(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.Pattern
    Find all mappings of this pattern in the target.
    matchAll(IReaction) - Method in class org.openscience.cdk.isomorphism.Pattern
    Find all mappings of this pattern in the target reaction.
    matchAll(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.Ullmann
     
    matchAll(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.VentoFoggia
    Find all mappings of this pattern in the target.
    matchAll(IAtomContainer) - Method in class org.openscience.cdk.smiles.smarts.SmartsPattern
    Obtain the mappings of the query pattern against the target compound.
    matched(int) - Method in class org.openscience.cdk.graph.Matching
    Determine if a vertex has a match.
    matched() - Method in class org.openscience.cdk.io.formats.IChemFormatMatcher.MatchResult
    Did the chem format match.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.ABINITFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.Aces2Format
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.ADFFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.CACheFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.CDKOWLFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.CIFFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.CMLFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.CrystClustFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.CTXFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.DaltonFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.GamessFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.Gaussian03Format
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.Gaussian90Format
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.Gaussian92Format
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.Gaussian94Format
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.Gaussian95Format
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.Gaussian98Format
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.HINFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(List<String>) - Method in interface org.openscience.cdk.io.formats.IChemFormatMatcher
    Method that checks whether the given lines are part of the format read by this reader.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.INChIFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.JaguarFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.MDLFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.MDLRXNFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(List<String>) - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format
    Method that checks whether the given lines are part of the format read by this reader.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.MDLV2000Format
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.MDLV3000Format
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.Mol2Format
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.MOPAC2002Format
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.MOPAC2007Format
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.MOPAC2009Format
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.MOPAC2012Format
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.MOPAC7Format
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.MOPAC93Format
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.MOPAC97Format
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.NWChemFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.PDBFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.PMPFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.PubChemASNFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(List<String>) - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
    Method that checks whether the given lines are part of the format read by this reader.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(List<String>) - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
    Method that checks whether the given lines are part of the format read by this reader.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.QChemFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.SDFFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.ShelXFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.SpartanFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.VASPFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(int, String) - Method in class org.openscience.cdk.io.formats.ZMatrixFormat
    Check whether a given line at a specified position (line number) could belong to this format.
    matches(IAtom, IAtom) - Method in class org.openscience.cdk.isomorphism.AtomMatcher
    Are the semantics of atom1 compatible with atom2.
    matches(IBond, IBond) - Method in class org.openscience.cdk.isomorphism.BondMatcher
    Determines if bond1 is compatible with bond2.
    matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.CTFileQueryBond
     
    matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom
    The matches implementation of the QueryAtom interface.
    matches(IAtom) - Method in interface org.openscience.cdk.isomorphism.matchers.IQueryAtom
    Returns true of the given atom matches this IQueryAtom.
    matches(IBond) - Method in interface org.openscience.cdk.isomorphism.matchers.IQueryBond
    Returns true of the given bond matches this IQueryBond.
    matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.OrderQueryBond
     
    matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.OrderQueryBondOrderOnly
     
    matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
     
    matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AliphaticAtom
     
    matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AliphaticSymbolAtom
     
    matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AnyAtom
     
    matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AnyOrderQueryBond
     
    matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AromaticAtom
     
    matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AromaticOrSingleQueryBond
     
    matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AromaticQueryBond
     
    matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AromaticSymbolAtom
     
    matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AtomicNumberAtom
     
    matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom
     
    matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ExplicitConnectionAtom
    Returns true of the given atom matches this IQueryAtom.
    matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.FormalChargeAtom
     
    matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.HybridizationNumberAtom
     
    matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.HydrogenAtom
     
    matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ImplicitHCountAtom
     
    matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom
     
    matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond
     
    matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.MassAtom
     
    matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.NonCHHeavyAtom
     
    matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.OrderQueryBond
     
    matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.PeriodicGroupNumberAtom
     
    matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ReactionRoleQueryAtom
     
    matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RecursiveSmartsAtom
     
    matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RingBond
     
    matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RingIdentifierAtom
     
    matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RingMembershipAtom
    Returns true of the given atom matches this IQueryAtom.
    matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.SmallestRingAtom
    Returns true of the given atom matches this IQueryAtom.
    matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom
     
    matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.SMARTSBond
     
    matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.StereoBond
     
    matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.TotalConnectionAtom
    Returns true of the given atom matches this IQueryAtom.
    matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.TotalHCountAtom
    Check if the total hydrogen count of the atom is equal to the query.
    matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.TotalRingConnectionAtom
    Returns true of the given atom matches this IQueryAtom.
    matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.TotalValencyAtom
    Returns true of the given atom matches this IQueryAtom.
    matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolAndChargeQueryAtom
     
    matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolChargeIDQueryAtom
     
    matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom
     
    matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom
    The matches implementation of the QueryAtom interface.
    matches(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.Pattern
    Determine if there is a mapping of this pattern in the target.
    matches(IReaction) - Method in class org.openscience.cdk.isomorphism.Pattern
    Determine if there is a mapping of this pattern in the target reaction.
    matches(IAtomContainer) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher
    Performs the pharmacophore matching.
    matches(IAtomContainer, boolean) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher
    Performs the pharmacophore matching.
    matches(IBond) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryAngleBond
    Checks whether the query angle constraint matches a target distance.
    matches(IAtom) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryAtom
    Checks whether this query atom matches a target atom.
    matches(IBond) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryBond
    Checks whether the query distance constraint matches a target distance.
    matches(IAtomContainer) - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool
    Perform a SMARTS match and check whether the query is present in the target molecule.
    matches(IAtomContainer, boolean) - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool
    Perform a SMARTS match and check whether the query is present in the target molecule.
    matches(IAtomContainer, IAtom) - Method in interface org.openscience.cdk.smsd.algorithm.matchers.AtomMatcher
    Deprecated.
     
    matches(IAtomContainer, IBond) - Method in interface org.openscience.cdk.smsd.algorithm.matchers.BondMatcher
    Deprecated.
     
    matches(IAtomContainer, IBond) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultBondMatcher
    Deprecated.
    matches(IAtomContainer, IAtom) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultMCSPlusAtomMatcher
    Deprecated.
    matches(IAtomContainer, IAtom) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultRGraphAtomMatcher
    Deprecated.
    matches(TargetProperties, IAtom) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFAtomMatcher
    Deprecated.
    matches(TargetProperties, IBond) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFBondMatcher
    Deprecated.
    matches(TargetProperties, IAtom) - Method in interface org.openscience.cdk.smsd.algorithm.matchers.VFAtomMatcher
    Deprecated.
     
    matches(TargetProperties, IBond) - Method in interface org.openscience.cdk.smsd.algorithm.matchers.VFBondMatcher
    Deprecated.
     
    matches(IBond) - Method in class org.openscience.cdk.smsd.helper.BondEnergy
    Deprecated.
     
    Matching - Class in org.openscience.cdk.graph
    A matching is an independent edge set of a graph.
    matchOccurence(int) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
    Matches the 'occurrence' condition with a provided maximum number of RGroup attachments.
    Matrix - Class in org.openscience.cdk.math
    This class contains a matrix.
    Matrix(int, int) - Constructor for class org.openscience.cdk.math.Matrix
    Creates a new Matrix.
    Matrix(double[][]) - Constructor for class org.openscience.cdk.math.Matrix
    Creates a Matrix with content of an array.
    matrix - Variable in class org.openscience.cdk.math.Matrix
    the content of this matrix
    MatrixNotInvertibleException - Exception in org.openscience.cdk.graph.invariant.exception
     
    MatrixNotInvertibleException() - Constructor for exception org.openscience.cdk.graph.invariant.exception.MatrixNotInvertibleException
     
    MAX_AXIS_ANGLE - Static variable in class org.openscience.cdk.stereo.StereoTool
    The maximum angle in radians for two lines to be 'diaxial'.
    MAX_FLAG_INDEX - Static variable in class org.openscience.cdk.CDKConstants
    Maximum flags array index.
    MAX_POINTER_INDEX - Static variable in class org.openscience.cdk.CDKConstants
    Maximum pointers array index.
    maxNextCharInd - Variable in class org.openscience.cdk.iupac.parser.SimpleCharStream
     
    maxNextCharInd - Variable in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
     
    maxSphere - Variable in class org.openscience.cdk.tools.HOSECodeGenerator
    How many spheres are we supposed inspect.
    maxX - Variable in class org.openscience.cdk.renderer.elements.Bounds
    Maximum x/y coordinates.
    maxY - Variable in class org.openscience.cdk.renderer.elements.Bounds
    Maximum x/y coordinates.
    mcb() - Static method in class org.openscience.cdk.graph.Cycles
    Create a cycle finder which will compute the minimum cycle basis (MCB) of a molecule.
    mcb(IAtomContainer) - Static method in class org.openscience.cdk.graph.Cycles
    Find the minimum cycle basis (MCB) of a molecule.
    McGregor - Class in org.openscience.cdk.smsd.algorithm.mcgregor
    Deprecated.
    SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    McGregor(IAtomContainer, IAtomContainer, List<List<Integer>>, boolean) - Constructor for class org.openscience.cdk.smsd.algorithm.mcgregor.McGregor
    Deprecated.
    Constructor for the McGregor algorithm.
    McGregor(IQueryAtomContainer, IAtomContainer, List<List<Integer>>) - Constructor for class org.openscience.cdk.smsd.algorithm.mcgregor.McGregor
    Deprecated.
    Constructor for the McGregor algorithm.
    McGregorChecks - Class in org.openscience.cdk.smsd.algorithm.mcgregor
    Deprecated.
    SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    McGregorChecks() - Constructor for class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
    Deprecated.
     
    McgregorHelper - Class in org.openscience.cdk.smsd.algorithm.mcgregor
    Deprecated.
    SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    McgregorHelper(boolean, int, List<Integer>, int, int, List<Integer>, List<Integer>, List<String>, List<String>, int, int, List<Integer>, List<Integer>, List<String>, List<String>) - Constructor for class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper
    Deprecated.
    Stores the variables
    MCSPlus - Class in org.openscience.cdk.smsd.algorithm.mcsplus
    Deprecated.
    SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    MCSPlus() - Constructor for class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlus
    Deprecated.
    Default constructor added
    MCSPlusHandler - Class in org.openscience.cdk.smsd.algorithm.mcsplus
    Deprecated.
    SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    MCSPlusHandler() - Constructor for class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler
    Deprecated.
    Constructor for the MCS Plus algorithm class
    MD - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    MDEC11 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
     
    MDEC12 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
     
    MDEC13 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
     
    MDEC14 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
     
    MDEC22 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
     
    MDEC23 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
     
    MDEC24 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
     
    MDEC33 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
     
    MDEC34 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
     
    MDEC44 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
     
    MDEDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
    Calculates the Molecular Distance Edge descriptor described in [Liu, S. and Cao, C. and Li, Z. , Approach to Estimation and Prediction for Normal Boiling Point (NBP) of Alkanes Based on a Novel Molecular Distance Edge (MDE) Vector, lambda, Journal of Chemical Information and Computer Sciences, 1998, 38:387-394].
    MDEDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
     
    MDEN11 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
     
    MDEN12 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
     
    MDEN13 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
     
    MDEN22 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
     
    MDEN23 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
     
    MDEN33 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
     
    MDEO11 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
     
    MDEO12 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
     
    MDEO22 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
     
    MDLFormat - Class in org.openscience.cdk.io.formats
    See here.
    MDLFormat() - Constructor for class org.openscience.cdk.io.formats.MDLFormat
     
    MDLMolConvention - Class in org.openscience.cdk.io.cml
    Implementation of the MDLMol Covention for CML.
    MDLMolConvention(IChemFile) - Constructor for class org.openscience.cdk.io.cml.MDLMolConvention
     
    MDLMolConvention(ICMLModule) - Constructor for class org.openscience.cdk.io.cml.MDLMolConvention
     
    MDLReader - Class in org.openscience.cdk.io
    Deprecated.
    This reader is only for molfiles without a version tag, typically the most common molfile now encountered is V2000 and the MDLV2000Reader should be used instead. The V2000 reader can actually read files missing the version tag when in relaxed mode.
    MDLReader() - Constructor for class org.openscience.cdk.io.MDLReader
    Deprecated.
     
    MDLReader(InputStream) - Constructor for class org.openscience.cdk.io.MDLReader
    Deprecated.
    Constructs a new MDLReader that can read Molecule from a given InputStream.
    MDLReader(InputStream, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLReader
    Deprecated.
     
    MDLReader(Reader) - Constructor for class org.openscience.cdk.io.MDLReader
    Deprecated.
    Constructs a new MDLReader that can read Molecule from a given Reader.
    MDLReader(Reader, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLReader
    Deprecated.
     
    MDLRXNFormat - Class in org.openscience.cdk.io.formats
    See here.
    MDLRXNFormat() - Constructor for class org.openscience.cdk.io.formats.MDLRXNFormat
     
    MDLRXNReader - Class in org.openscience.cdk.io
    Reads a molecule from an MDL RXN file [Dalby, A. and Nourse, J. G. and Hounshell, W. D. and Gushurst, A. K. and Grier, D. L. and Leland, B. A. and Laufer, J., Description of Several Chemical Structure File Formats Used by Computer Programs Developed at Molecular Design Limited, Journal of Chemical Information and Computer Sciences, 1992, 32:244-255].
    MDLRXNReader(Reader) - Constructor for class org.openscience.cdk.io.MDLRXNReader
    Constructs a new MDLReader that can read Molecule from a given Reader.
    MDLRXNReader(Reader, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLRXNReader
     
    MDLRXNReader(InputStream) - Constructor for class org.openscience.cdk.io.MDLRXNReader
     
    MDLRXNReader(InputStream, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLRXNReader
     
    MDLRXNReader() - Constructor for class org.openscience.cdk.io.MDLRXNReader
     
    MDLRXNV2000Reader - Class in org.openscience.cdk.io
    Reads a molecule from an MDL RXN file [Dalby, A. and Nourse, J. G. and Hounshell, W. D. and Gushurst, A. K. and Grier, D. L. and Leland, B. A. and Laufer, J., Description of Several Chemical Structure File Formats Used by Computer Programs Developed at Molecular Design Limited, Journal of Chemical Information and Computer Sciences, 1992, 32:244-255].
    MDLRXNV2000Reader(Reader) - Constructor for class org.openscience.cdk.io.MDLRXNV2000Reader
    Constructs a new MDLReader that can read Molecule from a given Reader.
    MDLRXNV2000Reader(Reader, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLRXNV2000Reader
     
    MDLRXNV2000Reader(InputStream) - Constructor for class org.openscience.cdk.io.MDLRXNV2000Reader
     
    MDLRXNV2000Reader(InputStream, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLRXNV2000Reader
     
    MDLRXNV2000Reader() - Constructor for class org.openscience.cdk.io.MDLRXNV2000Reader
     
    MDLRXNV3000Format - Class in org.openscience.cdk.io.formats
    See here.
    MDLRXNV3000Format() - Constructor for class org.openscience.cdk.io.formats.MDLRXNV3000Format
     
    MDLRXNV3000Reader - Class in org.openscience.cdk.io
    Class that implements the new MDL mol format introduced in August 2002.
    MDLRXNV3000Reader(Reader) - Constructor for class org.openscience.cdk.io.MDLRXNV3000Reader
     
    MDLRXNV3000Reader(Reader, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLRXNV3000Reader
     
    MDLRXNV3000Reader(InputStream) - Constructor for class org.openscience.cdk.io.MDLRXNV3000Reader
     
    MDLRXNV3000Reader(InputStream, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLRXNV3000Reader
     
    MDLRXNV3000Reader() - Constructor for class org.openscience.cdk.io.MDLRXNV3000Reader
     
    MDLRXNWriter - Class in org.openscience.cdk.io
    Writes a reaction to a MDL rxn or SDF file.
    MDLRXNWriter(Writer) - Constructor for class org.openscience.cdk.io.MDLRXNWriter
    Constructs a new MDLWriter that can write an array of Molecules to a Writer.
    MDLRXNWriter(OutputStream) - Constructor for class org.openscience.cdk.io.MDLRXNWriter
    Constructs a new MDLWriter that can write an array of Molecules to a given OutputStream.
    MDLRXNWriter() - Constructor for class org.openscience.cdk.io.MDLRXNWriter
     
    MDLV2000Format - Class in org.openscience.cdk.io.formats
     
    MDLV2000Format() - Constructor for class org.openscience.cdk.io.formats.MDLV2000Format
     
    MDLV2000Reader - Class in org.openscience.cdk.io
    Reads content from MDL molfiles and SD files.
    MDLV2000Reader() - Constructor for class org.openscience.cdk.io.MDLV2000Reader
     
    MDLV2000Reader(InputStream) - Constructor for class org.openscience.cdk.io.MDLV2000Reader
    Constructs a new MDLReader that can read Molecule from a given InputStream.
    MDLV2000Reader(InputStream, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLV2000Reader
     
    MDLV2000Reader(Reader) - Constructor for class org.openscience.cdk.io.MDLV2000Reader
    Constructs a new MDLReader that can read Molecule from a given Reader.
    MDLV2000Reader(Reader, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLV2000Reader
     
    MDLV2000Writer - Class in org.openscience.cdk.io
    Writes MDL molfiles, which contains a single molecule (see [Dalby, A. and Nourse, J. G. and Hounshell, W. D. and Gushurst, A. K. and Grier, D. L. and Leland, B. A. and Laufer, J., Description of Several Chemical Structure File Formats Used by Computer Programs Developed at Molecular Design Limited, Journal of Chemical Information and Computer Sciences, 1992, 32:244-255]).
    MDLV2000Writer(Writer) - Constructor for class org.openscience.cdk.io.MDLV2000Writer
    Constructs a new MDLWriter that can write an IAtomContainer to the MDL molfile format.
    MDLV2000Writer(OutputStream) - Constructor for class org.openscience.cdk.io.MDLV2000Writer
    Constructs a new MDLWriter that can write an IAtomContainer to a given OutputStream.
    MDLV2000Writer() - Constructor for class org.openscience.cdk.io.MDLV2000Writer
     
    MDLV2000Writer.SPIN_MULTIPLICITY - Enum in org.openscience.cdk.io
    Enumeration of all valid radical values.
    MDLV3000Format - Class in org.openscience.cdk.io.formats
     
    MDLV3000Format() - Constructor for class org.openscience.cdk.io.formats.MDLV3000Format
     
    MDLV3000Reader - Class in org.openscience.cdk.io
    Class that implements the MDL mol V3000 format.
    MDLV3000Reader(Reader) - Constructor for class org.openscience.cdk.io.MDLV3000Reader
     
    MDLV3000Reader(Reader, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLV3000Reader
     
    MDLV3000Reader(InputStream) - Constructor for class org.openscience.cdk.io.MDLV3000Reader
     
    MDLV3000Reader(InputStream, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLV3000Reader
     
    MDLV3000Reader() - Constructor for class org.openscience.cdk.io.MDLV3000Reader
     
    MDLV3000Writer - Class in org.openscience.cdk.io
    Ctab V3000 format output.
    MDLV3000Writer(Writer) - Constructor for class org.openscience.cdk.io.MDLV3000Writer
    Create a new V3000 writer, output to the provided JDK writer.
    MDLV3000Writer(OutputStream) - Constructor for class org.openscience.cdk.io.MDLV3000Writer
    Create a new V3000 writer, output to the provided JDK output stream.
    MDLV3000Writer() - Constructor for class org.openscience.cdk.io.MDLV3000Writer
    Default empty constructor.
    MDMolecule - Class in org.openscience.cdk.libio.md
     
    MDMolecule() - Constructor for class org.openscience.cdk.libio.md.MDMolecule
     
    MDMolecule(IAtomContainer) - Constructor for class org.openscience.cdk.libio.md.MDMolecule
     
    MDMoleculeConvention - Class in org.openscience.cdk.io.cml
    Implements a Convention for parsing an MDMolecule from CML.
    MDMoleculeConvention(IChemFile) - Constructor for class org.openscience.cdk.io.cml.MDMoleculeConvention
     
    MDMoleculeConvention(ICMLModule) - Constructor for class org.openscience.cdk.io.cml.MDMoleculeConvention
     
    MDMoleculeCustomizer - Class in org.openscience.cdk.libio.cml
    Customize persistence of MDMolecule by adding support for residues and charge groups.
    MDMoleculeCustomizer() - Constructor for class org.openscience.cdk.libio.cml.MDMoleculeCustomizer
     
    mechanism - Variable in class org.openscience.cdk.reaction.ReactionEngine
     
    MECURY - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    MEITMERIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    MEITNERIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    MENDELEVIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    MENDELEVIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    MERCURY - Static variable in enum org.openscience.cdk.config.Elements
     
    merge(ICountFingerprint) - Method in interface org.openscience.cdk.fingerprint.ICountFingerprint
    Merge all from fp into the current fingerprint.
    merge(ICountFingerprint) - Method in class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
     
    METH - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    method1(ICountFingerprint, ICountFingerprint) - Static method in class org.openscience.cdk.similarity.Tanimoto
    Calculates Tanimoto distance for two count fingerprints using method 1.
    method2(ICountFingerprint, ICountFingerprint) - Static method in class org.openscience.cdk.similarity.Tanimoto
    Calculates Tanimoto distance for two count fingerprints using method 2 [J.A. Grant, J.A. Haigh, B.T. Pickup, A. Nicholls and R.A. Sayle, Lingos, Finite State Machines, and Fast Similarity Searching, J. Chem. Inf. Model., 2006, 46:1912-1918, doi:10.1021/ci6002152].
    MG - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    MIN_COLINEAR_NORMAL - Static variable in class org.openscience.cdk.stereo.StereoTool
    The maximum tolerance for the normal calculated during colinearity.
    MinimalPathIterator - Class in org.openscience.cdk.graph
    Iterates over all shortest paths between two vertices in an undirected, unweighted graph.
    MinimalPathIterator(SimpleGraph, Object, Object) - Constructor for class org.openscience.cdk.graph.MinimalPathIterator
    Creates a minimal path iterator for the specified undirected graph.
    MinimumCycleBasis - Class in org.openscience.cdk.graph
    Compute the minimum cycle basis (MCB) of a graph.
    MinimumCycleBasis(int[][]) - Constructor for class org.openscience.cdk.graph.MinimumCycleBasis
    Generate the minimum cycle basis for a graph.
    minX - Variable in class org.openscience.cdk.renderer.elements.Bounds
    Minimum x/y coordinates.
    minY - Variable in class org.openscience.cdk.renderer.elements.Bounds
    Minimum x/y coordinates.
    MM2AtomTypeMatcher - Class in org.openscience.cdk.atomtype
    Deprecated.
    Incomplete and error prone - use at your own risk.
    MM2AtomTypeMatcher() - Constructor for class org.openscience.cdk.atomtype.MM2AtomTypeMatcher
    Deprecated.
    Constructor for the MMFF94AtomTypeMatcher object.
    MM2BasedAtomTypePattern - Class in org.openscience.cdk.modeling.builder3d
    Class stores hose code patterns to identify mm2 force field atom types.
    MM2BasedParameterSetReader - Class in org.openscience.cdk.modeling.builder3d
    AtomType list configurator that uses the ParameterSet originally defined in mm2.prm from tinker.
    MM2BasedParameterSetReader() - Constructor for class org.openscience.cdk.modeling.builder3d.MM2BasedParameterSetReader
    Constructor for the MM2BasedParameterSetReader object.
    MM_TO_POINT - Static variable in class org.openscience.cdk.depict.Depiction
    For converting MM coordinates to PS Point (1/72 inch)
    MMElementRule - Class in org.openscience.cdk.formula.rules
    This class validate if the occurrence of the IElements in the IMolecularFormula, for metabolites, are into a maximal limit according paper: .
    MMElementRule() - Constructor for class org.openscience.cdk.formula.rules.MMElementRule
    Constructor for the MMElementRule object.
    MMElementRule.Database - Enum in org.openscience.cdk.formula.rules
    A enumeration of the possible databases according the rules.
    MMElementRule.RangeMass - Enum in org.openscience.cdk.formula.rules
    A enumeration of the possible mass range according the rules.
    Mmff - Class in org.openscience.cdk.forcefield.mmff
    Facade to access Merck Molecular Force Field (MMFF) functions.
    Mmff() - Constructor for class org.openscience.cdk.forcefield.mmff.Mmff
     
    MMFF94AtomTypeMatcher - Class in org.openscience.cdk.atomtype
    Deprecated.
    use the newer Mmff.assignAtomTypes()
    MMFF94AtomTypeMatcher() - Constructor for class org.openscience.cdk.atomtype.MMFF94AtomTypeMatcher
    Deprecated.
    Constructor for the MMFF94AtomTypeMatcher object.
    MMFF94BasedAtomTypePattern - Class in org.openscience.cdk.modeling.builder3d
    Class stores hose code patterns to identify mm2 force field atom types
    MMFF94BasedParameterSetReader - Class in org.openscience.cdk.modeling.builder3d
    AtomType list configurator that uses the ParameterSet originally defined in mmff94.prm from moe.
    MMFF94BasedParameterSetReader() - Constructor for class org.openscience.cdk.modeling.builder3d.MMFF94BasedParameterSetReader
    Constructor for the MM2BasedParameterSetReader object
    MMFF94ParametersCall - Class in org.openscience.cdk.modeling.builder3d
    Set the right atoms order to get the parameters.
    MMFF94ParametersCall() - Constructor for class org.openscience.cdk.modeling.builder3d.MMFF94ParametersCall
     
    MMFF94PartialCharges - Class in org.openscience.cdk.charges
    The calculation of the MMFF94 partial charges.
    MMFF94PartialCharges() - Constructor for class org.openscience.cdk.charges.MMFF94PartialCharges
    Constructor for the MMFF94PartialCharges object
    MMFF_94_CHARGE - Static variable in class org.openscience.cdk.charges.MMFF94PartialCharges
     
    MMODFormat - Class in org.openscience.cdk.io.formats
    See here.
    MMODFormat() - Constructor for class org.openscience.cdk.io.formats.MMODFormat
     
    MN - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    MO - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    mode - Variable in class org.openscience.cdk.io.DefaultChemObjectReader
     
    mode - Variable in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader
     
    mode - Variable in class org.openscience.cdk.io.random.DefaultRandomAccessChemObjectReader
     
    MODE_EXACT - Static variable in class org.openscience.cdk.smarts.SmartsFragmentExtractor
    Sets the mode of the extractor to produce exact SMARTS.
    MODE_JCOMPOUNDMAPPER - Static variable in class org.openscience.cdk.smarts.SmartsFragmentExtractor
    Sets the mode of the extractor to produce SMARTS similar to JCompoundMapper.
    model2Molecule(Model, IChemObjectBuilder) - Static method in class org.openscience.cdk.libio.jena.Convertor
    Converts a Model into an IAtomContainer using the given IChemObjectBuilder.
    ModelBuilder3D - Class in org.openscience.cdk.modeling.builder3d
    The main class to generate the 3D coordinates of a molecule ModelBuilder3D.
    modelCenter - Variable in class org.openscience.cdk.renderer.AbstractRenderer
    The center point of the model (IAtomContainer, IAtomContainerSet, etc).
    modify(T) - Method in interface org.openscience.cdk.DynamicFactory.CreationModifier
     
    Mol2Format - Class in org.openscience.cdk.io.formats
    See here.
    Mol2Format() - Constructor for class org.openscience.cdk.io.formats.Mol2Format
     
    Mol2Reader - Class in org.openscience.cdk.io
    Reads a molecule from an Mol2 file, such as written by Sybyl.
    Mol2Reader(Reader) - Constructor for class org.openscience.cdk.io.Mol2Reader
    Constructs a new MDLReader that can read Molecule from a given Reader.
    Mol2Reader(InputStream) - Constructor for class org.openscience.cdk.io.Mol2Reader
     
    Mol2Reader() - Constructor for class org.openscience.cdk.io.Mol2Reader
     
    Mol2Writer - Class in org.openscience.cdk.io
    An output Writer that writes molecular data into the Tripos Mol2 format.
    Mol2Writer() - Constructor for class org.openscience.cdk.io.Mol2Writer
     
    Mol2Writer(Writer) - Constructor for class org.openscience.cdk.io.Mol2Writer
    Constructs a new Mol2 writer.
    Mol2Writer(OutputStream) - Constructor for class org.openscience.cdk.io.Mol2Writer
     
    molecular() - Method in class org.openscience.cdk.hash.HashGeneratorMaker
    Given the current configuration create an MoleculeHashGenerator.
    MolecularFormula - Class in org.openscience.cdk.formula
    Class defining a molecular formula object.
    MolecularFormula() - Constructor for class org.openscience.cdk.formula.MolecularFormula
    Constructs an empty MolecularFormula.
    MolecularFormula - Class in org.openscience.cdk.silent
    Class defining a molecular formula object.
    MolecularFormula() - Constructor for class org.openscience.cdk.silent.MolecularFormula
    Constructs an empty MolecularFormula.
    MolecularFormulaChecker - Class in org.openscience.cdk.formula
    Validate a molecular formula given in IMolecularformula object.
    MolecularFormulaChecker(List<IRule>) - Constructor for class org.openscience.cdk.formula.MolecularFormulaChecker
    Construct an instance of MolecularFormulaChecker.
    MolecularFormulaGenerator - Class in org.openscience.cdk.formula
    This class generates molecular formulas within given mass range and elemental composition.
    MolecularFormulaGenerator(IChemObjectBuilder, double, double, MolecularFormulaRange) - Constructor for class org.openscience.cdk.formula.MolecularFormulaGenerator
    Initiate the MolecularFormulaGenerator.
    MolecularFormulaManipulator - Class in org.openscience.cdk.tools.manipulator
    Class with convenience methods that provide methods to manipulate IMolecularFormula's.
    MolecularFormulaManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
     
    MolecularFormulaRange - Class in org.openscience.cdk.formula
    Class defining a expanded molecular formula object.
    MolecularFormulaRange() - Constructor for class org.openscience.cdk.formula.MolecularFormulaRange
    Constructs an empty MolecularFormulaExpand.
    MolecularFormulaRangeManipulator - Class in org.openscience.cdk.tools.manipulator
    Class with convenience methods that provide methods to manipulate MolecularFormulaRange's.
    MolecularFormulaRangeManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.MolecularFormulaRangeManipulator
     
    molecularFormulas() - Method in class org.openscience.cdk.debug.DebugAdductFormula
    Returns an Iterable for looping over all IMolecularFormula in this adduct formula.
    molecularFormulas() - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet
    Returns an Iterable for looping over all IMolecularFormula in this MolecularFormulaSet.
    molecularFormulas() - Method in class org.openscience.cdk.formula.AdductFormula
    Returns an Iterable for looping over all IMolecularFormula in this adduct formula.
    molecularFormulas() - Method in class org.openscience.cdk.formula.MolecularFormulaSet
    Returns an Iterable for looping over all IMolecularFormula in this MolecularFormulaSet.
    molecularFormulas() - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet
    Returns the array of IMolecularFormula of this chemObject.
    molecularFormulas() - Method in class org.openscience.cdk.silent.AdductFormula
    Returns an Iterable for looping over all IMolecularFormula in this adduct formula.
    molecularFormulas() - Method in class org.openscience.cdk.silent.MolecularFormulaSet
    Returns an Iterable for looping over all IMolecularFormula in this MolecularFormulaSet.
    MolecularFormulaSet - Class in org.openscience.cdk.formula
    Class defining an set object of MolecularFormulas.
    MolecularFormulaSet() - Constructor for class org.openscience.cdk.formula.MolecularFormulaSet
    Constructs an empty MolecularFormulaSet.
    MolecularFormulaSet(IMolecularFormula) - Constructor for class org.openscience.cdk.formula.MolecularFormulaSet
    Constructs a MolecularFormulaSet with a copy MolecularFormulaSet of another MolecularFormulaSet (A shallow copy, i.e., with the same objects as in the original MolecularFormulaSet).
    MolecularFormulaSet - Class in org.openscience.cdk.silent
    Class defining an set object of MolecularFormulas.
    MolecularFormulaSet() - Constructor for class org.openscience.cdk.silent.MolecularFormulaSet
    Constructs an empty MolecularFormulaSet.
    MolecularFormulaSet(IMolecularFormula) - Constructor for class org.openscience.cdk.silent.MolecularFormulaSet
    Constructs a MolecularFormulaSet with a copy MolecularFormulaSet of another MolecularFormulaSet (A shallow copy, i.e., with the same objects as in the original MolecularFormulaSet).
    MolecularFormulaSetManipulator - Class in org.openscience.cdk.tools.manipulator
    Class with convenience methods that provide methods to manipulate MolecularFormulaSet's.
    MolecularFormulaSetManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.MolecularFormulaSetManipulator
     
    molecule - Variable in class org.openscience.cdk.inchi.InChIToStructure
     
    MOLECULE - Static variable in class org.openscience.cdk.libio.jena.CDK
     
    molecule2Model(IAtomContainer) - Static method in class org.openscience.cdk.libio.jena.Convertor
    Converts a IAtomContainer into a Model representation using the CDK OWL.
    MoleculeBuilder - Class in org.openscience.cdk.iupac.parser
    Takes in parsed Tokens from NomParser and contains rules to convert those tokens to a Molecule.
    MoleculeBuilder(IChemObjectBuilder) - Constructor for class org.openscience.cdk.iupac.parser.MoleculeBuilder
     
    MoleculeBuilder() - Constructor for class org.openscience.cdk.iupac.parser.MoleculeBuilder
    Instantiates a builder using the DefaultChemObjectBuilder.
    moleculeCustomProperty - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
     
    MoleculeFactory - Class in org.openscience.cdk.templates
    Deprecated.
    Old CDK class primarily for testing, for CDK Tests please use TestMoleculeFactory in cdk-data (testjar).
    MoleculeFactory() - Constructor for class org.openscience.cdk.templates.MoleculeFactory
    Deprecated.
     
    MoleculeFeaturesTool - Class in org.openscience.cdk.tools.features
    Utility that helps determine which data features are present.
    MoleculeFeaturesTool() - Constructor for class org.openscience.cdk.tools.features.MoleculeFeaturesTool
     
    MoleculeFromSignatureBuilder - Class in org.openscience.cdk.signature
    Builds a molecule from a signature.
    MoleculeFromSignatureBuilder(IChemObjectBuilder) - Constructor for class org.openscience.cdk.signature.MoleculeFromSignatureBuilder
    Uses the chem object builder for making molecules.
    MoleculeGraphs - Class in org.openscience.cdk.graph
    Utility class to create a molecule graph for use with JGraphT.
    MoleculeHashGenerator - Interface in org.openscience.cdk.hash
    A hash function which generates a single 64-bit hash code for a molecule.
    MoleculeSanityCheck - Class in org.openscience.cdk.smsd.tools
    Deprecated.
    SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    MoleculeSanityCheck() - Constructor for class org.openscience.cdk.smsd.tools.MoleculeSanityCheck
    Deprecated.
     
    MoleculeSetManipulator - Class in org.openscience.cdk.tools.manipulator
     
    MoleculeSetManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
     
    MoleculeSetRenderer - Class in org.openscience.cdk.renderer
    A general renderer for IChemModels, IReactions, and IAtomContainers.
    MoleculeSetRenderer(List<IGenerator<IAtomContainer>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.MoleculeSetRenderer
    A renderer that generates diagrams using the specified generators and manages fonts with the supplied font manager.
    MoleculeSetRenderer(RendererModel, List<IGenerator<IAtomContainer>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.MoleculeSetRenderer
     
    MoleculeSignature - Class in org.openscience.cdk.signature
    A molecule signature is a way to produce AtomSignatures and to get the canonical [Faulon, J. L., Collins, M. J., and Carr, R. D., The Signature Molecular Descriptor. 4. Canonizing Molecules Using Extended Valence Sequences, Journal of Chemical Information and Computer Sciences, 2004, 44:427-436] signature string for a molecule.
    MoleculeSignature(IAtomContainer) - Constructor for class org.openscience.cdk.signature.MoleculeSignature
    Creates a signature that represents this molecule.
    MoleculeSignature(IAtomContainer, int) - Constructor for class org.openscience.cdk.signature.MoleculeSignature
    Creates a signature with a maximum height of height for molecule molecule.
    MoleculeSignatureLabellingAdaptor - Class in org.openscience.cdk.smsd.labelling
    Deprecated.
    This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    MoleculeSignatureLabellingAdaptor() - Constructor for class org.openscience.cdk.smsd.labelling.MoleculeSignatureLabellingAdaptor
    Deprecated.
     
    MolHandler - Class in org.openscience.cdk.smsd.tools
    Deprecated.
    A more recent version of SMSD is available at http://github.com/asad/smsd
    MolHandler(String, boolean, boolean) - Constructor for class org.openscience.cdk.smsd.tools.MolHandler
    Deprecated.
    Creates a new instance of MolHandler
    MolHandler(IAtomContainer, boolean, boolean) - Constructor for class org.openscience.cdk.smsd.tools.MolHandler
    Deprecated.
    Creates a new instance of MolHandler
    MOLYBDENUM - Static variable in enum org.openscience.cdk.config.Elements
     
    MOLYBDENUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    MomentOfInertiaDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
    A descriptor that calculates the moment of inertia and radius of gyration.
    MomentOfInertiaDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor
     
    Monomer - Class in org.openscience.cdk
    A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.
    Monomer() - Constructor for class org.openscience.cdk.Monomer
    Constructs a new Monomer.
    Monomer - Class in org.openscience.cdk.silent
    A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.
    Monomer() - Constructor for class org.openscience.cdk.silent.Monomer
    Constructs a new Monomer.
    MOPAC2002Format - Class in org.openscience.cdk.io.formats
     
    MOPAC2002Format() - Constructor for class org.openscience.cdk.io.formats.MOPAC2002Format
     
    MOPAC2007Format - Class in org.openscience.cdk.io.formats
     
    MOPAC2007Format() - Constructor for class org.openscience.cdk.io.formats.MOPAC2007Format
     
    MOPAC2009Format - Class in org.openscience.cdk.io.formats
     
    MOPAC2009Format() - Constructor for class org.openscience.cdk.io.formats.MOPAC2009Format
     
    MOPAC2012Format - Class in org.openscience.cdk.io.formats
     
    MOPAC2012Format() - Constructor for class org.openscience.cdk.io.formats.MOPAC2012Format
     
    MOPAC7Format - Class in org.openscience.cdk.io.formats
     
    MOPAC7Format() - Constructor for class org.openscience.cdk.io.formats.MOPAC7Format
     
    MOPAC7InputFormat - Class in org.openscience.cdk.io.formats
     
    MOPAC7InputFormat() - Constructor for class org.openscience.cdk.io.formats.MOPAC7InputFormat
     
    Mopac7Reader - Class in org.openscience.cdk.io
    Reads MOPAC output, extracts several electronic parameters and assigns them as a molecule properties.
    Mopac7Reader(Reader) - Constructor for class org.openscience.cdk.io.Mopac7Reader
    Constructs a new Mopac7reader that can read a molecule from a given Reader.
    Mopac7Reader(InputStream) - Constructor for class org.openscience.cdk.io.Mopac7Reader
    Constructs a new Mopac7reader that can read a molecule from a given InputStream.
    Mopac7Reader() - Constructor for class org.openscience.cdk.io.Mopac7Reader
    Constructs a new Mopac7reader that can read a molecule.
    Mopac7Writer - Class in org.openscience.cdk.io.program
    Prepares input file for running MOPAC.
    Mopac7Writer() - Constructor for class org.openscience.cdk.io.program.Mopac7Writer
    Creates a writer to serialize a molecule as Mopac7 input.
    Mopac7Writer(OutputStream) - Constructor for class org.openscience.cdk.io.program.Mopac7Writer
    Creates a writer to serialize a molecule as Mopac7 input.
    Mopac7Writer(Writer) - Constructor for class org.openscience.cdk.io.program.Mopac7Writer
    Creates a writer to serialize a molecule as Mopac7 input.
    MOPAC93Format - Class in org.openscience.cdk.io.formats
     
    MOPAC93Format() - Constructor for class org.openscience.cdk.io.formats.MOPAC93Format
     
    MOPAC97Format - Class in org.openscience.cdk.io.formats
     
    MOPAC97Format() - Constructor for class org.openscience.cdk.io.formats.MOPAC97Format
     
    MorganNumbersTools - Class in org.openscience.cdk.graph.invariant
    Compute the extended connectivity values (Morgan Numbers) [Morgan, H.L., The Generation of a Unique Machine Description for Chemical Structures - A Technique Developed at Chemical Abstracts Service., J.Chem.Doc., 1965, 5:107-113].
    MorganNumbersTools() - Constructor for class org.openscience.cdk.graph.invariant.MorganNumbersTools
     
    MoSSOutputFormat - Class in org.openscience.cdk.io.formats
     
    MoSSOutputFormat() - Constructor for class org.openscience.cdk.io.formats.MoSSOutputFormat
     
    MoSSOutputReader - Class in org.openscience.cdk.io
    Reader for MoSS output files [Unknown BibTeXML type: BOR2002] which present the results of a substructure mining study.
    MoSSOutputReader(Reader) - Constructor for class org.openscience.cdk.io.MoSSOutputReader
    Create a reader for MoSS output files from a Reader.
    MoSSOutputReader(InputStream) - Constructor for class org.openscience.cdk.io.MoSSOutputReader
    Create a reader for MoSS output files from an InputStream.
    MoSSOutputReader() - Constructor for class org.openscience.cdk.io.MoSSOutputReader
    Create a reader for MoSS output files from an empty string.
    mouseClicked(MouseEvent) - Method in class org.openscience.cdk.controller.SwingMouseEventRelay
     
    mouseClickedDouble(int, int) - Method in interface org.openscience.cdk.controller.IMouseEventRelay
    Event to signal that a mouse button has been double clicked.
    mouseClickedDown(int, int) - Method in interface org.openscience.cdk.controller.IMouseEventRelay
    Event to signal that the left mouse button has been pushed but not released yet.
    mouseClickedDownRight(int, int) - Method in interface org.openscience.cdk.controller.IMouseEventRelay
    Event to signal that the right mouse button has been pushed but not released yet.
    mouseClickedUp(int, int) - Method in interface org.openscience.cdk.controller.IMouseEventRelay
    Event to signal that the left mouse button has been released.
    mouseClickedUpRight(int, int) - Method in interface org.openscience.cdk.controller.IMouseEventRelay
    Event to signal that the right mouse button has been released.
    mouseDrag(int, int, int, int) - Method in interface org.openscience.cdk.controller.IMouseEventRelay
    Event to signal that a mouse has been dragged from one point to a next.
    mouseDragged(MouseEvent) - Method in class org.openscience.cdk.controller.SwingMouseEventRelay
     
    mouseEnter(int, int) - Method in interface org.openscience.cdk.controller.IMouseEventRelay
     
    mouseEntered(MouseEvent) - Method in class org.openscience.cdk.controller.SwingMouseEventRelay
     
    mouseExit(int, int) - Method in interface org.openscience.cdk.controller.IMouseEventRelay
     
    mouseExited(MouseEvent) - Method in class org.openscience.cdk.controller.SwingMouseEventRelay
     
    mouseMove(int, int) - Method in interface org.openscience.cdk.controller.IMouseEventRelay
    Event to signal that a mouse has been moved to the new coordinates.
    mouseMoved(MouseEvent) - Method in class org.openscience.cdk.controller.SwingMouseEventRelay
     
    mousePressed(MouseEvent) - Method in class org.openscience.cdk.controller.SwingMouseEventRelay
     
    mouseReleased(MouseEvent) - Method in class org.openscience.cdk.controller.SwingMouseEventRelay
     
    mouseWheelMovedBackward(int) - Method in interface org.openscience.cdk.controller.IMouseEventRelay
    Event to signal that the mouse wheel has been rotated a certain amount backward.
    mouseWheelMovedForward(int) - Method in interface org.openscience.cdk.controller.IMouseEventRelay
    Event to signal that the mouse wheel has been rotated a certain amount forward.
    MoveTo - Class in org.openscience.cdk.renderer.elements.path
    A MoveTo path element moves the drawing 'pen' without making any lines or curves and is commonly used to start a path or make gaps in the path.
    MoveTo(Point2d) - Constructor for class org.openscience.cdk.renderer.elements.path.MoveTo
    Make a move to path element.
    MoveTo(double[]) - Constructor for class org.openscience.cdk.renderer.elements.path.MoveTo
    Make a move to path element.
    MoveTo(double, double) - Constructor for class org.openscience.cdk.renderer.elements.path.MoveTo
    Make a move to path element.
    moveTo(Point2d) - Method in class org.openscience.cdk.renderer.elements.path.PathBuilder
    Make a move in the path, without drawing anything.
    MPQCFormat - Class in org.openscience.cdk.io.formats
    See here.
    MPQCFormat() - Constructor for class org.openscience.cdk.io.formats.MPQCFormat
     
    mul(Complex) - Method in class org.openscience.cdk.math.Complex
    Multiply this value with a complex value
    mul(IMatrix) - Method in class org.openscience.cdk.math.IMatrix
    Multiplikation from two matrices
    mul(IMatrix, IMatrix) - Method in class org.openscience.cdk.math.IMatrix
    Multiplikation from two matrices
    mul(IVector) - Method in class org.openscience.cdk.math.IMatrix
    Multiplikation from a vector and a matrix
    mul(IVector, IVector) - Method in class org.openscience.cdk.math.IMatrix
    Multiplikation from a vector and a matrix
    mul(Complex) - Method in class org.openscience.cdk.math.IMatrix
    Multiplikation from a scalar and a matrix
    mul(Complex, IMatrix) - Method in class org.openscience.cdk.math.IMatrix
    Multiplikation from a scalar and a matrix
    mul(double) - Method in class org.openscience.cdk.math.IVector
    Multiplication from a vectors with an double
    mul(double, IVector) - Method in class org.openscience.cdk.math.IVector
    Multiplication from a vectors with an double
    mul(Matrix) - Method in class org.openscience.cdk.math.Matrix
    Multiplies this Matrix with another one.
    mul(Vector) - Method in class org.openscience.cdk.math.Matrix
    Multiplies a Vector with this Matrix.
    mul(double) - Method in class org.openscience.cdk.math.Matrix
    Multiplies a scalar with this Matrix.
    mul(Quaternion) - Method in class org.openscience.cdk.math.Quaternion
     
    mul(double) - Method in class org.openscience.cdk.math.Quaternion
     
    mul(double) - Method in class org.openscience.cdk.math.Vector
    Multiplikation from a vectors with an double
    multipliers - Variable in class org.openscience.cdk.AtomContainerSet
    Defines the number of instances of a certain molecule in the set.
    multipliers - Variable in class org.openscience.cdk.silent.AtomContainerSet
    Defines the number of instances of a certain molecule in the set.
    multiply(double) - Method in class org.openscience.cdk.graph.invariant.GIMatrix
    Returns the result of the scalar multiplication of the matrix, that is the multiplication of every of its elements by a given number.
    multiply(GIMatrix) - Method in class org.openscience.cdk.graph.invariant.GIMatrix
    Returns the result of the matrix multiplication of this matrix by another one.
    multiply(Permutation) - Method in class org.openscience.cdk.group.Permutation
    Multiply this permutation by another such that for all i, this[i] = this[other[i]].
    multiplyLine(int, double) - Method in class org.openscience.cdk.graph.invariant.GIMatrix
    Returns the resulting matrix of an elementary linear operation that consists of multiplying a single line of the matrix by a constant.
    MurckoFragmenter - Class in org.openscience.cdk.fragment
    An implementation of the Murcko fragmenation method [Bemis, G.W. and Murcko, M.A. , The properties of known drugs. 1. Molecular Frameworks , Journal of Medicinal Chemistry, 1996, 39:2887-2893].
    MurckoFragmenter() - Constructor for class org.openscience.cdk.fragment.MurckoFragmenter
    Instantiate Murcko fragmenter.
    MurckoFragmenter(boolean, int) - Constructor for class org.openscience.cdk.fragment.MurckoFragmenter
    Instantiate Murcko fragmenter.
    MurckoFragmenter(boolean, int, MoleculeHashGenerator) - Constructor for class org.openscience.cdk.fragment.MurckoFragmenter
    Instantiate Murcko fragmenter.
    mutate(IAtomContainer) - Method in class org.openscience.cdk.structgen.RandomGenerator
    Randomly chooses four atoms and alters the bonding pattern between them according to rules described in "Faulon, JCICS 1996, 36, 731".

    N

    n() - Method in class org.openscience.cdk.DynamicFactory.ConstructorKey
    Access the number of parameters in the constructor.
    n - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    N - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    NA - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    name - Variable in class org.openscience.cdk.io.setting.IOSetting
     
    NAMES - Static variable in class org.openscience.cdk.CDKConstants
    A List of names.
    naturalAbundance - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom
    Natural abundance of this isotope.
    naturalAbundance - Variable in class org.openscience.cdk.Isotope
    Natural abundance of this isotope.
    naturalAbundance - Variable in class org.openscience.cdk.silent.Isotope
    Natural abundance of this isotope.
    NB - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    nComponents() - Method in class org.openscience.cdk.graph.ConnectedComponents
     
    ND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    NE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    negate() - Method in class org.openscience.cdk.math.Quaternion
     
    negate() - Method in class org.openscience.cdk.math.Vector
    Negates this vector
    NeighborList - Class in org.openscience.cdk.geometry.surface
    Creates a list of atoms neighboring each atom in the molecule.
    NeighborList(IAtom[], double) - Constructor for class org.openscience.cdk.geometry.surface.NeighborList
     
    neighbors() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.NodeBuilder
    Deprecated.
    Returns neighbors.
    neighbors() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.INode
    Deprecated.
    Returns neighbors.
    neighboursInBlock(Set<Integer>, int) - Method in interface org.openscience.cdk.group.Refinable
    Given a block (or cell) of a partition, determine the invariant that represents the intersection between the block and the neighbours of vertexIndex supplied.
    NEODYMIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    NEODYMIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    NEON - Static variable in enum org.openscience.cdk.config.Elements
     
    NEPTUNIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    NEPTUNIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    newAtom() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder
    Create a new atom using the default constructor.
    newAtom() - Method in class org.openscience.cdk.DefaultChemObjectBuilder
    Create a new atom using the default constructor.
    newAtom() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder
    Create a new atom using the default constructor.
    newAtom() - Method in class org.openscience.cdk.silent.SilentChemObjectBuilder
    Create a new atom using the default constructor.
    newAtomContainer() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder
    Create a new atom container using the default constructor.
    newAtomContainer() - Method in class org.openscience.cdk.DefaultChemObjectBuilder
    Create a new atom container using the default constructor.
    newAtomContainer() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder
    Create a new atom container using the default constructor.
    newAtomContainer() - Method in class org.openscience.cdk.silent.SilentChemObjectBuilder
    Create a new atom container using the default constructor.
    newAtomData() - Method in class org.openscience.cdk.io.cml.CMLCoreModule
    Clean all data about read atoms.
    newBond() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder
    Create a new bond using the default constructor.
    newBond() - Method in class org.openscience.cdk.DefaultChemObjectBuilder
    Create a new bond using the default constructor.
    newBond() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder
    Create a new bond using the default constructor.
    newBond() - Method in class org.openscience.cdk.silent.SilentChemObjectBuilder
    Create a new bond using the default constructor.
    newBondData() - Method in class org.openscience.cdk.io.cml.CMLCoreModule
    Clean all data about read bonds.
    newChemModel(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
    Create a new ChemModel containing an IAtomContainer.
    newCrystalData() - Method in class org.openscience.cdk.io.cml.CMLCoreModule
    Clean all data about read bonds.
    newFormulaData() - Method in class org.openscience.cdk.io.cml.CMLCoreModule
    Clean all data about read formulas.
    newInstance(Class<T>, Object...) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder
    Creates a new instance of an ICDKObject, using the constructor defined by the given parameters.
    newInstance(Class<T>, Object...) - Method in class org.openscience.cdk.DefaultChemObjectBuilder
    Creates a new instance of an ICDKObject, using the constructor defined by the given parameters.
    newInstance(Class<T>, Object...) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder
    Creates a new instance of an ICDKObject, using the constructor defined by the given parameters.
    newInstance(Class<T>, Object...) - Method in class org.openscience.cdk.silent.SilentChemObjectBuilder
    Creates a new instance of an ICDKObject, using the constructor defined by the given parameters.
    newMolecule() - Method in class org.openscience.cdk.io.cml.CMLCoreModule
    Clean all data about parsed data.
    newMoleculeData() - Method in class org.openscience.cdk.io.cml.CMLCoreModule
    Clean all data about the molecule itself.
    newSaturate(IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker
    Saturates a molecule by setting appropriate bond orders.
    newSaturate(IBond[], IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker
    Saturates a set of Bonds in an AtomContainer.
    newSaturate(IBond, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker
    Saturate atom by adjusting its bond orders.
    newSequence() - Method in class org.openscience.cdk.io.cml.PDBConvention
     
    newToken(int, String) - Static method in class org.openscience.cdk.iupac.parser.Token
    Returns a new Token object, by default.
    newToken(int) - Static method in class org.openscience.cdk.iupac.parser.Token
     
    newToken(int, String) - Static method in class org.openscience.cdk.smiles.smarts.parser.Token
    Returns a new Token object, by default.
    newToken(int) - Static method in class org.openscience.cdk.smiles.smarts.parser.Token
     
    next() - Method in class org.openscience.cdk.graph.AtomContainerPermutor
     
    next() - Method in class org.openscience.cdk.graph.MinimalPathIterator
     
    next() - Method in class org.openscience.cdk.io.iterator.IteratingMDLConformerReader
     
    next() - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundASNReader
     
    next() - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader
     
    next() - Method in class org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader
     
    next() - Method in class org.openscience.cdk.io.iterator.IteratingSDFReader
    Returns the next IAtomContainer.
    next() - Method in class org.openscience.cdk.io.iterator.IteratingSMILESReader
    Get the next molecule from the stream.
    next() - Method in class org.openscience.cdk.io.random.RandomAccessReader
     
    next - Variable in class org.openscience.cdk.iupac.parser.Token
    A reference to the next regular (non-special) token from the input stream.
    next - Variable in class org.openscience.cdk.smiles.smarts.parser.Token
    A reference to the next regular (non-special) token from the input stream.
    next() - Method in class org.openscience.cdk.smsd.labelling.AtomContainerAtomPermutor
    Deprecated.
    nextCandidate() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IState
    Deprecated.
    Returns the next candidate match.
    nextCandidate() - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFState
    Deprecated.
    Returns the next candidate match.
    nextElement() - Method in class org.openscience.cdk.formula.rules.RDBERule.Combinations
     
    nextIndex() - Method in class org.openscience.cdk.io.random.RandomAccessReader
     
    nextSphereNodes - Variable in class org.openscience.cdk.tools.HOSECodeGenerator
    Container for the node in the next sphere Assembled in a recursive method and then passed to the next recursion to become "sphereNodes".
    nextState(Match) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IState
    Deprecated.
    Returns a state in which the atoms in match have been added to the current mapping.
    nextState(Match) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFState
    Deprecated.
    Returns a state in which the atoms in match have been added to the current mapping.
    nextVASPToken(boolean) - Method in class org.openscience.cdk.io.VASPReader
    Find the next token of an VASP file.
    nextVASPTokenFollowing(String) - Method in class org.openscience.cdk.io.VASPReader
    Find the next token of a VASP file beginning with the *next* line.
    NI - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    NICKEL - Static variable in enum org.openscience.cdk.config.Elements
     
    NICKEL - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    NIOBIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    NIOBIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    NITRILE - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    NITRO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    NITROGEN - Static variable in enum org.openscience.cdk.config.Elements
     
    NitrogenRule - Class in org.openscience.cdk.formula.rules
    This class validate if the rule of nitrogen is kept.
    NitrogenRule() - Constructor for class org.openscience.cdk.formula.rules.NitrogenRule
    Constructor for the NitrogenRule object.
    NMRSHIFT_CARBON - Static variable in class org.openscience.cdk.CDKConstants
    Carbon NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.
    NMRSHIFT_DEUTERIUM - Static variable in class org.openscience.cdk.CDKConstants
    Deuterium NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.
    NMRSHIFT_FLUORINE - Static variable in class org.openscience.cdk.CDKConstants
    Fluorine NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.
    NMRSHIFT_HYDROGEN - Static variable in class org.openscience.cdk.CDKConstants
    Hydrogen NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.
    NMRSHIFT_NITROGEN - Static variable in class org.openscience.cdk.CDKConstants
    Nitrogen NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.
    NMRSHIFT_PHOSPORUS - Static variable in class org.openscience.cdk.CDKConstants
    Phosphorus NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.
    NO - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    NO_ATOMS - Static variable in class org.openscience.cdk.templates.AminoAcids
     
    NO_BONDS - Static variable in class org.openscience.cdk.templates.AminoAcids
     
    NO_MATCH - Static variable in interface org.openscience.cdk.io.formats.IChemFormatMatcher
    Convenience method for indicating a format did not match.
    NOBELIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    NOBELIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    Node - Interface in org.openscience.cdk.smiles.smarts.parser
    All AST nodes must implement this interface.
    nodeArity() - Method in class org.openscience.cdk.smiles.smarts.parser.JJTSMARTSParserState
     
    NodeBuilder - Class in org.openscience.cdk.smsd.algorithm.vflib.builder
    Deprecated.
    SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    NodeBuilder(VFAtomMatcher) - Constructor for class org.openscience.cdk.smsd.algorithm.vflib.builder.NodeBuilder
    Deprecated.
    Construct a node for a query atom
    nodeCreated() - Method in class org.openscience.cdk.smiles.smarts.parser.JJTSMARTSParserState
     
    nodes() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder
    Deprecated.
    Returns nodes of the query.
    nodes() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQuery
    Deprecated.
    Returns nodes of the query.
    NoHydrogenElement() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
     
    NomParser - Class in org.openscience.cdk.iupac.parser
    Deprecated.
    The OPSIN (http://opsin.ch.cam.ac.uk/) tool offers a more comprehensive alternative to this parsers functionality.
    NomParser(InputStream) - Constructor for class org.openscience.cdk.iupac.parser.NomParser
    Deprecated.
    Constructor with InputStream.
    NomParser(InputStream, String) - Constructor for class org.openscience.cdk.iupac.parser.NomParser
    Deprecated.
    Constructor with InputStream and supplied encoding
    NomParser(Reader) - Constructor for class org.openscience.cdk.iupac.parser.NomParser
    Deprecated.
    Constructor.
    NomParser(NomParserTokenManager) - Constructor for class org.openscience.cdk.iupac.parser.NomParser
    Deprecated.
    Constructor with generated Token Manager.
    NomParserConstants - Interface in org.openscience.cdk.iupac.parser
    Token literal values and constants.
    NomParserTokenManager - Class in org.openscience.cdk.iupac.parser
    Token Manager.
    NomParserTokenManager(SimpleCharStream) - Constructor for class org.openscience.cdk.iupac.parser.NomParserTokenManager
    Constructor.
    NomParserTokenManager(SimpleCharStream, int) - Constructor for class org.openscience.cdk.iupac.parser.NomParserTokenManager
    Constructor.
    NON - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    NonCHHeavyAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
    This matcher any heavy atom that is not C or H.
    NonCHHeavyAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.NonCHHeavyAtom
    Creates a new instance
    NonCHHeavyAtom() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
     
    NONE - Static variable in class org.openscience.cdk.tools.DataFeatures
    Indicated that no feature are defined.
    NORMAL - Static variable in class org.openscience.cdk.renderer.GraphRendererModel
    Paints the function normal
    normalize(IsotopePattern) - Static method in class org.openscience.cdk.formula.IsotopePatternManipulator
    Return the isotope pattern normalized to the highest abundance.
    normalize(Point3d) - Static method in class org.openscience.cdk.geometry.GeometryTools
    Normalizes a point.
    normalize(Point3d) - Static method in class org.openscience.cdk.geometry.GeometryUtil
    Normalizes a point.
    normalize(Matrix) - Method in class org.openscience.cdk.math.Matrix
    Normalizes the vectors of this matrix.
    normalize() - Method in class org.openscience.cdk.math.Quaternion
     
    normalize() - Method in class org.openscience.cdk.math.Vector
    Normalize this vector
    normalize(IAtomContainer, Document) - Static method in class org.openscience.cdk.normalize.Normalizer
    Deprecated.
    The method takes an XML files like the following:
    <replace-set>
    <replace>O=N=O</replace>
    <replacement>[O-][N+]=O</replacement>
    </replace-set>
    All parts in ac which are the same as replace will be changed according to replacement.
    Normalizer - Class in org.openscience.cdk.normalize
    Deprecated.
    The functionality provided by with class is better suited to SMIRKS
    Normalizer() - Constructor for class org.openscience.cdk.normalize.Normalizer
    Deprecated.
     
    NoSuchAtomException - Exception in org.openscience.cdk.exception
    Exception that is thrown when an Atom is requested or required that does not exist in the relevant environment.
    NoSuchAtomException(String) - Constructor for exception org.openscience.cdk.exception.NoSuchAtomException
    Constructs a new NoSuchAtomException with the given message.
    NoSuchAtomTypeException - Exception in org.openscience.cdk.exception
    Exception that may be thrown when an atom type is looked up or perceived but no such atom type was found.
    NoSuchAtomTypeException(String) - Constructor for exception org.openscience.cdk.exception.NoSuchAtomTypeException
    Constructs a new NoSuchAtomTypeException.
    not(IQueryAtom) - Static method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom
    Negate the provided expression.
    NOT - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    NotBond() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
     
    NotExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
     
    notify(String, String, int, int) - Method in class org.openscience.cdk.io.cml.CMLCoreModule
     
    notifyChanged() - Method in class org.openscience.cdk.ChemObject
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.ChemObject
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged() - Method in class org.openscience.cdk.debug.DebugAminoAcid
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugAminoAcid
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged() - Method in class org.openscience.cdk.debug.DebugAtom
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugAtom
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged() - Method in class org.openscience.cdk.debug.DebugAtomContainer
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugAtomContainer
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged() - Method in class org.openscience.cdk.debug.DebugAtomType
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugAtomType
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged() - Method in class org.openscience.cdk.debug.DebugBioPolymer
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugBioPolymer
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged() - Method in class org.openscience.cdk.debug.DebugBond
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugBond
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged() - Method in class org.openscience.cdk.debug.DebugChemFile
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugChemFile
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged() - Method in class org.openscience.cdk.debug.DebugChemModel
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugChemModel
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged() - Method in class org.openscience.cdk.debug.DebugChemObject
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugChemObject
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged() - Method in class org.openscience.cdk.debug.DebugChemSequence
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugChemSequence
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged() - Method in class org.openscience.cdk.debug.DebugCrystal
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugCrystal
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged() - Method in class org.openscience.cdk.debug.DebugElectronContainer
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugElectronContainer
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged() - Method in class org.openscience.cdk.debug.DebugElement
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugElement
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged() - Method in class org.openscience.cdk.debug.DebugIsotope
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugIsotope
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged() - Method in class org.openscience.cdk.debug.DebugLonePair
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugLonePair
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged() - Method in class org.openscience.cdk.debug.DebugMapping
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugMapping
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged() - Method in class org.openscience.cdk.debug.DebugMonomer
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugMonomer
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged() - Method in class org.openscience.cdk.debug.DebugPolymer
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugPolymer
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged() - Method in class org.openscience.cdk.debug.DebugReaction
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugReaction
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged() - Method in class org.openscience.cdk.debug.DebugReactionScheme
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugReactionScheme
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged() - Method in class org.openscience.cdk.debug.DebugReactionSet
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugReactionSet
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged() - Method in class org.openscience.cdk.debug.DebugRing
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugRing
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged() - Method in class org.openscience.cdk.debug.DebugSingleElectron
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugSingleElectron
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged() - Method in class org.openscience.cdk.debug.DebugStrand
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugStrand
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged() - Method in class org.openscience.cdk.debug.DebugSubstance
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugSubstance
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged() - Method in interface org.openscience.cdk.interfaces.IChemObject
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged(IChemObjectChangeEvent) - Method in interface org.openscience.cdk.interfaces.IChemObject
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged() - Method in class org.openscience.cdk.silent.ChemObject
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.ChemObject
    This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
    notionalToCartesian(double, double, double, double, double, double) - Static method in class org.openscience.cdk.geometry.CrystalGeometryTools
    Calculates Cartesian vectors for unit cell axes from axes lengths and angles between axes.
    NP - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    nPathsTo(int) - Method in class org.openscience.cdk.graph.ShortestPaths
    Access the number of possible paths to the end vertex.
    nPathsTo(IAtom) - Method in class org.openscience.cdk.graph.ShortestPaths
    Access the number of possible paths to the end atom.
    NS_CML - Static variable in class org.openscience.cdk.libio.cml.Convertor
     
    NULLVECTOR - Static variable in class org.openscience.cdk.math.Vector
    Null vector in 3 dimensional space
    numAtoms - Variable in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
     
    number() - Method in enum org.openscience.cdk.config.Elements
    The atomic number of the element.
    numberOfCycles() - Method in class org.openscience.cdk.graph.Cycles
    How many cycles are stored.
    numberOfElements() - Method in class org.openscience.cdk.group.Partition
    Calculate the size of the partition as the sum of the sizes of the cells.
    numberOfUnplacedHeavyAtoms(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
    Gets numberOfUnplacedHeavyAtoms (no Flag ISPLACED, no Hydrogens)
    numCycles() - Method in interface org.openscience.cdk.ringsearch.CyclicVertexSearch
    Returns the number of cycles (circuit rank, frère jacques number, num SSSR).
    numeric() - Method in enum org.openscience.cdk.interfaces.IBond.Order
    Access a numeric value for the number of bonded electron pairs.
    NumericalSurface - Class in org.openscience.cdk.geometry.surface
    A class representing the solvent accessible surface area surface of a molecule.
    NumericalSurface(IAtomContainer) - Constructor for class org.openscience.cdk.geometry.surface.NumericalSurface
    Constructor to initialize the surface calculation with default values.
    NumericalSurface(IAtomContainer, double, int) - Constructor for class org.openscience.cdk.geometry.surface.NumericalSurface
    Constructor to initialize the surface calculation with user specified values.
    numOfPopulatedbins() - Method in interface org.openscience.cdk.fingerprint.ICountFingerprint
    Returns the number of bins that are populated.
    numOfPopulatedbins() - Method in class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
     
    numRings() - Method in class org.openscience.cdk.ringsearch.RingSearch
    Access the number of rings found (aka.
    NWChemFormat - Class in org.openscience.cdk.io.formats
    See here.
    NWChemFormat() - Constructor for class org.openscience.cdk.io.formats.NWChemFormat
     

    O

    o - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    O - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    OATE - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    OBJECT_UNIQUE_POLICY - Static variable in class org.openscience.cdk.tools.IDCreator
    New ID generation policy - to generate IDs unique only in a molecule
    occupancies - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
     
    OCT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    of(IAtomContainer) - Static method in class org.openscience.cdk.stereo.Stereocenters
    Determine the stereocenter atoms in the provided container based on connectivity.
    ofClass(Class<T>, Object...) - Method in class org.openscience.cdk.DynamicFactory
    Construct an implementation using a constructor whose parameters match that of the provided objects.
    ofClass(Class<T>) - Method in class org.openscience.cdk.DynamicFactory
    Construct an implementation using the default constructor.
    ofNumber(int) - Static method in enum org.openscience.cdk.config.Elements
    Obtain the element with the specified atomic number.
    ofString(String) - Static method in enum org.openscience.cdk.config.Elements
    Obtain the element with the specified symbol or name.
    ofType(IBond, int) - Static method in class org.openscience.cdk.isomorphism.matchers.CTFileQueryBond
    Create a CTFileQueryBond of the specified type (from the MDL spec).
    ofValue(int) - Static method in enum org.openscience.cdk.io.MDLV2000Writer.SPIN_MULTIPLICITY
    Create a SPIN_MULTIPLICITY instance for the specified value.
    OICACID - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    OL - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    ONE - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    ONE_FIVE_SHIFT - Static variable in class org.openscience.cdk.tautomers.InChITautomerGenerator
    Generate InChI with -15T (1,5-shift tautomers) option.
    oneAttachLocation() - Method in class org.openscience.cdk.iupac.parser.NomParser
    Deprecated.
    Only one attach location specified, should be followed by a dash.
    OneElectronJob - Class in org.openscience.cdk.math.qm
    Calculates the orbitals and orbital energies of electron systems without electron electron interactions
    OneElectronJob(Orbitals) - Constructor for class org.openscience.cdk.math.qm.OneElectronJob
    Constructs a one electron job
    openNodeScope(Node) - Method in class org.openscience.cdk.smiles.smarts.parser.JJTSMARTSParserState
     
    OptionIOSetting - Class in org.openscience.cdk.io.setting
    An class for a reader setting which must be found in the list of possible settings.
    OptionIOSetting(String, IOSetting.Importance, String, List<String>, String) - Constructor for class org.openscience.cdk.io.setting.OptionIOSetting
    OptionIOSetting is IOSetting for which the value must be in the list of possible options.
    or(IBitFingerprint) - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
     
    or(IBitFingerprint) - Method in interface org.openscience.cdk.fingerprint.IBitFingerprint
    Performs a logical OR of the bits in this target bit set with the bits in the argument fingerprint.
    or(IBitFingerprint) - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
     
    or(IntArrayFingerprint) - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
     
    or(CycleFinder, CycleFinder) - Static method in class org.openscience.cdk.graph.Cycles
    Use an auxiliary cycle finder if the primary method was intractable.
    or(IQueryAtom, IQueryAtom) - Static method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom
    Disjunction the provided expressions.
    OR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    Orbit - Class in org.openscience.cdk.signature
    A list of atom indices, and the label of the orbit.
    Orbit(String, int) - Constructor for class org.openscience.cdk.signature.Orbit
     
    orbital() - Method in class org.openscience.cdk.hash.HashGeneratorMaker
    Discriminate atomic orbitals.
    Orbitals - Class in org.openscience.cdk.math.qm
    This class represents a set of orbitals
    Orbitals(IBasis) - Constructor for class org.openscience.cdk.math.qm.Orbitals
    Constructs orbitals with a specified base set
    Orbitals(IBasis, Matrix) - Constructor for class org.openscience.cdk.math.qm.Orbitals
    Constructs orbitals with a specified base set and a coefficient matrix
    OrBond() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
     
    order - Variable in class org.openscience.cdk.Bond
    The bond order of this bond.
    order(ILigand[]) - Static method in class org.openscience.cdk.geometry.cip.CIPTool
    Reorders the ILigand objects in the array according to the CIP rules.
    order() - Method in class org.openscience.cdk.group.Partition
    Sort the cells in increasing order.
    order() - Method in class org.openscience.cdk.group.PermutationGroup
    Calculates the size of the group.
    order - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
     
    order - Variable in class org.openscience.cdk.isomorphism.matchers.QueryBond
    The bond order of this query bond.
    order - Variable in class org.openscience.cdk.silent.Bond
    The bond order of this bond.
    order2Resource(IBond.Order) - Static method in class org.openscience.cdk.libio.jena.Convertor
    Create the Resource matching the given IBond.Order.
    OrderQueryBond - Class in org.openscience.cdk.isomorphism.matchers
     
    OrderQueryBond(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.OrderQueryBond
     
    OrderQueryBond(IQueryAtom, IQueryAtom, IBond.Order, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.OrderQueryBond
     
    OrderQueryBond - Class in org.openscience.cdk.isomorphism.matchers.smarts
    This matches a bond with a certain bond order.
    OrderQueryBond(IBond.Order, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.OrderQueryBond
    Creates a new instance
    OrderQueryBondOrderOnly - Class in org.openscience.cdk.isomorphism.matchers
    IQueryBond that matches IBond object only based on bond order, and disregarding any aromaticity flag.
    OrderQueryBondOrderOnly(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.OrderQueryBondOrderOnly
     
    OrderQueryBondOrderOnly(IQueryAtom, IQueryAtom, IBond.Order, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.OrderQueryBondOrderOnly
     
    OrExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
     
    org.openscience.cdk - package org.openscience.cdk
     
    org.openscience.cdk.aromaticity - package org.openscience.cdk.aromaticity
     
    org.openscience.cdk.atomtype - package org.openscience.cdk.atomtype
     
    org.openscience.cdk.atomtype.mapper - package org.openscience.cdk.atomtype.mapper
     
    org.openscience.cdk.charges - package org.openscience.cdk.charges
     
    org.openscience.cdk.config - package org.openscience.cdk.config
     
    org.openscience.cdk.config.atomtypes - package org.openscience.cdk.config.atomtypes
     
    org.openscience.cdk.config.fragments - package org.openscience.cdk.config.fragments
     
    org.openscience.cdk.config.isotopes - package org.openscience.cdk.config.isotopes
     
    org.openscience.cdk.controller - package org.openscience.cdk.controller
     
    org.openscience.cdk.debug - package org.openscience.cdk.debug
     
    org.openscience.cdk.depict - package org.openscience.cdk.depict
     
    org.openscience.cdk.dict - package org.openscience.cdk.dict
     
    org.openscience.cdk.event - package org.openscience.cdk.event
     
    org.openscience.cdk.exception - package org.openscience.cdk.exception
     
    org.openscience.cdk.fingerprint - package org.openscience.cdk.fingerprint
     
    org.openscience.cdk.fingerprint.model - package org.openscience.cdk.fingerprint.model
     
    org.openscience.cdk.forcefield.mmff - package org.openscience.cdk.forcefield.mmff
     
    org.openscience.cdk.formula - package org.openscience.cdk.formula
     
    org.openscience.cdk.formula.rules - package org.openscience.cdk.formula.rules
     
    org.openscience.cdk.fragment - package org.openscience.cdk.fragment
     
    org.openscience.cdk.geometry - package org.openscience.cdk.geometry
     
    org.openscience.cdk.geometry.alignment - package org.openscience.cdk.geometry.alignment
     
    org.openscience.cdk.geometry.cip - package org.openscience.cdk.geometry.cip
     
    org.openscience.cdk.geometry.cip.rules - package org.openscience.cdk.geometry.cip.rules
     
    org.openscience.cdk.geometry.surface - package org.openscience.cdk.geometry.surface
     
    org.openscience.cdk.geometry.volume - package org.openscience.cdk.geometry.volume
     
    org.openscience.cdk.graph - package org.openscience.cdk.graph
     
    org.openscience.cdk.graph.invariant - package org.openscience.cdk.graph.invariant
     
    org.openscience.cdk.graph.invariant.exception - package org.openscience.cdk.graph.invariant.exception
     
    org.openscience.cdk.graph.matrix - package org.openscience.cdk.graph.matrix
     
    org.openscience.cdk.graph.rebond - package org.openscience.cdk.graph.rebond
     
    org.openscience.cdk.group - package org.openscience.cdk.group
     
    org.openscience.cdk.hash - package org.openscience.cdk.hash
     
    org.openscience.cdk.hash.stereo - package org.openscience.cdk.hash.stereo
     
    org.openscience.cdk.inchi - package org.openscience.cdk.inchi
     
    org.openscience.cdk.index - package org.openscience.cdk.index
     
    org.openscience.cdk.interfaces - package org.openscience.cdk.interfaces
     
    org.openscience.cdk.io - package org.openscience.cdk.io
     
    org.openscience.cdk.io.cml - package org.openscience.cdk.io.cml
     
    org.openscience.cdk.io.formats - package org.openscience.cdk.io.formats
     
    org.openscience.cdk.io.inchi - package org.openscience.cdk.io.inchi
     
    org.openscience.cdk.io.iterator - package org.openscience.cdk.io.iterator
     
    org.openscience.cdk.io.iterator.event - package org.openscience.cdk.io.iterator.event
     
    org.openscience.cdk.io.listener - package org.openscience.cdk.io.listener
     
    org.openscience.cdk.io.program - package org.openscience.cdk.io.program
     
    org.openscience.cdk.io.pubchemxml - package org.openscience.cdk.io.pubchemxml
     
    org.openscience.cdk.io.random - package org.openscience.cdk.io.random
     
    org.openscience.cdk.io.rdf - package org.openscience.cdk.io.rdf
     
    org.openscience.cdk.io.setting - package org.openscience.cdk.io.setting
     
    org.openscience.cdk.isomorphism - package org.openscience.cdk.isomorphism
     
    org.openscience.cdk.isomorphism.matchers - package org.openscience.cdk.isomorphism.matchers
     
    org.openscience.cdk.isomorphism.matchers.smarts - package org.openscience.cdk.isomorphism.matchers.smarts
     
    org.openscience.cdk.isomorphism.mcss - package org.openscience.cdk.isomorphism.mcss
     
    org.openscience.cdk.iupac.parser - package org.openscience.cdk.iupac.parser
     
    org.openscience.cdk.layout - package org.openscience.cdk.layout
     
    org.openscience.cdk.libio.cml - package org.openscience.cdk.libio.cml
     
    org.openscience.cdk.libio.jena - package org.openscience.cdk.libio.jena
     
    org.openscience.cdk.libio.md - package org.openscience.cdk.libio.md
     
    org.openscience.cdk.math - package org.openscience.cdk.math
     
    org.openscience.cdk.math.qm - package org.openscience.cdk.math.qm
     
    org.openscience.cdk.modeling.builder3d - package org.openscience.cdk.modeling.builder3d
     
    org.openscience.cdk.normalize - package org.openscience.cdk.normalize
     
    org.openscience.cdk.pharmacophore - package org.openscience.cdk.pharmacophore
     
    org.openscience.cdk.protein - package org.openscience.cdk.protein
     
    org.openscience.cdk.protein.data - package org.openscience.cdk.protein.data
     
    org.openscience.cdk.qsar - package org.openscience.cdk.qsar
     
    org.openscience.cdk.qsar.descriptors.atomic - package org.openscience.cdk.qsar.descriptors.atomic
     
    org.openscience.cdk.qsar.descriptors.atompair - package org.openscience.cdk.qsar.descriptors.atompair
     
    org.openscience.cdk.qsar.descriptors.bond - package org.openscience.cdk.qsar.descriptors.bond
     
    org.openscience.cdk.qsar.descriptors.molecular - package org.openscience.cdk.qsar.descriptors.molecular
     
    org.openscience.cdk.qsar.descriptors.protein - package org.openscience.cdk.qsar.descriptors.protein
     
    org.openscience.cdk.qsar.descriptors.substance - package org.openscience.cdk.qsar.descriptors.substance
     
    org.openscience.cdk.qsar.result - package org.openscience.cdk.qsar.result
     
    org.openscience.cdk.reaction - package org.openscience.cdk.reaction
     
    org.openscience.cdk.reaction.mechanism - package org.openscience.cdk.reaction.mechanism
     
    org.openscience.cdk.reaction.type - package org.openscience.cdk.reaction.type
     
    org.openscience.cdk.reaction.type.parameters - package org.openscience.cdk.reaction.type.parameters
     
    org.openscience.cdk.renderer - package org.openscience.cdk.renderer
     
    org.openscience.cdk.renderer.color - package org.openscience.cdk.renderer.color
     
    org.openscience.cdk.renderer.elements - package org.openscience.cdk.renderer.elements
     
    org.openscience.cdk.renderer.elements.path - package org.openscience.cdk.renderer.elements.path
     
    org.openscience.cdk.renderer.font - package org.openscience.cdk.renderer.font
     
    org.openscience.cdk.renderer.generators - package org.openscience.cdk.renderer.generators
     
    org.openscience.cdk.renderer.generators.parameter - package org.openscience.cdk.renderer.generators.parameter
     
    org.openscience.cdk.renderer.generators.standard - package org.openscience.cdk.renderer.generators.standard
     
    org.openscience.cdk.renderer.selection - package org.openscience.cdk.renderer.selection
     
    org.openscience.cdk.renderer.visitor - package org.openscience.cdk.renderer.visitor
     
    org.openscience.cdk.ringsearch - package org.openscience.cdk.ringsearch
     
    org.openscience.cdk.ringsearch.cyclebasis - package org.openscience.cdk.ringsearch.cyclebasis
     
    org.openscience.cdk.sgroup - package org.openscience.cdk.sgroup
     
    org.openscience.cdk.signature - package org.openscience.cdk.signature
     
    org.openscience.cdk.silent - package org.openscience.cdk.silent
     
    org.openscience.cdk.similarity - package org.openscience.cdk.similarity
     
    org.openscience.cdk.smarts - package org.openscience.cdk.smarts
     
    org.openscience.cdk.smiles - package org.openscience.cdk.smiles
     
    org.openscience.cdk.smiles.smarts - package org.openscience.cdk.smiles.smarts
     
    org.openscience.cdk.smiles.smarts.parser - package org.openscience.cdk.smiles.smarts.parser
     
    org.openscience.cdk.smsd - package org.openscience.cdk.smsd
     
    org.openscience.cdk.smsd.algorithm.matchers - package org.openscience.cdk.smsd.algorithm.matchers
     
    org.openscience.cdk.smsd.algorithm.mcgregor - package org.openscience.cdk.smsd.algorithm.mcgregor
     
    org.openscience.cdk.smsd.algorithm.mcsplus - package org.openscience.cdk.smsd.algorithm.mcsplus
     
    org.openscience.cdk.smsd.algorithm.rgraph - package org.openscience.cdk.smsd.algorithm.rgraph
     
    org.openscience.cdk.smsd.algorithm.single - package org.openscience.cdk.smsd.algorithm.single
     
    org.openscience.cdk.smsd.algorithm.vflib - package org.openscience.cdk.smsd.algorithm.vflib
     
    org.openscience.cdk.smsd.algorithm.vflib.builder - package org.openscience.cdk.smsd.algorithm.vflib.builder
     
    org.openscience.cdk.smsd.algorithm.vflib.interfaces - package org.openscience.cdk.smsd.algorithm.vflib.interfaces
     
    org.openscience.cdk.smsd.algorithm.vflib.map - package org.openscience.cdk.smsd.algorithm.vflib.map
     
    org.openscience.cdk.smsd.algorithm.vflib.query - package org.openscience.cdk.smsd.algorithm.vflib.query
     
    org.openscience.cdk.smsd.filters - package org.openscience.cdk.smsd.filters
     
    org.openscience.cdk.smsd.global - package org.openscience.cdk.smsd.global
     
    org.openscience.cdk.smsd.helper - package org.openscience.cdk.smsd.helper
     
    org.openscience.cdk.smsd.interfaces - package org.openscience.cdk.smsd.interfaces
     
    org.openscience.cdk.smsd.labelling - package org.openscience.cdk.smsd.labelling
     
    org.openscience.cdk.smsd.ring - package org.openscience.cdk.smsd.ring
     
    org.openscience.cdk.smsd.tools - package org.openscience.cdk.smsd.tools
     
    org.openscience.cdk.stereo - package org.openscience.cdk.stereo
     
    org.openscience.cdk.structgen - package org.openscience.cdk.structgen
     
    org.openscience.cdk.structgen.stochastic - package org.openscience.cdk.structgen.stochastic
     
    org.openscience.cdk.structgen.stochastic.operator - package org.openscience.cdk.structgen.stochastic.operator
     
    org.openscience.cdk.tautomers - package org.openscience.cdk.tautomers
     
    org.openscience.cdk.templates - package org.openscience.cdk.templates
     
    org.openscience.cdk.templates.saturatedhydrocarbons - package org.openscience.cdk.templates.saturatedhydrocarbons
     
    org.openscience.cdk.tools - package org.openscience.cdk.tools
     
    org.openscience.cdk.tools.diff - package org.openscience.cdk.tools.diff
     
    org.openscience.cdk.tools.diff.tree - package org.openscience.cdk.tools.diff.tree
     
    org.openscience.cdk.tools.features - package org.openscience.cdk.tools.features
     
    org.openscience.cdk.tools.manipulator - package org.openscience.cdk.tools.manipulator
     
    org.openscience.cdk.tools.periodictable - package org.openscience.cdk.tools.periodictable
     
    org.openscience.cdk.validate - package org.openscience.cdk.validate
     
    orthonormalize(Matrix) - Method in class org.openscience.cdk.math.Matrix
    Orthonormalize the vectors of this matrix by Gram-Schmidt.
    OS - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    OSMIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    OSMIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    other(int) - Method in class org.openscience.cdk.graph.Matching
    Access the vertex matched with 'v'.
    outline(double) - Method in class org.openscience.cdk.renderer.elements.GeneralPath
    Outline the general path with the specified stroke size.
    outlineOf(Shape, double, Color) - Static method in class org.openscience.cdk.renderer.elements.GeneralPath
    Create an outline path of the specified Java 2D Shape and color.
    output - Variable in class org.openscience.cdk.inchi.InChIGenerator
     
    output - Variable in class org.openscience.cdk.inchi.InChIToStructure
     
    OvalElement - Class in org.openscience.cdk.renderer.elements
    An oval element (should) have both a width and a height.
    OvalElement(double, double, Color) - Constructor for class org.openscience.cdk.renderer.elements.OvalElement
    Make an oval with a default radius of 10.
    OvalElement(double, double, double, Color) - Constructor for class org.openscience.cdk.renderer.elements.OvalElement
    Make an oval with the supplied radius.
    OvalElement(double, double, double, boolean, Color) - Constructor for class org.openscience.cdk.renderer.elements.OvalElement
    Make an oval with a particular fill and color.
    OVERAREA - Static variable in class org.openscience.cdk.renderer.GraphRendererModel
    Paints the area over the function
    OverlapResolver - Class in org.openscience.cdk.layout
    Deprecated.
    does not resolve overlaps correctly
    OverlapResolver() - Constructor for class org.openscience.cdk.layout.OverlapResolver
    Deprecated.
     
    OverlapResolver.OverlapPair - Class in org.openscience.cdk.layout
    Deprecated.
    A little helper class to store pairs of overlapping atoms.
    OverlapResolver.OverlapPair(IChemObject, IChemObject) - Constructor for class org.openscience.cdk.layout.OverlapResolver.OverlapPair
    Deprecated.
    Constructor for the OverlapPair object.
    OWLAtomTypeHandler - Class in org.openscience.cdk.config.atomtypes
    SAX Handler for the OWLAtomTypeReader.
    OWLAtomTypeHandler(IChemObjectBuilder) - Constructor for class org.openscience.cdk.config.atomtypes.OWLAtomTypeHandler
    Constructs a new AtomTypeHandler and will create IAtomType implementations using the given IChemObjectBuilder.
    OWLAtomTypeMappingHandler - Class in org.openscience.cdk.config.atomtypes
    SAX Handler for the OWLAtomTypeMappingReader.
    OWLAtomTypeMappingHandler() - Constructor for class org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingHandler
    Constructs a new OWLAtomTypeMappingHandler.
    OWLAtomTypeMappingReader - Class in org.openscience.cdk.config.atomtypes
    XML Reader for the OWLBasedAtomTypeConfigurator.
    OWLAtomTypeMappingReader(Reader) - Constructor for class org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingReader
    Instantiates the XML based AtomTypeReader.
    OWLAtomTypeReader - Class in org.openscience.cdk.config.atomtypes
    XML Reader for the OWLBasedAtomTypeConfigurator.
    OWLAtomTypeReader(Reader) - Constructor for class org.openscience.cdk.config.atomtypes.OWLAtomTypeReader
    Instantiates the XML based AtomTypeReader.
    OWLBasedAtomTypeConfigurator - Class in org.openscience.cdk.config
    AtomType resource that reads the atom type configuration from an OWL file.
    OWLBasedAtomTypeConfigurator() - Constructor for class org.openscience.cdk.config.OWLBasedAtomTypeConfigurator
     
    OWLFile - Class in org.openscience.cdk.dict
    Dictionary with entries build from an OWL file.
    OWLFile() - Constructor for class org.openscience.cdk.dict.OWLFile
     
    OWLReact - Class in org.openscience.cdk.dict
    Dictionary with entries build from an OWL React.
    OWLReact() - Constructor for class org.openscience.cdk.dict.OWLReact
    Constructor of the OWLReact object.
    OXO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    OXYGEN - Static variable in enum org.openscience.cdk.config.Elements
     
    OxygenAtomCountDescriptor - Class in org.openscience.cdk.qsar.descriptors.substance
    Descriptor that returns the number of oxygens in the chemical formula.
    OxygenAtomCountDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.substance.OxygenAtomCountDescriptor
     
    OYLCHLORIDE - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.

    P

    p - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    P - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    PA - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    paint(IDrawVisitor, IRenderingElement) - Method in class org.openscience.cdk.renderer.AbstractRenderer
    The target method for paintChemModel, paintReaction, and paintMolecule.
    paint(IAtomContainer, IDrawVisitor) - Method in class org.openscience.cdk.renderer.AtomContainerRenderer
    Paint an IChemObject.
    paint(IAtomContainer, IDrawVisitor, Rectangle2D, boolean) - Method in class org.openscience.cdk.renderer.AtomContainerRenderer
    Paint a molecule (an IAtomContainer).
    paint(IChemModel, IDrawVisitor) - Method in class org.openscience.cdk.renderer.ChemModelRenderer
    Paint an IChemModel using the IDrawVisitor at a scale determined by the bond length in RendererModel.
    paint(IChemModel, IDrawVisitor, Rectangle2D, boolean) - Method in class org.openscience.cdk.renderer.ChemModelRenderer
    Paint a ChemModel.
    paint(T, IDrawVisitor) - Method in interface org.openscience.cdk.renderer.IRenderer
    Paint an IChemObject.
    paint(T, IDrawVisitor, Rectangle2D, boolean) - Method in interface org.openscience.cdk.renderer.IRenderer
    Paint the chem object within the specified bounds.
    paint(IAtomContainerSet, IDrawVisitor) - Method in class org.openscience.cdk.renderer.MoleculeSetRenderer
    Paint an IChemObject.
    paint(IAtomContainerSet, IDrawVisitor, Rectangle2D, boolean) - Method in class org.openscience.cdk.renderer.MoleculeSetRenderer
    Paint a set of molecules.
    paint(IReaction, IDrawVisitor) - Method in class org.openscience.cdk.renderer.ReactionRenderer
    Paint an IChemObject.
    paint(IReaction, IDrawVisitor, Rectangle2D, boolean) - Method in class org.openscience.cdk.renderer.ReactionRenderer
    Paint a reaction.
    paint(IReactionSet, IDrawVisitor) - Method in class org.openscience.cdk.renderer.ReactionSetRenderer
    Paint an IChemObject.
    paint(IReactionSet, IDrawVisitor, Rectangle2D, boolean) - Method in class org.openscience.cdk.renderer.ReactionSetRenderer
    Paint a set of reactions.
    PALLADIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    PALLADIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    ParameterReact - Class in org.openscience.cdk.reaction.type.parameters
    Class which defines the allowed parameters of a reaction.
    ParameterReact() - Constructor for class org.openscience.cdk.reaction.type.parameters.ParameterReact
     
    paramsMap - Variable in class org.openscience.cdk.reaction.ReactionEngine
     
    paramsMap2 - Variable in class org.openscience.cdk.reaction.ReactionEngine
     
    parityARef1 - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
     
    parityARef2 - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
     
    parityARef3 - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
     
    parityARef4 - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
     
    parityAtomsGiven - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
     
    parityGiven - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
     
    parse(BitSet, BitSet, boolean, boolean) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
    Parsing of the RGraph.
    parse(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
    This method parses a Smarts String and returns an instance of QueryAtomContainer
    parse(BitSet, BitSet, boolean, boolean, TimeManager) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
    Deprecated.
    Parsing of the CDKRGraph.
    parseAtomCharges(XMLStreamReader, IAtomContainer) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
     
    parseAtomElements(XMLStreamReader, IAtomContainer) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
     
    parseAuxInfo(String, long[]) - Static method in class org.openscience.cdk.graph.invariant.InChINumbersTools
    Parse the atom numbering from the auxinfo.
    parseCompoundsBlock(XMLStreamReader) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
     
    parseCtabKey(String) - Static method in enum org.openscience.cdk.sgroup.SgroupType
     
    ParseException - Exception in org.openscience.cdk.iupac.parser
    This exception is thrown when parse errors are encountered.
    ParseException(Token, int[][], String[]) - Constructor for exception org.openscience.cdk.iupac.parser.ParseException
    This constructor is used by the method "generateParseException" in the generated parser.
    ParseException() - Constructor for exception org.openscience.cdk.iupac.parser.ParseException
    The following constructors are for use by you for whatever purpose you can think of.
    ParseException(String) - Constructor for exception org.openscience.cdk.iupac.parser.ParseException
    Constructor with message.
    ParseException - Exception in org.openscience.cdk.smiles.smarts.parser
    This exception is thrown when parse errors are encountered.
    ParseException(Token, int[][], String[]) - Constructor for exception org.openscience.cdk.smiles.smarts.parser.ParseException
    This constructor is used by the method "generateParseException" in the generated parser.
    ParseException() - Constructor for exception org.openscience.cdk.smiles.smarts.parser.ParseException
    The following constructors are for use by you for whatever purpose you can think of.
    ParseException(String) - Constructor for exception org.openscience.cdk.smiles.smarts.parser.ParseException
    Constructor with message.
    parseMolecule(XMLStreamReader, IChemObjectBuilder) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
     
    parserAtomBlock(XMLStreamReader, IAtomContainer) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
     
    parserBondBlock(XMLStreamReader, IAtomContainer) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
     
    parserCompoundInfoData(XMLStreamReader, IAtomContainer) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
     
    parserCoordBlock(XMLStreamReader, IAtomContainer) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
     
    parseReactionSmiles(String) - Method in class org.openscience.cdk.smiles.SmilesParser
    Parse a reaction SMILES.
    parseSmiles(String) - Method in class org.openscience.cdk.smiles.SmilesParser
    Parses a SMILES string and returns a structure (IAtomContainer).
    parseSubstance(XMLStreamReader) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
     
    PART_OF_RING_OF_SIZE - Static variable in class org.openscience.cdk.CDKConstants
    Used as property key for indicating the ring size of a certain atom type.
    PartialAtomicChargeColors - Class in org.openscience.cdk.renderer.color
    Class defining the color which with atoms are colored.
    PartialAtomicChargeColors() - Constructor for class org.openscience.cdk.renderer.color.PartialAtomicChargeColors
     
    partialCharges(IAtomContainer) - Method in class org.openscience.cdk.forcefield.mmff.Mmff
    Assign the partial charges, all existing charges are cleared.
    partialCharges - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
     
    PartialFilledStructureMerger - Class in org.openscience.cdk.structgen.stochastic
    Randomly generates a single, connected, correctly bonded structure from a number of fragments.
    PartialFilledStructureMerger() - Constructor for class org.openscience.cdk.structgen.stochastic.PartialFilledStructureMerger
    Constructor for the PartialFilledStructureMerger object.
    PartialPiChargeDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
    The calculation of pi partial charges in pi-bonded systems of an heavy atom was made by Saller-Gasteiger.
    PartialPiChargeDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor
    Constructor for the PartialPiChargeDescriptor object
    PartialSigmaChargeDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
    The calculation of sigma partial charges in sigma-bonded systems of an heavy atom was made by Marsilli-Gasteiger.
    PartialSigmaChargeDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor
    Constructor for the PartialSigmaChargeDescriptor object
    PartialTChargeMMFF94Descriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
    The calculation of total partial charges of an heavy atom is based on MMFF94 model.
    PartialTChargeMMFF94Descriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor
    Constructor for the PartialTChargeMMFF94Descriptor object
    PartialTChargePEOEDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
    The calculation of total partial charges of an heavy atom is based on Partial Equalization of Electronegativity method (PEOE-PEPE) from Gasteiger.
    PartialTChargePEOEDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor
    Constructor for the PartialTChargePEOEDescriptor object
    Partition - Class in org.openscience.cdk.group
    A partition of a set of integers, such as the discrete partition {{1}, {2}, {3}, {4}} or the unit partition {{1, 2, 3, 4}} or an intermediate like {{1, 2}, {3, 4}}.
    Partition() - Constructor for class org.openscience.cdk.group.Partition
    Creates a new, empty partition with no cells.
    Partition(Partition) - Constructor for class org.openscience.cdk.group.Partition
    Copy constructor to make one partition from another.
    Partition(int[][]) - Constructor for class org.openscience.cdk.group.Partition
    Constructor to make a partition from an array of int arrays.
    partitionIntoMolecules(IAtomContainer) - Static method in class org.openscience.cdk.graph.ConnectivityChecker
    Partitions the atoms in an AtomContainer into covalently connected components.
    partitionIntoMolecules(IAtomContainer, int[]) - Static method in class org.openscience.cdk.graph.ConnectivityChecker
     
    partitionNonRingPartners(IAtom, IRing, IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.layout.RingPlacer
    Partition the bonding partners of a given atom into ring atoms and non-ring atoms
    partitionPartners(IAtom, IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.layout.AtomPlacer
    Partition the bonding partners of a given atom into placed (coordinates assinged) and not placed.
    PartitionRefinement - Class in org.openscience.cdk.group
    Factory for partition refiners.
    PartitionRefinement() - Constructor for class org.openscience.cdk.group.PartitionRefinement
     
    PartitionRefinement.AtomRefinerBuilder - Class in org.openscience.cdk.group
     
    PartitionRefinement.AtomRefinerBuilder() - Constructor for class org.openscience.cdk.group.PartitionRefinement.AtomRefinerBuilder
     
    PartitionRefinement.BondRefinerBuilder - Class in org.openscience.cdk.group
     
    PartitionRefinement.BondRefinerBuilder() - Constructor for class org.openscience.cdk.group.PartitionRefinement.BondRefinerBuilder
     
    partitionRings(IRingSet) - Static method in class org.openscience.cdk.ringsearch.RingPartitioner
    Partitions a RingSet into RingSets of connected rings.
    PartitionRingsFromComplexRing(String) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor
     
    PathBuilder - Class in org.openscience.cdk.renderer.elements.path
    Builder class for paths.
    PathBuilder() - Constructor for class org.openscience.cdk.renderer.elements.path.PathBuilder
    Make a new path builder with a default color of black.
    PathBuilder(Color) - Constructor for class org.openscience.cdk.renderer.elements.path.PathBuilder
    Make a path builder that will make a path with a particular color.
    PathEdge - Class in org.openscience.cdk.smsd.ring
    Deprecated.
    This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK and a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    PathEdge(List<IAtom>) - Constructor for class org.openscience.cdk.smsd.ring.PathEdge
    Deprecated.
     
    PathElement - Class in org.openscience.cdk.renderer.elements.path
    A path element.
    PathElement(Type) - Constructor for class org.openscience.cdk.renderer.elements.path.PathElement
    Create a path element.
    PathElement - Class in org.openscience.cdk.renderer.elements
    A path composed of points.
    PathElement(List<Point2d>, Color) - Constructor for class org.openscience.cdk.renderer.elements.PathElement
    Make a path from the list of points.
    PathGraph - Class in org.openscience.cdk.smsd.ring
    Deprecated.
    This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK and a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    PathGraph(IAtomContainer) - Constructor for class org.openscience.cdk.smsd.ring.PathGraph
    Deprecated.
     
    paths() - Method in class org.openscience.cdk.fingerprint.ShortestPathWalker
    Access a set of all shortest paths.
    paths() - Method in class org.openscience.cdk.graph.AllCycles
    The paths describing all simple cycles in the given graph.
    paths() - Method in class org.openscience.cdk.graph.Cycles
     
    paths() - Method in class org.openscience.cdk.graph.EssentialCycles
    The paths for each essential cycle.
    paths() - Method in class org.openscience.cdk.graph.MinimumCycleBasis
    The paths of all cycles in the minimum cycle basis.
    paths() - Method in class org.openscience.cdk.graph.RelevantCycles
    Reconstruct the paths of all relevant cycles.
    paths() - Method in class org.openscience.cdk.graph.TripletShortCycles
    Access the vertex paths for all cycles of the basis.
    pathsTo(int) - Method in class org.openscience.cdk.graph.ShortestPaths
    Reconstruct all shortest paths to the provided end vertex.
    pathsTo(IAtom) - Method in class org.openscience.cdk.graph.ShortestPaths
    Reconstruct all shortest paths to the provided end vertex.
    pathTo(int) - Method in class org.openscience.cdk.graph.ShortestPaths
    Reconstruct a shortest path to the provided end vertex.
    pathTo(IAtom) - Method in class org.openscience.cdk.graph.ShortestPaths
    Reconstruct a shortest path to the provided end atom.
    PathTools - Class in org.openscience.cdk.graph
    Tools class with methods for handling molecular graphs.
    PathTools() - Constructor for class org.openscience.cdk.graph.PathTools
     
    Pattern - Class in org.openscience.cdk.isomorphism
    A structural pattern for finding an exact matching in a target compound.
    Pattern() - Constructor for class org.openscience.cdk.isomorphism.Pattern
     
    PB - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    pBlockMetals() - Method in class org.openscience.cdk.iupac.parser.NomParser
    Deprecated.
     
    PCCompoundASNReader - Class in org.openscience.cdk.io
    Reads an object from ASN formated input for PubChem Compound entries.
    PCCompoundASNReader(Reader) - Constructor for class org.openscience.cdk.io.PCCompoundASNReader
    Construct a new reader from a Reader type object.
    PCCompoundASNReader(InputStream) - Constructor for class org.openscience.cdk.io.PCCompoundASNReader
     
    PCCompoundASNReader() - Constructor for class org.openscience.cdk.io.PCCompoundASNReader
     
    PCCompoundXMLReader - Class in org.openscience.cdk.io
    Reads an object from ASN.1 XML formated input for PubChem Compound entries.
    PCCompoundXMLReader(Reader) - Constructor for class org.openscience.cdk.io.PCCompoundXMLReader
    Construct a new reader from a Reader type object.
    PCCompoundXMLReader(InputStream) - Constructor for class org.openscience.cdk.io.PCCompoundXMLReader
     
    PCCompoundXMLReader() - Constructor for class org.openscience.cdk.io.PCCompoundXMLReader
     
    PCModelFormat - Class in org.openscience.cdk.io.formats
    See here.
    PCModelFormat() - Constructor for class org.openscience.cdk.io.formats.PCModelFormat
     
    PCSubstanceXMLReader - Class in org.openscience.cdk.io
    Reads an object from ASN formated input for PubChem Compound entries.
    PCSubstanceXMLReader(Reader) - Constructor for class org.openscience.cdk.io.PCSubstanceXMLReader
    Construct a new reader from a Reader type object.
    PCSubstanceXMLReader(InputStream) - Constructor for class org.openscience.cdk.io.PCSubstanceXMLReader
     
    PCSubstanceXMLReader() - Constructor for class org.openscience.cdk.io.PCSubstanceXMLReader
     
    PD - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    PDBAtom - Class in org.openscience.cdk.protein.data
    Represents the idea of an atom as used in PDB files.
    PDBAtom(IElement) - Constructor for class org.openscience.cdk.protein.data.PDBAtom
    Constructs an IPDBAtom from a Element.
    PDBAtom(String) - Constructor for class org.openscience.cdk.protein.data.PDBAtom
    Constructs an IPDBAtom from a String containing an element symbol.
    PDBAtom(String, Point3d) - Constructor for class org.openscience.cdk.protein.data.PDBAtom
    Constructs an IPDBAtom from an Element and a Point3d.
    PDBAtom - Class in org.openscience.cdk.silent
    Represents the idea of an atom as used in PDB files.
    PDBAtom(IElement) - Constructor for class org.openscience.cdk.silent.PDBAtom
    Constructs an IPDBAtom from a Element.
    PDBAtom(String) - Constructor for class org.openscience.cdk.silent.PDBAtom
    Constructs an IPDBAtom from a String containing an element symbol.
    PDBAtom(String, Point3d) - Constructor for class org.openscience.cdk.silent.PDBAtom
    Constructs an IPDBAtom from an Element and a Point3d.
    PDBAtomCustomizer - Class in org.openscience.cdk.libio.cml
    ICMLCustomizer for the libio-cml Convertor to be able to export details for IPDBAtom's.
    PDBAtomCustomizer() - Constructor for class org.openscience.cdk.libio.cml.PDBAtomCustomizer
     
    PDBConvention - Class in org.openscience.cdk.io.cml
    Implements the PDB convention used by PDB2CML.
    PDBConvention(IChemFile) - Constructor for class org.openscience.cdk.io.cml.PDBConvention
     
    PDBConvention(ICMLModule) - Constructor for class org.openscience.cdk.io.cml.PDBConvention
     
    PDBFormat - Class in org.openscience.cdk.io.formats
    See here.
    PDBFormat() - Constructor for class org.openscience.cdk.io.formats.PDBFormat
     
    PDBMLFormat - Class in org.openscience.cdk.io.formats
    XML version of the PDB format.
    PDBMLFormat() - Constructor for class org.openscience.cdk.io.formats.PDBMLFormat
     
    PDBMonomer - Class in org.openscience.cdk.protein.data
    Represents the idea of an monomer as used in PDB files.
    PDBMonomer() - Constructor for class org.openscience.cdk.protein.data.PDBMonomer
     
    PDBMonomer - Class in org.openscience.cdk.silent
    Represents the idea of an monomer as used in PDB files.
    PDBMonomer() - Constructor for class org.openscience.cdk.silent.PDBMonomer
     
    PDBPolymer - Class in org.openscience.cdk.protein.data
    An entry in the PDB database.
    PDBPolymer() - Constructor for class org.openscience.cdk.protein.data.PDBPolymer
    Constructs a new Polymer to store the IMonomers.
    PDBPolymer - Class in org.openscience.cdk.silent
    An entry in the PDB database.
    PDBPolymer() - Constructor for class org.openscience.cdk.silent.PDBPolymer
    Constructs a new Polymer to store the IMonomers.
    PDBReader - Class in org.openscience.cdk.io
    Reads the contents of a PDBFile.
    PDBReader(InputStream) - Constructor for class org.openscience.cdk.io.PDBReader
    Constructs a new PDBReader that can read Molecules from a given InputStream.
    PDBReader(Reader) - Constructor for class org.openscience.cdk.io.PDBReader
    Constructs a new PDBReader that can read Molecules from a given Reader.
    PDBReader() - Constructor for class org.openscience.cdk.io.PDBReader
     
    PDBStrand - Class in org.openscience.cdk.protein.data
    An entry in the PDB database.
    PDBStrand() - Constructor for class org.openscience.cdk.protein.data.PDBStrand
    Constructs a new Polymer to store the Monomers.
    PDBStructure - Class in org.openscience.cdk.protein.data
    Holder for secundary protein structure elements.
    PDBStructure() - Constructor for class org.openscience.cdk.protein.data.PDBStructure
     
    PDBStructure - Class in org.openscience.cdk.silent
    Holder for secundary protein structure elements.
    PDBStructure() - Constructor for class org.openscience.cdk.silent.PDBStructure
     
    PDBWriter - Class in org.openscience.cdk.io
    Saves small molecules in a rudimentary PDB format.
    PDBWriter() - Constructor for class org.openscience.cdk.io.PDBWriter
     
    PDBWriter(Writer) - Constructor for class org.openscience.cdk.io.PDBWriter
    Creates a PDB writer.
    PDBWriter(OutputStream) - Constructor for class org.openscience.cdk.io.PDBWriter
     
    PDF_FMT - Static variable in class org.openscience.cdk.depict.Depiction
    Portable Document Format (PDF) format key.
    peekNode() - Method in class org.openscience.cdk.smiles.smarts.parser.JJTSMARTSParserState
     
    PENT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    percieveAtomTypesAndConfigureAtoms(IAtomContainer) - Static method in class org.openscience.cdk.normalize.SMSDNormalizer
    Deprecated.
    Convenience method to perceive atom types for all IAtoms in the IAtomContainer, using the CDKAtomTypeMatcher.
    percieveAtomTypesAndConfigureAtoms(IAtomContainer) - Static method in class org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator
    Deprecated.
    Convenience method to perceive atom types for all IAtoms in the IAtomContainer, using the CDKAtomTypeMatcher.
    percieveAtomTypesAndConfigureAtoms(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
    Convenience method to perceive atom types for all IAtoms in the IAtomContainer, using the CDKAtomTypeMatcher.
    percieveAtomTypesAndConfigureUnsetProperties(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
    Convenience method to perceive atom types for all IAtoms in the IAtomContainer, using the CDKAtomTypeMatcher.
    perfect(int[][], BitSet) - Method in class org.openscience.cdk.graph.Matching
    Attempt to augment the matching such that it is perfect over the subset of vertices in the provided graph.
    period() - Method in enum org.openscience.cdk.config.Elements
    Return the period in the periodic table this element belongs to.
    PeriodicGroupNumber() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
     
    PeriodicGroupNumberAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
    This matcher checks the periodic group number of an atom.
    PeriodicGroupNumberAtom(int, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.PeriodicGroupNumberAtom
    Creates a new instance
    periodicTable - Variable in class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor
     
    PeriodicTable - Class in org.openscience.cdk.tools.periodictable
    Represents elements of the Periodic Table.
    PeriodicTable() - Constructor for class org.openscience.cdk.tools.periodictable.PeriodicTable
     
    PeriodicTablePositionDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
    This class returns the period in the periodic table of an atom belonging to an atom container
    Parameters for this descriptor:
    Name Default Description no parameters
    PeriodicTablePositionDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor
    Constructor for the PeriodicTablePositionDescriptor object
    peripherals() - Method in class org.openscience.cdk.stereo.ExtendedTetrahedral
    The neighbouring peripherals atoms, these are attached to the terminal atoms in the cumulated system.
    Permutation - Class in org.openscience.cdk.group
    A permutation with some associated methods to multiply, invert, and convert to cycle strings.
    Permutation(int) - Constructor for class org.openscience.cdk.group.Permutation
    Constructs an identity permutation with size elements.
    Permutation(int...) - Constructor for class org.openscience.cdk.group.Permutation
    Make a permutation from a set of values such that p[i] = x for the value x at position i.
    Permutation(Permutation) - Constructor for class org.openscience.cdk.group.Permutation
    Construct a permutation from another one by cloning the values.
    PermutationGroup - Class in org.openscience.cdk.group
    A permutation group with a Schreier-Sims representation.
    PermutationGroup(int) - Constructor for class org.openscience.cdk.group.PermutationGroup
    Make a group with just a single identity permutation of size n.
    PermutationGroup(Permutation) - Constructor for class org.openscience.cdk.group.PermutationGroup
    Creates the initial group, with the base base.
    PermutationGroup(int, List<Permutation>) - Constructor for class org.openscience.cdk.group.PermutationGroup
    Creates a group from a set of generators.
    PermutationGroup.Backtracker - Interface in org.openscience.cdk.group
    An interface for use with the apply method, which runs through all the permutations in this group.
    permute(int[], IAtomContainer) - Static method in class org.openscience.cdk.smsd.labelling.AtomContainerAtomPermutor
    Deprecated.
     
    Permutor - Class in org.openscience.cdk.graph
    General permutation generator, that uses orderly generation by ranking and unranking.
    Permutor(int) - Constructor for class org.openscience.cdk.graph.Permutor
    Create a permutor that will generate permutations of numbers up to size.
    Permutor - Class in org.openscience.cdk.smsd.labelling
    Deprecated.
    This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    Permutor(int) - Constructor for class org.openscience.cdk.smsd.labelling.Permutor
    Deprecated.
    Create a permutor that will generate permutations of numbers up to size.
    perturbed() - Method in class org.openscience.cdk.hash.HashGeneratorMaker
    Discriminate atoms experiencing uniform environments.
    PetitjeanNumberDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
    According to the Petitjean definition, the eccentricity of a vertex corresponds to the distance from that vertex to the most remote vertex in the graph.
    PetitjeanNumberDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor
    Constructor for the PetitjeanNumberDescriptor object
    PetitjeanShapeIndexDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
    Evaluates the Petitjean shape indices, These original Petitjean number was described by Petitjean ([ Petitjean, M. , Applications of the radius-diameter diagram to the classification of topological and geometrical shapes of chemical compounds, Journal of Chemical Information and Computer Science, 1992, 32:331-337]) and considered the molecular graph.
    PetitjeanShapeIndexDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor
     
    PharmacophoreAngleBond - Class in org.openscience.cdk.pharmacophore
    Represents an angle relationship between three pharmacophore groups.
    PharmacophoreAngleBond(PharmacophoreAtom, PharmacophoreAtom, PharmacophoreAtom) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreAngleBond
    Create a pharmacophore distance constraint.
    PharmacophoreAtom - Class in org.openscience.cdk.pharmacophore
    A representation of a pharmacophore group.
    PharmacophoreAtom(String, String, Point3d) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreAtom
    Create a pharmacophore group.
    PharmacophoreAtom(PharmacophoreAtom) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreAtom
    Create a pharmacophore group.
    PharmacophoreBond - Class in org.openscience.cdk.pharmacophore
    Represents a distance relationship between two pharmacophore groups.
    PharmacophoreBond(PharmacophoreAtom, PharmacophoreAtom) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreBond
    Create a pharmacophore distance constraint.
    PharmacophoreMatcher - Class in org.openscience.cdk.pharmacophore
    Identifies atoms whose 3D arrangement matches a specified pharmacophore query.
    PharmacophoreMatcher() - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreMatcher
    An empty constructor.
    PharmacophoreMatcher(PharmacophoreQuery) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreMatcher
    Initialize the matcher with a query.
    PharmacophoreQuery - Class in org.openscience.cdk.pharmacophore
    Represents a colleciton of pharmacophore groups and constraints.
    PharmacophoreQuery() - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreQuery
     
    PharmacophoreQueryAngleBond - Class in org.openscience.cdk.pharmacophore
    Represents a pharmacophore query angle constraint.
    PharmacophoreQueryAngleBond() - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreQueryAngleBond
     
    PharmacophoreQueryAngleBond(PharmacophoreQueryAtom, PharmacophoreQueryAtom, PharmacophoreQueryAtom, double, double) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreQueryAngleBond
    Create a query angle constraint between three query groups.
    PharmacophoreQueryAngleBond(PharmacophoreQueryAtom, PharmacophoreQueryAtom, PharmacophoreQueryAtom, double) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreQueryAngleBond
    Create a query angle constraint between three query groups.
    PharmacophoreQueryAtom - Class in org.openscience.cdk.pharmacophore
    Represents a query pharmacophore group.
    PharmacophoreQueryAtom(String, String) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreQueryAtom
    Creat a new query pharmacophore group
    PharmacophoreQueryBond - Class in org.openscience.cdk.pharmacophore
    Represents a pharmacophore query distance constraint.
    PharmacophoreQueryBond() - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreQueryBond
     
    PharmacophoreQueryBond(PharmacophoreQueryAtom, PharmacophoreQueryAtom, double, double) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreQueryBond
    Create a query distance constraint between two query groups.
    PharmacophoreQueryBond(PharmacophoreQueryAtom, PharmacophoreQueryAtom, double) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreQueryBond
    Create a query distance constraint between two query groups.
    PharmacophoreUtils - Class in org.openscience.cdk.pharmacophore
    Provides some utility methods for pharmacophore handling.
    PharmacophoreUtils() - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreUtils
     
    PHENYL - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    PHOSPHORUS - Static variable in enum org.openscience.cdk.config.Elements
     
    PhysicalConstants - Class in org.openscience.cdk
    An class providing predefined properties of physical constants.
    PhysicalConstants() - Constructor for class org.openscience.cdk.PhysicalConstants
     
    PI_BOND_COUNT - Static variable in class org.openscience.cdk.CDKConstants
    Used as property key for indicating the HOSE code for a certain atom type.
    PiBondingMovementReaction - Class in org.openscience.cdk.reaction.type
    IReactionProcess which tries to reproduce the delocalization of electrons which are unsaturated bonds from conjugated rings.
    PiBondingMovementReaction() - Constructor for class org.openscience.cdk.reaction.type.PiBondingMovementReaction
    Constructor of the PiBondingMovementReaction object
    piBonds() - Static method in class org.openscience.cdk.aromaticity.ElectronDonation
    A very simple aromaticity model which only allows atoms adjacent to cyclic pi bonds.
    pickBFgraph() - Method in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
     
    pickDFgraph() - Method in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
     
    PiContactDetectionDescriptor - Class in org.openscience.cdk.qsar.descriptors.atompair
    This class checks if two atoms have pi-contact (this is true when there is one and the same conjugated pi-system which contains both atoms, or directly linked neighbours of the atoms).
    PiContactDetectionDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor
    Constructor for the PiContactDetectionDescriptor object.
    PiElectronegativity - Class in org.openscience.cdk.charges
    Calculation of the electronegativity of orbitals of a molecule by the method Gasteiger based on electronegativity is given by X = a + bq + c(q*q).
    PiElectronegativity() - Constructor for class org.openscience.cdk.charges.PiElectronegativity
    Constructor for the PiElectronegativity object.
    PiElectronegativity(int, int) - Constructor for class org.openscience.cdk.charges.PiElectronegativity
    Constructor for the Electronegativity object.
    PiElectronegativityDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
    Pi electronegativity is given by X = a + bq + c(q*q)
    Parameters for this descriptor:
    Name Default Description maxIterations 0 Number of maximum iterations
    PiElectronegativityDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor
    Constructor for the PiElectronegativityDescriptor object
    placeAliphaticHeavyChain(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
    Method assigns 3D coordinates to the heavy atoms in an aliphatic chain.
    placeFusedRing(IRing, IAtomContainer, Vector2d, double) - Method in class org.openscience.cdk.layout.RingPlacer
    Generated coordinates for a given ring, which is fused to another ring.
    placeHydrogens2D(IAtomContainer, double) - Method in class org.openscience.cdk.layout.HydrogenPlacer
    Place all hydrogens connected to atoms which have already been laid out.
    placeHydrogens2D(IAtomContainer, IAtom) - Method in class org.openscience.cdk.layout.HydrogenPlacer
    Place hydrogens connected to the given atom using the average bond length in the container.
    placeHydrogens2D(IAtomContainer, IAtom, double) - Method in class org.openscience.cdk.layout.HydrogenPlacer
    Place hydrogens connected to the provided atom atom using the specified bondLength.
    placeLinearChain(IAtomContainer, Vector2d, double) - Method in class org.openscience.cdk.layout.AtomPlacer
    Places the atoms in a linear chain.
    placeRing(IRing, IAtomContainer, Point2d, Vector2d, double) - Method in class org.openscience.cdk.layout.RingPlacer
    Generated coordinates for a given ring.
    placeRing(IRing, Point2d, double) - Method in class org.openscience.cdk.layout.RingPlacer
    Place ring with default start angles, using RingPlacer.defaultAngles.
    placeRing(IRing, Point2d, double, Map<Integer, Double>) - Method in class org.openscience.cdk.layout.RingPlacer
    Place ring with user provided angles.
    placeRingSubstituents(IRingSet, double) - Method in class org.openscience.cdk.layout.RingPlacer
    Positions the aliphatic substituents of a ring system
    placeSpiroRing(IRing, IAtomContainer, Point2d, Vector2d, double) - Method in class org.openscience.cdk.layout.RingPlacer
    Generated coordinates for a given ring, which is connected to a spiro ring.
    PLANE_TOLERANCE - Static variable in class org.openscience.cdk.stereo.StereoTool
     
    PLATINUM - Static variable in enum org.openscience.cdk.config.Elements
     
    PLATINUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    PLUS - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    PLUTOMNIUM - Static variable in enum org.openscience.cdk.config.Elements
    Deprecated.
    PLUTONIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    PLUTONIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    PM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    PMPConvention - Class in org.openscience.cdk.io.cml
    Implementation of the PMPMol Covention for CML.
    PMPConvention(IChemFile) - Constructor for class org.openscience.cdk.io.cml.PMPConvention
     
    PMPConvention(ICMLModule) - Constructor for class org.openscience.cdk.io.cml.PMPConvention
     
    PMPFormat - Class in org.openscience.cdk.io.formats
     
    PMPFormat() - Constructor for class org.openscience.cdk.io.formats.PMPFormat
     
    PMPReader - Class in org.openscience.cdk.io
    Reads an frames from a PMP formated input.
    PMPReader(Reader) - Constructor for class org.openscience.cdk.io.PMPReader
     
    PMPReader(InputStream) - Constructor for class org.openscience.cdk.io.PMPReader
     
    PMPReader() - Constructor for class org.openscience.cdk.io.PMPReader
     
    PNG_FMT - Static variable in class org.openscience.cdk.depict.Depiction
    Portable Network Graphics (PNG) format key.
    PO - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    Point - Class in org.openscience.cdk.graph.rebond
     
    Point(double, double, double) - Constructor for class org.openscience.cdk.graph.rebond.Point
     
    point2d - Variable in class org.openscience.cdk.Atom
    A 2D point specifying the location of this atom in a 2D coordinate space.
    point2d - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom
    A 2D point specifying the location of this atom in a 2D coordinate space.
    point2d - Variable in class org.openscience.cdk.silent.Atom
    A 2D point specifying the location of this atom in a 2D coordinate space.
    Point2dDifference - Class in org.openscience.cdk.tools.diff.tree
    Difference between two boolean[]'s.
    point3d - Variable in class org.openscience.cdk.Atom
    A 3 point specifying the location of this atom in a 3D coordinate space.
    point3d - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom
    A 3 point specifying the location of this atom in a 3D coordinate space.
    point3d - Variable in class org.openscience.cdk.silent.Atom
    A 3 point specifying the location of this atom in a 3D coordinate space.
    Point3dDifference - Class in org.openscience.cdk.tools.diff.tree
    Difference between two boolean[]'s.
    points() - Method in class org.openscience.cdk.renderer.elements.path.Close
    Get the points in the path.
    points(double[]) - Method in class org.openscience.cdk.renderer.elements.path.Close
    Load the provided array with the specified coordinates of this path element.
    points() - Method in class org.openscience.cdk.renderer.elements.path.CubicTo
    Get the points in the path.
    points(double[]) - Method in class org.openscience.cdk.renderer.elements.path.CubicTo
    Load the provided array with the specified coordinates of this path element.
    points() - Method in class org.openscience.cdk.renderer.elements.path.LineTo
    Get the points in the path.
    points(double[]) - Method in class org.openscience.cdk.renderer.elements.path.LineTo
    Load the provided array with the specified coordinates of this path element.
    points() - Method in class org.openscience.cdk.renderer.elements.path.MoveTo
    Get the points in the path.
    points(double[]) - Method in class org.openscience.cdk.renderer.elements.path.MoveTo
    Load the provided array with the specified coordinates of this path element.
    points() - Method in class org.openscience.cdk.renderer.elements.path.PathElement
    Deprecated.
    points(double[]) - Method in class org.openscience.cdk.renderer.elements.path.PathElement
    Load the provided array with the specified coordinates of this path element.
    points() - Method in class org.openscience.cdk.renderer.elements.path.QuadTo
    Get the points in the path.
    points(double[]) - Method in class org.openscience.cdk.renderer.elements.path.QuadTo
    Load the provided array with the specified coordinates of this path element.
    points - Variable in class org.openscience.cdk.renderer.elements.PathElement
    The points that make up the path.
    Polarizability - Class in org.openscience.cdk.charges
    Calculation of the polarizability of a molecule by the method of Kang and Jhon and Gasteiger based on [Kang, Y.K. and Jhon, M.S., Additivity of Atomic Static Polarizabilities and Dispersion Coefficients, Theoretica Chimica Acta, 1982, 61:41-48] and [Gasteiger, J. and Hutchings, M.G., Quantitative Models of Gas-Phase Proton Transfer Reactions Involving Alcohols, Ethers, and their Thio analogs. Correlation Analyses Based on Residual Electronegativity and Effective Polarizability, J. Amer. Chem. Soc., 1984, 106:6489-6495] Limitations in parameterization of atoms: H, Csp3, Csp2, Csp2arom, Csp3, Nsp3, Nsp2, Nsp3, P, Osp3 and Osp2.
    Polarizability() - Constructor for class org.openscience.cdk.charges.Polarizability
    Constructor for the Polarizability object.
    POLONIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    POLONIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    Polymer - Class in org.openscience.cdk
    Subclass of Molecule to store Polymer specific attributes that a Polymer has.
    Polymer() - Constructor for class org.openscience.cdk.Polymer
    Constructs a new Polymer to store the Monomers.
    Polymer - Class in org.openscience.cdk.silent
    Subclass of Molecule to store Polymer specific attributes that a Polymer has.
    Polymer() - Constructor for class org.openscience.cdk.silent.Polymer
    Constructs a new Polymer to store the Monomers.
    pop() - Method in class org.openscience.cdk.io.cml.CMLModuleStack
    Retrieves and deletes to last added entry.
    pop() - Method in class org.openscience.cdk.ringsearch.Queue
    Deprecated.
    Returns an Object from the queue
    popNode() - Method in class org.openscience.cdk.smiles.smarts.parser.JJTSMARTSParserState
     
    populatePolygonCorners(List<IAtom>, Point2d, double, double, double) - Method in class org.openscience.cdk.layout.AtomPlacer
    Populates the corners of a polygon with atoms.
    position - Variable in class org.openscience.cdk.renderer.elements.TextGroupElement.Child
    The position of the child relative to the parent.
    POSITION_FORMAT - Variable in class org.openscience.cdk.io.PDBWriter
     
    possibleAtomTypes(IAtomContainer, IAtom) - Method in interface org.openscience.cdk.atomtype.IAtomTypeGuesser
    Method that returns an iterator with a suitable list of atom types given the provided atom.
    possibleAtomTypes(IAtomContainer, IAtom) - Method in class org.openscience.cdk.atomtype.StructGenAtomTypeGuesser
    Finds the AtomType matching the Atom's element symbol, formal charge and hybridization state.
    PostFilter - Class in org.openscience.cdk.smsd.filters
    Deprecated.
    SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    PostFilter() - Constructor for class org.openscience.cdk.smsd.filters.PostFilter
    Deprecated.
     
    POTASSIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    POTASSIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    POVRayFormat - Class in org.openscience.cdk.io.formats
    See here.
    POVRayFormat() - Constructor for class org.openscience.cdk.io.formats.POVRayFormat
     
    PQSChemFormat - Class in org.openscience.cdk.io.formats
    See here.
    PQSChemFormat() - Constructor for class org.openscience.cdk.io.formats.PQSChemFormat
     
    PR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    PRASEODYMIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    PRASEODYMIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    predict(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.model.Bayesian
    For a given molecule, determines its fingerprints and uses them to calculate a Bayesian prediction.
    predict(String) - Method in class org.openscience.cdk.tools.BremserOneSphereHOSECodePredictor
     
    predictFull(String) - Method in class org.openscience.cdk.tools.BremserOneSphereHOSECodePredictor
     
    predictIP(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.tools.IonizationPotentialTool
    Deprecated.
    Method which is predict the Ionization Potential from given atom.
    predictIP(IAtomContainer, IBond) - Static method in class org.openscience.cdk.tools.IonizationPotentialTool
    Deprecated.
    Method which is predict the Ionization Potential from given atom.
    prefixConstruct() - Method in class org.openscience.cdk.iupac.parser.NomParser
    Deprecated.
    Allows 1 or more prefixes
    prefixFunctionalGroups() - Method in class org.openscience.cdk.iupac.parser.NomParser
    Deprecated.
     
    prefixType() - Method in class org.openscience.cdk.iupac.parser.NomParser
    Deprecated.
     
    prepare(IAtomContainer, boolean) - Static method in class org.openscience.cdk.isomorphism.matchers.smarts.SmartsMatchers
    Do not use - temporary method until the SMARTS packages are cleaned up.
    prepareNode(IAtomContainer) - Method in class org.openscience.cdk.graph.invariant.EquivalentClassPartitioner
    Prepare the node identifier.
    prevCharIsCR - Variable in class org.openscience.cdk.iupac.parser.SimpleCharStream
     
    prevCharIsCR - Variable in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
     
    prevCharIsLF - Variable in class org.openscience.cdk.iupac.parser.SimpleCharStream
     
    prevCharIsLF - Variable in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
     
    previous() - Method in class org.openscience.cdk.io.random.RandomAccessReader
     
    previousIndex() - Method in class org.openscience.cdk.io.random.RandomAccessReader
     
    Primes - Class in org.openscience.cdk.math
    Deprecated.
    Primes() - Constructor for class org.openscience.cdk.math.Primes
    Deprecated.
     
    PrimitiveAtomExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
     
    printIncidenceMatrix() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis
    Deprecated.
     
    printInt2D(int[][]) - Static method in class org.openscience.cdk.tools.SwissArmyKnife
    Deprecated.
    Returns a string representation of a 2D int matrix for printing or listing to the console.
    printPaths() - Method in class org.openscience.cdk.smsd.ring.PathGraph
    Deprecated.
     
    PRIORITY - Static variable in class org.openscience.cdk.layout.AtomPlacer
     
    prioritySubstituents() - Method in class org.openscience.cdk.iupac.parser.NomParser
    Deprecated.
    Things which have sub chains branching off them but the molecule has no main chain.
    prioritySubstituentsFunGroups() - Method in class org.openscience.cdk.iupac.parser.NomParser
    Deprecated.
    Things which have sub chains branching off them and the molecule does have a main chain.
    ProblemMarker - Class in org.openscience.cdk.validate
    Tool to mark IChemObject's as having a problem.
    ProblemMarker() - Constructor for class org.openscience.cdk.validate.ProblemMarker
     
    process() - Method in class org.openscience.cdk.io.iterator.event.EventCMLReader
    Starts the reading of the CML file.
    process(IAtomContainer) - Method in class org.openscience.cdk.qsar.DescriptorEngine
    Calculates all available (or only those specified) descriptors for a molecule.
    process(IAtomContainer, IAtomContainer, List<Integer>, List<Integer>, int) - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.QueryProcessor
    Deprecated.
     
    process(IQueryAtomContainer, IAtomContainer, List<Integer>, List<Integer>, int) - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.QueryProcessor
    Deprecated.
     
    process(int, int, List<Integer>, List<Integer>, List<Integer>, List<Integer>, int) - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.QueryProcessor
    Deprecated.
     
    process(IAtomContainer, List<Integer>, int, List<Integer>, List<String>, List<Integer>, int) - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.TargetProcessor
    Deprecated.
     
    process(int, List<Integer>, int, List<Integer>, List<String>, List<Integer>, int, List<Integer>, List<String>) - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.TargetProcessor
    Deprecated.
     
    processConnections(String, IAtomContainer, int) - Method in class org.openscience.cdk.io.inchi.INChIContentProcessorTool
    Processes the content from the connections field of the INChI.
    processContent() - Method in class org.openscience.cdk.io.random.RandomAccessReader
    The reader is already set to read the record buffer.
    processContent() - Method in class org.openscience.cdk.io.random.RandomAccessSDFReader
     
    processFormula(IAtomContainer, String) - Method in class org.openscience.cdk.io.inchi.INChIContentProcessorTool
    Processes the content from the formula field of the INChI.
    processIOSettingQuestion(IOSetting) - Method in interface org.openscience.cdk.io.listener.IChemObjectIOListener
    Prompted when the IO filter needs information to process the file.
    processIOSettingQuestion(IOSetting) - Method in class org.openscience.cdk.io.listener.PropertiesListener
    Processes the IOSettings by listing the question, giving the options and asking the user to provide their choice.
    processIOSettingQuestion(IOSetting) - Method in class org.openscience.cdk.io.listener.SwingGUIListener
    Processes the IOSettings by listing the question, giving the options and asking the user to provide their choice.
    processIOSettingQuestion(IOSetting) - Method in class org.openscience.cdk.io.listener.TextGUIListener
    Processes the IOSettings by listing the question, giving the options and asking the user to provide their choice.
    products - Variable in class org.openscience.cdk.Reaction
     
    products - Variable in class org.openscience.cdk.silent.Reaction
     
    ProductsBoxGenerator - Class in org.openscience.cdk.renderer.generators
    Generate the symbols for radicals.
    ProductsBoxGenerator() - Constructor for class org.openscience.cdk.renderer.generators.ProductsBoxGenerator
     
    project(List<RMap>, IAtomContainer, int) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
    Projects a list of RMap on a molecule.
    project(List<CDKRMap>, IAtomContainer, int) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
    Deprecated.
    Projects atom list of CDKRMap on atom molecule.
    project2D(IAtomContainer) - Static method in class org.openscience.cdk.geometry.Projector
     
    project2D(IAtomContainer, HashMap<IAtom, Point2d>) - Static method in class org.openscience.cdk.geometry.Projector
     
    projectG1(BitSet) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
    Projects a RGraph bitset on the source graph G1.
    projectG1(BitSet) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
    Deprecated.
    Projects a CDKRGraph bitset on the source graph G1.
    projectG2(BitSet) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
    Projects a RGraph bitset on the source graph G2.
    projectG2(BitSet) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
    Deprecated.
    Projects a CDKRGraph bitset on the source graph G2.
    Projection - Enum in org.openscience.cdk.stereo
    Stereochemistry projection types.
    projections - Variable in class org.openscience.cdk.stereo.StereoElementFactory
     
    projectList(List<List<RMap>>, IAtomContainer, int) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
    Projects a list of RMapsList on a molecule.
    projectList(List<List<CDKRMap>>, IAtomContainer, int) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
    Deprecated.
    Projects atom list of RMapsList on atom molecule.
    Projector - Class in org.openscience.cdk.geometry
    Tool to make projections from 3D to 2D.
    Projector() - Constructor for class org.openscience.cdk.geometry.Projector
     
    PROMETHIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    PROMETHIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    PROP - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    PropertiesListener - Class in org.openscience.cdk.io.listener
    Answers the questions by looking up the values in a Properties object.
    PropertiesListener(Properties) - Constructor for class org.openscience.cdk.io.listener.PropertiesListener
     
    proposeStructure() - Method in class org.openscience.cdk.structgen.RandomGenerator
    Proposes a structure which can be accepted or rejected by an external entity.
    PROTACTINIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    PROTACTINIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    ProteinBuilderTool - Class in org.openscience.cdk.tools
    Class that facilitates building protein structures.
    ProteinBuilderTool() - Constructor for class org.openscience.cdk.tools.ProteinBuilderTool
     
    proteinGridToPmesh(String) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
    Method writes the protein grid points to pmesh format.
    ProteinPocketFinder - Class in org.openscience.cdk.protein
    The detection of pocket and cavities in a bioPolymer is done similar to the program LIGSITE [Hendlich, M. and Rippmann, F. and Bernickel, G. , LIGSITE: Automatic and efficient detection of potential small molecule-binding sites in proteins, Journal of Molecular Graphics and Modelling, 1997, 15:359-363].
    ProteinPocketFinder(String, boolean) - Constructor for class org.openscience.cdk.protein.ProteinPocketFinder
     
    ProteinPocketFinder(String, double, boolean) - Constructor for class org.openscience.cdk.protein.ProteinPocketFinder
     
    ProteinPocketFinder(String, double[][][]) - Constructor for class org.openscience.cdk.protein.ProteinPocketFinder
     
    ProteinPocketFinder(IBioPolymer, double[][][]) - Constructor for class org.openscience.cdk.protein.ProteinPocketFinder
     
    ProtonAffinityHOSEDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
    This class returns the proton affinity of an atom containing.
    ProtonAffinityHOSEDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor
    Constructor for the ProtonAffinityDescriptor object.
    ProtonTotalPartialChargeDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
    The calculation of partial charges of an heavy atom and its protons is based on Gasteiger Marsili (PEOE).
    ProtonTotalPartialChargeDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor
    Constructor for the ProtonTotalPartialChargeDescriptor object
    PS_FMT - Static variable in class org.openscience.cdk.depict.Depiction
    PostScript (PS) format key.
    PSEUDOATOM - Static variable in class org.openscience.cdk.libio.jena.CDK
     
    PseudoAtom - Class in org.openscience.cdk
    Represents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc.
    PseudoAtom() - Constructor for class org.openscience.cdk.PseudoAtom
    Constructs an empty PseudoAtom.
    PseudoAtom(String) - Constructor for class org.openscience.cdk.PseudoAtom
    Constructs an Atom from a String containing an element symbol.
    PseudoAtom(IElement) - Constructor for class org.openscience.cdk.PseudoAtom
    Constructs an PseudoAtom from a IAtom.
    PseudoAtom(String, Point3d) - Constructor for class org.openscience.cdk.PseudoAtom
    Constructs an Atom from an Element and a Point3d.
    PseudoAtom(String, Point2d) - Constructor for class org.openscience.cdk.PseudoAtom
    Constructs an Atom from an Element and a Point2d.
    PseudoAtom - Class in org.openscience.cdk.silent
    Represents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc.
    PseudoAtom() - Constructor for class org.openscience.cdk.silent.PseudoAtom
    Constructs an empty PseudoAtom.
    PseudoAtom(String) - Constructor for class org.openscience.cdk.silent.PseudoAtom
    Constructs an Atom from a String containing an element symbol.
    PseudoAtom(IElement) - Constructor for class org.openscience.cdk.silent.PseudoAtom
    Constructs an PseudoAtom from a IAtom.
    PseudoAtom(String, Point3d) - Constructor for class org.openscience.cdk.silent.PseudoAtom
    Constructs an Atom from an Element and a Point3d.
    PseudoAtom(String, Point2d) - Constructor for class org.openscience.cdk.silent.PseudoAtom
    Constructs an Atom from an Element and a Point2d.
    pspGridToPmesh(String) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
    Method writes the PSP points (≥minPSPocket) to pmesh format.
    PT - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    PU - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    PubChemASNFormat - Class in org.openscience.cdk.io.formats
     
    PubChemASNFormat() - Constructor for class org.openscience.cdk.io.formats.PubChemASNFormat
     
    PubChemCompoundsXMLFormat - Class in org.openscience.cdk.io.formats
     
    PubChemCompoundsXMLFormat() - Constructor for class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
     
    PubChemCompoundXMLFormat - Class in org.openscience.cdk.io.formats
     
    PubChemCompoundXMLFormat() - Constructor for class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
     
    PubchemFingerprinter - Class in org.openscience.cdk.fingerprint
    Generates a Pubchem fingerprint for a molecule.
    PubchemFingerprinter(IChemObjectBuilder) - Constructor for class org.openscience.cdk.fingerprint.PubchemFingerprinter
     
    PubChemFormat - Class in org.openscience.cdk.io.formats
    See here.
    PubChemFormat() - Constructor for class org.openscience.cdk.io.formats.PubChemFormat
     
    PubChemSubstancesASNFormat - Class in org.openscience.cdk.io.formats
     
    PubChemSubstancesASNFormat() - Constructor for class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
     
    PubChemSubstancesXMLFormat - Class in org.openscience.cdk.io.formats
     
    PubChemSubstancesXMLFormat() - Constructor for class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
     
    PubChemSubstanceXMLFormat - Class in org.openscience.cdk.io.formats
     
    PubChemSubstanceXMLFormat() - Constructor for class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
     
    PubChemXMLHelper - Class in org.openscience.cdk.io.pubchemxml
    Helper class to parse PubChem XML documents.
    PubChemXMLHelper(IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
     
    push(ICMLModule) - Method in class org.openscience.cdk.io.cml.CMLModuleStack
    Adds an entry to the stack.
    push(Object) - Method in class org.openscience.cdk.ringsearch.Queue
    Deprecated.
    Places an Object into the queue
    pushNode(Node) - Method in class org.openscience.cdk.smiles.smarts.parser.JJTSMARTSParserState
     
    putInOrder(String[], IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
     
    putValue(SgroupKey, Object) - Method in class org.openscience.cdk.sgroup.Sgroup
    Store an attribute for the Sgroup.
    PYRIDINE_RING - Static variable in class org.openscience.cdk.tools.AtomTypeTools
     
    PYRIMIDINE_RING - Static variable in class org.openscience.cdk.tools.AtomTypeTools
     
    PYROLE_RING - Static variable in class org.openscience.cdk.tools.AtomTypeTools
     

    Q

    Q_MARK - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    QChemFormat - Class in org.openscience.cdk.io.formats
    See here.
    QChemFormat() - Constructor for class org.openscience.cdk.io.formats.QChemFormat
     
    QSARConvention - Class in org.openscience.cdk.io.cml
    This is an implementation for the CDK convention.
    QSARConvention(IChemFile) - Constructor for class org.openscience.cdk.io.cml.QSARConvention
     
    QSARConvention(ICMLModule) - Constructor for class org.openscience.cdk.io.cml.QSARConvention
     
    QSARCustomizer - Class in org.openscience.cdk.libio.cml
    Customizer for the libio-cml Convertor to be able to export details for QSAR descriptors calculated for Molecules.
    QSARCustomizer() - Constructor for class org.openscience.cdk.libio.cml.QSARCustomizer
     
    QUADRUPLEBOND - Static variable in class org.openscience.cdk.libio.jena.CDK
     
    quadTo(Point2d, Point2d) - Method in class org.openscience.cdk.renderer.elements.path.PathBuilder
    Make a quadratic curve in the path, with one control point.
    QuadTo - Class in org.openscience.cdk.renderer.elements.path
    Make a quadratic curve in the path.
    QuadTo(Point2d, Point2d) - Constructor for class org.openscience.cdk.renderer.elements.path.QuadTo
    Make a quad curve.
    QuadTo(double[]) - Constructor for class org.openscience.cdk.renderer.elements.path.QuadTo
    Make a quad curve path element.
    QuadTo(double, double, double, double) - Constructor for class org.openscience.cdk.renderer.elements.path.QuadTo
    Make a quad curve path element.
    Quaternion - Class in org.openscience.cdk.math
    This class handles quaternions.
    Quaternion() - Constructor for class org.openscience.cdk.math.Quaternion
     
    Quaternion(double, double, double, double) - Constructor for class org.openscience.cdk.math.Quaternion
     
    Quaternion(Vector, double) - Constructor for class org.openscience.cdk.math.Quaternion
    Generate a quaternion from a rotation axis and an angle
    Quaternion(double, double, double) - Constructor for class org.openscience.cdk.math.Quaternion
    Generate a quaternion from spherical coordinates and a rotation angle
    QueryAtom - Class in org.openscience.cdk.isomorphism.matchers
     
    QueryAtom(String, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryAtom
     
    QueryAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryAtom
     
    QueryAtomContainer - Class in org.openscience.cdk.isomorphism.matchers
     
    QueryAtomContainer(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
    Constructs an empty AtomContainer.
    QueryAtomContainer(IAtomContainer, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
    Constructs an AtomContainer with a copy of the atoms and electronContainers of another AtomContainer (A shallow copy, i.e., with the same objects as in the original AtomContainer).
    QueryAtomContainer(int, int, int, int, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
    Constructs an empty AtomContainer that will contain a certain number of atoms and electronContainers.
    QueryAtomContainerCreator - Class in org.openscience.cdk.isomorphism.matchers
     
    QueryAtomContainerCreator() - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
     
    QueryBond - Class in org.openscience.cdk.isomorphism.matchers
    Implements the concept of a "query bond" between two or more atoms.
    QueryBond(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryBond
    Constructs an empty query bond.
    QueryBond(IAtom, IAtom, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryBond
    Constructs a query bond with a single query bond order..
    QueryBond(IAtom, IAtom, IBond.Order, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryBond
    Constructs a query bond with a given order.
    QueryBond(IAtom[], IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryBond
    Constructs a multi-center query bond, with undefined order and no stereo information.
    QueryBond(IAtom[], IBond.Order, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryBond
    Constructs a multi-center query bond, with a specified order and no stereo information.
    QueryBond(IAtom, IAtom, IBond.Order, IBond.Stereo, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryBond
    Constructs a query bond with a given order and stereo orientation from an array of atoms.
    QueryChemObject - Class in org.openscience.cdk.isomorphism.matchers
     
    QueryChemObject(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryChemObject
     
    QueryCompiler - Class in org.openscience.cdk.smsd.algorithm.vflib.query
    Deprecated.
    SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    QueryCompiler(IAtomContainer, boolean) - Constructor for class org.openscience.cdk.smsd.algorithm.vflib.query.QueryCompiler
    Deprecated.
    Construct query object from the molecule
    QueryCompiler(IQueryAtomContainer) - Constructor for class org.openscience.cdk.smsd.algorithm.vflib.query.QueryCompiler
    Deprecated.
    Construct query object from the molecule
    QueryProcessor - Class in org.openscience.cdk.smsd.algorithm.mcgregor
    Deprecated.
    SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    QueryProcessor(List<String>, List<String>, String[], int, int, List<Integer>, List<String>, int, List<Integer>, List<String>) - Constructor for class org.openscience.cdk.smsd.algorithm.mcgregor.QueryProcessor
    Deprecated.
    Query molecule
    question - Variable in class org.openscience.cdk.io.setting.IOSetting
     
    Queue - Class in org.openscience.cdk.ringsearch
    Deprecated.
    internal implemenation detail from SSSRFinder, do not use
    Queue() - Constructor for class org.openscience.cdk.ringsearch.Queue
    Deprecated.
    Constructs an empty Queue

    R

    R - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    r - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    R_BOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    R_BRACKET - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    R_PAREN - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    RA - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    RAD_30 - Static variable in class org.openscience.cdk.layout.RingPlacer
     
    RAD_30 - Static variable in class org.openscience.cdk.layout.StructureDiagramGenerator
     
    radical() - Method in class org.openscience.cdk.hash.HashGeneratorMaker
    Discriminate free radicals.
    RadicalChargeSiteInitiationHReaction - Class in org.openscience.cdk.reaction.type
    IReactionProcess which participate mass spectrum process.
    RadicalChargeSiteInitiationHReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalChargeSiteInitiationHReaction
    Constructor of the RadicalChargeSiteInitiationHReaction object
    RadicalChargeSiteInitiationReaction - Class in org.openscience.cdk.reaction.type
    IReactionProcess which participate mass spectrum process.
    RadicalChargeSiteInitiationReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalChargeSiteInitiationReaction
    Constructor of the RadicalChargeSiteInitiationReaction object
    RadicalGenerator - Class in org.openscience.cdk.renderer.generators
    Generate the symbols for radicals.
    RadicalGenerator() - Constructor for class org.openscience.cdk.renderer.generators.RadicalGenerator
     
    RadicalSiteHrAlphaReaction - Class in org.openscience.cdk.reaction.type
    This reaction could be represented as [A*]-(C)_2-C3[H] => A([H])-(C_2)-[C3*].
    RadicalSiteHrAlphaReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalSiteHrAlphaReaction
    Constructor of the RadicalSiteHrAlphaReaction object
    RadicalSiteHrBetaReaction - Class in org.openscience.cdk.reaction.type
    This reaction could be represented as [A*]-(C)_3-C4[H] => A([H])-(C_3)-[C4*].
    RadicalSiteHrBetaReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalSiteHrBetaReaction
    Constructor of the RadicalSiteHrBetaReaction object
    RadicalSiteHrDeltaReaction - Class in org.openscience.cdk.reaction.type
    This reaction could be represented as [A*]-(C)_4-C5[H] => A([H])-(C_4)-[C5*].
    RadicalSiteHrDeltaReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalSiteHrDeltaReaction
    Constructor of the RadicalSiteHrDeltaReaction object
    RadicalSiteHrGammaReaction - Class in org.openscience.cdk.reaction.type
    This reaction could be represented as [A*]-C1-C2-C3[H] => A([H])-C1-C2-[C3*].
    RadicalSiteHrGammaReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalSiteHrGammaReaction
    Constructor of the RadicalSiteHrGammaReaction object
    RadicalSiteInitiationHReaction - Class in org.openscience.cdk.reaction.type
    IReactionProcess which participate mass spectrum process.
    RadicalSiteInitiationHReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalSiteInitiationHReaction
    Constructor of the RadicalSiteInitiationHReaction object
    RadicalSiteInitiationReaction - Class in org.openscience.cdk.reaction.type
    IReactionProcess which participate mass spectrum process.
    RadicalSiteInitiationReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalSiteInitiationReaction
    Constructor of the RadicalSiteInitiationReaction object
    RadicalSiteIonizationMechanism - Class in org.openscience.cdk.reaction.mechanism
    This mechanism extracts an atom because of the stabilization of a radical.
    RadicalSiteIonizationMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.RadicalSiteIonizationMechanism
     
    RadicalSiteRearrangementMechanism - Class in org.openscience.cdk.reaction.mechanism
    This mechanism displaces an Atom or substructure (R) from one position to an other.
    RadicalSiteRearrangementMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.RadicalSiteRearrangementMechanism
     
    RadicalSiteRrAlphaReaction - Class in org.openscience.cdk.reaction.type
    This reaction could be represented as [A*]-(C)_2-C3[R] => A([RH])-(C_2)-[C3*].
    RadicalSiteRrAlphaReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalSiteRrAlphaReaction
    Constructor of the RadicalSiteRrAlphaReaction object
    RadicalSiteRrBetaReaction - Class in org.openscience.cdk.reaction.type
    This reaction could be represented as [A*]-(C)_3-C4[R] => A([R])-(C_3)-[C4*].
    RadicalSiteRrBetaReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalSiteRrBetaReaction
    Constructor of the RadicalSiteRrBetaReaction object
    RadicalSiteRrDeltaReaction - Class in org.openscience.cdk.reaction.type
    This reaction could be represented as [A*]-(C)_4-C5[R] => A([R])-(C_4)-[C5*].
    RadicalSiteRrDeltaReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalSiteRrDeltaReaction
    Constructor of the RadicalSiteRrDeltaReaction object
    RadicalSiteRrGammaReaction - Class in org.openscience.cdk.reaction.type
    This reaction could be represented as [A*]-(C)_5-C6[R] => A([R])-(C_5)-[C6*].
    RadicalSiteRrGammaReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalSiteRrGammaReaction
    Constructor of the RadicalSiteRrGammaReaction object
    RADIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    RADIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    radius - Variable in class org.openscience.cdk.renderer.elements.OvalElement
    The radius of the oval.
    RADON - Static variable in enum org.openscience.cdk.config.Elements
     
    raFile - Variable in class org.openscience.cdk.io.random.RandomAccessReader
     
    RandomAccessReader - Class in org.openscience.cdk.io.random
    Random access to text files of compounds.
    RandomAccessReader(File, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.random.RandomAccessReader
    Reads the file and builds an index file, if the index file doesn't already exist.
    RandomAccessReader(File, IChemObjectBuilder, IReaderListener) - Constructor for class org.openscience.cdk.io.random.RandomAccessReader
    Reads the file and builds an index file, if the index file doesn't already exist.
    RandomAccessSDFReader - Class in org.openscience.cdk.io.random
    Random access of SDF file.
    RandomAccessSDFReader(File, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.random.RandomAccessSDFReader
     
    RandomAccessSDFReader(File, IChemObjectBuilder, IReaderListener) - Constructor for class org.openscience.cdk.io.random.RandomAccessSDFReader
     
    randomBit() - Static method in class org.openscience.cdk.math.RandomNumbersTool
    Generates a random bit: either 0 or 1.
    randomBoolean() - Static method in class org.openscience.cdk.math.RandomNumbersTool
    Generates a random boolean.
    randomDouble() - Static method in class org.openscience.cdk.math.RandomNumbersTool
    Generates a random double between 0 and 1.
    randomDouble(double, double) - Static method in class org.openscience.cdk.math.RandomNumbersTool
    Generates a random double between the specified values.
    randomFloat() - Static method in class org.openscience.cdk.math.RandomNumbersTool
    Generates a random float between 0 and 1.
    randomFloat(float, float) - Static method in class org.openscience.cdk.math.RandomNumbersTool
    Generates a random float between the specified values.
    RandomGenerator - Class in org.openscience.cdk.structgen
    RandomGenerator is a generator of constitutional isomers.
    RandomGenerator(IAtomContainer) - Constructor for class org.openscience.cdk.structgen.RandomGenerator
    Constructs a RandomGenerator with a given starting structure.
    randomInt() - Static method in class org.openscience.cdk.math.RandomNumbersTool
    Generates a random integer between 0 and 1.
    randomInt(int, int) - Static method in class org.openscience.cdk.math.RandomNumbersTool
    Generates a random integer between the specified values.
    randomLong() - Static method in class org.openscience.cdk.math.RandomNumbersTool
    Generates a random long between 0 and 1.
    randomLong(long, long) - Static method in class org.openscience.cdk.math.RandomNumbersTool
    Generates a random long between the specified values.
    randomNext() - Method in class org.openscience.cdk.graph.AtomContainerPermutor
    Get a new container, but randomly skip forwards in the list of possible permutations to generate it.
    RandomNumber - Class in org.openscience.cdk.fingerprint
    Generates pseudorandom numbers using the MersenneTwister method from commons-math.
    RandomNumber() - Constructor for class org.openscience.cdk.fingerprint.RandomNumber
     
    RandomNumbersTool - Class in org.openscience.cdk.math
    Class supplying useful methods to generate random numbers.
    RandomNumbersTool() - Constructor for class org.openscience.cdk.math.RandomNumbersTool
     
    range - Variable in class org.openscience.cdk.fingerprint.model.Bayesian
     
    RasmolColors - Class in org.openscience.cdk.renderer.color
    Atom coloring following RasMol/Chime Color scheme http://www.umass.edu/microbio/rasmol/rascolor.htm.
    RasmolColors() - Constructor for class org.openscience.cdk.renderer.color.RasmolColors
     
    RawCopyFormat - Class in org.openscience.cdk.io.formats
    See here.
    RawCopyFormat() - Constructor for class org.openscience.cdk.io.formats.RawCopyFormat
     
    RB - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    RDBERule - Class in org.openscience.cdk.formula.rules
    Ring Double Bond Equivalents (RDBE) or Double Bond Equivalents (DBE) are calculated from valence values of elements contained in a formula and should tell the number of bonds - or rings.
    RDBERule() - Constructor for class org.openscience.cdk.formula.rules.RDBERule
    Constructor for the RDBE object.
    RDBERule.Combinations - Class in org.openscience.cdk.formula.rules
     
    RDBERule.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.
    RDFCalculator - Class in org.openscience.cdk.geometry
    Calculator of radial distribution functions.
    RDFCalculator(double, double, double, double) - Constructor for class org.openscience.cdk.geometry.RDFCalculator
    Constructs a RDF calculator that calculates a unweighted, digitized RDF function.
    RDFCalculator(double, double, double, double, IRDFWeightFunction) - Constructor for class org.openscience.cdk.geometry.RDFCalculator
    Constructs a RDF calculator that calculates a digitized RDF function.
    rdFields - Variable in class org.openscience.cdk.io.MDLRXNWriter
     
    RDFProtonDescriptor_G3R - Class in org.openscience.cdk.qsar.descriptors.atomic
    This class calculates G3R proton descriptors used in neural networks for H1 NMR shift [Aires-de-Sousa, J. and Hemmer, M.C. and Gasteiger, J., Prediction of 1H NMR Chemical Shifts Using Neural Networks, J. Chem. Inf. Mod., 2002, 74:80-90].
    RDFProtonDescriptor_G3R() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R
    Constructor for the RDFProtonDescriptor object
    RDFProtonDescriptor_GDR - Class in org.openscience.cdk.qsar.descriptors.atomic
    This class calculates GDR proton descriptors used in neural networks for H1 NMR shift [Aires-de-Sousa, J. and Hemmer, M.C. and Gasteiger, J., Prediction of 1H NMR Chemical Shifts Using Neural Networks, J. Chem. Inf. Mod., 2002, 74:80-90].
    RDFProtonDescriptor_GDR() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR
    Constructor for the RDFProtonDescriptor object
    RDFProtonDescriptor_GHR - Class in org.openscience.cdk.qsar.descriptors.atomic
    This class calculates GHR proton descriptors used in neural networks for H1 NMR shift [Aires-de-Sousa, J. and Hemmer, M.C. and Gasteiger, J., Prediction of 1H NMR Chemical Shifts Using Neural Networks, J. Chem. Inf. Mod., 2002, 74:80-90].
    RDFProtonDescriptor_GHR() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR
    Constructor for the RDFProtonDescriptor object
    RDFProtonDescriptor_GHR_topol - Class in org.openscience.cdk.qsar.descriptors.atomic
    This class calculates GHR topological proton descriptors used in neural networks for H1 NMR shift [Aires-de-Sousa, J. and Hemmer, M.C. and Gasteiger, J., Prediction of 1H NMR Chemical Shifts Using Neural Networks, J. Chem. Inf. Mod., 2002, 74:80-90].
    RDFProtonDescriptor_GHR_topol() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol
    Constructor for the RDFProtonDescriptor object
    RDFProtonDescriptor_GSR - Class in org.openscience.cdk.qsar.descriptors.atomic
    This class calculates GDR proton descriptors used in neural networks for H1 NMR shift [Aires-de-Sousa, J. and Hemmer, M.C. and Gasteiger, J., Prediction of 1H NMR Chemical Shifts Using Neural Networks, J. Chem. Inf. Mod., 2002, 74:80-90].
    RDFProtonDescriptor_GSR() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR
    Constructor for the RDFProtonDescriptor object
    RE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    reactants - Variable in class org.openscience.cdk.Reaction
     
    reactants - Variable in class org.openscience.cdk.silent.Reaction
     
    ReactantsBoxGenerator - Class in org.openscience.cdk.renderer.generators
    Generate the symbols for radicals.
    ReactantsBoxGenerator() - Constructor for class org.openscience.cdk.renderer.generators.ReactantsBoxGenerator
     
    Reaction - Class in org.openscience.cdk
    Represents the idea of a chemical reaction.
    Reaction() - Constructor for class org.openscience.cdk.Reaction
    Constructs an empty, forward reaction.
    Reaction - Class in org.openscience.cdk.silent
    Represents the idea of a chemical reaction.
    Reaction() - Constructor for class org.openscience.cdk.silent.Reaction
    Constructs an empty, forward reaction.
    REACTION_CONDITIONS - Static variable in class org.openscience.cdk.CDKConstants
    Property for reaction objects where the conditions of reactions can be placed.
    REACTION_GROUP - Static variable in class org.openscience.cdk.CDKConstants
    Property used for reactions when converted to/from molecules.
    REACTION_ROLE - Static variable in class org.openscience.cdk.CDKConstants
    Property used for reactions when converted to/from molecules.
    ReactionArrowGenerator - Class in org.openscience.cdk.renderer.generators
    Generate the arrow for a reaction.
    ReactionArrowGenerator() - Constructor for class org.openscience.cdk.renderer.generators.ReactionArrowGenerator
     
    ReactionBoxGenerator - Class in org.openscience.cdk.renderer.generators
    Generate the symbols for radicals.
    ReactionBoxGenerator() - Constructor for class org.openscience.cdk.renderer.generators.ReactionBoxGenerator
     
    ReactionChain - Class in org.openscience.cdk.reaction
    Classes that extends the definition of reaction to a chain reaction.
    ReactionChain() - Constructor for class org.openscience.cdk.reaction.ReactionChain
     
    ReactionEngine - Class in org.openscience.cdk.reaction
    The base class for all chemical reactions objects in this cdk.
    ReactionEngine() - Constructor for class org.openscience.cdk.reaction.ReactionEngine
    Constructor of the ReactionEngine object.
    ReactionExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
     
    ReactionManipulator - Class in org.openscience.cdk.tools.manipulator
     
    ReactionManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.ReactionManipulator
     
    ReactionPlusGenerator - Class in org.openscience.cdk.renderer.generators
    Generate the arrow for a reaction.
    ReactionPlusGenerator() - Constructor for class org.openscience.cdk.renderer.generators.ReactionPlusGenerator
     
    ReactionRenderer - Class in org.openscience.cdk.renderer
    A general renderer for IChemModels, IReactions, and IAtomContainers.
    ReactionRenderer(List<IGenerator<IAtomContainer>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.ReactionRenderer
    A renderer that generates diagrams using the specified generators and manages fonts with the supplied font manager.
    ReactionRenderer(RendererModel, List<IGenerator<IAtomContainer>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.ReactionRenderer
     
    ReactionRenderer(List<IGenerator<IAtomContainer>>, List<IGenerator<IReaction>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.ReactionRenderer
    A renderer that draws IReactions with the passed IGenerator for both IAtomContainer and IReaction content.
    ReactionRole - Enum in org.openscience.cdk
     
    ReactionRoleQueryAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
    Matches atoms with a particular role in a reaction.
    ReactionRoleQueryAtom(IChemObjectBuilder, int) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.ReactionRoleQueryAtom
     
    reactions() - Method in class org.openscience.cdk.debug.DebugReactionSet
    Get an iterator for this reaction set.
    reactions() - Method in interface org.openscience.cdk.interfaces.IReactionSet
    Returns the Iterable over Reactions of this container.
    reactions() - Method in class org.openscience.cdk.ReactionSet
    Get an iterator for this reaction set.
    reactions() - Method in class org.openscience.cdk.silent.ReactionSet
    Get an iterator for this reaction set.
    ReactionSceneGenerator - Class in org.openscience.cdk.renderer.generators
    Generator for general reaction scene components.
    ReactionSceneGenerator() - Constructor for class org.openscience.cdk.renderer.generators.ReactionSceneGenerator
     
    ReactionSceneGenerator.ArrowHeadWidth - Class in org.openscience.cdk.renderer.generators
    Double which indicates how wide the arrow head is in screen pixels.
    ReactionSceneGenerator.ArrowHeadWidth() - Constructor for class org.openscience.cdk.renderer.generators.ReactionSceneGenerator.ArrowHeadWidth
     
    ReactionSceneGenerator.ShowReactionBoxes - Class in org.openscience.cdk.renderer.generators
    Boolean that indicates if boxes are drawn around the reaction.
    ReactionSceneGenerator.ShowReactionBoxes() - Constructor for class org.openscience.cdk.renderer.generators.ReactionSceneGenerator.ShowReactionBoxes
     
    ReactionScheme - Class in org.openscience.cdk
    Classes that extends the definition of reaction to a scheme.
    ReactionScheme() - Constructor for class org.openscience.cdk.ReactionScheme
    Constructs an empty ReactionScheme.
    ReactionScheme - Class in org.openscience.cdk.silent
    Classes that extends the definition of reaction to a scheme.
    ReactionScheme() - Constructor for class org.openscience.cdk.silent.ReactionScheme
    Constructs an empty ReactionScheme.
    ReactionSchemeManipulator - Class in org.openscience.cdk.tools.manipulator
     
    ReactionSchemeManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator
     
    reactionSchemes() - Method in class org.openscience.cdk.debug.DebugReactionScheme
    Returns an Iterable for looping over all IMolecularScheme in this ReactionScheme.
    reactionSchemes() - Method in interface org.openscience.cdk.interfaces.IReactionScheme
    Returns an Iterable for looping over all IMolecularScheme in this ReactionScheme.
    reactionSchemes() - Method in class org.openscience.cdk.ReactionScheme
    Returns an Iterable for looping over all IMolecularScheme in this ReactionScheme.
    reactionSchemes() - Method in class org.openscience.cdk.silent.ReactionScheme
    Returns an Iterable for looping over all IMolecularScheme in this ReactionScheme.
    ReactionSet - Class in org.openscience.cdk
    A set of reactions, for example those taking part in a reaction.
    ReactionSet() - Constructor for class org.openscience.cdk.ReactionSet
    Constructs an empty ReactionSet.
    ReactionSet - Class in org.openscience.cdk.silent
    A set of reactions, for example those taking part in a reaction.
    ReactionSet() - Constructor for class org.openscience.cdk.silent.ReactionSet
    Constructs an empty ReactionSet.
    ReactionSetManipulator - Class in org.openscience.cdk.tools.manipulator
     
    ReactionSetManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
     
    ReactionSetRenderer - Class in org.openscience.cdk.renderer
    A general renderer for IChemModels, IReactions, and IAtomContainers.
    ReactionSetRenderer(List<IGenerator<IAtomContainer>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.ReactionSetRenderer
    A renderer that generates diagrams using the specified generators and manages fonts with the supplied font manager.
    ReactionSetRenderer(RendererModel, List<IGenerator<IAtomContainer>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.ReactionSetRenderer
     
    ReactionSetRenderer(List<IGenerator<IAtomContainer>>, List<IGenerator<IReaction>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.ReactionSetRenderer
    A renderer that generates diagrams using the specified generators for IAtomContainers and IReactionSets and manages fonts with the supplied font manager.
    ReactionSetRenderer(RendererModel, List<IGenerator<IAtomContainer>>, List<IGenerator<IReaction>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.ReactionSetRenderer
     
    ReactionSpecification - Class in org.openscience.cdk.reaction
    Class that is used to distribute reactions specifications.
    ReactionSpecification(String, String, String, String) - Constructor for class org.openscience.cdk.reaction.ReactionSpecification
    Container for specifying the type of reaction.
    REACTIVE_CENTER - Static variable in class org.openscience.cdk.CDKConstants
    Flag is set if a chemobject has reactive center.
    read(T) - Method in class org.openscience.cdk.io.CIFReader
    Read a ChemFile from input.
    read(T) - Method in class org.openscience.cdk.io.CMLReader
    Read a IChemObject from input.
    read(T) - Method in class org.openscience.cdk.io.CrystClustReader
     
    read(T) - Method in class org.openscience.cdk.io.CTXReader
     
    read(T) - Method in class org.openscience.cdk.io.GamessReader
     
    read(T) - Method in class org.openscience.cdk.io.Gaussian03Reader
     
    read(T) - Method in class org.openscience.cdk.io.Gaussian98Reader
     
    read(T) - Method in class org.openscience.cdk.io.GhemicalMMReader
     
    read(T) - Method in class org.openscience.cdk.io.HINReader
    Reads the content from a HIN input.
    read(T) - Method in class org.openscience.cdk.io.INChIPlainTextReader
    Reads a IChemObject of type object from input.
    read(T) - Method in class org.openscience.cdk.io.INChIReader
    Reads a IChemObject of type object from input.
    read(T) - Method in interface org.openscience.cdk.io.ISimpleChemObjectReader
    Reads an IChemObject of type "object" from input.
    read(T) - Method in class org.openscience.cdk.io.MDLReader
    Deprecated.
    Takes an object which subclasses IChemObject, e.g.
    read(T) - Method in class org.openscience.cdk.io.MDLRXNReader
    Takes an object which subclasses IChemObject, e.g.Molecule, and will read this (from file, database, internet etc).
    read(T) - Method in class org.openscience.cdk.io.MDLRXNV2000Reader
    Takes an object which subclasses IChemObject, e.g.Molecule, and will read this (from file, database, internet etc).
    read(T) - Method in class org.openscience.cdk.io.MDLRXNV3000Reader
     
    read(T) - Method in class org.openscience.cdk.io.MDLV2000Reader
    Takes an object which subclasses IChemObject, e.g.
    read(T) - Method in class org.openscience.cdk.io.MDLV3000Reader
     
    read(T) - Method in class org.openscience.cdk.io.Mol2Reader
     
    read(T) - Method in class org.openscience.cdk.io.Mopac7Reader
     
    read(T) - Method in class org.openscience.cdk.io.MoSSOutputReader
    Read a IAtomContainerSet from the input source.
    read(T) - Method in class org.openscience.cdk.io.PCCompoundASNReader
     
    read(T) - Method in class org.openscience.cdk.io.PCCompoundXMLReader
     
    read(T) - Method in class org.openscience.cdk.io.PCSubstanceXMLReader
     
    read(T) - Method in class org.openscience.cdk.io.PDBReader
    Takes an object which subclasses IChemObject, e.g.
    read(T) - Method in class org.openscience.cdk.io.PMPReader
    reads the content from a PMP input.
    read(T) - Method in class org.openscience.cdk.io.rdf.CDKOWLReader
    Reads an IChemObject of type "object" from input.
    read(T) - Method in class org.openscience.cdk.io.RGroupQueryReader
    Check input IChemObject and proceed to parse.
    read(T) - Method in class org.openscience.cdk.io.ShelXReader
    Read a ChemFile from input.
    read(T) - Method in class org.openscience.cdk.io.SMILESReader
    Reads the content from a XYZ input.
    read(T) - Method in class org.openscience.cdk.io.VASPReader
     
    read(T) - Method in class org.openscience.cdk.io.XYZReader
    reads the content from a XYZ input.
    read(T) - Method in class org.openscience.cdk.io.ZMatrixReader
    Returns a IChemObject of type object bye reading from the input.
    readAtomBlock(IAtomContainer) - Method in class org.openscience.cdk.io.MDLV3000Reader
    Reads the atoms, coordinates and charges.
    readAtomTypeMappings() - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingReader
    Reads the atom type mappings from the data file.
    readAtomTypes(IChemObjectBuilder) - Method in class org.openscience.cdk.config.atomtypes.AtomTypeReader
    Reads the atom types from the data file.
    readAtomTypes(IChemObjectBuilder) - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeReader
    Reads the atom types from the data file.
    readAtomTypes(IChemObjectBuilder) - Method in class org.openscience.cdk.config.CDKBasedAtomTypeConfigurator
    Reads the atom types from the CDK based atom type list.
    readAtomTypes(IChemObjectBuilder) - Method in interface org.openscience.cdk.config.IAtomTypeConfigurator
    Reads a set of configured AtomType's into a List.
    readAtomTypes(IChemObjectBuilder) - Method in class org.openscience.cdk.config.OWLBasedAtomTypeConfigurator
    Reads the atom types from the OWL based atom type list.
    readAtomTypes(IChemObjectBuilder) - Method in class org.openscience.cdk.config.TXTBasedAtomTypeConfigurator
    Reads a text based configuration file.
    readBondBlock(IAtomContainer) - Method in class org.openscience.cdk.io.MDLV3000Reader
    Reads the bond atoms, order and stereo configuration.
    readChar() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
    Read a character.
    readChar() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
    Read a character.
    readConnectionTable(IChemObjectBuilder) - Method in class org.openscience.cdk.io.MDLV3000Reader
     
    readContent(int) - Method in class org.openscience.cdk.io.random.RandomAccessReader
    Reads the record text content into a String.
    readDictionary(Reader, String) - Method in class org.openscience.cdk.dict.DictionaryDatabase
    Reads a custom dictionary into the database.
    ReaderEvent - Class in org.openscience.cdk.io
    Signals that something has happened in a file reader.
    ReaderEvent(Object) - Constructor for class org.openscience.cdk.io.ReaderEvent
    Creates a reader event.
    ReaderFactory - Class in org.openscience.cdk.io
    A factory for creating ChemObjectReaders.
    ReaderFactory() - Constructor for class org.openscience.cdk.io.ReaderFactory
    Constructs a ReaderFactory which tries to detect the format in the first 65536 chars.
    ReaderFactory(int) - Constructor for class org.openscience.cdk.io.ReaderFactory
    Constructs a ReaderFactory which tries to detect the format in the first given number of chars.
    readHeader(IAtomContainer) - Method in class org.openscience.cdk.io.MDLV3000Reader
     
    readIsotopes() - Method in class org.openscience.cdk.config.isotopes.IsotopeReader
    Triggers the XML parsing of the data file and returns the read Isotopes.
    readLine() - Method in class org.openscience.cdk.io.MDLV3000Reader
     
    readMolecule(IChemObjectBuilder) - Method in class org.openscience.cdk.io.MDLV3000Reader
     
    ReadNCISdfFileAsTemplate(String) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor
     
    readParameterSets(IChemObjectBuilder) - Method in class org.openscience.cdk.modeling.builder3d.MM2BasedParameterSetReader
    The main method which parses through the force field configuration file
    readParameterSets(IChemObjectBuilder) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94BasedParameterSetReader
    The main method which parses through the force field configuration file
    readPharmacophoreDefinitions(String) - Static method in class org.openscience.cdk.pharmacophore.PharmacophoreUtils
    Read in a set of pharmacophore definitions to create pharmacophore queries.
    readPharmacophoreDefinitions(InputStream) - Static method in class org.openscience.cdk.pharmacophore.PharmacophoreUtils
    Read in a set of pharmacophore definitions to create pharmacophore queries.
    readRecord(int) - Method in interface org.openscience.cdk.io.random.IRandomAccessChemObjectReader
     
    readRecord(int) - Method in class org.openscience.cdk.io.random.RandomAccessReader
    Returns the object at given record No.
    readSGroup(IAtomContainer) - Method in class org.openscience.cdk.io.MDLV3000Reader
    Reads labels.
    real - Variable in class org.openscience.cdk.math.Complex
    The real part of this value
    realmatrix - Variable in class org.openscience.cdk.math.IMatrix
    the real part of the content
    realvector - Variable in class org.openscience.cdk.math.IVector
    The real part of this vector
    RearrangementAnionReaction - Class in org.openscience.cdk.reaction.type
    IReactionProcess which participate in movement resonance.
    RearrangementAnionReaction() - Constructor for class org.openscience.cdk.reaction.type.RearrangementAnionReaction
    Constructor of the RearrangementAnionReaction object
    RearrangementCationReaction - Class in org.openscience.cdk.reaction.type
    IReactionProcess which participate in movement resonance.
    RearrangementCationReaction() - Constructor for class org.openscience.cdk.reaction.type.RearrangementCationReaction
    Constructor of the RearrangementCharge2Reaction object
    RearrangementChargeMechanism - Class in org.openscience.cdk.reaction.mechanism
    This mechanism displaces the charge(radical, charge + or charge -) because of a double bond which is associated.
    RearrangementChargeMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.RearrangementChargeMechanism
     
    RearrangementLonePairReaction - Class in org.openscience.cdk.reaction.type
    IReactionProcess which participate in movement resonance.
    RearrangementLonePairReaction() - Constructor for class org.openscience.cdk.reaction.type.RearrangementLonePairReaction
    Constructor of the RearrangementLonePairReaction object
    RearrangementRadicalReaction - Class in org.openscience.cdk.reaction.type
    IReactionProcess which participate in movement resonance.
    RearrangementRadicalReaction() - Constructor for class org.openscience.cdk.reaction.type.RearrangementRadicalReaction
    Constructor of the RearrangementRadicalReaction object
    rebond(IAtomContainer) - Method in class org.openscience.cdk.graph.rebond.RebondTool
    Rebonding using a Binary Space Partition Tree.
    RebondTool - Class in org.openscience.cdk.graph.rebond
    Provides tools to rebond a molecule from 3D coordinates only.
    RebondTool(double, double, double) - Constructor for class org.openscience.cdk.graph.rebond.RebondTool
     
    recolor(Color) - Method in class org.openscience.cdk.renderer.elements.GeneralPath
    Recolor the path with the specified color.
    records - Variable in class org.openscience.cdk.io.random.RandomAccessReader
     
    RectangleElement - Class in org.openscience.cdk.renderer.elements
    A rectangle, with width and height.
    RectangleElement(double, double, double, double, Color) - Constructor for class org.openscience.cdk.renderer.elements.RectangleElement
    Make a rectangle from two opposite corners (x1, y1) and (x2, y2).
    RectangleElement(double, double, double, double, boolean, Color) - Constructor for class org.openscience.cdk.renderer.elements.RectangleElement
    Make a rectangle centered on (x, y).
    RecursiveSmartsAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
    This matches recursive smarts atoms.
    RecursiveSmartsAtom(IQueryAtomContainer) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.RecursiveSmartsAtom
    Creates a new instance
    RecursiveSmartsExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
     
    Refinable - Interface in org.openscience.cdk.group
    Implementors are graph-like objects that are refinable by the equitable and discrete partition refiners.
    refine(IAtomContainer) - Method in interface org.openscience.cdk.group.AtomContainerDiscretePartitionRefiner
    Refine an atom container, which has the side effect of calculating the automorphism group.
    refine(IAtomContainer, Partition) - Method in interface org.openscience.cdk.group.AtomContainerDiscretePartitionRefiner
    Refine an atom partition based on the connectivity in the atom container.
    register(Class<? extends T>) - Method in class org.openscience.cdk.DynamicFactory
    Registers a class with the factory.
    register(Class<T>, Class<? extends T>) - Method in class org.openscience.cdk.DynamicFactory
    Explicitly register a concrete class with a provided interface.
    register(Class<S>, Class<T>, DynamicFactory.CreationModifier<T>) - Method in class org.openscience.cdk.DynamicFactory
    Explicitly register a concrete class with a provided interface and a given modifier.
    register(Class<S>, Constructor<T>) - Method in class org.openscience.cdk.DynamicFactory
    Register a specific constructor with an explicit interface.
    register(Class<S>, Constructor<T>, DynamicFactory.CreationModifier<T>) - Method in class org.openscience.cdk.DynamicFactory
    Register a specific constructor with a creation modifier to an explicit interface.
    register(DynamicFactory.ConstructorKey, DynamicFactory.Creator<T>) - Method in class org.openscience.cdk.DynamicFactory
    Register a constructor key with a defined DynamicFactory.Creator.
    registerConvention(String, ICMLModule) - Method in class org.openscience.cdk.io.cml.CMLHandler
     
    registerConvention(String, ICMLModule) - Method in class org.openscience.cdk.io.CMLReader
     
    registerCustomizer(ICMLCustomizer) - Method in class org.openscience.cdk.io.CMLWriter
     
    registerCustomizer(ICMLCustomizer) - Method in class org.openscience.cdk.libio.cml.Convertor
     
    registerFontSizeMapping(double, int) - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
    For a particular zoom level, register a font point-size so that this size of font will be used when the zoom is at this level.
    registerFormat(IChemFormatMatcher) - Method in class org.openscience.cdk.io.FormatFactory
    Registers a format for detection.
    registerFormat(IChemFormatMatcher) - Method in class org.openscience.cdk.io.ReaderFactory
    Registers a format for detection.
    registerParameters(IGenerator<? extends IChemObject>) - Method in class org.openscience.cdk.renderer.RendererModel
    Registers rendering parameters from IGenerators with this model.
    registerWriter(Class<?>) - Method in class org.openscience.cdk.io.WriterFactory
     
    ReInit(InputStream) - Method in class org.openscience.cdk.iupac.parser.NomParser
    Deprecated.
    Reinitialise.
    ReInit(InputStream, String) - Method in class org.openscience.cdk.iupac.parser.NomParser
    Deprecated.
    Reinitialise.
    ReInit(Reader) - Method in class org.openscience.cdk.iupac.parser.NomParser
    Deprecated.
    Reinitialise.
    ReInit(NomParserTokenManager) - Method in class org.openscience.cdk.iupac.parser.NomParser
    Deprecated.
    Reinitialise.
    ReInit(SimpleCharStream) - Method in class org.openscience.cdk.iupac.parser.NomParserTokenManager
    Reinitialise parser.
    ReInit(SimpleCharStream, int) - Method in class org.openscience.cdk.iupac.parser.NomParserTokenManager
    Reinitialise parser.
    ReInit(Reader, int, int, int) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
    Reinitialise.
    ReInit(Reader, int, int) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
    Reinitialise.
    ReInit(Reader) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
    Reinitialise.
    ReInit(InputStream, String, int, int, int) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
    Reinitialise.
    ReInit(InputStream, int, int, int) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
    Reinitialise.
    ReInit(InputStream, String) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
    Reinitialise.
    ReInit(InputStream) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
    Reinitialise.
    ReInit(InputStream, String, int, int) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
    Reinitialise.
    ReInit(InputStream, int, int) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
    Reinitialise.
    ReInit(Reader, int, int, int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
    Reinitialise.
    ReInit(Reader, int, int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
    Reinitialise.
    ReInit(Reader) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
    Reinitialise.
    ReInit(InputStream, String, int, int, int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
    Reinitialise.
    ReInit(InputStream, int, int, int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
    Reinitialise.
    ReInit(InputStream, String) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
    Reinitialise.
    ReInit(InputStream) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
    Reinitialise.
    ReInit(InputStream, String, int, int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
    Reinitialise.
    ReInit(InputStream, int, int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
    Reinitialise.
    ReInit(InputStream) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
    Reinitialise.
    ReInit(InputStream, String) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
    Reinitialise.
    ReInit(Reader) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
    Reinitialise.
    ReInit(SMARTSParserTokenManager) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
    Reinitialise.
    ReInit(SimpleCharStream) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager
    Reinitialise parser.
    ReInit(SimpleCharStream, int) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager
    Reinitialise parser.
    relatedChemObjects() - Method in class org.openscience.cdk.debug.DebugMapping
    Returns an Iterable to the two IChemObjects.
    relatedChemObjects() - Method in interface org.openscience.cdk.interfaces.IMapping
    Returns an Iterable to the two IChemObjects.
    relatedChemObjects() - Method in class org.openscience.cdk.Mapping
    Returns an Iterable to the two IChemObjects.
    relatedChemObjects() - Method in class org.openscience.cdk.silent.Mapping
    Returns an Iterable to the two IChemObjects.
    relevant() - Static method in class org.openscience.cdk.graph.Cycles
    Create a cycle finder which will compute the relevant cycle basis (RC) of a molecule.
    relevant(IAtomContainer) - Static method in class org.openscience.cdk.graph.Cycles
    Find the relevant cycles of a molecule.
    RELEVANT_RINGS - Static variable in class org.openscience.cdk.CDKConstants
    The relevant rings computed for this molecule.
    RelevantCycles - Class in org.openscience.cdk.graph
    Compute the relevant cycles (CR) of a graph.
    RelevantCycles(int[][]) - Constructor for class org.openscience.cdk.graph.RelevantCycles
    Generate the relevant cycle basis for a graph.
    relevantCycles() - Method in class org.openscience.cdk.ringsearch.cyclebasis.CycleBasis
    Deprecated.
    Returns the essential cycles of this cycle basis.
    relevantCycles() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis
    Deprecated.
     
    REMARK - Static variable in class org.openscience.cdk.CDKConstants
    A remark for a IChemObject.
    remove(IAtomContainer) - Method in class org.openscience.cdk.AtomContainer
    Removes all atoms and electronContainers of a given atomcontainer from this container.
    remove(Object) - Method in class org.openscience.cdk.ConformerContainer
    Remove the specified conformer.
    remove(int) - Method in class org.openscience.cdk.ConformerContainer
    Removes the conformer at the specified position.
    remove(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugAminoAcid
    Removes all atoms and electronContainers of a given atomcontainer from this container.
    remove(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainer
    Removes all atoms and electronContainers of a given atomcontainer from this container.
    remove(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugBioPolymer
    Removes all atoms and electronContainers of a given atomcontainer from this container.
    remove(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugCrystal
    Removes all atoms and electronContainers of a given atomcontainer from this container.
    remove(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugMonomer
    Removes all atoms and electronContainers of a given atomcontainer from this container.
    remove(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugPolymer
    Removes all atoms and electronContainers of a given atomcontainer from this container.
    remove(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugRing
    Removes all atoms and electronContainers of a given atomcontainer from this container.
    remove(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugStrand
    Removes all atoms and electronContainers of a given atomcontainer from this container.
    remove() - Method in class org.openscience.cdk.graph.AtomContainerPermutor
     
    remove() - Method in class org.openscience.cdk.graph.MinimalPathIterator
     
    remove(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
    Removes all atoms and electronContainers of a given atomcontainer from this container.
    remove() - Method in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader
    File IO generally does not support removing of entries.
    remove() - Method in class org.openscience.cdk.io.iterator.event.DefaultEventChemObjectReader
    File IO generally does not support removing of entries.
    remove() - Method in class org.openscience.cdk.io.iterator.IteratingMDLConformerReader
     
    remove() - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundASNReader
     
    remove() - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader
     
    remove() - Method in class org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader
     
    remove() - Method in class org.openscience.cdk.io.iterator.IteratingSDFReader
     
    remove() - Method in class org.openscience.cdk.io.iterator.IteratingSMILESReader
     
    remove() - Method in class org.openscience.cdk.io.random.RandomAccessSDFReader
     
    remove(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
    Removes all atoms and electronContainers of a given atomcontainer from this container.
    remove(int) - Method in class org.openscience.cdk.signature.Orbit
    Removes an atom index from the orbit.
    remove(IAtomContainer) - Method in class org.openscience.cdk.silent.AtomContainer
    Removes all atoms and electronContainers of a given atomcontainer from this container.
    remove() - Method in class org.openscience.cdk.smsd.labelling.AtomContainerAtomPermutor
    Deprecated.
    remove(IAtom) - Method in class org.openscience.cdk.smsd.ring.PathGraph
    Deprecated.
     
    remove(IMolecularFormulaSet, IMolecularFormula, IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaSetManipulator
    Remove all those IMolecularFormula which are not fit theirs IElement occurrence into a limits.
    remove(IMolecularFormulaSet, MolecularFormulaRange) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaSetManipulator
    Remove all those IMolecularFormula which are not fit theirs IElement occurrence into a limits.
    removeAcidicOxygen(IAminoAcid) - Static method in class org.openscience.cdk.tools.manipulator.AminoAcidManipulator
    Removes the singly bonded oxygen from the acid group of the AminoAcid.
    removeAll(Collection<?>) - Method in class org.openscience.cdk.ConformerContainer
     
    removeAllAtomContainers() - Method in class org.openscience.cdk.AtomContainerSet
    Removes all AtomContainer from this container.
    removeAllAtomContainers() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
    Removes all AtomContainer from this container.
    removeAllAtomContainers() - Method in class org.openscience.cdk.debug.DebugSubstance
    Removes all AtomContainer from this container.
    removeAllAtomContainers() - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
    Removes all AtomContainer from this container.
    removeAllAtomContainers() - Method in class org.openscience.cdk.silent.AtomContainerSet
    Removes all AtomContainer from this container.
    removeAllBonds() - Method in class org.openscience.cdk.AtomContainer
    Removes all Bonds from this container.
    removeAllBonds() - Method in class org.openscience.cdk.debug.DebugAminoAcid
    Removes all Bonds from this container.
    removeAllBonds() - Method in class org.openscience.cdk.debug.DebugAtomContainer
    Removes all Bonds from this container.
    removeAllBonds() - Method in class org.openscience.cdk.debug.DebugBioPolymer
    Removes all Bonds from this container.
    removeAllBonds() - Method in class org.openscience.cdk.debug.DebugCrystal
    Removes all Bonds from this container.
    removeAllBonds() - Method in class org.openscience.cdk.debug.DebugMonomer
    Removes all Bonds from this container.
    removeAllBonds() - Method in class org.openscience.cdk.debug.DebugPolymer
    Removes all Bonds from this container.
    removeAllBonds() - Method in class org.openscience.cdk.debug.DebugRing
    Removes all Bonds from this container.
    removeAllBonds() - Method in class org.openscience.cdk.debug.DebugStrand
    Removes all Bonds from this container.
    removeAllBonds() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
    Removes all Bonds from this container.
    removeAllBonds() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
    Removes all Bonds from this container.
    removeAllBonds() - Method in class org.openscience.cdk.silent.AtomContainer
    Removes all Bonds from this container.
    removeAllElectronContainers() - Method in class org.openscience.cdk.AtomContainer
    Removes electronContainers from this container.
    removeAllElectronContainers() - Method in class org.openscience.cdk.debug.DebugAminoAcid
    Removes electronContainers from this container.
    removeAllElectronContainers() - Method in class org.openscience.cdk.debug.DebugAtomContainer
    Removes electronContainers from this container.
    removeAllElectronContainers() - Method in class org.openscience.cdk.debug.DebugBioPolymer
    Removes electronContainers from this container.
    removeAllElectronContainers() - Method in class org.openscience.cdk.debug.DebugCrystal
    Removes electronContainers from this container.
    removeAllElectronContainers() - Method in class org.openscience.cdk.debug.DebugMonomer
    Removes electronContainers from this container.
    removeAllElectronContainers() - Method in class org.openscience.cdk.debug.DebugPolymer
    Removes electronContainers from this container.
    removeAllElectronContainers() - Method in class org.openscience.cdk.debug.DebugRing
    Removes electronContainers from this container.
    removeAllElectronContainers() - Method in class org.openscience.cdk.debug.DebugStrand
    Removes electronContainers from this container.
    removeAllElectronContainers() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
    Removes electronContainers from this container.
    removeAllElectronContainers() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
    Removes electronContainers from this container.
    removeAllElectronContainers() - Method in class org.openscience.cdk.silent.AtomContainer
    Removes electronContainers from this container.
    removeAllElements() - Method in class org.openscience.cdk.AtomContainer
    Removes all atoms, bonds and stereo elements from this container.
    removeAllElements() - Method in class org.openscience.cdk.debug.DebugAminoAcid
    Removes all atoms, bonds and stereo elements from this container.
    removeAllElements() - Method in class org.openscience.cdk.debug.DebugAtomContainer
    Removes all atoms, bonds and stereo elements from this container.
    removeAllElements() - Method in class org.openscience.cdk.debug.DebugBioPolymer
    Removes all atoms, bonds and stereo elements from this container.
    removeAllElements() - Method in class org.openscience.cdk.debug.DebugCrystal
    Removes all atoms, bonds and stereo elements from this container.
    removeAllElements() - Method in class org.openscience.cdk.debug.DebugMonomer
    Removes all atoms, bonds and stereo elements from this container.
    removeAllElements() - Method in class org.openscience.cdk.debug.DebugPolymer
    Removes all atoms, bonds and stereo elements from this container.
    removeAllElements() - Method in class org.openscience.cdk.debug.DebugRing
    Removes all atoms, bonds and stereo elements from this container.
    removeAllElements() - Method in class org.openscience.cdk.debug.DebugStrand
    Removes all atoms, bonds and stereo elements from this container.
    removeAllElements() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
    Removes all atoms, bonds and stereo elements from this container.
    removeAllElements() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
    Removes all atoms and bond from this container.
    removeAllElements() - Method in class org.openscience.cdk.silent.AtomContainer
    Removes all atoms, bonds and stereo elements from this container.
    removeAllIsotopes() - Method in class org.openscience.cdk.debug.DebugMolecularFormula
    Removes all isotopes of this molecular formula.
    removeAllIsotopes() - Method in class org.openscience.cdk.formula.MolecularFormula
    Removes all isotopes of this molecular formula.
    removeAllIsotopes() - Method in class org.openscience.cdk.formula.MolecularFormulaRange
    Removes all isotopes of this molecular formula.
    removeAllIsotopes() - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
    Removes all isotopes of this molecular formula.
    removeAllIsotopes() - Method in class org.openscience.cdk.silent.MolecularFormula
    Removes all isotopes of this molecular formula.
    removeAllMolecularFormulas() - Method in class org.openscience.cdk.debug.DebugAdductFormula
    Removes all IMolecularFormula from this chemObject.
    removeAllMolecularFormulas() - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet
    Removes all IMolecularFormula from this chemObject.
    removeAllMolecularFormulas() - Method in class org.openscience.cdk.formula.AdductFormula
    Removes all IMolecularFormula from this chemObject.
    removeAllMolecularFormulas() - Method in class org.openscience.cdk.formula.MolecularFormulaSet
    Removes all IMolecularFormula from this chemObject.
    removeAllMolecularFormulas() - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet
    Removes all IMolecularFormula of this IMolecularFormulaSet.
    removeAllMolecularFormulas() - Method in class org.openscience.cdk.silent.AdductFormula
    Removes all IMolecularFormula from this chemObject.
    removeAllMolecularFormulas() - Method in class org.openscience.cdk.silent.MolecularFormulaSet
    Removes all IMolecularFormula from this chemObject.
    removeAllReactions() - Method in class org.openscience.cdk.debug.DebugReactionSet
    Removes all Reactions from this container.
    removeAllReactions() - Method in interface org.openscience.cdk.interfaces.IReactionSet
    Removes all reactions from this set.
    removeAllReactions() - Method in class org.openscience.cdk.ReactionSet
    Removes all Reactions from this container.
    removeAllReactions() - Method in class org.openscience.cdk.silent.ReactionSet
    Removes all Reactions from this container.
    removeAllReactionSchemes() - Method in class org.openscience.cdk.debug.DebugReactionScheme
    Removes all IReactionScheme from this chemObject.
    removeAllReactionSchemes() - Method in interface org.openscience.cdk.interfaces.IReactionScheme
    Removes all IReactionScheme from this chemObject.
    removeAllReactionSchemes() - Method in class org.openscience.cdk.ReactionScheme
    Removes all IReactionScheme from this chemObject.
    removeAllReactionSchemes() - Method in class org.openscience.cdk.silent.ReactionScheme
    Removes all IReactionScheme from this chemObject.
    removeAromaticityFlagsFromHoseCode(String) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
     
    removeAtom(int) - Method in class org.openscience.cdk.AtomContainer
    Removes the atom at the given position from the AtomContainer.
    removeAtom(IAtom) - Method in class org.openscience.cdk.AtomContainer
    Removes the given atom from the AtomContainer.
    removeAtom(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid
    Removes the atom at the given position from the AtomContainer.
    removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
    Removes the given atom from the AtomContainer.
    removeAtom(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer
    Removes the atom at the given position from the AtomContainer.
    removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
    Removes the given atom from the AtomContainer.
    removeAtom(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer
    Removes the atom at the given position from the AtomContainer.
    removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
    Removes the given atom from the AtomContainer.
    removeAtom(int) - Method in class org.openscience.cdk.debug.DebugCrystal
    Removes the atom at the given position from the AtomContainer.
    removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
    Removes the given atom from the AtomContainer.
    removeAtom(int) - Method in class org.openscience.cdk.debug.DebugMonomer
    Removes the atom at the given position from the AtomContainer.
    removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
    Removes the given atom from the AtomContainer.
    removeAtom(int) - Method in class org.openscience.cdk.debug.DebugPolymer
    Removes the atom at the given position from the AtomContainer.
    removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
    Removes the given atom from the AtomContainer.
    removeAtom(int) - Method in class org.openscience.cdk.debug.DebugRing
    Removes the atom at the given position from the AtomContainer.
    removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
    Removes the given atom from the AtomContainer.
    removeAtom(int) - Method in class org.openscience.cdk.debug.DebugStrand
    Removes the atom at the given position from the AtomContainer.
    removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
    Removes the given atom from the AtomContainer.
    removeAtom(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
    Removes the atom at the given position from the AtomContainer.
    removeAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
    Removes the given atom from the AtomContainer.
    removeAtom(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
    Removes the atom at the given position from the AtomContainer.
    removeAtom(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
    Removes the given atom from the AtomContainer.
    removeAtom(int) - Method in class org.openscience.cdk.silent.AtomContainer
    Removes the atom at the given position from the AtomContainer.
    removeAtom(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
    Removes the given atom from the AtomContainer.
    removeAtomAndConnectedElectronContainers(IAtom) - Method in class org.openscience.cdk.AtomContainer
    Removes the given atom and all connected electronContainers from the AtomContainer.
    removeAtomAndConnectedElectronContainers(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
    Removes the given atom and all connected electronContainers from the AtomContainer.
    removeAtomAndConnectedElectronContainers(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
    Removes the given atom and all connected electronContainers from the AtomContainer.
    removeAtomAndConnectedElectronContainers(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
    Removes the given atom and all connected electronContainers from the AtomContainer.
    removeAtomAndConnectedElectronContainers(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
    Removes the given atom and all connected electronContainers from the AtomContainer.
    removeAtomAndConnectedElectronContainers(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
    Removes the given atom and all connected electronContainers from the AtomContainer.
    removeAtomAndConnectedElectronContainers(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
    Removes the given atom and all connected electronContainers from the AtomContainer.
    removeAtomAndConnectedElectronContainers(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
    Removes the given atom and all connected electronContainers from the AtomContainer.
    removeAtomAndConnectedElectronContainers(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
    Removes the given atom and all connected electronContainers from the AtomContainer.
    removeAtomAndConnectedElectronContainers(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
    Removes the given atom and all connected electronContainers from the AtomContainer.
    removeAtomAndConnectedElectronContainers(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
    Removes the given atom and all connected electronContainers from the AtomContainer.
    removeAtomAndConnectedElectronContainers(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
    Removes the given atom and all connected electronContainers from the AtomContainer.
    removeAtomAndConnectedElectronContainers(IAtomContainerSet, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
     
    removeAtomAndConnectedElectronContainers(IChemModel, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
    Remove an Atom and the connected ElectronContainers from all AtomContainers inside an IChemModel.
    removeAtomAndConnectedElectronContainers(IAtomContainerSet, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
     
    removeAtomAndConnectedElectronContainers(IReaction, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
     
    removeAtomAndConnectedElectronContainers(IReactionSet, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
     
    removeAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.AtomContainerSet
    Removes an AtomContainer from this container.
    removeAtomContainer(int) - Method in class org.openscience.cdk.AtomContainerSet
    Removes an AtomContainer from this container.
    removeAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
    Removes an AtomContainer from this container.
    removeAtomContainer(int) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
    Removes an AtomContainer from this container.
    removeAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugSubstance
    Removes an AtomContainer from this container.
    removeAtomContainer(int) - Method in class org.openscience.cdk.debug.DebugSubstance
    Removes an AtomContainer from this container.
    removeAtomContainer(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
    Removes an AtomContainer from this container.
    removeAtomContainer(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
    Removes an AtomContainer from this container.
    removeAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.silent.AtomContainerSet
    Removes an AtomContainer from this container.
    removeAtomContainer(int) - Method in class org.openscience.cdk.silent.AtomContainerSet
    Removes an AtomContainer from this container.
    removeAtomVectors() - Method in class org.openscience.cdk.Vibration
    Removes all atom vectors from this vibration.
    removeBond(int) - Method in class org.openscience.cdk.AtomContainer
    Removes the bond at the given position from the AtomContainer.
    removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.AtomContainer
    Removes the bond that connects the two given atoms.
    removeBond(IBond) - Method in class org.openscience.cdk.AtomContainer
    Removes the bond from this container.
    removeBond(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid
    Removes the bond at the given position from the AtomContainer.
    removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
    Removes the bond that connects the two given atoms.
    removeBond(IBond) - Method in class org.openscience.cdk.debug.DebugAminoAcid
    Removes the bond from this container.
    removeBond(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer
    Removes the bond at the given position from the AtomContainer.
    removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
    Removes the bond that connects the two given atoms.
    removeBond(IBond) - Method in class org.openscience.cdk.debug.DebugAtomContainer
    Removes the bond from this container.
    removeBond(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer
    Removes the bond at the given position from the AtomContainer.
    removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
    Removes the bond that connects the two given atoms.
    removeBond(IBond) - Method in class org.openscience.cdk.debug.DebugBioPolymer
    Removes the bond from this container.
    removeBond(int) - Method in class org.openscience.cdk.debug.DebugCrystal
    Removes the bond at the given position from the AtomContainer.
    removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
    Removes the bond that connects the two given atoms.
    removeBond(IBond) - Method in class org.openscience.cdk.debug.DebugCrystal
    Removes the bond from this container.
    removeBond(int) - Method in class org.openscience.cdk.debug.DebugMonomer
    Removes the bond at the given position from the AtomContainer.
    removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
    Removes the bond that connects the two given atoms.
    removeBond(IBond) - Method in class org.openscience.cdk.debug.DebugMonomer
    Removes the bond from this container.
    removeBond(int) - Method in class org.openscience.cdk.debug.DebugPolymer
    Removes the bond at the given position from the AtomContainer.
    removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
    Removes the bond that connects the two given atoms.
    removeBond(IBond) - Method in class org.openscience.cdk.debug.DebugPolymer
    Removes the bond from this container.
    removeBond(int) - Method in class org.openscience.cdk.debug.DebugRing
    Removes the bond at the given position from the AtomContainer.
    removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugRing
    Removes the bond that connects the two given atoms.
    removeBond(IBond) - Method in class org.openscience.cdk.debug.DebugRing
    Removes the bond from this container.
    removeBond(int) - Method in class org.openscience.cdk.debug.DebugStrand
    Removes the bond at the given position from the AtomContainer.
    removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
    Removes the bond that connects the two given atoms.
    removeBond(IBond) - Method in class org.openscience.cdk.debug.DebugStrand
    Removes the bond from this container.
    removeBond(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
    Removes the bond at the given position from the AtomContainer.
    removeBond(IAtom, IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
    Removes the bond that connects the two given atoms.
    removeBond(IBond) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
    Removes the bond from this container.
    removeBond(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
    Removes the bond at the given position from the AtomContainer.
    removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
    Removes the bond that connects the two given atoms.
    removeBond(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
    Removes the bond from this container.
    removeBond(int) - Method in class org.openscience.cdk.silent.AtomContainer
    Removes the bond at the given position from the AtomContainer.
    removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
    Removes the bond that connects the two given atoms.
    removeBond(IBond) - Method in class org.openscience.cdk.silent.AtomContainer
    Removes the bond from this container.
    removeCDKChangeListener(ICDKChangeListener) - Method in class org.openscience.cdk.renderer.RendererModel
    Removes a change listener from the list of listeners.
    removeCell(int) - Method in class org.openscience.cdk.group.Partition
    Removes the cell at the specified index.
    removeChemModel(int) - Method in class org.openscience.cdk.ChemSequence
    Remove a ChemModel from this ChemSequence.
    removeChemModel(int) - Method in class org.openscience.cdk.debug.DebugChemSequence
    Remove a ChemModel from this ChemSequence.
    removeChemModel(int) - Method in interface org.openscience.cdk.interfaces.IChemSequence
    Remove a ChemModel from this ChemSequence.
    removeChemModel(int) - Method in class org.openscience.cdk.silent.ChemSequence
    Remove a ChemModel from this ChemSequence.
    removeChemObjectIOListener(IChemObjectIOListener) - Method in class org.openscience.cdk.io.ChemObjectIO
    Removes a IChemObjectIOListener from this IChemObjectIO.
    removeChemObjectIOListener(IChemObjectIOListener) - Method in interface org.openscience.cdk.io.IChemObjectIO
    Removes a IChemObjectIOListener from this IChemObjectIO.
    removeChemObjectIOListener(IChemObjectIOListener) - Method in class org.openscience.cdk.io.random.DefaultRandomAccessChemObjectReader
     
    removeChemObjectIOListener(IChemObjectIOListener) - Method in class org.openscience.cdk.io.random.RandomAccessReader
     
    removeChemSequence(int) - Method in class org.openscience.cdk.ChemFile
    Removes a ChemSequence from this container.
    removeChemSequence(int) - Method in class org.openscience.cdk.debug.DebugChemFile
    Removes a ChemSequence from this container.
    removeChemSequence(int) - Method in interface org.openscience.cdk.interfaces.IChemFile
    Removes the IChemSequence at the given position from this container.
    removeChemSequence(int) - Method in class org.openscience.cdk.silent.ChemFile
    Removes a ChemSequence from this container.
    removeElectronContainer(int) - Method in class org.openscience.cdk.AtomContainer
    Removes the bond at the given position from this container.
    removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.AtomContainer
    Removes this ElectronContainer from this container.
    removeElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid
    Removes the bond at the given position from this container.
    removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugAminoAcid
    Removes this ElectronContainer from this container.
    removeElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer
    Removes the bond at the given position from this container.
    removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainer
    Removes this ElectronContainer from this container.
    removeElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer
    Removes the bond at the given position from this container.
    removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugBioPolymer
    Removes this ElectronContainer from this container.
    removeElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugCrystal
    Removes the bond at the given position from this container.
    removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugCrystal
    Removes this ElectronContainer from this container.
    removeElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugMonomer
    Removes the bond at the given position from this container.
    removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugMonomer
    Removes this ElectronContainer from this container.
    removeElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugPolymer
    Removes the bond at the given position from this container.
    removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugPolymer
    Removes this ElectronContainer from this container.
    removeElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugRing
    Removes the bond at the given position from this container.
    removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugRing
    Removes this ElectronContainer from this container.
    removeElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugStrand
    Removes the bond at the given position from this container.
    removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugStrand
    Removes this ElectronContainer from this container.
    removeElectronContainer(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
    Removes the bond at the given position from this container.
    removeElectronContainer(IElectronContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
    Removes this ElectronContainer from this container.
    removeElectronContainer(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
    Removes the bond at the given position from this container.
    removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
    Removes this ElectronContainer from this container.
    removeElectronContainer(int) - Method in class org.openscience.cdk.silent.AtomContainer
    Removes the bond at the given position from this container.
    removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.silent.AtomContainer
    Removes this ElectronContainer from this container.
    removeElectronContainer(IAtomContainerSet, IElectronContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
     
    removeElectronContainer(IChemModel, IElectronContainer) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
    Remove an ElectronContainer from all AtomContainers inside an IChemModel.
    removeElectronContainer(IAtomContainerSet, IElectronContainer) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
     
    removeElectronContainer(IReaction, IElectronContainer) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
     
    removeElectronContainer(IReactionSet, IElectronContainer) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
     
    removeElement(IMolecularFormula, IElement) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
    Removes all isotopes from a given element in the MolecularFormula.
    removeHydrogens(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
    Create an copy of the org structure with explicit hydrogens removed.
    removeHydrogensAndPreserveAtomID(IAtomContainer) - Static method in class org.openscience.cdk.normalize.SMSDNormalizer
    Deprecated.
    Returns IAtomContainer without Hydrogen.
    removeHydrogensExceptSingleAndPreserveAtomID(IAtomContainer) - Static method in class org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator
    Deprecated.
    Returns IAtomContainer without Hydrogen.
    removeHydrogensPreserveMultiplyBonded(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
    Deprecated.
    removeIsotope(IIsotope) - Method in class org.openscience.cdk.debug.DebugMolecularFormula
    Removes the given isotope from the MolecularFormula.
    removeIsotope(IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormula
    Removes the given isotope from the MolecularFormula.
    removeIsotope(IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormulaRange
    Removes the given isotope from the MolecularFormulaExpand.
    removeIsotope(IIsotope) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
    Removes the given isotope from the MolecularFormula.
    removeIsotope(IIsotope) - Method in class org.openscience.cdk.silent.MolecularFormula
    Removes the given isotope from the MolecularFormula.
    removeListener(IChemObjectListener) - Method in class org.openscience.cdk.ChemObject
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAminoAcid
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAtom
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAtomContainer
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAtomType
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugBioPolymer
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugBond
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugChemFile
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugChemModel
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugChemObject
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugChemSequence
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugCrystal
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugElectronContainer
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugElement
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugIsotope
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugLonePair
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugMapping
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugMonomer
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugPolymer
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugReaction
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugReactionScheme
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugReactionSet
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugRing
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugSingleElectron
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugStrand
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugSubstance
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    removeListener(IChemObjectListener) - Method in interface org.openscience.cdk.interfaces.IChemObject
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    removeListener(IChemObjectListener) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    removeListener(IChemObjectListener) - Method in class org.openscience.cdk.silent.ChemObject
    Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
    removeLonePair(int) - Method in class org.openscience.cdk.AtomContainer
    Removes the lone pair at the given position from the AtomContainer.
    removeLonePair(ILonePair) - Method in class org.openscience.cdk.AtomContainer
    Removes the lone pair from the AtomContainer.
    removeLonePair(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid
    Removes the lone pair at the given position from the AtomContainer.
    removeLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugAminoAcid
    Removes the lone pair from the AtomContainer.
    removeLonePair(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer
    Removes the lone pair at the given position from the AtomContainer.
    removeLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugAtomContainer
    Removes the lone pair from the AtomContainer.
    removeLonePair(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer
    Removes the lone pair at the given position from the AtomContainer.
    removeLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugBioPolymer
    Removes the lone pair from the AtomContainer.
    removeLonePair(int) - Method in class org.openscience.cdk.debug.DebugCrystal
    Removes the lone pair at the given position from the AtomContainer.
    removeLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugCrystal
    Removes the lone pair from the AtomContainer.
    removeLonePair(int) - Method in class org.openscience.cdk.debug.DebugMonomer
    Removes the lone pair at the given position from the AtomContainer.
    removeLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugMonomer
    Removes the lone pair from the AtomContainer.
    removeLonePair(int) - Method in class org.openscience.cdk.debug.DebugPolymer
    Removes the lone pair at the given position from the AtomContainer.
    removeLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugPolymer
    Removes the lone pair from the AtomContainer.
    removeLonePair(int) - Method in class org.openscience.cdk.debug.DebugRing
    Removes the lone pair at the given position from the AtomContainer.
    removeLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugRing
    Removes the lone pair from the AtomContainer.
    removeLonePair(int) - Method in class org.openscience.cdk.debug.DebugStrand
    Removes the lone pair at the given position from the AtomContainer.
    removeLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugStrand
    Removes the lone pair from the AtomContainer.
    removeLonePair(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
    Removes the lone pair at the given position from the AtomContainer.
    removeLonePair(ILonePair) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
    Removes the lone pair from the AtomContainer.
    removeLonePair(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
    Removes the lone pair at the given position from the AtomContainer.
    removeLonePair(ILonePair) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
    Removes the lone pair from the AtomContainer.
    removeLonePair(int) - Method in class org.openscience.cdk.silent.AtomContainer
    Removes the lone pair at the given position from the AtomContainer.
    removeLonePair(ILonePair) - Method in class org.openscience.cdk.silent.AtomContainer
    Removes the lone pair from the AtomContainer.
    removeLoopBonds(IAtomContainer, int) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor
     
    removeMapping(int) - Method in interface org.openscience.cdk.interfaces.IReaction
    Removes a mapping between the reactant and product side to this Reaction.
    removeMapping(int) - Method in class org.openscience.cdk.Reaction
    Removes a mapping between the reactant and product side to this Reaction.
    removeMapping(int) - Method in class org.openscience.cdk.silent.Reaction
    Removes a mapping between the reactant and product side to this Reaction.
    removeMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugAdductFormula
    Removes an IMolecularFormula from this chemObject.
    removeMolecularFormula(int) - Method in class org.openscience.cdk.debug.DebugAdductFormula
    Removes an MolecularFormula from this chemObject.
    removeMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet
    Removes an IMolecularFormula from this chemObject.
    removeMolecularFormula(int) - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet
    Removes an MolecularFormula from this chemObject.
    removeMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.formula.AdductFormula
    Removes an IMolecularFormula from this chemObject.
    removeMolecularFormula(int) - Method in class org.openscience.cdk.formula.AdductFormula
    Removes an MolecularFormula from this chemObject.
    removeMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.formula.MolecularFormulaSet
    Removes an IMolecularFormula from this chemObject.
    removeMolecularFormula(int) - Method in class org.openscience.cdk.formula.MolecularFormulaSet
    Removes an MolecularFormula from this chemObject.
    removeMolecularFormula(IMolecularFormula) - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet
    Removes the given IMolecularFormula from the IMolecularFormulaSet.
    removeMolecularFormula(int) - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet
    Removes the IMolecularFormula at the given position from the IMolecularFormulaSet.
    removeMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.silent.AdductFormula
    Removes an IMolecularFormula from this chemObject.
    removeMolecularFormula(int) - Method in class org.openscience.cdk.silent.AdductFormula
    Removes an MolecularFormula from this chemObject.
    removeMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.silent.MolecularFormulaSet
    Removes an IMolecularFormula from this chemObject.
    removeMolecularFormula(int) - Method in class org.openscience.cdk.silent.MolecularFormulaSet
    Removes an MolecularFormula from this chemObject.
    removeMolecule(IAtomContainer) - Method in class org.openscience.cdk.layout.TemplateHandler
     
    removeMonomer(String) - Method in class org.openscience.cdk.debug.DebugBioPolymer
    Removes a particular monomer, specified by its name.
    removeMonomer(String) - Method in class org.openscience.cdk.debug.DebugPolymer
    Removes a particular monomer, specified by its name.
    removeMonomer(String) - Method in class org.openscience.cdk.debug.DebugStrand
    Removes a particular monomer, specified by its name.
    removeMonomer(String) - Method in interface org.openscience.cdk.interfaces.IPolymer
    Removes a particular monomer, specified by its name.
    removeMonomer(String) - Method in interface org.openscience.cdk.interfaces.IStrand
    Removes a particular monomer, specified by its name.
    removeMonomer(String) - Method in class org.openscience.cdk.Polymer
    Removes a particular monomer, specified by its name.
    removeMonomer(String) - Method in class org.openscience.cdk.silent.Polymer
    Removes a particular monomer, specified by its name.
    removeMonomer(String) - Method in class org.openscience.cdk.silent.Strand
    Removes a particular monomer, specified by its name.
    removeMonomer(String) - Method in class org.openscience.cdk.Strand
    Removes a particular monomer, specified by its name.
    removeNonChiralHydrogens(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
    Produces an AtomContainer without explicit non stereo-relevant Hs but with H count from one with Hs.
    removeParents(Collection<Sgroup>) - Method in class org.openscience.cdk.sgroup.Sgroup
    Remove the specified parent associations from this Sgroup.
    removeProperty(Object) - Method in class org.openscience.cdk.ChemObject
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugAminoAcid
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugAtom
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugAtomContainer
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugAtomType
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugBioPolymer
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugBond
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugChemFile
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugChemModel
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugChemObject
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugChemSequence
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugCrystal
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugElectronContainer
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugElement
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugIsotope
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugLonePair
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugMapping
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugMolecularFormula
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugMonomer
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugPolymer
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugReaction
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugReactionScheme
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugReactionSet
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugRing
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugSingleElectron
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugStrand
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugSubstance
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.formula.MolecularFormula
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in interface org.openscience.cdk.interfaces.IChemObject
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.silent.ChemObject
    Removes a property for a IChemObject.
    removeProperty(Object) - Method in class org.openscience.cdk.silent.MolecularFormula
    Removes a property for a IChemObject.
    removeReaction(IReaction) - Method in class org.openscience.cdk.debug.DebugReactionSet
    Removes all instances of a reaction from this IReactionSet.
    removeReaction(int) - Method in interface org.openscience.cdk.interfaces.IReactionSet
    Remove a reaction from this set.
    removeReaction(IReaction) - Method in interface org.openscience.cdk.interfaces.IReactionSet
    Removes all instances of a reaction from this IReactionSet.
    removeReaction(int) - Method in class org.openscience.cdk.ReactionSet
    Remove a reaction from this set.
    removeReaction(IReaction) - Method in class org.openscience.cdk.ReactionSet
     
    removeReaction(int) - Method in class org.openscience.cdk.silent.ReactionSet
    Remove a reaction from this set.
    removeReaction(IReaction) - Method in class org.openscience.cdk.silent.ReactionSet
     
    removeReactionScheme(IReactionScheme) - Method in interface org.openscience.cdk.interfaces.IReactionScheme
    Removes an IReactionScheme from this chemObject.
    removeReactionScheme(IReactionScheme) - Method in class org.openscience.cdk.ReactionScheme
    Removes an IReactionScheme from this chemObject.
    removeReactionScheme(IReactionScheme) - Method in class org.openscience.cdk.silent.ReactionScheme
    Removes an IReactionScheme from this chemObject.
    removeRecurringMappings(List<Integer>) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
    Deprecated.
     
    removeRedundantArcs(int, int, List<Integer>, McgregorHelper) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
    Deprecated.
    The function is called in function partsearch.
    removeRedundantMappingsForSingleAtomCase(List<CDKRMap>) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
    Deprecated.
     
    removeSingleElectron(int) - Method in class org.openscience.cdk.AtomContainer
    Removes the single electron at the given position from the AtomContainer.
    removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.AtomContainer
    Removes the single electron from the AtomContainer.
    removeSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid
    Removes the single electron at the given position from the AtomContainer.
    removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAminoAcid
    Removes the single electron from the AtomContainer.
    removeSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer
    Removes the single electron at the given position from the AtomContainer.
    removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAtomContainer
    Removes the single electron from the AtomContainer.
    removeSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer
    Removes the single electron at the given position from the AtomContainer.
    removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugBioPolymer
    Removes the single electron from the AtomContainer.
    removeSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugCrystal
    Removes the single electron at the given position from the AtomContainer.
    removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugCrystal
    Removes the single electron from the AtomContainer.
    removeSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugMonomer
    Removes the single electron at the given position from the AtomContainer.
    removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugMonomer
    Removes the single electron from the AtomContainer.
    removeSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugPolymer
    Removes the single electron at the given position from the AtomContainer.
    removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugPolymer
    Removes the single electron from the AtomContainer.
    removeSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugRing
    Removes the single electron at the given position from the AtomContainer.
    removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugRing
    Removes the single electron from the AtomContainer.
    removeSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugStrand
    Removes the single electron at the given position from the AtomContainer.
    removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugStrand
    Removes the single electron from the AtomContainer.
    removeSingleElectron(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
    Removes the single electron at the given position from the AtomContainer.
    removeSingleElectron(ISingleElectron) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
    Removes the single electron from the AtomContainer.
    removeSingleElectron(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
    Removes the single electron at the given position from the AtomContainer.
    removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
    Removes the single electron from the AtomContainer.
    removeSingleElectron(int) - Method in class org.openscience.cdk.silent.AtomContainer
    Removes the single electron at the given position from the AtomContainer.
    removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.silent.AtomContainer
    Removes the single electron from the AtomContainer.
    removeStrand(String) - Method in class org.openscience.cdk.BioPolymer
    Removes a particular strand, specified by its name.
    removeStrand(String) - Method in class org.openscience.cdk.debug.DebugBioPolymer
    Removes a particular strand, specified by its name.
    removeStrand(String) - Method in interface org.openscience.cdk.interfaces.IBioPolymer
    Removes a particular strand, specified by its name.
    removeStrand(String) - Method in class org.openscience.cdk.silent.BioPolymer
    Removes a particular strand, specified by its name.
    removeSubGraph(List<List<CDKRMap>>) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
    Deprecated.
     
    removeSymbol(String) - Method in class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom
    Remove a symbol from this QueryAtom
    removeSymbol(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom
    Remove a symbol from this QueryAtom
    removeTreeStructure(BinaryTree) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
    Deprecated.
     
    removeValidator(IValidator) - Method in class org.openscience.cdk.validate.ValidatorEngine
     
    RemovingSEofBMechanism - Class in org.openscience.cdk.reaction.mechanism
    This mechanism extracts a single electron from a bonding orbital which located in an bond.
    RemovingSEofBMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.RemovingSEofBMechanism
     
    RemovingSEofNBMechanism - Class in org.openscience.cdk.reaction.mechanism
    This mechanism extracts a single electron from a non-bonding orbital which located in a ILonePair container.
    RemovingSEofNBMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.RemovingSEofNBMechanism
     
    rendererModel - Variable in class org.openscience.cdk.renderer.AbstractRenderer
    The renderer model is final as it is not intended to be replaced.
    RendererModel - Class in org.openscience.cdk.renderer
    Model for IRenderer that contains settings for drawing objects.
    RendererModel() - Constructor for class org.openscience.cdk.renderer.RendererModel
    Construct a renderer model with no parameters.
    RendererModel.ColorHash - Class in org.openscience.cdk.renderer
    The color hash is used to color substructures.
    RendererModel.ColorHash() - Constructor for class org.openscience.cdk.renderer.RendererModel.ColorHash
     
    RendererModel.ExternalHighlightColor - Class in org.openscience.cdk.renderer
    The color used to highlight external selections.
    RendererModel.ExternalHighlightColor() - Constructor for class org.openscience.cdk.renderer.RendererModel.ExternalHighlightColor
     
    RendererModel.MarkedOutput - Class in org.openscience.cdk.renderer
    If format supports it (e.g.
    RendererModel.MarkedOutput() - Constructor for class org.openscience.cdk.renderer.RendererModel.MarkedOutput
     
    RendererModel.Padding - Class in org.openscience.cdk.renderer
    Padding between molecules in a grid or row.
    RendererModel.Padding() - Constructor for class org.openscience.cdk.renderer.RendererModel.Padding
     
    RendererModel.SelectionColor - Class in org.openscience.cdk.renderer
    Color of a selection.
    RendererModel.SelectionColor() - Constructor for class org.openscience.cdk.renderer.RendererModel.SelectionColor
     
    RendererModel.TitleColor - Class in org.openscience.cdk.renderer
    Color of title text.
    RendererModel.TitleColor() - Constructor for class org.openscience.cdk.renderer.RendererModel.TitleColor
     
    RendererModel.TitleFontScale - Class in org.openscience.cdk.renderer
    Size of title font relative compared to atom symbols
    RendererModel.TitleFontScale() - Constructor for class org.openscience.cdk.renderer.RendererModel.TitleFontScale
     
    repaint(IDrawVisitor) - Method in class org.openscience.cdk.renderer.AbstractRenderer
    Repaint using the cached diagram.
    repaint(IDrawVisitor) - Method in class org.openscience.cdk.renderer.ChemModelRenderer
    Repaint using the cached diagram.
    replaceAtomByAtom(IAtomContainer, IAtom, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
    Substitute one atom in a container for another adjusting bonds, single electrons, lone pairs, and stereochemistry as required.
    replaceAtomContainer(int, IAtomContainer) - Method in class org.openscience.cdk.AtomContainerSet
    Replace the AtomContainer at a specific position (array has to be large enough).
    replaceAtomContainer(int, IAtomContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
    Replace the AtomContainer at a specific position (array has to be large enough).
    replaceAtomContainer(int, IAtomContainer) - Method in class org.openscience.cdk.debug.DebugSubstance
    Replace the AtomContainer at a specific position (array has to be large enough).
    replaceAtomContainer(int, IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
    Replace the AtomContainer at a specific position (array has to be large enough).
    replaceAtomContainer(int, IAtomContainer) - Method in class org.openscience.cdk.silent.AtomContainerSet
    Replace the AtomContainer at a specific position (array has to be large enough).
    reportErrors - Variable in class org.openscience.cdk.io.cml.CMLErrorHandler
     
    repVal - Variable in class org.openscience.cdk.io.VASPReader
     
    REQUIRE_EXPLICIT_HYDROGENS - Static variable in class org.openscience.cdk.atomtype.CDKAtomTypeMatcher
     
    REQUIRE_NOTHING - Static variable in class org.openscience.cdk.atomtype.CDKAtomTypeMatcher
     
    rescaleBondLength(IAtom, IAtom, Point3d) - Static method in class org.openscience.cdk.geometry.AtomTools
    Rescales Point2 so that length 1-2 is sum of covalent radii.
    rescaleBondLength(IAtom, IAtom, Point3d) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
    Rescales Point2 so that length 1-2 is sum of covalent radii.
    reset() - Method in interface org.openscience.cdk.hash.stereo.StereoEncoder
    Reset the stereo-encoders, any currently perceived configurations will be re-activated.
    reset() - Method in class org.openscience.cdk.renderer.AtomContainerRenderer
    Reset the draw center and model center, and set the zoom to 100%.
    reset() - Method in class org.openscience.cdk.smiles.smarts.parser.JJTSMARTSParserState
     
    reset(String) - Method in class org.openscience.cdk.tools.FormatStringBuffer
    Reset this FormatStringBuffer.
    reset() - Method in class org.openscience.cdk.tools.FormatStringBuffer
    Reset this FormatStringBuffer with the format string given in the constructor or last call to reset(String).
    resetCEdgesSize() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
    Deprecated.
     
    resetDEdgesSize() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
    Deprecated.
     
    resetFlags(IAtomContainer) - Static method in class org.openscience.cdk.graph.PathTools
     
    resetFlags(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor
     
    resetTimeOut() - Method in class org.openscience.cdk.smsd.Isomorphism
    Deprecated.
     
    resetVirtualCounts() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
    Reset the virtual counts.
    reshape(int, int) - Method in class org.openscience.cdk.math.IMatrix
    Resize the matrix
    reshape(int) - Method in class org.openscience.cdk.math.IVector
    Resize this vector
    Residue - Class in org.openscience.cdk.libio.md
    A residue is a named, numbered collection of atoms in an MDMolecule.
    Residue() - Constructor for class org.openscience.cdk.libio.md.Residue
    Empty constructor
    Residue(IAtomContainer, int, MDMolecule) - Constructor for class org.openscience.cdk.libio.md.Residue
    Constructor to create a Residue based on an AC, a number, and a MDMolecule.
    RESIDUE_FORMAT - Variable in class org.openscience.cdk.io.PDBWriter
     
    RESIDUE_NAME - Static variable in class org.openscience.cdk.templates.AminoAcids
     
    RESIDUE_NAME_SHORT - Static variable in class org.openscience.cdk.templates.AminoAcids
     
    resize(long[][], int) - Method in class org.openscience.cdk.io.random.RandomAccessReader
     
    resolveEntity(String, String, String, String) - Method in class org.openscience.cdk.io.cml.CMLResolver
    Not implemented, but uses resolveEntity(String publicId, String systemId) instead.
    resolveEntity(String, String) - Method in class org.openscience.cdk.io.cml.CMLResolver
    Resolves SYSTEM and PUBLIC identifiers for CML DTDs.
    resolveOverlap(IAtomContainer, IRingSet) - Method in class org.openscience.cdk.layout.OverlapResolver
    Deprecated.
    Main method to be called to resolve overlap situations.
    resource2Order(Resource) - Static method in class org.openscience.cdk.libio.jena.Convertor
    Converts a Resource object into the matching IBond.Order.
    REST_H - Static variable in class org.openscience.cdk.CDKConstants
    A property to indicate RestH being true or false.
    retainAll(Collection<?>) - Method in class org.openscience.cdk.ConformerContainer
     
    returnChemFile() - Method in class org.openscience.cdk.io.cml.CMLCoreModule
     
    returnChemFile() - Method in interface org.openscience.cdk.io.cml.ICMLModule
     
    reverse(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
    Returns a new Reaction object which is the reverse of the given Reaction.
    RGraph - Class in org.openscience.cdk.isomorphism.mcss
    This class implements the Resolution Graph (RGraph).
    RGraph() - Constructor for class org.openscience.cdk.isomorphism.mcss.RGraph
    Constructor for the RGraph object and creates an empty RGraph.
    RGroup - Class in org.openscience.cdk.isomorphism.matchers
    Represents a single substitute structure in an RGroupList.
    RGroup() - Constructor for class org.openscience.cdk.isomorphism.matchers.RGroup
     
    RGroupList - Class in org.openscience.cdk.isomorphism.matchers
    Represents a list of Rgroup substitutes to be associated with some RGroupQuery.
    RGroupList(int) - Constructor for class org.openscience.cdk.isomorphism.matchers.RGroupList
    Default constructor.
    RGroupList(int, boolean, String, int) - Constructor for class org.openscience.cdk.isomorphism.matchers.RGroupList
    Constructor with attributes given.
    RGroupQuery - Class in org.openscience.cdk.isomorphism.matchers
    Represents information contained in a Symyx RGfile (R-group query file).
    It contains a root structure (the scaffold if you like), a map with R-group definitions (each of which can contain multiple substitutes) and a map with attachment points.
    RGroupQuery(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.RGroupQuery
     
    RGroupQueryFormat - Class in org.openscience.cdk.io.formats
    Format for Symyx RGfiles (Rgroup query files).
    RGroupQueryFormat() - Constructor for class org.openscience.cdk.io.formats.RGroupQueryFormat
     
    RGroupQueryReader - Class in org.openscience.cdk.io
    A reader for Symyx' Rgroup files (RGFiles).
    RGroupQueryReader() - Constructor for class org.openscience.cdk.io.RGroupQueryReader
    Default constructor, input not set.
    RGroupQueryReader(InputStream) - Constructor for class org.openscience.cdk.io.RGroupQueryReader
    Constructs a new RgroupQueryReader that can read RgroupAtomContainerSet from a given InputStream.
    RGroupQueryReader(Reader) - Constructor for class org.openscience.cdk.io.RGroupQueryReader
    Constructs a new RgroupQueryReader that can read RgroupAtomContainerSet from a given Reader.
    RGroupQueryWriter - Class in org.openscience.cdk.io
    A writer for Symyx' Rgroup files (RGFiles).
    An RGfile describes a single molecular query with Rgroups.
    RGroupQueryWriter(Writer) - Constructor for class org.openscience.cdk.io.RGroupQueryWriter
    Constructs a new writer that can write an IRGroupQuery to the Symx RGFile format.
    RGroupQueryWriter() - Constructor for class org.openscience.cdk.io.RGroupQueryWriter
    Zero argument constructor.
    RH - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    RHENIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    RHENIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    RHODIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    RHODIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    Ring - Class in org.openscience.cdk
    Class representing a ring structure in a molecule.
    Ring() - Constructor for class org.openscience.cdk.Ring
    Constructs an empty ring.
    Ring(IAtomContainer) - Constructor for class org.openscience.cdk.Ring
    Constructs a ring from the atoms in an IAtomContainer object.
    Ring(int, String) - Constructor for class org.openscience.cdk.Ring
    Constructs a ring that will have a certain number of atoms of the given elements.
    Ring(int) - Constructor for class org.openscience.cdk.Ring
    Constructs an empty ring that will have a certain size.
    Ring - Class in org.openscience.cdk.silent
    Class representing a ring structure in a molecule.
    Ring() - Constructor for class org.openscience.cdk.silent.Ring
    Constructs an empty ring.
    Ring(IAtomContainer) - Constructor for class org.openscience.cdk.silent.Ring
    Constructs a ring from the atoms in an IAtomContainer object.
    Ring(int, String) - Constructor for class org.openscience.cdk.silent.Ring
    Constructs a ring that will have a certain number of atoms of the given elements.
    Ring(int) - Constructor for class org.openscience.cdk.silent.Ring
    Constructs an empty ring that will have a certain size.
    RING_CONNECTIONS - Static variable in class org.openscience.cdk.CDKConstants
    This property indicates how many ring bonds are connected to the given atom.
    RING_SIZES - Static variable in class org.openscience.cdk.CDKConstants
    This property will contain an ArrayList of Integers.
    ringAlreadyInSet(IRing, IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator
    Checks - and returns 'true' - if a certain ring is already stored in the ringset.
    RingBond - Class in org.openscience.cdk.isomorphism.matchers.smarts
    This smarts bond matches any bond that is in a ring.
    RingBond(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.RingBond
    Creates a new instance
    RingConnectivity() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
     
    RingElement - Class in org.openscience.cdk.renderer.elements
    A ring is just a circle - in other words, an oval whose width and height are the same.
    RingElement(double, double, double, Color) - Constructor for class org.openscience.cdk.renderer.elements.RingElement
    Make a ring element centered on (x, y) with radius and color given.
    RingFilter - Class in org.openscience.cdk.smsd.ring
    Deprecated.
    This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK and a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    RingFilter(AtomMatcher, RingFinder) - Constructor for class org.openscience.cdk.smsd.ring.RingFilter
    Deprecated.
     
    RingFinder - Interface in org.openscience.cdk.smsd.ring
    Deprecated.
    This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    ringFragments() - Method in class org.openscience.cdk.ringsearch.RingSearch
    Extract the cyclic atom and bond fragments of the container.
    RingGenerator - Class in org.openscience.cdk.renderer.generators
    Generates just the aromatic indicators for rings : circles, or light-gray inner bonds, depending on the value of CDKStyleAromaticity.
    RingGenerator() - Constructor for class org.openscience.cdk.renderer.generators.RingGenerator
    Make a generator for ring elements.
    RingGenerator.CDKStyleAromaticity - Class in org.openscience.cdk.renderer.generators
    Depicts aromaticity of rings in the original CDK style.
    RingGenerator.CDKStyleAromaticity() - Constructor for class org.openscience.cdk.renderer.generators.RingGenerator.CDKStyleAromaticity
     
    RingGenerator.MaxDrawableAromaticRing - Class in org.openscience.cdk.renderer.generators
    The maximum ring size for which an aromatic ring should be drawn.
    RingGenerator.MaxDrawableAromaticRing() - Constructor for class org.openscience.cdk.renderer.generators.RingGenerator.MaxDrawableAromaticRing
     
    RingGenerator.RingProportion - Class in org.openscience.cdk.renderer.generators
    The proportion of a ring bounds to use to draw the ring.
    RingGenerator.RingProportion() - Constructor for class org.openscience.cdk.renderer.generators.RingGenerator.RingProportion
     
    RingGenerator.ShowAromaticity - Class in org.openscience.cdk.renderer.generators
    Determines whether rings should be drawn with a circle if they are aromatic.
    RingGenerator.ShowAromaticity() - Constructor for class org.openscience.cdk.renderer.generators.RingGenerator.ShowAromaticity
     
    RingIdentifier() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
     
    RingIdentifierAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
    This encapsulates an atom with a ring identifier, with an optional ring bond specified.
    RingIdentifierAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.RingIdentifierAtom
     
    RingManipulator - Class in org.openscience.cdk.tools.manipulator
     
    RingManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.RingManipulator
     
    RingMembership() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
     
    RingMembershipAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
    This query is found in a specified number of ring.
    RingMembershipAtom(int, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.RingMembershipAtom
    Ring membership query atom.
    RingPartitioner - Class in org.openscience.cdk.ringsearch
    Partitions a RingSet into RingSets of connected rings.
    RingPartitioner() - Constructor for class org.openscience.cdk.ringsearch.RingPartitioner
     
    RingPlacer - Class in org.openscience.cdk.layout
    Class providing methods for generating coordinates for ring atoms.
    RingPlacer() - Constructor for class org.openscience.cdk.layout.RingPlacer
    The empty constructor.
    RingSearch - Class in org.openscience.cdk.ringsearch
    Efficiently search for atoms that are members of a ring.
    RingSearch(IAtomContainer) - Constructor for class org.openscience.cdk.ringsearch.RingSearch
    Create a new RingSearch for the specified container.
    RingSearch(IAtomContainer, int[][]) - Constructor for class org.openscience.cdk.ringsearch.RingSearch
    Create a new RingSearch for the specified container and graph.
    RingSearch(IAtomContainer, CyclicVertexSearch) - Constructor for class org.openscience.cdk.ringsearch.RingSearch
    Create a new RingSearch for the specified container using the provided search.
    ringSet - Variable in class org.openscience.cdk.ChemModel
    A RingSet.
    ringSet - Variable in class org.openscience.cdk.renderer.generators.BasicBondGenerator
    Necessary for calculating inner-ring bond elements.
    RingSet - Class in org.openscience.cdk
    Maintains a set of Ring objects.
    RingSet() - Constructor for class org.openscience.cdk.RingSet
    The constructor.
    ringSet - Variable in class org.openscience.cdk.silent.ChemModel
    A RingSet.
    RingSet - Class in org.openscience.cdk.silent
    Maintains a set of Ring objects.
    RingSet() - Constructor for class org.openscience.cdk.silent.RingSet
    The constructor.
    RingSetManipulator - Class in org.openscience.cdk.tools.manipulator
     
    RingSetManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.RingSetManipulator
     
    RingSizeComparator - Class in org.openscience.cdk.tools.manipulator
     
    RingSizeComparator(int) - Constructor for class org.openscience.cdk.tools.manipulator.RingSizeComparator
    Constructs a new comparator to sort rings by size.
    RMap - Class in org.openscience.cdk.isomorphism.mcss
    An RMap implements the association between an edge (bond) in G1 and an edge (bond) in G2, G1 and G2 being the compared graphs in a RGraph context.
    RMap(int, int) - Constructor for class org.openscience.cdk.isomorphism.mcss.RMap
    Constructor for the RMap.
    RN - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    RNode - Class in org.openscience.cdk.isomorphism.mcss
    Node of the resolution graph (RGraph) An RNode represents an association between two edges of the source graphs G1 and G2 that are compared.
    RNode(int, int) - Constructor for class org.openscience.cdk.isomorphism.mcss.RNode
    Constructor for the RNode object.
    rocAUC - Variable in class org.openscience.cdk.fingerprint.model.Bayesian
     
    rocType - Variable in class org.openscience.cdk.fingerprint.model.Bayesian
     
    rocX - Variable in class org.openscience.cdk.fingerprint.model.Bayesian
     
    rocY - Variable in class org.openscience.cdk.fingerprint.model.Bayesian
     
    ROENTGENIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    ROLE_AGENT - Static variable in class org.openscience.cdk.isomorphism.matchers.smarts.ReactionRoleQueryAtom
     
    ROLE_ANY - Static variable in class org.openscience.cdk.isomorphism.matchers.smarts.ReactionRoleQueryAtom
     
    ROLE_PRODUCT - Static variable in class org.openscience.cdk.isomorphism.matchers.smarts.ReactionRoleQueryAtom
     
    ROLE_REACTANT - Static variable in class org.openscience.cdk.isomorphism.matchers.smarts.ReactionRoleQueryAtom
     
    RoleAgent - Static variable in class org.openscience.cdk.isomorphism.matchers.smarts.ReactionRoleQueryAtom
     
    RoleProduct - Static variable in class org.openscience.cdk.isomorphism.matchers.smarts.ReactionRoleQueryAtom
     
    RoleReactant - Static variable in class org.openscience.cdk.isomorphism.matchers.smarts.ReactionRoleQueryAtom
     
    root() - Method in class org.openscience.cdk.renderer.elements.Bounds
    Access the root rendering element, it contains all elements added to the bounds so far.
    ROOT_LABEL - Static variable in class org.openscience.cdk.isomorphism.matchers.RGroup
    Standard label/title to be used for the root atom container.
    rootNode() - Method in class org.openscience.cdk.smiles.smarts.parser.JJTSMARTSParserState
     
    rootNode - Variable in class org.openscience.cdk.tools.HOSECodeGenerator
     
    RotatableBondsCountDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
    The number of rotatable bonds is given by the SMARTS specified by Daylight on SMARTS tutorial
    RotatableBondsCountDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor
    Constructor for the RotatableBondsCountDescriptor object
    rotate(IAtomContainer, Point2d, double) - Static method in class org.openscience.cdk.geometry.GeometryTools
    Rotates a molecule around a given center by a given angle.
    rotate(IAtom, Point3d, Point3d, double) - Static method in class org.openscience.cdk.geometry.GeometryTools
    Rotates a 3D point about a specified line segment by a specified angle.
    rotate(IAtomContainer, Point2d, double) - Static method in class org.openscience.cdk.geometry.GeometryUtil
    Rotates a molecule around a given center by a given angle.
    rotate(IAtom, Point3d, Point3d, double) - Static method in class org.openscience.cdk.geometry.GeometryUtil
    Rotates a 3D point about a specified line segment by a specified angle.
    rotate(Vector3d, Vector3d, double) - Static method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
    Rotates a vector around an axis.
    rotateAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.geometry.alignment.KabschAlignment
    Rotates the IAtomContainer coordinates by the rotation matrix.
    rows - Variable in class org.openscience.cdk.math.IMatrix
    the count of rows of the matrix
    rows - Variable in class org.openscience.cdk.math.Matrix
    the number of rows of this matrix
    RssWriter - Class in org.openscience.cdk.io
    Generates an RSS feed.
    RssWriter() - Constructor for class org.openscience.cdk.io.RssWriter
     
    RU - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    RUBIDIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    RUBIDIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    RuleOfFiveDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
    This Class contains a method that returns the number failures of the Lipinski's Rule Of 5.
    RuleOfFiveDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor
    Constructor for the RuleOfFiveDescriptor object.
    RUTHENIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    RUTHENIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    RUTHERFORDIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    RUTHERFORDIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.

    S

    s - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    S - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    S_BOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    SAMARIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    sample(IAtomContainer) - Static method in class org.openscience.cdk.structgen.VicinitySampler
    Choose any possible quadruple of the set of atoms in ac and establish all of the possible bonding schemes according to Faulon's equations.
    SANARIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    saturate(IAtomContainer) - Method in class org.openscience.cdk.tools.AtomTypeAwareSaturationChecker
    saturate(IAtomContainer) - Method in interface org.openscience.cdk.tools.IDeduceBondOrderTool
     
    saturate(IAtomContainer) - Method in class org.openscience.cdk.tools.LonePairElectronChecker
    Saturates a molecule by setting appropriate number lone pair electrons.
    saturate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.LonePairElectronChecker
    Saturates an IAtom by adding the appropriate number lone pairs.
    saturate(IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker
    The method is known to fail for certain compounds.
    saturate(IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
    Saturates a molecule by setting appropriate bond orders.
    saturate(IBond[], IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
    Saturates a set of Bonds in an AtomContainer.
    saturateByIncreasingBondOrder(IBond, IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
    Tries to saturate a bond by increasing its bond orders by 1.0.
    saturateRingSystems(IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker
     
    SaturationChecker - Class in org.openscience.cdk.tools
    Provides methods for checking whether an atoms valences are saturated with respect to a particular atom type.
    SaturationChecker() - Constructor for class org.openscience.cdk.tools.SaturationChecker
     
    saveIndex(File) - Method in class org.openscience.cdk.io.random.RandomAccessReader
     
    SB - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    SC - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    scaleMolecule(IAtomContainer, Dimension, double) - Static method in class org.openscience.cdk.geometry.GeometryTools
    Scales a molecule such that it fills a given percentage of a given dimension.
    scaleMolecule(IAtomContainer, double) - Static method in class org.openscience.cdk.geometry.GeometryTools
    Multiplies all the coordinates of the atoms of the given molecule with the scalefactor.
    scaleMolecule(IAtomContainer, double[], double) - Static method in class org.openscience.cdk.geometry.GeometryUtil
    Scales a molecule such that it fills a given percentage of a given dimension.
    scaleMolecule(IAtomContainer, double) - Static method in class org.openscience.cdk.geometry.GeometryUtil
    Multiplies all the coordinates of the atoms of the given molecule with the scalefactor.
    scalePredictor(double) - Method in class org.openscience.cdk.fingerprint.model.Bayesian
    Converts a raw Bayesian prediction and transforms it into a probability-like range, i.e.
    SCANDIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    SCANDIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    SDFFormat - Class in org.openscience.cdk.io.formats
    See here.
    SDFFormat() - Constructor for class org.openscience.cdk.io.formats.SDFFormat
     
    SDFWriter - Class in org.openscience.cdk.io
    Writes MDL SD files ([Dalby, A. and Nourse, J. G. and Hounshell, W. D. and Gushurst, A. K. and Grier, D. L. and Leland, B. A. and Laufer, J., Description of Several Chemical Structure File Formats Used by Computer Programs Developed at Molecular Design Limited, Journal of Chemical Information and Computer Sciences, 1992, 32:244-255]).
    SDFWriter(BufferedWriter) - Constructor for class org.openscience.cdk.io.SDFWriter
    Create an SDfile writer that will output directly to the provided buffered writer.
    SDFWriter(Writer) - Constructor for class org.openscience.cdk.io.SDFWriter
    Create an SDfile writer, the provided writer is buffered if it's not an instance of BufferedWriter.
    SDFWriter(OutputStream) - Constructor for class org.openscience.cdk.io.SDFWriter
    Create an SDfile writer, the provided output stream is wrapped in a UTF-8 buffered writer.
    SDFWriter() - Constructor for class org.openscience.cdk.io.SDFWriter
     
    SDFWriter(Writer, Set<String>) - Constructor for class org.openscience.cdk.io.SDFWriter
    Constructs a new SDFWriter that writes to the given Writer.
    SDFWriter(OutputStream, Set<String>) - Constructor for class org.openscience.cdk.io.SDFWriter
    Constructs a new SdfWriter that can write to a given OutputStream.
    SDFWriter(Set<String>) - Constructor for class org.openscience.cdk.io.SDFWriter
    Writes SD-File to a String including the given properties
    se - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    SE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    SEABORGIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    SEABORGIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    search(IAtomContainer, IAtomContainer, BitSet, BitSet, boolean, boolean) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
    General RGraph parsing method (usually not used directly) This method is the entry point for the recursive search adapted to the atom container input.
    search(IAtomContainer, IAtomContainer, BitSet, BitSet, boolean, boolean, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
    Deprecated.
    General Rgraph parsing method (usually not used directly) This method is the entry point for the recursive search adapted to the atom container input.
    searchCorrespondingAtom(int, int, int, List<Integer>) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
    Deprecated.
     
    searchMCS(boolean) - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler
    Deprecated.
    Initialise the MCS search algorithm.
    searchMCS(boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler
    Deprecated.
    Initialise the MCS search algorithm.
    searchMCS(boolean) - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler
    Deprecated.
    Initialise the MCS search algorithm.
    searchMCS(boolean) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler
    Deprecated.
    Initialise the MCS search algorithm.
    searchMCS(boolean) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCSAlgorithm
    Deprecated.
    Initialise the MCS search algorithm.
    secondPointX - Variable in class org.openscience.cdk.renderer.elements.LineElement
    The x-coordinate of the second point.
    secondPointY - Variable in class org.openscience.cdk.renderer.elements.LineElement
    The y-coordinate of the second point.
    select(IChemModel) - Method in class org.openscience.cdk.renderer.selection.AbstractSelection
    Perform a selection by some method.
    select(IChemModel) - Method in interface org.openscience.cdk.renderer.selection.IChemObjectSelection
    Perform a selection by some method.
    SelectionVisibility - Class in org.openscience.cdk.renderer.generators.standard
    Extended existing symbol visibility options to account for selection of atoms in the standard generator.
    SELENIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    SELENIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    SERIAL_FORMAT - Variable in class org.openscience.cdk.io.PDBWriter
     
    serialise() - Method in class org.openscience.cdk.fingerprint.model.Bayesian
    Converts the current model into a serialised string representation.
    set(int, IAtomContainer) - Method in class org.openscience.cdk.ConformerContainer
     
    set(int, boolean) - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
     
    set(int) - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
     
    set(int, boolean) - Method in interface org.openscience.cdk.fingerprint.IBitFingerprint
    Sets the bit at the specified index to the specified value.
    set(int) - Method in interface org.openscience.cdk.fingerprint.IBitFingerprint
    Sets the bit at the specified index to true.
    set(int, boolean) - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
     
    set(int) - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
     
    set(int, int) - Method in class org.openscience.cdk.group.Permutation
    Set the value at the specified index.
    set(IChemObject) - Method in class org.openscience.cdk.io.random.RandomAccessReader
     
    set(Class<T>, U) - Method in class org.openscience.cdk.renderer.RendererModel
    Sets the IGeneratorParameter for the active IRenderer.
    set(MolHandler, MolHandler) - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler
    Deprecated.
    Initialise the query and target molecule.
    set(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler
    Deprecated.
    Initialise the query and target molecule.
    set(MolHandler, MolHandler) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler
    Deprecated.
    Initialise the query and target molecule.
    set(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler
    Deprecated.
    Initialise the query and target molecule.
    set(MolHandler, MolHandler) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler
    Deprecated.
    Initialise the query and target molecule.
    set(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler
    Deprecated.
    Initialise the query and target molecule.
    set(MolHandler, MolHandler) - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler
    Deprecated.
    Initialise the query and target molecule.
    set(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler
    Deprecated.
    Initialise the query and target molecule.
    set(MolHandler, MolHandler) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler
    Deprecated.
    Initialise the query and target molecule.
    set(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler
    Deprecated.
    Initialise the query and target molecule.
    set(MolHandler, MolHandler) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler
    Deprecated.
    Initialise the query and target molecule.
    set(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler
    Deprecated.
    Initialise the query and target molecule.
    set(MolHandler, MolHandler) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler
    Deprecated.
    Initialise the query and target molecule.
    set(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler
    Deprecated.
    Initialise the query and target molecule.
    set(List<Map<Integer, Integer>>) - Method in class org.openscience.cdk.smsd.helper.FinalMappings
    Deprecated.
    Sets mapping list
    set(List<Map<Integer, Integer>>) - Method in interface org.openscience.cdk.smsd.interfaces.IFinalMapping
    Deprecated.
    Sets mapping list
    set(MolHandler, MolHandler) - Method in interface org.openscience.cdk.smsd.interfaces.IMCSBase
    Deprecated.
    Initialise the query and target molecule.
    set(IQueryAtomContainer, IAtomContainer) - Method in interface org.openscience.cdk.smsd.interfaces.IMCSBase
    Deprecated.
    Initialise the query and target molecule.
    SET_UNIQUE_POLICY - Static variable in class org.openscience.cdk.tools.IDCreator
    Old ID generation policy - to generate IDs unique over the entire set
    setA(Vector3d) - Method in class org.openscience.cdk.Crystal
    Sets the A unit cell axes in Cartesian coordinates in a Euclidean space.
    setA(Vector3d) - Method in class org.openscience.cdk.debug.DebugCrystal
    Sets the A unit cell axes in Cartesian coordinates in a Euclidean space.
    setA(Vector3d) - Method in interface org.openscience.cdk.interfaces.ICrystal
    Sets the A unit cell axes in carthesian coordinates in a eucledian space.
    setA(Vector3d) - Method in class org.openscience.cdk.silent.Crystal
    Sets the A unit cell axes in Cartesian coordinates in a Euclidean space.
    setAbout(String) - Method in class org.openscience.cdk.io.RssWriter
     
    setAlignMappedReaction(boolean) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
    Set whether reaction reactants should be allignned to their product.
    setAllMap(boolean) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
    Sets the 'finAllMap' option.
    setAllMap(boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
    Deprecated.
    Sets the 'finAllMap' option.
    setAllStructure(boolean) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
    Sets the 'AllStructres' option.
    setAllStructure(boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
    Deprecated.
    Sets the 'AllStructres' option.
    setAltLoc(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom
    set the Alternate location indicator of this atom.
    setAltLoc(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
    set the Alternate location indicator of this atom.
    setAltLoc(String) - Method in class org.openscience.cdk.protein.data.PDBAtom
    set the Alternate location indicator of this atom.
    setAltLoc(String) - Method in class org.openscience.cdk.silent.PDBAtom
    set the Alternate location indicator of this atom.
    setAlwaysV3000(boolean) - Method in class org.openscience.cdk.io.SDFWriter
     
    setArcs(IAtomContainer, IAtomContainer, int, int, List<Integer>, List<Integer>, List<String>, List<String>, List<Integer>, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
    Deprecated.
     
    setAromaticity(Aromaticity) - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool
    Set the aromaticity perception to use.
    setArrayValue(double[][]) - Method in class org.openscience.cdk.graph.invariant.GIMatrix
    Resets the value of the matrix to the given array of double numbers.
    setAsPermutation(int) - Method in class org.openscience.cdk.group.Partition
    Fill the elements of a permutation from the first element of each cell, up to the point upTo.
    setAtom(int, IAtom) - Method in class org.openscience.cdk.AtomContainer
    Sets the atom at position number in [0,..].
    setAtom(IAtom, int) - Method in class org.openscience.cdk.Bond
    Sets an Atom in this bond.
    setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
    Sets the atom at position number in [0,..].
    setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
    Sets the atom at position number in [0,..].
    setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
    Sets the atom at position number in [0,..].
    setAtom(IAtom, int) - Method in class org.openscience.cdk.debug.DebugBond
    Sets an Atom in this bond.
    setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
    Sets the atom at position number in [0,..].
    setAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugLonePair
    Sets the associated Atom.
    setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
    Sets the atom at position number in [0,..].
    setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
    Sets the atom at position number in [0,..].
    setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugRing
    Sets the atom at position number in [0,..].
    setAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugSingleElectron
    Sets the associated Atom.
    setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
    Sets the atom at position number in [0,..].
    setAtom(int, IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
    Set the atom at position number in [0,..].
    setAtom(IAtom, int) - Method in interface org.openscience.cdk.interfaces.IBond
    Sets an Atom in this bond.
    setAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.ILonePair
    Sets the associated Atom.
    setAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.ISingleElectron
    Sets the associated Atom.
    setAtom(int, IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
    Sets the atom at position number in [0,..].
    setAtom(IAtom, int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
    Sets an atom in this query bond.
    setAtom(IQueryAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RingIdentifierAtom
     
    setAtom(IAtom) - Method in class org.openscience.cdk.LonePair
    Sets the associated Atom.
    setAtom(int, IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
    Sets the atom at position number in [0,..].
    setAtom(IAtom, int) - Method in class org.openscience.cdk.silent.Bond
    Sets an Atom in this bond.
    setAtom(IAtom) - Method in class org.openscience.cdk.silent.LonePair
    Sets the associated Atom.
    setAtom(IAtom) - Method in class org.openscience.cdk.silent.SingleElectron
    Sets the associated Atom.
    setAtom(IAtom) - Method in class org.openscience.cdk.SingleElectron
    Sets the associated Atom.
    setAtom(IAtom) - Method in class org.openscience.cdk.smiles.InvPair
     
    setAtomAt(IAtom, int) - Method in class org.openscience.cdk.Association
    Sets an Atom in this Association.
    setAtomAt(IAtom, int) - Method in class org.openscience.cdk.isomorphism.matchers.OrderQueryBond
     
    setAtomAt(IAtom, int) - Method in class org.openscience.cdk.isomorphism.matchers.OrderQueryBondOrderOnly
     
    setAtomCheckRadius(double) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
     
    setAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.structgen.SingleStructureRandomGenerator
    Sets the AtomContainer attribute of the SingleStructureRandomGenerator object.
    setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugAtom
    Sets the atomic number of this element.
    setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugAtomType
    Sets the atomic number of this element.
    setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugElement
    Sets the atomic number of this element.
    setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
    Sets the atomic number of this element.
    setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugIsotope
    Sets the atomic number of this element.
    setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
    Sets the atomic number of this element.
    setAtomicNumber(Integer) - Method in class org.openscience.cdk.Element
    Sets the atomic number of this element.
    setAtomicNumber(Integer) - Method in interface org.openscience.cdk.interfaces.IElement
    Sets the atomic number of this element.
    setAtomicNumber(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
    Sets the atomic number of this element.
    setAtomicNumber(Integer) - Method in class org.openscience.cdk.silent.Element
    Sets the atomic number of this element.
    setAtomPlacer(AtomPlacer) - Method in class org.openscience.cdk.layout.RingPlacer
     
    setAtomProperties(IAtomContainer, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
    Sets a property on all Atoms in the given container.
    setAtomProperties(IAtomContainerSet, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
     
    setAtomProperties(IChemModel, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
    Sets the AtomProperties of all Atoms inside an IChemModel.
    setAtomProperties(IAtomContainerSet, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
     
    setAtomProperties(IReaction, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
     
    setAtomProperties(IReactionSet, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
     
    setAtoms(IAtom[]) - Method in class org.openscience.cdk.Association
    Sets the array of atoms making up this Association.
    setAtoms(IAtom[]) - Method in class org.openscience.cdk.AtomContainer
    Sets the array of atoms of this AtomContainer.
    setAtoms(IAtom[]) - Method in class org.openscience.cdk.Bond
    Sets the array of atoms making up this bond.
    setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugAminoAcid
    Sets the array of atoms of this AtomContainer.
    setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugAtomContainer
    Sets the array of atoms of this AtomContainer.
    setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugBioPolymer
    Sets the array of atoms of this AtomContainer.
    setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugBond
    Sets the array of atoms making up this bond.
    setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugCrystal
    Sets the array of atoms of this AtomContainer.
    setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugMonomer
    Sets the array of atoms of this AtomContainer.
    setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugPolymer
    Sets the array of atoms of this AtomContainer.
    setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugRing
    Sets the array of atoms of this AtomContainer.
    setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugStrand
    Sets the array of atoms of this AtomContainer.
    setAtoms(IAtom[]) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
    Sets the array of atoms of this AtomContainer.
    setAtoms(IAtom[]) - Method in interface org.openscience.cdk.interfaces.IBond
    Sets the array of atoms making up this bond.
    setAtoms(IAtom[]) - Method in class org.openscience.cdk.isomorphism.matchers.OrderQueryBond
     
    setAtoms(IAtom[]) - Method in class org.openscience.cdk.isomorphism.matchers.OrderQueryBondOrderOnly
     
    setAtoms(IAtom[]) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
    Sets the array of atoms of this AtomContainer.
    setAtoms(IAtom[]) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
    Sets the array of atoms making up this query bond.
    setAtoms(IAtom[]) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond
     
    setAtoms(IAtom[]) - Method in class org.openscience.cdk.silent.AtomContainer
    Sets the array of atoms of this AtomContainer.
    setAtoms(IAtom[]) - Method in class org.openscience.cdk.silent.Bond
    Sets the array of atoms making up this bond.
    setAtomTypeName(String) - Method in class org.openscience.cdk.AtomType
    Sets the if attribute of the AtomType object.
    setAtomTypeName(String) - Method in class org.openscience.cdk.debug.DebugAtom
    Sets the if attribute of the AtomType object.
    setAtomTypeName(String) - Method in class org.openscience.cdk.debug.DebugAtomType
    Sets the if attribute of the AtomType object.
    setAtomTypeName(String) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
    Sets the if attribute of the AtomType object.
    setAtomTypeName(String) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
    Sets the if attribute of the AtomType object.
    setAtomTypeName(String) - Method in interface org.openscience.cdk.interfaces.IAtomType
    Sets the if attribute of the AtomType object.
    setAtomTypeName(String) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
    Sets the if attribute of the AtomType object.
    setAtomTypeName(String) - Method in class org.openscience.cdk.silent.AtomType
    Sets the if attribute of the AtomType object.
    setAtomTypes(List<IAtomType>) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
    Sets the atomTypes attribute of the ForceFieldConfigurator object
    setAttachPointNum(int) - Method in interface org.openscience.cdk.interfaces.IPseudoAtom
    Set the attachment point number.
    setAttachPointNum(int) - Method in class org.openscience.cdk.PseudoAtom
    Set the attachment point number.
    setAttachPointNum(int) - Method in class org.openscience.cdk.silent.PseudoAtom
    Set the attachment point number.
    setB(Vector3d) - Method in class org.openscience.cdk.Crystal
    Sets the B unit cell axes in Cartesian coordinates.
    setB(Vector3d) - Method in class org.openscience.cdk.debug.DebugCrystal
    Sets the B unit cell axes in Cartesian coordinates.
    setB(Vector3d) - Method in interface org.openscience.cdk.interfaces.ICrystal
    Sets the B unit cell axes in carthesian coordinates.
    setB(Vector3d) - Method in class org.openscience.cdk.silent.Crystal
    Sets the B unit cell axes in Cartesian coordinates.
    setBasis(int[], int[], int[], double[], Vector[], IAtom[]) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
    Set up basis with gauss funktions f(x,y,z) = (x-rx)^nx * (y-ry)^ny * (z-rz)^nz * exp(-alpha*(r-ri)^2).
    setBehaveAsBitFingerprint(boolean) - Method in interface org.openscience.cdk.fingerprint.ICountFingerprint
    Changes behaviour, if true is given the count fingerprint will behave as a bit fingerprint and return 0 or 1 for counts.
    setBehaveAsBitFingerprint(boolean) - Method in class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
     
    setBondInSensitiveTimeOut(double) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
    Deprecated.
    set timeout in mins (default 1.00 min) for bond insensitive searches
    setBondInSensitiveTimeOut(double) - Method in class org.openscience.cdk.smsd.Isomorphism
    Deprecated.
    set timeout in mins (default 1.00 min) for bond insensitive searches
    setBondLength(double) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
    Set the bond length used for laying out the molecule.
    setBondMatchFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultBondMatcher
    Deprecated.
     
    setBondMatchFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultMCSPlusAtomMatcher
    Deprecated.
     
    setBondMatchFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultRGraphAtomMatcher
    Deprecated.
     
    setBondMatchFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFAtomMatcher
    Deprecated.
     
    setBondMatchFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFBondMatcher
    Deprecated.
     
    setBondMatchFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler
    Deprecated.
     
    setBondMatchFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler
    Deprecated.
     
    setBondMatchFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler
    Deprecated.
     
    setBondOrderSum(Double) - Method in class org.openscience.cdk.AtomType
    Sets the the exact bond order sum attribute of the AtomType object.
    setBondOrderSum(Double) - Method in class org.openscience.cdk.debug.DebugAtom
    Sets the the exact bond order sum attribute of the AtomType object.
    setBondOrderSum(Double) - Method in class org.openscience.cdk.debug.DebugAtomType
    Sets the the exact bond order sum attribute of the AtomType object.
    setBondOrderSum(Double) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
    Sets the the exact bond order sum attribute of the AtomType object.
    setBondOrderSum(Double) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
    Sets the the exact bond order sum attribute of the AtomType object.
    setBondOrderSum(Double) - Method in interface org.openscience.cdk.interfaces.IAtomType
    Sets the the exact bond order sum attribute of the AtomType object.
    setBondOrderSum(Double) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
    Sets the the exact bond order sum attribute of the AtomType object.
    setBondOrderSum(Double) - Method in class org.openscience.cdk.silent.AtomType
    Sets the the exact bond order sum attribute of the AtomType object.
    setBonds(IBond[]) - Method in class org.openscience.cdk.AtomContainer
    Sets the array of bonds of this AtomContainer.
    setBonds(IBond[]) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
    Sets the array of bonds of this AtomContainer.
    setBonds(IBond[]) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
    Sets the array of bonds of this AtomContainer.
    setBonds(IBond[]) - Method in class org.openscience.cdk.silent.AtomContainer
    Sets the array of bonds of this AtomContainer.
    setBondSensitiveTimeOut(double) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
    Deprecated.
    set timeout in mins (default 0.10 min) for bond sensitive searches
    setBondSensitiveTimeOut(double) - Method in class org.openscience.cdk.smsd.Isomorphism
    Deprecated.
    set timeout in mins (default 0.10 min) for bond sensitive searches
    setBuilder(IChemObjectBuilder) - Method in class org.openscience.cdk.stereo.DoubleBondStereochemistry
    Sets a new IChemObjectBuilder.
    setBuilder(IChemObjectBuilder) - Method in class org.openscience.cdk.stereo.TetrahedralChirality
    Sets a new IChemObjectBuilder.
    setC(Vector3d) - Method in class org.openscience.cdk.Crystal
    Sets the C unit cell axes in Cartesian coordinates.
    setC(Vector3d) - Method in class org.openscience.cdk.debug.DebugCrystal
    Sets the C unit cell axes in Cartesian coordinates.
    setC(Vector3d) - Method in interface org.openscience.cdk.interfaces.ICrystal
    Sets the C unit cell axes in carthesian coordinates.
    setC(Vector3d) - Method in class org.openscience.cdk.silent.Crystal
    Sets the C unit cell axes in Cartesian coordinates.
    setChainID(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom
    set the Chain identifier of this atom.
    setChainID(String) - Method in class org.openscience.cdk.debug.DebugPDBMonomer
    Sets the Chain ID of this monomer.
    setChainID(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
    set the Chain identifier of this atom.
    setChainID(String) - Method in interface org.openscience.cdk.interfaces.IPDBMonomer
    Sets the Chain ID of this monomer.
    setChainID(String) - Method in class org.openscience.cdk.protein.data.PDBAtom
    set the Chain identifier of this atom.
    setChainID(String) - Method in class org.openscience.cdk.protein.data.PDBMonomer
     
    setChainID(String) - Method in class org.openscience.cdk.silent.PDBAtom
    set the Chain identifier of this atom.
    setChainID(String) - Method in class org.openscience.cdk.silent.PDBMonomer
     
    setCharge(Double) - Method in class org.openscience.cdk.Atom
    Sets the partial charge of this atom.
    setCharge(Integer) - Method in class org.openscience.cdk.debug.DebugAdductFormula
    No use this method.
    setCharge(Double) - Method in class org.openscience.cdk.debug.DebugAtom
    Sets the partial charge of this atom.
    setCharge(Double) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
    Sets the partial charge of this atom.
    setCharge(Integer) - Method in class org.openscience.cdk.debug.DebugMolecularFormula
    Sets the charge of this IMolecularFormula, since there is no atom associated with the charge the number of a given isotope is not modified.
    setCharge(Double) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
    Sets the partial charge of this atom.
    setCharge(Integer) - Method in class org.openscience.cdk.formula.AdductFormula
    Deprecated. 
    setCharge(double) - Method in class org.openscience.cdk.formula.IsotopePattern
    Set the charge in this pattern.
    setCharge(Integer) - Method in class org.openscience.cdk.formula.MolecularFormula
    Sets the charge of this IMolecularFormula, since there is no atom associated with the charge the number of a given isotope is not modified.
    setCharge(Integer) - Method in interface org.openscience.cdk.interfaces.IAdductFormula
    Sets the partial charge of this adduct formula.
    setCharge(Double) - Method in interface org.openscience.cdk.interfaces.IAtom
    Sets the partial charge of this atom.
    setCharge(Integer) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
    Sets the charge of this IMolecularFormula, since there is no atom associated with the charge the number of a given isotope is not modified.
    setCharge(Double) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
    Sets the partial charge of this atom.
    setCharge(Integer) - Method in class org.openscience.cdk.silent.AdductFormula
    Deprecated. 
    setCharge(Double) - Method in class org.openscience.cdk.silent.Atom
    Sets the partial charge of this atom.
    setCharge(Integer) - Method in class org.openscience.cdk.silent.MolecularFormula
    Sets the charge of this IMolecularFormula, since there is no atom associated with the charge the number of a given isotope is not modified.
    setChargeGroups(List<ChargeGroup>) - Method in class org.openscience.cdk.libio.md.MDMolecule
     
    setCharges(IAtomContainer) - Method in class org.openscience.cdk.charges.AtomTypeCharges
    Sets initial charges for atom types.
    setChemFilters(boolean, boolean, boolean) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
    Deprecated.
    initialize query and target molecules.
    setChemFilters(boolean, boolean, boolean) - Method in class org.openscience.cdk.smsd.Isomorphism
    Deprecated.
    initialize query and target molecules.
    setChemObjectReader(ISimpleChemObjectReader) - Method in class org.openscience.cdk.io.random.RandomAccessReader
     
    setChiCatHydrogen(double) - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
    Sets chi_cat value for hydrogen, because H poses a special problem due to lack of possible second ionisation.
    setClassName(String) - Method in class org.openscience.cdk.dict.Entry
     
    setClipboardContent(IAtomContainer) - Method in class org.openscience.cdk.renderer.RendererModel
    Sets the atoms and bonds on the Renderer2D clipboard.
    setClockwise(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom
     
    setCoefficients(Matrix) - Method in class org.openscience.cdk.math.qm.Orbitals
    Set a coefficient matrix
    setColumn(int, GIMatrix) - Method in class org.openscience.cdk.graph.invariant.GIMatrix
    Sets the column of the matrix at the specified index to a new value.
    setContractOnHetero(boolean) - Method in class org.openscience.cdk.depict.Abbreviations
    Set whether abbreviations should be further contracted when they are connected to a heteroatom, for example -NH-Boc becomes -NHBoc.
    setCountElectrons(int) - Method in class org.openscience.cdk.math.qm.Orbitals
    Sets the count of electrons, which occupies the orbitals
    setCovalentRadius(Double) - Method in class org.openscience.cdk.AtomType
    Sets the covalent radius for this AtomType.
    setCovalentRadius(Double) - Method in class org.openscience.cdk.debug.DebugAtom
    Sets the covalent radius for this AtomType.
    setCovalentRadius(Double) - Method in class org.openscience.cdk.debug.DebugAtomType
    Sets the covalent radius for this AtomType.
    setCovalentRadius(Double) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
    Sets the covalent radius for this AtomType.
    setCovalentRadius(Double) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
    Sets the covalent radius for this AtomType.
    setCovalentRadius(Double) - Method in interface org.openscience.cdk.interfaces.IAtomType
    Sets the covalent radius for this AtomType.
    setCovalentRadius(Double) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
    Sets the covalent radius for this AtomType.
    setCovalentRadius(Double) - Method in class org.openscience.cdk.silent.AtomType
    Sets the covalent radius for this AtomType.
    setCreator(String) - Method in class org.openscience.cdk.io.RssWriter
     
    setCreatormap(Map) - Method in class org.openscience.cdk.io.RssWriter
     
    setCrystal(ICrystal) - Method in class org.openscience.cdk.ChemModel
    Sets the Crystal contained in this ChemModel.
    setCrystal(ICrystal) - Method in class org.openscience.cdk.debug.DebugChemModel
    Sets the Crystal contained in this ChemModel.
    setCrystal(ICrystal) - Method in interface org.openscience.cdk.interfaces.IChemModel
    Sets the Crystal contained in this ChemModel.
    setCrystal(ICrystal) - Method in class org.openscience.cdk.silent.ChemModel
    Sets the Crystal contained in this ChemModel.
    setCurr(long) - Method in class org.openscience.cdk.smiles.InvPair
    Set the value of the seed.
    setDatemap(Map) - Method in class org.openscience.cdk.io.RssWriter
     
    setDebugEnabled(boolean) - Method in class org.openscience.cdk.tools.SystemOutLoggingTool
    Protected method which must not be used, except for testing purposes.
    setDebugStream(PrintStream) - Method in class org.openscience.cdk.iupac.parser.NomParserTokenManager
    Set debug output.
    setDebugStream(PrintStream) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager
    Set debug output.
    setDefaultReactions() - Method in class org.openscience.cdk.tools.StructureResonanceGenerator
    Set the default reactions that must be presents to generate the resonance.
    setDefaultRestrictions() - Method in class org.openscience.cdk.formula.MassToFormulaTool
    Deprecated.
    Set the default restrictions that must be presents in the molecular formula.
    setDefinition(String) - Method in class org.openscience.cdk.dict.Entry
     
    setDegree(int) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom
     
    setDescription(String) - Method in class org.openscience.cdk.dict.Entry
     
    setDescription(String) - Method in class org.openscience.cdk.io.RssWriter
     
    setDescriptorInstances(List<IDescriptor>) - Method in class org.openscience.cdk.qsar.DescriptorEngine
    Set the list of Descriptor objects.
    setDescriptorMetadata(String) - Method in class org.openscience.cdk.dict.Entry
     
    setDescriptorSpecifications(List<IImplementationSpecification>) - Method in class org.openscience.cdk.qsar.DescriptorEngine
    Set the list of DescriptorSpecification objects.
    setDetails(String) - Method in class org.openscience.cdk.validate.ValidationTest
     
    setDim(int[]) - Method in class org.openscience.cdk.tools.GridGenerator
     
    setDimension(double, double) - Method in class org.openscience.cdk.tools.GridGenerator
    Method sets the maximal 3d dimensions to given min and max values.
    setDimension(double[], boolean) - Method in class org.openscience.cdk.tools.GridGenerator
    Method sets the maximal 3d dimensions to given min and max values.
    setDimension(double, double, double, double, double, double) - Method in class org.openscience.cdk.tools.GridGenerator
    Method sets the maximal 3d dimensions to given min and max values.
    setDirection(IReaction.Direction) - Method in class org.openscience.cdk.debug.DebugReaction
    Sets the direction of the reaction.
    setDirection(IReaction.Direction) - Method in interface org.openscience.cdk.interfaces.IReaction
    Sets the direction of the reaction.
    setDirection(IReaction.Direction) - Method in class org.openscience.cdk.Reaction
    Sets the direction of the reaction.
    setDirection(IReaction.Direction) - Method in class org.openscience.cdk.silent.Reaction
    Sets the direction of the reaction.
    setDisplayMode(int) - Method in class org.openscience.cdk.renderer.GraphRendererModel
    Set the display mode
    setDocumentProperty(String, String) - Method in class org.openscience.cdk.io.iterator.event.EventCMLHandler
    Procedure required by the CDOInterface.
    setDrawCenter(double, double) - Method in class org.openscience.cdk.renderer.AbstractRenderer
    Set the point on the screen to draw the diagram.
    setElectronCount(Integer) - Method in class org.openscience.cdk.debug.DebugBond
    Sets the number of electrons in this electron container.
    setElectronCount(Integer) - Method in class org.openscience.cdk.debug.DebugElectronContainer
    Sets the number of electrons in this electron container.
    setElectronCount(Integer) - Method in class org.openscience.cdk.debug.DebugLonePair
    Sets the number of electrons in this electron container.
    setElectronCount(Integer) - Method in class org.openscience.cdk.debug.DebugSingleElectron
    Sets the number of electrons in this electron container.
    setElectronCount(Integer) - Method in class org.openscience.cdk.ElectronContainer
    Sets the number of electrons in this electron container.
    setElectronCount(Integer) - Method in interface org.openscience.cdk.interfaces.IElectronContainer
    Sets the number of electrons in this electron container.
    setElectronCount(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
    Sets the number of electrons in this bond
    setElectronCount(Integer) - Method in class org.openscience.cdk.silent.ElectronContainer
    Sets the number of electrons in this electron container.
    setEnabled(String, boolean) - Method in class org.openscience.cdk.depict.Abbreviations
    Set whether an abbreviation is enabled or disabled.
    setEndChainID(Character) - Method in class org.openscience.cdk.debug.DebugPDBStructure
    set the ending Chain identifier of this structure.
    setEndChainID(Character) - Method in interface org.openscience.cdk.interfaces.IPDBStructure
    set the ending Chain identifier of this structure.
    setEndChainID(Character) - Method in class org.openscience.cdk.protein.data.PDBStructure
    set the ending Chain identifier of this structure.
    setEndChainID(Character) - Method in class org.openscience.cdk.silent.PDBStructure
    set the ending Chain identifier of this structure.
    setEndInsertionCode(Character) - Method in class org.openscience.cdk.debug.DebugPDBStructure
    set the ending Code for insertion of residues of this structure.
    setEndInsertionCode(Character) - Method in interface org.openscience.cdk.interfaces.IPDBStructure
    set the ending Code for insertion of residues of this structure.
    setEndInsertionCode(Character) - Method in class org.openscience.cdk.protein.data.PDBStructure
    set the ending Code for insertion of residues of this structure.
    setEndInsertionCode(Character) - Method in class org.openscience.cdk.silent.PDBStructure
    set the ending Code for insertion of residues of this structure.
    setEndSequenceNumber(Integer) - Method in class org.openscience.cdk.debug.DebugPDBStructure
    set the ending sequence number of this structure.
    setEndSequenceNumber(Integer) - Method in interface org.openscience.cdk.interfaces.IPDBStructure
    set the ending sequence number of this structure.
    setEndSequenceNumber(Integer) - Method in class org.openscience.cdk.protein.data.PDBStructure
    set the ending sequence number of this structure.
    setEndSequenceNumber(Integer) - Method in class org.openscience.cdk.silent.PDBStructure
    set the ending sequence number of this structure.
    setEqual(BinaryTree) - Method in class org.openscience.cdk.smsd.helper.BinaryTree
    Deprecated.
    Set equal node
    setErrorHandler(IChemObjectReaderErrorHandler) - Method in class org.openscience.cdk.io.DefaultChemObjectReader
    Sets an error handler that is sent events when file format issues occur.
    setErrorHandler(IChemObjectReaderErrorHandler) - Method in interface org.openscience.cdk.io.IChemObjectReader
    Sets an error handler that is sent events when file format issues occur.
    setErrorHandler(IChemObjectReaderErrorHandler) - Method in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader
    Sets an error handler that is sent events when file format issues occur.
    setExactMass(Double) - Method in class org.openscience.cdk.debug.DebugAtom
    Sets the ExactMass attribute of the Isotope object.
    setExactMass(Double) - Method in class org.openscience.cdk.debug.DebugAtomType
    Sets the ExactMass attribute of the Isotope object.
    setExactMass(Double) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
    Sets the ExactMass attribute of the Isotope object.
    setExactMass(Double) - Method in class org.openscience.cdk.debug.DebugIsotope
    Sets the ExactMass attribute of the Isotope object.
    setExactMass(Double) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
    Sets the ExactMass attribute of the Isotope object.
    setExactMass(Double) - Method in class org.openscience.cdk.FragmentAtom
     
    setExactMass(Double) - Method in interface org.openscience.cdk.interfaces.IIsotope
    Sets the ExactMass attribute of the Isotope object.
    setExactMass(Double) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
    Sets the ExactMass attribute of the Isotope object.
    setExactMass(Double) - Method in class org.openscience.cdk.Isotope
    Sets the ExactMass attribute of the Isotope object.
    setExactMass(Double) - Method in class org.openscience.cdk.silent.FragmentAtom
     
    setExactMass(Double) - Method in class org.openscience.cdk.silent.Isotope
    Sets the ExactMass attribute of the Isotope object.
    setExpanded(boolean) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
    Sets whether this atom is to be fully drawn and not just in the abbreviated form.
    setExpanded(boolean) - Method in class org.openscience.cdk.FragmentAtom
     
    setExpanded(boolean) - Method in interface org.openscience.cdk.interfaces.IFragmentAtom
    Sets whether this atom is to be fully drawn and not just in the abbreviated form.
    setExpanded(boolean) - Method in class org.openscience.cdk.silent.FragmentAtom
     
    setExtendGrid(double) - Method in class org.openscience.cdk.tools.GridGenerator
     
    setExtension(BitSet) - Method in class org.openscience.cdk.isomorphism.mcss.RNode
    Sets the extension attribute of the RNode object.
    setExtension(BitSet) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode
    Deprecated.
    Sets the extension attribute of the RNode object
    setExternalSelectedPart(IAtomContainer) - Method in class org.openscience.cdk.renderer.RendererModel
    Set externally selected atoms.
    setFirstAttachmentPoint(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.RGroup
     
    setFirstGraphSize(int) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
    Sets the size of the first of the two compared graphs.
    setFirstGraphSize(int) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
    Deprecated.
    Sets the size of the first of the two compared graphs.
    setFlag(int, boolean) - Method in class org.openscience.cdk.ChemObject
    Sets the value of some flag.
    setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugAminoAcid
    Sets the value of some flag.
    setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugAtom
    Sets the value of some flag.
    setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugAtomContainer
    Sets the value of some flag.
    setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
    Sets the value of some flag.
    setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugAtomType
    Sets the value of some flag.
    setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugBioPolymer
    Sets the value of some flag.
    setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugBond
    Sets the value of some flag.
    setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugChemFile
    Sets the value of some flag.
    setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugChemModel
    Sets the value of some flag.
    setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugChemObject
    Sets the value of some flag.
    setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugChemSequence
    Sets the value of some flag.
    setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugCrystal
    Sets the value of some flag.
    setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugElectronContainer
    Sets the value of some flag.
    setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugElement
    Sets the value of some flag.
    setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
    Sets the value of some flag.
    setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugIsotope
    Sets the value of some flag.
    setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugLonePair
    Sets the value of some flag.
    setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugMapping
    Sets the value of some flag.
    setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugMonomer
    Sets the value of some flag.
    setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugPolymer
    Sets the value of some flag.
    setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
    Sets the value of some flag.
    setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugReaction
    Sets the value of some flag.
    setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugReactionScheme
    Sets the value of some flag.
    setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugReactionSet
    Sets the value of some flag.
    setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugRing
    Sets the value of some flag.
    setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugSingleElectron
    Sets the value of some flag.
    setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugStrand
    Sets the value of some flag.
    setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugSubstance
    Sets the value of some flag.
    setFlag(int, boolean) - Method in interface org.openscience.cdk.interfaces.IChemObject
    Sets the value of some flag.
    setFlag(int, boolean) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
    Sets the value of some flag.
    setFlag(int, boolean) - Method in class org.openscience.cdk.silent.ChemObject
    Sets the value of some flag.
    setFlags(boolean[]) - Method in class org.openscience.cdk.ChemObject
    Sets the whole set of flags.
    setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugAminoAcid
    Sets the whole set of flags.
    setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugAtom
    Sets the whole set of flags.
    setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugAtomContainer
    Sets the whole set of flags.
    setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
    Sets the whole set of flags.
    setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugAtomType
    Sets the whole set of flags.
    setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugBioPolymer
    Sets the whole set of flags.
    setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugBond
    Sets the whole set of flags.
    setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugChemFile
    Sets the whole set of flags.
    setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugChemModel
    Sets the whole set of flags.
    setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugChemObject
    Sets the whole set of flags.
    setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugChemSequence
    Sets the whole set of flags.
    setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugCrystal
    Sets the whole set of flags.
    setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugElectronContainer
    Sets the whole set of flags.
    setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugElement
    Sets the whole set of flags.
    setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
    Sets the whole set of flags.
    setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugIsotope
    Sets the whole set of flags.
    setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugLonePair
    Sets the whole set of flags.
    setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugMapping
    Sets the whole set of flags.
    setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugMonomer
    Sets the whole set of flags.
    setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugPolymer
    Sets the whole set of flags.
    setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
    Sets the whole set of flags.
    setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugReaction
    Sets the whole set of flags.
    setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugReactionScheme
    Sets the whole set of flags.
    setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugReactionSet
    Sets the whole set of flags.
    setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugRing
    Sets the whole set of flags.
    setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugSingleElectron
    Sets the whole set of flags.
    setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugStrand
    Sets the whole set of flags.
    setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugSubstance
    Sets the whole set of flags.
    setFlags(boolean[]) - Method in interface org.openscience.cdk.interfaces.IChemObject
    Sets the whole set of flags.
    setFlags(boolean[]) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
    Sets the whole set of flags.
    setFlags(boolean[]) - Method in class org.openscience.cdk.silent.ChemObject
    Sets the whole set of flags.
    setFontForZoom(double) - Method in class org.openscience.cdk.renderer.font.AWTFontManager
    For a particular zoom level, set the appropriate font size to use.
    setFontForZoom(double) - Method in interface org.openscience.cdk.renderer.font.IFontManager
    For a particular zoom level, set the appropriate font size to use.
    setFontManager(IFontManager) - Method in class org.openscience.cdk.renderer.visitor.AWTDrawVisitor
    The font manager must be set by any renderer that uses this class! This manager is needed to keep track of fonts of the right size.
    setFontManager(IFontManager) - Method in interface org.openscience.cdk.renderer.visitor.IDrawVisitor
    Sets the IFontManager this IDrawVisitor should use.
    setFontName(String) - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
    Set the font name ('Arial', 'Times New Roman') and so on.
    setFontName(String) - Method in interface org.openscience.cdk.renderer.font.IFontManager
    Set the font name ('Arial', 'Times New Roman') and so on.
    setFontStyle(IFontManager.FontStyle) - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
    Set the font style.
    setFontStyle(IFontManager.FontStyle) - Method in interface org.openscience.cdk.renderer.font.IFontManager
    Set the font style.
    setForbidden(BitSet) - Method in class org.openscience.cdk.isomorphism.mcss.RNode
    Sets the forbidden attribute of the RNode object.
    setForbidden(BitSet) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode
    Deprecated.
    Sets the forbidden attribute of the RNode object
    setForceFieldConfigurator(String, IChemObjectBuilder) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
    Constructor for the ForceFieldConfigurator object
    setFormalCharge(Integer) - Method in class org.openscience.cdk.AtomType
    Sets the formal charge of this atom.
    setFormalCharge(Integer) - Method in class org.openscience.cdk.debug.DebugAtom
    Sets the formal charge of this atom.
    setFormalCharge(Integer) - Method in class org.openscience.cdk.debug.DebugAtomType
    Sets the formal charge of this atom.
    setFormalCharge(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
    Sets the formal charge of this atom.
    setFormalCharge(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
    Sets the formal charge of this atom.
    setFormalCharge(Integer) - Method in interface org.openscience.cdk.interfaces.IAtomType
    Sets the formal charge of this atom.
    setFormalCharge(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
    Sets the formal charge of this atom.
    setFormalCharge(Integer) - Method in class org.openscience.cdk.silent.AtomType
    Sets the formal charge of this atom.
    setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.AtomType
    Sets the formal neighbour count of this atom.
    setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.debug.DebugAtom
    Sets the formal neighbour count of this atom.
    setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.debug.DebugAtomType
    Sets the formal neighbour count of this atom.
    setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
    Sets the formal neighbour count of this atom.
    setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
    Sets the formal neighbour count of this atom.
    setFormalNeighbourCount(Integer) - Method in interface org.openscience.cdk.interfaces.IAtomType
    Sets the formal neighbour count of this atom.
    setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
    Sets the formal neighbour count of this atom.
    setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.silent.AtomType
    Sets the formal neighbour count of this atom.
    setFormula(IMolecularFormula) - Method in class org.openscience.cdk.formula.IsotopeContainer
    Set IMolecularFormula object of this container.
    setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.Atom
    Sets a point specifying the location of this atom in a Crystal unit cell.
    setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugAtom
    Sets a point specifying the location of this atom in a Crystal unit cell.
    setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
    Sets a point specifying the location of this atom in a Crystal unit cell.
    setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
    Sets a point specifying the location of this atom in a Crystal unit cell.
    setFractionalPoint3d(Point3d) - Method in interface org.openscience.cdk.interfaces.IAtom
    Sets a point specifying the location of this atom in a Crystal unit cell.
    setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
    Sets a point specifying the location of this atom in a Crystal unit cell.
    setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.silent.Atom
    Sets a point specifying the location of this atom in a Crystal unit cell.
    setFragment(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
    Sets the fully expended form of the IFragmentAtom.
    setFragment(IAtomContainer) - Method in class org.openscience.cdk.FragmentAtom
     
    setFragment(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IFragmentAtom
    Sets the fully expended form of the IFragmentAtom.
    setFragment(IAtomContainer) - Method in class org.openscience.cdk.silent.FragmentAtom
     
    setGrid(double[][][]) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
     
    setGrid(double[][][]) - Method in class org.openscience.cdk.tools.GridGenerator
     
    setGroup(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.matchers.RGroup
     
    setHashPseudoAtoms(boolean) - Method in class org.openscience.cdk.fingerprint.Fingerprinter
     
    setHCount(int) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom
     
    setHetAtom(Boolean) - Method in class org.openscience.cdk.debug.DebugPDBAtom
    Mark the atom as a heteroatom.
    setHetAtom(Boolean) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
    Mark the atom as a heteroatom.
    setHetAtom(Boolean) - Method in class org.openscience.cdk.protein.data.PDBAtom
     
    setHetAtom(Boolean) - Method in class org.openscience.cdk.silent.PDBAtom
     
    setHighlightedAtom(IAtom) - Method in class org.openscience.cdk.renderer.RendererModel
    Sets the atom currently highlighted.
    setHighlightedBond(IBond) - Method in class org.openscience.cdk.renderer.RendererModel
    Sets the Bond currently highlighted.
    setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.AtomType
    Sets the hybridization of this atom.
    setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.debug.DebugAtom
    Sets the hybridization of this atom.
    setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.debug.DebugAtomType
    Sets the hybridization of this atom.
    setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
    Sets the hybridization of this atom.
    setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
    Sets the hybridization of this atom.
    setHybridization(IAtomType.Hybridization) - Method in interface org.openscience.cdk.interfaces.IAtomType
    Sets the hybridization of this atom.
    setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
    Sets the hybridization of this atom.
    setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.silent.AtomType
    Sets the hybridization of this atom.
    setICode(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom
    set the Code for insertion of residues of this atom.
    setICode(String) - Method in class org.openscience.cdk.debug.DebugPDBMonomer
    Sets the ICode of this monomer.
    setICode(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
    set the Code for insertion of residues of this atom.
    setICode(String) - Method in interface org.openscience.cdk.interfaces.IPDBMonomer
    Sets the ICode of this monomer.
    setICode(String) - Method in class org.openscience.cdk.protein.data.PDBAtom
    set the Code for insertion of residues of this atom.
    setICode(String) - Method in class org.openscience.cdk.protein.data.PDBMonomer
     
    setICode(String) - Method in class org.openscience.cdk.silent.PDBAtom
    set the Code for insertion of residues of this atom.
    setICode(String) - Method in class org.openscience.cdk.silent.PDBMonomer
     
    setID(String) - Method in class org.openscience.cdk.ChemObject
    Sets the identifier (ID) of this object.
    setID(String) - Method in class org.openscience.cdk.debug.DebugAminoAcid
    Sets the identifier (ID) of this object.
    setID(String) - Method in class org.openscience.cdk.debug.DebugAtom
    Sets the identifier (ID) of this object.
    setID(String) - Method in class org.openscience.cdk.debug.DebugAtomContainer
    Sets the identifier (ID) of this object.
    setID(String) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
    Sets the identifier (ID) of this object.
    setID(String) - Method in class org.openscience.cdk.debug.DebugAtomType
    Sets the identifier (ID) of this object.
    setID(String) - Method in class org.openscience.cdk.debug.DebugBioPolymer
    Sets the identifier (ID) of this object.
    setID(String) - Method in class org.openscience.cdk.debug.DebugBond
    Sets the identifier (ID) of this object.
    setID(String) - Method in class org.openscience.cdk.debug.DebugChemFile
    Sets the identifier (ID) of this object.
    setID(String) - Method in class org.openscience.cdk.debug.DebugChemModel
    Sets the identifier (ID) of this object.
    setID(String) - Method in class org.openscience.cdk.debug.DebugChemObject
    Sets the identifier (ID) of this object.
    setID(String) - Method in class org.openscience.cdk.debug.DebugChemSequence
    Sets the identifier (ID) of this object.
    setID(String) - Method in class org.openscience.cdk.debug.DebugCrystal
    Sets the identifier (ID) of this object.
    setID(String) - Method in class org.openscience.cdk.debug.DebugElectronContainer
    Sets the identifier (ID) of this object.
    setID(String) - Method in class org.openscience.cdk.debug.DebugElement
    Sets the identifier (ID) of this object.
    setID(String) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
    Sets the identifier (ID) of this object.
    setID(String) - Method in class org.openscience.cdk.debug.DebugIsotope
    Sets the identifier (ID) of this object.
    setID(String) - Method in class org.openscience.cdk.debug.DebugLonePair
    Sets the identifier (ID) of this object.
    setID(String) - Method in class org.openscience.cdk.debug.DebugMapping
    Sets the identifier (ID) of this object.
    setID(String) - Method in class org.openscience.cdk.debug.DebugMonomer
    Sets the identifier (ID) of this object.
    setID(String) - Method in class org.openscience.cdk.debug.DebugPolymer
    Sets the identifier (ID) of this object.
    setID(String) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
    Sets the identifier (ID) of this object.
    setID(String) - Method in class org.openscience.cdk.debug.DebugReaction
    Sets the identifier (ID) of this object.
    setID(String) - Method in class org.openscience.cdk.debug.DebugReactionScheme
    Sets the identifier (ID) of this object.
    setID(String) - Method in class org.openscience.cdk.debug.DebugReactionSet
    Sets the identifier (ID) of this object.
    setID(String) - Method in class org.openscience.cdk.debug.DebugRing
    Sets the identifier (ID) of this object.
    setID(String) - Method in class org.openscience.cdk.debug.DebugSingleElectron
    Sets the identifier (ID) of this object.
    setID(String) - Method in class org.openscience.cdk.debug.DebugStrand
    Sets the identifier (ID) of this object.
    setID(String) - Method in class org.openscience.cdk.debug.DebugSubstance
    Sets the identifier (ID) of this object.
    setID(String) - Method in class org.openscience.cdk.dict.Entry
     
    setID(String) - Method in interface org.openscience.cdk.interfaces.IChemObject
    Sets the identifier (ID) of this object.
    setID(String) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
    Sets the identifier (ID) of this object.
    setID(String) - Method in class org.openscience.cdk.silent.ChemObject
    Sets the identifier (ID) of this object.
    setId1(int) - Method in class org.openscience.cdk.isomorphism.mcss.RMap
    Sets the id1 attribute of the RMap object.
    setId1(int) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMap
    Deprecated.
    Sets the id1 attribute of the CDKRMap object
    setId2(int) - Method in class org.openscience.cdk.isomorphism.mcss.RMap
    Sets the id2 attribute of the RMap object.
    setId2(int) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMap
    Deprecated.
    Sets the id2 attribute of the CDKRMap object
    setIDPolicy(int) - Static method in class org.openscience.cdk.tools.IDCreator
    Alters the policy of ID generation.
    setIgnoreAromaticBonds(boolean) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory
    Deprecated.
    "the use of aromatic bonds is strongly discouraged" - InChI FAQ, the InChI will fail for many compounds if ignore aromatic bonds is not enabled and the compound have aromatic flags.
    setImagelink(String) - Method in class org.openscience.cdk.io.RssWriter
     
    setImaginaryPart(double) - Method in class org.openscience.cdk.math.Complex
    Sets the imaginary part of this value
    setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.Atom
    Sets the number of implicit hydrogen count of this atom.
    setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.debug.DebugAtom
    Sets the number of implicit hydrogen count of this atom.
    setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
    Sets the number of implicit hydrogen count of this atom.
    setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
    Sets the number of implicit hydrogen count of this atom.
    setImplicitHydrogenCount(Integer) - Method in interface org.openscience.cdk.interfaces.IAtom
    Sets the implicit hydrogen count of this atom.
    setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
    Sets the number of implicit hydrogen count of this atom.
    setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.silent.Atom
    Sets the number of implicit hydrogen count of this atom.
    setInchimap(Map) - Method in class org.openscience.cdk.io.RssWriter
     
    setIndexCreated(boolean) - Method in class org.openscience.cdk.io.random.RandomAccessReader
     
    setInputReader(Reader) - Method in class org.openscience.cdk.io.listener.TextGUIListener
    Overwrites the default reader from which the input is taken.
    setInputStream(InputStream) - Method in class org.openscience.cdk.config.CDKBasedAtomTypeConfigurator
    Sets the file containing the configuration data.
    setInputStream(InputStream) - Method in interface org.openscience.cdk.config.IAtomTypeConfigurator
    Sets the file containing the configuration data.
    setInputStream(InputStream) - Method in class org.openscience.cdk.config.OWLBasedAtomTypeConfigurator
    Sets the file containing the configuration data.
    setInputStream(InputStream) - Method in class org.openscience.cdk.config.TXTBasedAtomTypeConfigurator
    Sets the file containing the configuration data.
    setInputStream(InputStream) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
    Sets the inputStream attribute of the ForceFieldConfigurator object
    setInputStream(InputStream) - Method in class org.openscience.cdk.modeling.builder3d.MM2BasedParameterSetReader
    Sets the file containing the config data.
    setInputStream(InputStream) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94BasedParameterSetReader
    Sets the file containing the config data
    setIntensity(double) - Method in class org.openscience.cdk.formula.IsotopeContainer
    Set the intensity value of this container.
    setInterrupted(boolean) - Method in class org.openscience.cdk.smiles.DeduceBondSystemTool
    Deprecated.
    Sets if the calculation should be interrupted.
    setInterrupted(boolean) - Method in class org.openscience.cdk.smiles.FixBondOrdersTool
    Deprecated.
    Sets if the calculation should be interrupted.
    setIsAromatic(boolean) - Method in class org.openscience.cdk.Atom
    Mark this atom as being aromatic.
    setIsAromatic(boolean) - Method in class org.openscience.cdk.Bond
    Mark this bond as being aromatic.
    setIsAromatic(boolean) - Method in interface org.openscience.cdk.interfaces.IAtom
    Mark this atom as being aromatic.
    setIsAromatic(boolean) - Method in interface org.openscience.cdk.interfaces.IBond
    Mark this bond as being aromatic.
    setIsAromatic(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
    Mark this atom as being aromatic.
    setIsAromatic(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
    Mark this bond as being aromatic.
    setIsAromatic(boolean) - Method in class org.openscience.cdk.silent.Atom
    Mark this atom as being aromatic.
    setIsAromatic(boolean) - Method in class org.openscience.cdk.silent.Bond
    Mark this bond as being aromatic.
    setIsInRing(boolean) - Method in class org.openscience.cdk.Atom
    Mark this atom as being in a ring.
    setIsInRing(boolean) - Method in class org.openscience.cdk.Bond
    Mark this bond as being in a ring.
    setIsInRing(boolean) - Method in interface org.openscience.cdk.interfaces.IAtom
    Mark this atom as being in a ring.
    setIsInRing(boolean) - Method in interface org.openscience.cdk.interfaces.IBond
    Mark this bond as being in a ring.
    setIsInRing(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
    Mark this atom as being in a ring.
    setIsInRing(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
    Mark this bond as being in a ring.
    setIsInRing(boolean) - Method in class org.openscience.cdk.silent.Atom
    Mark this atom as being in a ring.
    setIsInRing(boolean) - Method in class org.openscience.cdk.silent.Bond
    Mark this bond as being in a ring.
    setLabel(String) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
    Sets the label of this PseudoAtom.
    setLabel(String) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
    Sets the label of this PseudoAtom.
    setLabel(String) - Method in class org.openscience.cdk.dict.Entry
     
    setLabel(String) - Method in interface org.openscience.cdk.interfaces.IPseudoAtom
    Sets the label of this PseudoAtom.
    setLabel(String) - Method in class org.openscience.cdk.PseudoAtom
    Sets the label of this PseudoAtom.
    setLabel(String) - Method in class org.openscience.cdk.silent.PseudoAtom
    Sets the label of this PseudoAtom.
    setLast(long) - Method in class org.openscience.cdk.smiles.InvPair
     
    setLatticeConstant(double) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
     
    setLatticeConstant(double) - Method in class org.openscience.cdk.tools.GridGenerator
     
    setLeft(IQueryAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom
    Deprecated.
    setLeft(IQueryBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond
     
    setLength(int) - Method in class org.openscience.cdk.iupac.parser.AttachedGroup
    Setter for property length.
    setLevel(IOSetting.Importance) - Method in class org.openscience.cdk.io.listener.SwingGUIListener
     
    setLevel(IOSetting.Importance) - Method in class org.openscience.cdk.io.listener.TextGUIListener
     
    setLine(int, GIMatrix) - Method in class org.openscience.cdk.graph.invariant.GIMatrix
    Sets the line of the matrix at the specified index to a new value.
    setLink(String) - Method in class org.openscience.cdk.io.RssWriter
     
    setLinkageRadius(double) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
     
    setLinkmap(Map) - Method in class org.openscience.cdk.io.RssWriter
     
    setLocations(List<Token>) - Method in class org.openscience.cdk.iupac.parser.AttachedGroup
    Setter for property locations.
    setLoggingToolClass(Class<? extends ILoggingTool>) - Static method in class org.openscience.cdk.tools.LoggingToolFactory
    Sets the ILoggingTool implementation to be used.
    setMappings(List<Map<Integer, Integer>>) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
    Deprecated.
    Set mapping solutions
    setMass(double) - Method in class org.openscience.cdk.formula.IsotopeContainer
    Set the mass value of this container.
    setMassNumber(Integer) - Method in class org.openscience.cdk.debug.DebugAtom
    Sets the atomic mass of this element.
    setMassNumber(Integer) - Method in class org.openscience.cdk.debug.DebugAtomType
    Sets the atomic mass of this element.
    setMassNumber(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
    Sets the atomic mass of this element.
    setMassNumber(Integer) - Method in class org.openscience.cdk.debug.DebugIsotope
    Sets the atomic mass of this element.
    setMassNumber(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
    Sets the atomic mass of this element.
    setMassNumber(Integer) - Method in interface org.openscience.cdk.interfaces.IIsotope
    Sets the atomic mass of this element.
    setMassNumber(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
    Sets the atomic mass of this element.
    setMassNumber(Integer) - Method in class org.openscience.cdk.Isotope
    Sets the atomic mass of this element.
    setMassNumber(Integer) - Method in class org.openscience.cdk.silent.Isotope
    Sets the atomic mass of this element.
    setMatchBond(boolean) - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
    Deprecated.
     
    setMatchBonds(boolean) - Method in class org.openscience.cdk.smsd.Isomorphism
    Deprecated.
     
    setMatchingAtoms(int[]) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom
    Set the atoms of a target molecule that correspond to this group.
    setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.AtomType
    Sets the MaxBondOrder attribute of the AtomType object.
    setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.debug.DebugAtom
    Sets the MaxBondOrder attribute of the AtomType object.
    setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.debug.DebugAtomType
    Sets the MaxBondOrder attribute of the AtomType object.
    setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
    Sets the MaxBondOrder attribute of the AtomType object.
    setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
    Sets the MaxBondOrder attribute of the AtomType object.
    setMaxBondOrder(IBond.Order) - Method in interface org.openscience.cdk.interfaces.IAtomType
    Sets the MaxBondOrder attribute of the AtomType object.
    setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
    Sets the MaxBondOrder attribute of the AtomType object.
    setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.silent.AtomType
    Sets the MaxBondOrder attribute of the AtomType object.
    setMaxGasteigerDamp(double) - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
    Sets the maxGasteigerDamp attribute of the GasteigerMarsiliPartialCharges object.
    setMaxGasteigerIters(double) - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
    Sets the maxGasteigerIters attribute of the GasteigerMarsiliPartialCharges object.
    setMaxGasteigerIters(int) - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges
    Sets the maxGasteigerIters attribute of the GasteigerPEPEPartialCharges object.
    setMaximalStructures(int) - Method in class org.openscience.cdk.tools.StructureResonanceGenerator
    Set the number maximal of resonance structures to be found.
    setMaximumNeighbors(int) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultMCSPlusAtomMatcher
    Deprecated.
     
    setMaximumNeighbors(int) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultRGraphAtomMatcher
    Deprecated.
     
    setMaximumNeighbors(int) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFAtomMatcher
    Deprecated.
     
    setMaxIteration(int) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
    Sets the maxIteration for the RGraph parsing.
    setMaxIteration(int) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
    Deprecated.
    Sets the maxIteration for the CDKRGraph parsing.
    setMaxIterations(int) - Method in class org.openscience.cdk.charges.Electronegativity
    set the maximum number of Iterations.
    setMaxIterations(int) - Method in class org.openscience.cdk.charges.PiElectronegativity
    set the maximum number of Iterations.
    setMaxResonStruc(int) - Method in class org.openscience.cdk.charges.Electronegativity
    set the maximum number of resonance structures.
    setMaxResonStruc(int) - Method in class org.openscience.cdk.charges.PiElectronegativity
    set the maximum number of resonance structures.
    setMaxResoStruc(int) - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges
    Sets the maximum resonance structures to be searched.
    setMechanism(String) - Method in class org.openscience.cdk.dict.EntryReact
    Set the mechanism of this reaction.
    setMinimumFragmentSize(int) - Method in class org.openscience.cdk.fragment.ExhaustiveFragmenter
    Set the minimum fragment size.
    setMinPSCluster(int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
     
    setMinPSPocket(int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
     
    setMM2Parameters(IChemObjectBuilder) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
    Sets the parameters attribute of the ForceFieldConfigurator object, default is mm2 force field
    setMMFF94Parameters(IChemObjectBuilder) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
     
    setMode(int) - Method in class org.openscience.cdk.smarts.SmartsFragmentExtractor
    Set the mode of SMARTS substructure selection
    setModelCenter(double, double) - Method in class org.openscience.cdk.renderer.AbstractRenderer
    Set the position of the center of the model.
    setMolecule(IAtomContainer) - Method in class org.openscience.cdk.layout.AtomPlacer
    Sets the molecule the AtomPlacer currently works with
    setMolecule(IAtomContainer) - Method in class org.openscience.cdk.layout.RingPlacer
     
    setMolecule(IAtomContainer, boolean) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
     
    setMolecule(IAtomContainer, boolean, Set<IAtom>, Set<IBond>) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
    Assigns a molecule to be laid out.
    setMolecule(IAtomContainer) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
    Assings a molecule to be layed out.
    setMolecule(IAtomContainer) - Method in class org.openscience.cdk.structgen.RandomGenerator
    Assigns a starting structure to this generator.
    setMoleculeSet(IAtomContainerSet) - Method in class org.openscience.cdk.ChemModel
    Sets the MoleculeSet of this ChemModel.
    setMoleculeSet(IAtomContainerSet) - Method in class org.openscience.cdk.debug.DebugChemModel
    Sets the MoleculeSet of this ChemModel.
    setMoleculeSet(IAtomContainerSet) - Method in interface org.openscience.cdk.interfaces.IChemModel
    Sets the IAtomContainerSet of this ChemModel.
    setMoleculeSet(IAtomContainerSet) - Method in class org.openscience.cdk.silent.ChemModel
    Sets the MoleculeSet of this ChemModel.
    setMonoIsotope(IsotopeContainer) - Method in class org.openscience.cdk.formula.IsotopePattern
    Set the mono isotope object.
    setMonomerName(String) - Method in class org.openscience.cdk.debug.DebugAminoAcid
    Sets the name of the Monomer object.
    setMonomerName(String) - Method in class org.openscience.cdk.debug.DebugMonomer
    Sets the name of the Monomer object.
    setMonomerName(String) - Method in interface org.openscience.cdk.interfaces.IMonomer
    Set the name of the Monomer object.
    setMonomerName(String) - Method in class org.openscience.cdk.Monomer
    Sets the name of the Monomer object.
    setMonomerName(String) - Method in class org.openscience.cdk.silent.Monomer
    Sets the name of the Monomer object.
    setMonomerType(String) - Method in class org.openscience.cdk.debug.DebugAminoAcid
    Sets the type of the Monomer object.
    setMonomerType(String) - Method in class org.openscience.cdk.debug.DebugMonomer
    Sets the type of the Monomer object.
    setMonomerType(String) - Method in interface org.openscience.cdk.interfaces.IMonomer
    Set the type of the Monomer object.
    setMonomerType(String) - Method in class org.openscience.cdk.Monomer
    Sets the type of the Monomer object.
    setMonomerType(String) - Method in class org.openscience.cdk.silent.Monomer
    Sets the type of the Monomer object.
    setMultiMap(Map) - Method in class org.openscience.cdk.io.RssWriter
     
    setMultiplier(IAtomContainer, Double) - Method in class org.openscience.cdk.AtomContainerSet
    Sets the coefficient of a AtomContainer to a given value.
    setMultiplier(int, Double) - Method in class org.openscience.cdk.AtomContainerSet
    Sets the coefficient of a AtomContainer to a given value.
    setMultiplier(IAtomContainer, Double) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
    Sets the coefficient of a AtomContainer to a given value.
    setMultiplier(int, Double) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
    Sets the coefficient of a AtomContainer to a given value.
    setMultiplier(IAtomContainer, Double) - Method in class org.openscience.cdk.debug.DebugSubstance
    Sets the coefficient of a AtomContainer to a given value.
    setMultiplier(int, Double) - Method in class org.openscience.cdk.debug.DebugSubstance
    Sets the coefficient of a AtomContainer to a given value.
    setMultiplier(IAtomContainer, Double) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
    Sets the coefficient of a AtomContainer to a given value.
    setMultiplier(int, Double) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
    Sets the coefficient of a AtomContainer to a given value.
    setMultiplier(IAtomContainer, Double) - Method in class org.openscience.cdk.silent.AtomContainerSet
    Sets the coefficient of a AtomContainer to a given value.
    setMultiplier(int, Double) - Method in class org.openscience.cdk.silent.AtomContainerSet
    Sets the coefficient of a AtomContainer to a given value.
    setMultipliers(Double[]) - Method in class org.openscience.cdk.AtomContainerSet
    Sets the multipliers of the AtomContainers.
    setMultipliers(Double[]) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
    Sets the multipliers of the AtomContainers.
    setMultipliers(Double[]) - Method in class org.openscience.cdk.debug.DebugSubstance
    Sets the multipliers of the AtomContainers.
    setMultipliers(Double[]) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
    Sets the multipliers of the AtomContainers.
    setMultipliers(Double[]) - Method in class org.openscience.cdk.silent.AtomContainerSet
    Sets the multipliers of the AtomContainers.
    setName(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom
    set the Atom name of this atom.
    setName(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
    set the Atom name of this atom.
    setName(String) - Method in class org.openscience.cdk.iupac.parser.AttachedGroup
    Setter for property name.
    setName(String) - Method in class org.openscience.cdk.libio.md.Residue
     
    setName(String) - Method in class org.openscience.cdk.protein.data.PDBAtom
    set the Atom name of this atom.
    setName(String) - Method in class org.openscience.cdk.silent.PDBAtom
    set the Atom name of this atom.
    setNaturalAbundance(Double) - Method in class org.openscience.cdk.debug.DebugAtom
    Sets the NaturalAbundance attribute of the Isotope object.
    setNaturalAbundance(Double) - Method in class org.openscience.cdk.debug.DebugAtomType
    Sets the NaturalAbundance attribute of the Isotope object.
    setNaturalAbundance(Double) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
    Sets the NaturalAbundance attribute of the Isotope object.
    setNaturalAbundance(Double) - Method in class org.openscience.cdk.debug.DebugIsotope
    Sets the NaturalAbundance attribute of the Isotope object.
    setNaturalAbundance(Double) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
    Sets the NaturalAbundance attribute of the Isotope object.
    setNaturalAbundance(Double) - Method in interface org.openscience.cdk.interfaces.IIsotope
    Sets the NaturalAbundance attribute of the Isotope object.
    setNaturalAbundance(Double) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
    Sets the NaturalAbundance attribute of the Isotope object.
    setNaturalAbundance(Double) - Method in class org.openscience.cdk.Isotope
    Sets the NaturalAbundance attribute of the Isotope object.
    setNaturalAbundance(Double) - Method in class org.openscience.cdk.silent.Isotope
    Sets the NaturalAbundance attribute of the Isotope object.
    setNewMatrix(boolean) - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregor
    Deprecated.
    set a new Matrix.
    setNoteComments(String[]) - Method in class org.openscience.cdk.fingerprint.model.Bayesian
    Sets the comments for the model, which is a list of strings containing arbitrary content.
    setNoteOrigin(String) - Method in class org.openscience.cdk.fingerprint.model.Bayesian
    Provides an arbitrary string that briefly describes the model origin, which may include authors, data source keywords, or other pertinent information.
    setNotEqual(BinaryTree) - Method in class org.openscience.cdk.smsd.helper.BinaryTree
    Deprecated.
    Set not equal node
    setNoteTitle(String) - Method in class org.openscience.cdk.fingerprint.model.Bayesian
    Provides an arbitrary title string that briefly summarises the model.
    setNotification(boolean) - Method in class org.openscience.cdk.ChemObject
     
    setNotification(boolean) - Method in class org.openscience.cdk.debug.DebugChemObject
    Set a flag to use or not use notification.
    setNotification(boolean) - Method in interface org.openscience.cdk.interfaces.IChemObject
    Set a flag to use or not use notification.
    setNotification(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
     
    setNotification(boolean) - Method in class org.openscience.cdk.renderer.RendererModel
    Dis- or enables sending around change notifications.
    setNotification(boolean) - Method in class org.openscience.cdk.silent.ChemObject
     
    setNS(String) - Method in class org.openscience.cdk.dict.Dictionary
     
    setNumAtoms(int) - Method in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
     
    setNumber(int) - Method in class org.openscience.cdk.libio.md.ChargeGroup
     
    setNumber(int) - Method in class org.openscience.cdk.libio.md.Residue
     
    setObjectProperty(String, String, String) - Method in class org.openscience.cdk.io.iterator.event.EventCMLHandler
    Procedure required by the CDOInterface.
    setOccupancy(Double) - Method in class org.openscience.cdk.debug.DebugPDBAtom
    set the Occupancy of this atom.
    setOccupancy(Double) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
    set the Occupancy of this atom.
    setOccupancy(Double) - Method in class org.openscience.cdk.protein.data.PDBAtom
    set the Occupancy of this atom.
    setOccupancy(Double) - Method in class org.openscience.cdk.silent.PDBAtom
    set the Occupancy of this atom.
    setOccurrence(String) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
    Picky setter for occurrence fields.
    setOfMolecules - Variable in class org.openscience.cdk.ChemModel
    A MoleculeSet.
    setOfMolecules - Variable in class org.openscience.cdk.silent.ChemModel
    A MoleculeSet.
    setOfReactions - Variable in class org.openscience.cdk.ChemModel
    A ReactionSet.
    setOfReactions - Variable in class org.openscience.cdk.silent.ChemModel
    A ReactionSet.
    seTolerance(double) - Method in class org.openscience.cdk.formula.IsotopePatternSimilarity
    Set the tolerance of the mass accuracy.
    setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom
     
    setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom
    setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond
     
    setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolAndChargeQueryAtom
     
    setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolChargeIDQueryAtom
     
    setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom
     
    setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom
     
    setOrder(IBond.Order) - Method in class org.openscience.cdk.Bond
    Sets the bond order of this bond.
    setOrder(IBond.Order) - Method in class org.openscience.cdk.debug.DebugBond
    Sets the bond order of this bond.
    setOrder(IBond.Order) - Method in interface org.openscience.cdk.interfaces.IBond
    Sets the bond order of this bond.
    setOrder(IBond.Order) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
    Sets the bond order of this query bond.
    setOrder(IBond.Order) - Method in class org.openscience.cdk.silent.Bond
    Sets the bond order of this bond.
    setOutputWriter(Writer) - Method in class org.openscience.cdk.io.listener.PropertiesListener
    Overwrites the default writer to which the output is directed.
    setOutputWriter(Writer) - Method in class org.openscience.cdk.io.listener.TextGUIListener
    Overwrites the default writer to which the output is directed.
    setOverrideBondWidth(double) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
    Set the width to use for all bonds, overriding any standard bond widths.
    setOverrideColor(Color) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
    Set the color to use for all bonds, overriding the standard bond colors.
    setOxt(Boolean) - Method in class org.openscience.cdk.debug.DebugPDBAtom
    Change the state of this atom in being the PDB OXT atom.
    setOxt(Boolean) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
    Change the state of this atom in being the PDB OXT atom.
    setOxt(Boolean) - Method in class org.openscience.cdk.protein.data.PDBAtom
     
    setOxt(Boolean) - Method in class org.openscience.cdk.silent.PDBAtom
     
    setParameter(boolean) - Method in interface org.openscience.cdk.reaction.type.parameters.IParameterReact
    Set the parameter to take account.
    setParameter(boolean) - Method in class org.openscience.cdk.reaction.type.parameters.ParameterReact
    Set the parameter to take account.
    setParameterList(List<IParameterReact>) - Method in interface org.openscience.cdk.reaction.IReactionProcess
    Sets the parameters for this reaction.
    setParameterList(List<IParameterReact>) - Method in class org.openscience.cdk.reaction.ReactionEngine
    Returns the current parameter Map for this reaction.
    setParameters(String, String, String) - Method in class org.openscience.cdk.dict.EntryReact
    Set the parameters of the reaction.
    setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.ChargeRule
    Sets the parameters attribute of the ChargeRule object.
    setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.ElementRule
    Sets the parameters attribute of the ElementRule object.
    setParameters(Object[]) - Method in interface org.openscience.cdk.formula.rules.IRule
    Sets the parameters for this rule.
    setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.IsotopePatternRule
    Sets the parameters attribute of the IsotopePatternRule object.
    setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.MMElementRule
    Sets the parameters attribute of the MMElementRule object.
    setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.NitrogenRule
    Sets the parameters attribute of the NitrogenRule object.
    setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.RDBERule
    Sets the parameters attribute of the RDBE object.
    setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.ToleranceRangeRule
    Sets the parameters attribute of the ToleranceRangeRule object.
    setParameters(Map<String, Object>) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
    Sets the parameters attribute of the ForceFieldConfigurator object
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor
    This descriptor does not have any parameter to be set.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor
    This descriptor does have any parameter.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor
    This descriptor does have any parameter.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor
    This descriptor does have any parameter.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor
    Sets the parameters attribute of the BondsToAtomDescriptor object
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor
    This descriptor does have any parameter.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor
    Sets the parameters attribute of the DistanceToAtomDescriptor object
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor
    This descriptor does have any parameter.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor
    This descriptor does have any parameter.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor
    This descriptor does have any parameter.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor
    This descriptor does have any parameter.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor
    Deprecated.
    This descriptor does have any parameter.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor
    Sets the parameters attribute of the IsProtonInAromaticSystemDescriptor object
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInConjugatedPiSystemDescriptor
    Sets the parameters attribute of the IsProtonInConjugatedPiSystemDescriptor object
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor
    Sets the parameters attribute of the PartialPiChargeDescriptor object
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor
    Sets the parameters attribute of the PartialSigmaChargeDescriptor object
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor
    This descriptor does not have any parameter to be set.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor
    This descriptor does not have any parameter to be set.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor
    This descriptor does not have any parameter to be set.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor
    Sets the parameters attribute of the PiElectronegativityDescriptor object
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor
    This descriptor does have any parameter.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor
    This descriptor does not have any parameter to be set.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R
    Sets the parameters attribute of the RDFProtonDescriptor object
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR
    Sets the parameters attribute of the RDFProtonDescriptor object
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR
    Sets the parameters attribute of the RDFProtonDescriptor object
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol
    Sets the parameters attribute of the RDFProtonDescriptor object
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR
    Sets the parameters attribute of the RDFProtonDescriptor object
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor
    Sets the parameters attribute of the SigmaElectronegativityDescriptor object
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor
    Sets the parameters attribute of the StabilizationPlusChargeDescriptor object
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor
    This descriptor does have any parameter.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor
    Sets the parameters attribute of the PiContactDetectionDescriptor object.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptor
     
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor
    This descriptor does have any parameter.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor
    This descriptor does have any parameter.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor
    This descriptor does have any parameter.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor
    This descriptor does have any parameter.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor
    Deprecated.
    This descriptor does have any parameter.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor
    Sets the parameters for this descriptor.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
     
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor
    Sets the parameters attribute of the AminoAcidsCountDescriptor object.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor
    Sets the parameters attribute of the APolDescriptor object.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor
    Sets the parameters attribute of the AromaticAtomsCountDescriptor object.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor
    Sets the parameters attribute of the AromaticBondsCountDescriptor object.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor
    Sets the parameters attribute of the AtomCountDescriptor object.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
     
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
     
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
     
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor
    Sets the parameters for this descriptor.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor
    Sets the parameters attribute of the BCUTDescriptor object.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor
    Sets the parameters attribute of the BondCountDescriptor object
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor
    Sets the parameters attribute of the BPolDescriptor object
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor
    Sets the parameters attribute of the GravitationalIndexDescriptor object.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
     
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
     
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
     
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
     
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor
    Sets the parameters attribute of the CPSADescriptor object.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor
    Sets the parameters attribute of the EccentricConnectivityIndexDescriptor object
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor
    Sets the parameters for this descriptor.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor
    Sets the parameters for this descriptor.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor
    Sets the parameters attribute of the FragmentComplexityDescriptor object.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor
    Sets the parameters attribute of the GravitationalIndexDescriptor object.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor
    Sets the parameters attribute of the HBondAcceptorCountDescriptor object.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor
    Sets the parameter of this HBondDonorCountDescriptor instance.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor
    Sets the parameters attribute of the HybridizationRatioDescriptor object.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor
    Deprecated.
    Sets the parameters attribute of the IPMolecularLearningDescriptor object
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor
    Sets the parameters attribute of the KappaShapeIndicesDescriptor object
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor
    Sets the parameters attribute of the descriptor.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor
    Sets the parameters attribute of the LargestChain object.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor
    Sets the parameters attribute of the LargestPiSystemDescriptor object.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor
    Sets the parameters attribute of the PetitjeanNumberDescriptor object
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor
    Sets the parameters attribute of the LongestAliphaticChainDescriptor object.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor
    This IDescriptor does not have any parameters.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
    Sets the parameters attribute of the WeightDescriptor object.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor
    Sets the parameters attribute of the MomentOfInertiaDescriptor object.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor
    Sets the parameters attribute of the PetitjeanNumberDescriptor object
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor
    Sets the parameters attribute of the PetitjeanShapeIndexDescriptor object.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor
    Sets the parameters attribute of the RotatableBondsCountDescriptor object
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor
    Sets the parameters attribute of the RuleOfFiveDescriptor object.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor
    Set parameters: ignored, there are none.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor
    Sets the parameters attribute of the TPSADescriptor object.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor
    Sets the parameters for this descriptor.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor
    Sets the parameters attribute of the VAdjMaDescriptor object
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor
    Sets the parameters attribute of the WeightDescriptor object.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor
    Sets the parameters attribute of the WeightedPathDescriptor object.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor
    Sets the parameters attribute of the WHIMDescriptor object.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor
    Sets the parameters attribute of the WienerNumbersDescriptor object.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor
    Sets the parameters attribute of the XLogPDescriptor object.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor
    Sets the parameters attribute of the ZagrebIndexDescriptor object.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor
    Sets the parameters attribute of the TaeAminoAcidDescriptor object.
    setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.substance.OxygenAtomCountDescriptor
    Sets the parameters for this descriptor.
    setParameters(Object[]) - Method in interface org.openscience.cdk.qsar.IDescriptor
    Sets the parameters for this descriptor.
    setParameterSet(Map) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
    Constructor for the setParameterSet object.
    setParentMolecule(MDMolecule) - Method in class org.openscience.cdk.libio.md.ChargeGroup
     
    setParentMolecule(MDMolecule) - Method in class org.openscience.cdk.libio.md.Residue
     
    setPathLimit(int) - Method in class org.openscience.cdk.fingerprint.Fingerprinter
     
    setPermutation(int[]) - Method in class org.openscience.cdk.graph.Permutor
    Set the currently used permutation.
    setPermutation(int[]) - Method in class org.openscience.cdk.smsd.labelling.Permutor
    Deprecated.
    Set the currently used permutation.
    setPharmacophoreQuery(PharmacophoreQuery) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher
    Set a pharmacophore query.
    setPocketSize(int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
     
    setPoint2d(Point2d) - Method in class org.openscience.cdk.Atom
    Sets a point specifying the location of this atom in a 2D space.
    setPoint2d(Point2d) - Method in class org.openscience.cdk.debug.DebugAtom
    Sets a point specifying the location of this atom in a 2D space.
    setPoint2d(Point2d) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
    Sets a point specifying the location of this atom in a 2D space.
    setPoint2d(Point2d) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
    Sets a point specifying the location of this atom in a 2D space.
    setPoint2d(Point2d) - Method in interface org.openscience.cdk.interfaces.IAtom
    Sets a point specifying the location of this atom in a 2D space.
    setPoint2d(Point2d) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
    Sets a point specifying the location of this atom in a 2D space.
    setPoint2d(Point2d) - Method in class org.openscience.cdk.silent.Atom
    Sets a point specifying the location of this atom in a 2D space.
    setPoint3d(Point3d) - Method in class org.openscience.cdk.Atom
    Sets a point specifying the location of this atom in 3D space.
    setPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugAtom
    Sets a point specifying the location of this atom in 3D space.
    setPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
    Sets a point specifying the location of this atom in 3D space.
    setPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
    Sets a point specifying the location of this atom in 3D space.
    setPoint3d(Point3d) - Method in interface org.openscience.cdk.interfaces.IAtom
    Sets a point specifying the location of this atom in 3D space.
    setPoint3d(Point3d) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
    Sets a point specifying the location of this atom in 3D space.
    setPoint3d(Point3d) - Method in class org.openscience.cdk.silent.Atom
    Sets a point specifying the location of this atom in 3D space.
    setPreservingAromaticity(boolean) - Method in class org.openscience.cdk.smiles.SmilesParser
    Deprecated.
    setPrime() - Method in class org.openscience.cdk.smiles.InvPair
    Sets the prime number based on the current seed.
    setProductCoefficient(IAtomContainer, Double) - Method in class org.openscience.cdk.debug.DebugReaction
    Sets the coefficient of a a product to a given value.
    setProductCoefficient(IAtomContainer, Double) - Method in interface org.openscience.cdk.interfaces.IReaction
    Sets the coefficient of a a product to a given value.
    setProductCoefficient(IAtomContainer, Double) - Method in class org.openscience.cdk.Reaction
    Sets the coefficient of a a product to a given value.
    setProductCoefficient(IAtomContainer, Double) - Method in class org.openscience.cdk.silent.Reaction
    Sets the coefficient of a a product to a given value.
    setProductCoefficients(Double[]) - Method in class org.openscience.cdk.debug.DebugReaction
    Sets the coefficient of the products.
    setProductCoefficients(Double[]) - Method in interface org.openscience.cdk.interfaces.IReaction
    Sets the coefficient of the products.
    setProductCoefficients(Double[]) - Method in class org.openscience.cdk.Reaction
    Sets the coefficient of the products.
    setProductCoefficients(Double[]) - Method in class org.openscience.cdk.silent.Reaction
    Sets the coefficient of the products.
    setProducts(IAtomContainerSet) - Method in class org.openscience.cdk.debug.DebugReaction
    Assigns a MoleculeSet to the products of this reaction.
    setProducts(IAtomContainerSet) - Method in interface org.openscience.cdk.interfaces.IReaction
    Assigns a IAtomContaineSet to the products of this reaction.
    setProducts(IAtomContainerSet) - Method in class org.openscience.cdk.Reaction
    Assigns a MoleculeSet to the products of this reaction.
    setProducts(IAtomContainerSet) - Method in class org.openscience.cdk.silent.Reaction
    Assigns a MoleculeSet to the products of this reaction.
    setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.ChemObject
    Set the properties of this object to the provided map (shallow copy).
    setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugChemObject
    Set the properties of this object to the provided map (shallow copy).
    setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugMolecularFormula
    Sets the properties of this object.
    setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.formula.MolecularFormula
    Sets the properties of this object.
    setProperties(Map<Object, Object>) - Method in interface org.openscience.cdk.interfaces.IChemObject
    Set the properties of this object to the provided map (shallow copy).
    setProperties(Map<Object, Object>) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
    Sets the properties of this object.I should integrate into ChemObject.
    setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
    Set the properties of this object to the provided map (shallow copy).
    setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.silent.ChemObject
    Set the properties of this object to the provided map (shallow copy).
    setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.silent.MolecularFormula
    Sets the properties of this object.
    setProperty(Object, Object) - Method in class org.openscience.cdk.ChemObject
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugAminoAcid
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugAtom
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugAtomContainer
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugAtomType
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugBioPolymer
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugBond
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugChemFile
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugChemModel
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugChemObject
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugChemSequence
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugCrystal
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugElectronContainer
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugElement
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugIsotope
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugLonePair
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugMapping
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugMolecularFormula
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugMonomer
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugPolymer
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugReaction
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugReactionScheme
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugReactionSet
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugRing
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugSingleElectron
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugStrand
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugSubstance
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.formula.MolecularFormula
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in interface org.openscience.cdk.interfaces.IChemObject
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.silent.ChemObject
    Sets a property for a IChemObject.
    setProperty(Object, Object) - Method in class org.openscience.cdk.silent.MolecularFormula
    Sets a property for a IChemObject.
    setProtein(IBioPolymer) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
     
    setProteinInterior(int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
     
    setPublisher(String) - Method in class org.openscience.cdk.io.RssWriter
     
    setQueryCacheSize(int) - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool
    Set the maximum size of the query cache.
    setRandom(Random) - Static method in class org.openscience.cdk.math.RandomNumbersTool
    Sets the base generator to be used by this class.
    setRandomSeed(long) - Static method in class org.openscience.cdk.math.RandomNumbersTool
    Sets the seed of this random number generator using a single long seed.
    setRank(int) - Method in class org.openscience.cdk.graph.Permutor
    Set the permutation to use, given its rank.
    setRank(int) - Method in class org.openscience.cdk.smsd.labelling.Permutor
    Deprecated.
    Set the permutation to use, given its rank.
    setRAtom(double) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
     
    setRawContent(Object) - Method in class org.openscience.cdk.dict.Entry
     
    setRdFields(Map<String, Object>) - Method in class org.openscience.cdk.io.MDLRXNWriter
    Here you can set a map which will be used to build rd fields in the file.
    setReactantCoefficient(IAtomContainer, Double) - Method in class org.openscience.cdk.debug.DebugReaction
    Sets the coefficient of a a reactant to a given value.
    setReactantCoefficient(IAtomContainer, Double) - Method in interface org.openscience.cdk.interfaces.IReaction
    Sets the coefficient of a a reactant to a given value.
    setReactantCoefficient(IAtomContainer, Double) - Method in class org.openscience.cdk.Reaction
    Sets the coefficient of a a reactant to a given value.
    setReactantCoefficient(IAtomContainer, Double) - Method in class org.openscience.cdk.silent.Reaction
    Sets the coefficient of a a reactant to a given value.
    setReactantCoefficients(Double[]) - Method in class org.openscience.cdk.debug.DebugReaction
    Sets the coefficients of the reactants.
    setReactantCoefficients(Double[]) - Method in interface org.openscience.cdk.interfaces.IReaction
    Sets the coefficients of the reactants.
    setReactantCoefficients(Double[]) - Method in class org.openscience.cdk.Reaction
    Sets the coefficients of the reactants.
    setReactantCoefficients(Double[]) - Method in class org.openscience.cdk.silent.Reaction
    Sets the coefficients of the reactants.
    setReactants(IAtomContainerSet) - Method in class org.openscience.cdk.debug.DebugReaction
    Assigns a MoleculeSet to the reactants in this reaction.
    setReactants(IAtomContainerSet) - Method in interface org.openscience.cdk.interfaces.IReaction
    Assigns a IAtomContaineSet to the reactants in this reaction.
    setReactants(IAtomContainerSet) - Method in class org.openscience.cdk.Reaction
    Assigns a MoleculeSet to the reactants in this reaction.
    setReactants(IAtomContainerSet) - Method in class org.openscience.cdk.silent.Reaction
    Assigns a MoleculeSet to the reactants in this reaction.
    SetReactionCenter - Class in org.openscience.cdk.reaction.type.parameters
    Class extension of ParameterReact class which defines if a reaction is set already the reaction center in the reactants.
    SetReactionCenter() - Constructor for class org.openscience.cdk.reaction.type.parameters.SetReactionCenter
     
    setReactionMetadata(String) - Method in class org.openscience.cdk.dict.EntryReact
     
    setReactions(List<IReactionProcess>) - Method in class org.openscience.cdk.tools.StructureResonanceGenerator
    Set the reactions that must be used in the generation of the resonance.
    setReactionSet(IReactionSet) - Method in class org.openscience.cdk.ChemModel
    Sets the ReactionSet contained in this ChemModel.
    setReactionSet(IReactionSet) - Method in class org.openscience.cdk.debug.DebugChemModel
    Sets the ReactionSet contained in this ChemModel.
    setReactionSet(IReactionSet) - Method in interface org.openscience.cdk.interfaces.IChemModel
    Sets the ReactionSet contained in this ChemModel.
    setReactionSet(IReactionSet) - Method in class org.openscience.cdk.silent.ChemModel
    Sets the ReactionSet contained in this ChemModel.
    setReader(Reader) - Method in class org.openscience.cdk.io.CIFReader
     
    setReader(InputStream) - Method in class org.openscience.cdk.io.CIFReader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.CMLReader
    This method must not be used; XML reading requires the use of an InputStream.
    setReader(InputStream) - Method in class org.openscience.cdk.io.CMLReader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.CrystClustReader
     
    setReader(InputStream) - Method in class org.openscience.cdk.io.CrystClustReader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.CTXReader
     
    setReader(InputStream) - Method in class org.openscience.cdk.io.CTXReader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.GamessReader
     
    setReader(InputStream) - Method in class org.openscience.cdk.io.GamessReader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.Gaussian03Reader
     
    setReader(InputStream) - Method in class org.openscience.cdk.io.Gaussian03Reader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.Gaussian98Reader
    Sets the reader attribute of the Gaussian98Reader object.
    setReader(InputStream) - Method in class org.openscience.cdk.io.Gaussian98Reader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.GhemicalMMReader
     
    setReader(InputStream) - Method in class org.openscience.cdk.io.GhemicalMMReader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.HINReader
     
    setReader(InputStream) - Method in class org.openscience.cdk.io.HINReader
     
    setReader(Reader) - Method in interface org.openscience.cdk.io.IChemObjectReader
    Sets the Reader from which this ChemObjectReader should read the contents.
    setReader(InputStream) - Method in interface org.openscience.cdk.io.IChemObjectReader
    Sets the InputStream from which this ChemObjectReader should read the contents.
    setReader(Reader) - Method in class org.openscience.cdk.io.INChIPlainTextReader
     
    setReader(InputStream) - Method in class org.openscience.cdk.io.INChIPlainTextReader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.INChIReader
    This method must not be used; XML reading requires the use of an InputStream.
    setReader(InputStream) - Method in class org.openscience.cdk.io.INChIReader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.iterator.event.EventCMLReader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundASNReader
     
    setReader(InputStream) - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundASNReader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader
     
    setReader(InputStream) - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader
     
    setReader(InputStream) - Method in class org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.iterator.IteratingSDFReader
     
    setReader(InputStream) - Method in class org.openscience.cdk.io.iterator.IteratingSDFReader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.iterator.IteratingSMILESReader
     
    setReader(InputStream) - Method in class org.openscience.cdk.io.iterator.IteratingSMILESReader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.MDLReader
    Deprecated.
     
    setReader(InputStream) - Method in class org.openscience.cdk.io.MDLReader
    Deprecated.
     
    setReader(Reader) - Method in class org.openscience.cdk.io.MDLRXNReader
     
    setReader(InputStream) - Method in class org.openscience.cdk.io.MDLRXNReader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.MDLRXNV2000Reader
     
    setReader(InputStream) - Method in class org.openscience.cdk.io.MDLRXNV2000Reader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.MDLRXNV3000Reader
     
    setReader(InputStream) - Method in class org.openscience.cdk.io.MDLRXNV3000Reader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.MDLV2000Reader
     
    setReader(InputStream) - Method in class org.openscience.cdk.io.MDLV2000Reader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.MDLV3000Reader
     
    setReader(InputStream) - Method in class org.openscience.cdk.io.MDLV3000Reader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.Mol2Reader
     
    setReader(InputStream) - Method in class org.openscience.cdk.io.Mol2Reader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.Mopac7Reader
     
    setReader(InputStream) - Method in class org.openscience.cdk.io.Mopac7Reader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.MoSSOutputReader
    Sets the Reader from which this ChemObjectReader should read the contents.
    setReader(InputStream) - Method in class org.openscience.cdk.io.MoSSOutputReader
    Sets the InputStream from which this ChemObjectReader should read the contents.
    setReader(Reader) - Method in class org.openscience.cdk.io.PCCompoundASNReader
     
    setReader(InputStream) - Method in class org.openscience.cdk.io.PCCompoundASNReader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.PCCompoundXMLReader
     
    setReader(InputStream) - Method in class org.openscience.cdk.io.PCCompoundXMLReader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.PCSubstanceXMLReader
     
    setReader(InputStream) - Method in class org.openscience.cdk.io.PCSubstanceXMLReader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.PDBReader
     
    setReader(InputStream) - Method in class org.openscience.cdk.io.PDBReader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.PMPReader
     
    setReader(InputStream) - Method in class org.openscience.cdk.io.PMPReader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.random.RandomAccessSDFReader
     
    setReader(InputStream) - Method in class org.openscience.cdk.io.random.RandomAccessSDFReader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.rdf.CDKOWLReader
    Deprecated. 
    setReader(InputStream) - Method in class org.openscience.cdk.io.rdf.CDKOWLReader
    Sets the InputStream from which this ChemObjectReader should read the contents.
    setReader(Reader) - Method in class org.openscience.cdk.io.RGroupQueryReader
    Sets the input Reader.
    setReader(InputStream) - Method in class org.openscience.cdk.io.RGroupQueryReader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.ShelXReader
     
    setReader(InputStream) - Method in class org.openscience.cdk.io.ShelXReader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.SMILESReader
     
    setReader(InputStream) - Method in class org.openscience.cdk.io.SMILESReader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.VASPReader
     
    setReader(InputStream) - Method in class org.openscience.cdk.io.VASPReader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.XYZReader
     
    setReader(InputStream) - Method in class org.openscience.cdk.io.XYZReader
     
    setReader(Reader) - Method in class org.openscience.cdk.io.ZMatrixReader
     
    setReader(InputStream) - Method in class org.openscience.cdk.io.ZMatrixReader
     
    setReaderMode(IChemObjectReader.Mode) - Method in class org.openscience.cdk.io.DefaultChemObjectReader
     
    setReaderMode(IChemObjectReader.Mode) - Method in interface org.openscience.cdk.io.IChemObjectReader
    Sets the reader mode.
    setReaderMode(IChemObjectReader.Mode) - Method in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader
     
    setReaderMode(IChemObjectReader.Mode) - Method in class org.openscience.cdk.io.random.DefaultRandomAccessChemObjectReader
     
    setRealPart(double) - Method in class org.openscience.cdk.math.Complex
    Sets the real part of this complex value
    setRecord(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom
    set one entire line from the PDB entry file which describe the IPDBAtom.
    setRecord(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
    Set one entire line from the PDB entry file which describe the IPDBAtom.
    setRecord(String) - Method in class org.openscience.cdk.protein.data.PDBAtom
    set one entire line from the PDB entry file which describe the IPDBAtom.
    setRecord(String) - Method in class org.openscience.cdk.silent.PDBAtom
    set one entire line from the PDB entry file which describe the IPDBAtom.
    setRendererModel(RendererModel) - Method in class org.openscience.cdk.renderer.visitor.AWTDrawVisitor
    Sets the RendererModel this IDrawVisitor should use.
    setRendererModel(RendererModel) - Method in interface org.openscience.cdk.renderer.visitor.IDrawVisitor
    Sets the RendererModel this IDrawVisitor should use.
    setRepresentation(String) - Method in class org.openscience.cdk.dict.EntryReact
    Set the representation of the reaction.
    setRequiredRGroupNumber(int) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
     
    setResidues(List<Residue>) - Method in class org.openscience.cdk.libio.md.MDMolecule
     
    setResName(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom
    set the Residue name of this atom.
    setResName(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
    set the Residue name of this atom.
    setResName(String) - Method in class org.openscience.cdk.protein.data.PDBAtom
    set the Residue name of this atom.
    setResName(String) - Method in class org.openscience.cdk.silent.PDBAtom
    set the Residue name of this atom.
    setResSeq(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom
    set the Residue sequence number of this atom.
    setResSeq(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
    set the Residue sequence number of this atom.
    setResSeq(String) - Method in interface org.openscience.cdk.interfaces.IPDBMonomer
    Sets the sequence identifier of this monomer.
    setResSeq(String) - Method in class org.openscience.cdk.protein.data.PDBAtom
    set the Residue sequence number of this atom.
    setResSeq(String) - Method in class org.openscience.cdk.protein.data.PDBMonomer
     
    setResSeq(String) - Method in class org.openscience.cdk.silent.PDBAtom
    set the Residue sequence number of this atom.
    setResSeq(String) - Method in class org.openscience.cdk.silent.PDBMonomer
     
    setRestH(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
     
    setRestrictions(List<IRule>) - Method in class org.openscience.cdk.formula.MassToFormulaTool
    Deprecated.
    Set the restrictions that must be presents in the molecular formula.
    setRGroupDefinitions(Map<Integer, RGroupList>) - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
    Setter for the R-group definitions (substituents).
    setRGroupDefinitions(Map<Integer, RGroupList>) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
     
    setRGroupNumber(int) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
    Setter for rGroupNumber, checks for valid range.
    setRGroups(List<RGroup>) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
     
    setRight(IQueryAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom
    Deprecated.
    setRight(IQueryBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond
     
    setRingBond(IQueryBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RingIdentifierAtom
     
    setRingSet(IRingSet) - Method in class org.openscience.cdk.atomtype.EStateAtomTypeMatcher
     
    setRingSet(IRingSet) - Method in class org.openscience.cdk.ChemModel
    Sets the RingSet of this ChemModel.
    setRingSet(IRingSet) - Method in class org.openscience.cdk.debug.DebugChemModel
    Sets the RingSet of this ChemModel.
    setRingSet(IRingSet) - Method in interface org.openscience.cdk.interfaces.IChemModel
    Sets the RingSet of this ChemModel.
    setRingSet(IRingSet) - Method in class org.openscience.cdk.silent.ChemModel
    Sets the RingSet of this ChemModel.
    setRMap(RMap) - Method in class org.openscience.cdk.isomorphism.mcss.RNode
    Sets the rMap attribute of the RNode object.
    setRMap(CDKRMap) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode
    Deprecated.
    Sets the rMap attribute of the RNode object
    setrMap(CDKRMap) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode
    Deprecated.
    Sets resolution map/graph
    setRootAttachmentPoints(Map<IAtom, Map<Integer, IBond>>) - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
    Setter for root attachment points = bonds that connect R pseudo-atoms to the scaffold.
    setRootAttachmentPoints(Map<IAtom, Map<Integer, IBond>>) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
     
    setRootStructure(IAtomContainer) - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
    Setter for the root structure of this R-Group.
    setRootStructure(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
     
    setRounding(boolean) - Method in class org.openscience.cdk.renderer.visitor.AWTDrawVisitor
    Set whether we should we round coordinates to ints, this tries to circumvent graphical glitches from AWT where floating points are truncated (e.g.
    setRSolvent(double) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
     
    setScale(IAtomContainer) - Method in class org.openscience.cdk.renderer.AtomContainerRenderer
    Set the scale for an IAtomContainer.
    setScale(IChemModel) - Method in class org.openscience.cdk.renderer.ChemModelRenderer
    Set the scale for an IChemModel.
    setScale(T) - Method in interface org.openscience.cdk.renderer.IRenderer
    Set the scale for an IChemObject.
    setScale(IAtomContainerSet) - Method in class org.openscience.cdk.renderer.MoleculeSetRenderer
    Set the scale for an IAtomContainerSet.
    setScale(IReaction) - Method in class org.openscience.cdk.renderer.ReactionRenderer
    Set the scale for an IReaction.
    setScale(IReactionSet) - Method in class org.openscience.cdk.renderer.ReactionSetRenderer
    Set the scale for an IReactionSet.
    setSecondAttachmentPoint(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.RGroup
     
    setSecondGraphSize(int) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
    Returns the size of the second of the two compared graphs.
    setSecondGraphSize(int) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
    Deprecated.
    Returns the size of the second of the two compared graphs.
    setSegID(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom
    set the Segment identifier, left-justified of this atom.
    setSegID(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
    set the Segment identifier, left-justified of this atom.
    setSegID(String) - Method in class org.openscience.cdk.protein.data.PDBAtom
    set the Segment identifier, left-justified of this atom.
    setSegID(String) - Method in class org.openscience.cdk.silent.PDBAtom
    set the Segment identifier, left-justified of this atom.
    setSelection(IChemObjectSelection) - Method in class org.openscience.cdk.renderer.RendererModel
    Set the selected IChemObjects.
    setSerial(Integer) - Method in class org.openscience.cdk.debug.DebugPDBAtom
    set the Atom serial number of this atom.
    setSerial(Integer) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
    set the Atom serial number of this atom.
    setSerial(Integer) - Method in class org.openscience.cdk.protein.data.PDBAtom
    set the Atom serial number of this atom.
    setSerial(Integer) - Method in class org.openscience.cdk.silent.PDBAtom
    set the Atom serial number of this atom.
    setSetting(String) - Method in class org.openscience.cdk.io.setting.BooleanIOSetting
    Sets the setting for a certain question.
    setSetting(String) - Method in class org.openscience.cdk.io.setting.IntegerIOSetting
    Sets the setting for a certain question.
    setSetting(String) - Method in class org.openscience.cdk.io.setting.IOSetting
    Sets the setting for a certain question.
    setSetting(String) - Method in class org.openscience.cdk.io.setting.OptionIOSetting
    Sets the setting for a certain question.
    setSetting(int) - Method in class org.openscience.cdk.io.setting.OptionIOSetting
    Sets the setting for a certain question.
    setSetting(String) - Method in class org.openscience.cdk.io.setting.StringIOSetting
    Sets the setting for a certain question.
    setSingleOrDoubleFlags(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
    Assigns CDKConstants.SINGLE_OR_DOUBLE flags to the bonds of a container.
    setSkip(boolean) - Method in class org.openscience.cdk.io.iterator.IteratingSDFReader
    Indicate whether the reader should skip over SDF records that cause problems.
    setSmarts(String) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom
    Set the SMARTS for the group.
    setSmarts(String) - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool
    Set a new SMARTS pattern.
    setSolvantValue(int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
     
    setSource(IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
    Deprecated.
    Set source molecule
    setSpaceGroup(String) - Method in class org.openscience.cdk.Crystal
    Sets the space group of this crystal.
    setSpaceGroup(String) - Method in class org.openscience.cdk.debug.DebugCrystal
    Sets the space group of this crystal.
    setSpaceGroup(String) - Method in interface org.openscience.cdk.interfaces.ICrystal
    Sets the space group of this crystal.
    setSpaceGroup(String) - Method in class org.openscience.cdk.silent.Crystal
    Sets the space group of this crystal.
    setStackLength(int) - Method in interface org.openscience.cdk.tools.ILoggingTool
    Sets the number of StackTraceElements to be printed in DEBUG mode when calling debug(Throwable).
    setStackLength(int) - Method in class org.openscience.cdk.tools.LoggingTool
    Sets the number of StackTraceElements to be printed in DEBUG mode when calling debug(Throwable).
    setStackLength(int) - Method in class org.openscience.cdk.tools.SystemOutLoggingTool
    Sets the number of StackTraceElements to be printed in DEBUG mode when calling debug(Throwable).
    setStart(long) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
     
    setStartChainID(Character) - Method in class org.openscience.cdk.debug.DebugPDBStructure
    set the start Chain identifier of this structure.
    setStartChainID(Character) - Method in interface org.openscience.cdk.interfaces.IPDBStructure
    set the start Chain identifier of this structure.
    setStartChainID(Character) - Method in class org.openscience.cdk.protein.data.PDBStructure
    set the start Chain identifier of this structure.
    setStartChainID(Character) - Method in class org.openscience.cdk.silent.PDBStructure
    set the start Chain identifier of this structure.
    setStartInsertionCode(Character) - Method in class org.openscience.cdk.debug.DebugPDBStructure
    set the start Chain identifier of this structure.
    setStartInsertionCode(Character) - Method in interface org.openscience.cdk.interfaces.IPDBStructure
    set the start Chain identifier of this structure.
    setStartInsertionCode(Character) - Method in class org.openscience.cdk.protein.data.PDBStructure
    set the start Chain identifier of this structure.
    setStartInsertionCode(Character) - Method in class org.openscience.cdk.silent.PDBStructure
    set the start Chain identifier of this structure.
    setStartSequenceNumber(Integer) - Method in class org.openscience.cdk.debug.DebugPDBStructure
    set the start sequence number of this structure.
    setStartSequenceNumber(Integer) - Method in interface org.openscience.cdk.interfaces.IPDBStructure
    set the start sequence number of this structure.
    setStartSequenceNumber(Integer) - Method in class org.openscience.cdk.protein.data.PDBStructure
    set the start sequence number of this structure.
    setStartSequenceNumber(Integer) - Method in class org.openscience.cdk.silent.PDBStructure
    set the start sequence number of this structure.
    setStepSize(int) - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
    Set the StepSize attribute of the GasteigerMarsiliPartialCharges object.
    setStepSize(int) - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges
    Set the StepSize attribute of the GasteigerMarsiliPartialCharges object.
    setStereo(IBond.Stereo) - Method in class org.openscience.cdk.Bond
    Sets the stereo descriptor for this bond.
    setStereo(IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugBond
    Sets the stereo descriptor for this bond.
    setStereo(IBond.Stereo) - Method in interface org.openscience.cdk.interfaces.IBond
    Sets the stereo descriptor for this bond.
    setStereo(ITetrahedralChirality.Stereo) - Method in interface org.openscience.cdk.interfaces.ITetrahedralChirality
    Set the stereochemistry of this tetrahedral centre.
    setStereo(IBond.Stereo) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
    Sets the stereo descriptor for this query bond.
    setStereo(IBond.Stereo) - Method in class org.openscience.cdk.silent.Bond
    Sets the stereo descriptor for this bond.
    setStereo(ITetrahedralChirality.Stereo) - Method in class org.openscience.cdk.stereo.TetrahedralChirality
    Set the stereochemistry of this tetrahedral centre.
    setStereoElements(List<IStereoElement>) - Method in class org.openscience.cdk.AtomContainer
    Set the stereo elements - this will replace the existing instance with a new instance.
    setStereoElements(List<IStereoElement>) - Method in class org.openscience.cdk.debug.DebugAtomContainer
    Set the stereo elements - this will replace the existing instance with a new instance.
    setStereoElements(List<IStereoElement>) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
    Set the stereo elements - this will replace the existing instance with a new instance.
    setStereoElements(List<IStereoElement>) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
     
    setStereoElements(List<IStereoElement>) - Method in class org.openscience.cdk.silent.AtomContainer
    Set the stereo elements - this will replace the existing instance with a new instance.
    setStereoParity(Integer) - Method in class org.openscience.cdk.Atom
    Sets the stereo parity for this atom.
    setStereoParity(Integer) - Method in class org.openscience.cdk.debug.DebugAtom
    Sets the stereo parity for this atom.
    setStereoParity(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
    Dummy method: the stereo parity is undefined, final.
    setStereoParity(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
    Dummy method: the stereo parity is undefined, final.
    setStereoParity(Integer) - Method in interface org.openscience.cdk.interfaces.IAtom
    Deprecated.
    use IStereoElements for storing stereochemistry
    setStereoParity(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
    Sets the stereo parity for this atom.
    setStereoParity(Integer) - Method in class org.openscience.cdk.PseudoAtom
    Dummy method: the stereo parity is undefined, final.
    setStereoParity(Integer) - Method in class org.openscience.cdk.silent.Atom
    Sets the stereo parity for this atom.
    setStereoParity(Integer) - Method in class org.openscience.cdk.silent.PseudoAtom
    Dummy method: the stereo parity is undefined, final.
    setStrandName(String) - Method in class org.openscience.cdk.debug.DebugStrand
    Sets the name of the Strand object.
    setStrandName(String) - Method in interface org.openscience.cdk.interfaces.IStrand
    Set the name of the Strand object.
    setStrandName(String) - Method in class org.openscience.cdk.silent.Strand
    Sets the name of the Strand object.
    setStrandName(String) - Method in class org.openscience.cdk.Strand
    Sets the name of the Strand object.
    setStrandType(String) - Method in class org.openscience.cdk.debug.DebugStrand
    Sets the type of the Strand object.
    setStrandType(String) - Method in interface org.openscience.cdk.interfaces.IStrand
    Set the type of the Strand object.
    setStrandType(String) - Method in class org.openscience.cdk.silent.Strand
    Sets the type of the Strand object.
    setStrandType(String) - Method in class org.openscience.cdk.Strand
    Sets the type of the Strand object.
    setStructureType(String) - Method in class org.openscience.cdk.debug.DebugPDBStructure
    set the Structure Type of this structure.
    setStructureType(String) - Method in interface org.openscience.cdk.interfaces.IPDBStructure
    set the Structure Type of this structure.
    setStructureType(String) - Method in class org.openscience.cdk.protein.data.PDBStructure
    set the Structure Type of this structure.
    setStructureType(String) - Method in class org.openscience.cdk.silent.PDBStructure
    set the Structure Type of this structure.
    setSubgraph(List<Integer>) - Method in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
     
    setSubscript(String) - Method in class org.openscience.cdk.sgroup.Sgroup
    Set the subscript value.
    setSwitchingAtom(IAtom) - Method in class org.openscience.cdk.libio.md.ChargeGroup
     
    setSymbol(String) - Method in class org.openscience.cdk.debug.DebugAtom
    Sets the element symbol of this element.
    setSymbol(String) - Method in class org.openscience.cdk.debug.DebugAtomType
    Sets the element symbol of this element.
    setSymbol(String) - Method in class org.openscience.cdk.debug.DebugElement
    Sets the element symbol of this element.
    setSymbol(String) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
    Sets the element symbol of this element.
    setSymbol(String) - Method in class org.openscience.cdk.debug.DebugIsotope
    Sets the element symbol of this element.
    setSymbol(String) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
    Sets the element symbol of this element.
    setSymbol(String) - Method in class org.openscience.cdk.Element
    Sets the element symbol of this element.
    setSymbol(String) - Method in interface org.openscience.cdk.interfaces.IElement
    Sets the element symbol of this element.
    setSymbol(String) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
    Sets the element symbol of this element.
    setSymbol(String) - Method in class org.openscience.cdk.silent.Element
    Sets the element symbol of this element.
    setSymbol(String) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultMCSPlusAtomMatcher
    Deprecated.
     
    setSymbol(String) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultRGraphAtomMatcher
    Deprecated.
     
    setSymbol(String) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFAtomMatcher
    Deprecated.
     
    setTabSize(int) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
     
    setTabSize(int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
     
    setTarget(IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
    Deprecated.
    Set target molecule
    setTempFactor(Double) - Method in class org.openscience.cdk.debug.DebugPDBAtom
    set the Temperature factor of this atom.
    setTempFactor(Double) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
    set the Temperature factor of this atom.
    setTempFactor(Double) - Method in class org.openscience.cdk.protein.data.PDBAtom
    set the Temperature factor of this atom.
    setTempFactor(Double) - Method in class org.openscience.cdk.silent.PDBAtom
    set the Temperature factor of this atom.
    setTemplateHandler(TemplateHandler) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
    Deprecated.
    substructure templates are no longer used for layout but those provided here will be converted to identity templates
    setTimeManager(TimeManager) - Static method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlus
    Deprecated.
     
    setTimeManager(TimeManager) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
    Deprecated.
     
    setTimeManager(TimeManager) - Static method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper
    Deprecated.
     
    setTimeManager(TimeManager) - Static method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper
    Deprecated.
     
    setTimeout(long) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
    Sets the time in milliseconds until the substructure search will be breaked.
    setTimeout(long) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
    Sets the time in milliseconds until the substructure search will be breaked.
    setTimeout(long) - Method in class org.openscience.cdk.ringsearch.AllRingsFinder
    Deprecated.
    use the new threshold (during construction)
    setTimeOut(double) - Method in class org.openscience.cdk.smsd.global.TimeOut
    Deprecated.
    set cutoff value for time out eg.
    setTimeoutFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
    Deprecated.
    Set time out flag
    setTimeOutFlag(boolean) - Method in class org.openscience.cdk.smsd.global.TimeOut
    Deprecated.
    Set true if timeout occures else false
    setTimezone(String) - Method in class org.openscience.cdk.io.RssWriter
     
    setting - Variable in class org.openscience.cdk.io.setting.IOSetting
     
    SettingManager<T extends ISetting> - Class in org.openscience.cdk.io.setting
    Provides dynamic management of settings.
    SettingManager() - Constructor for class org.openscience.cdk.io.setting.SettingManager
     
    setTitle(String) - Method in class org.openscience.cdk.io.RssWriter
     
    setTitle(String) - Method in class org.openscience.cdk.renderer.GraphRendererModel
    Set the main title
    setTitlemap(Map) - Method in class org.openscience.cdk.io.RssWriter
     
    setTo(Permutation) - Method in class org.openscience.cdk.group.Permutation
    Alter a permutation by setting it to the values in the other permutation.
    setToolTipTextMap(Map<IAtom, String>) - Method in class org.openscience.cdk.renderer.RendererModel
    Sets the toolTipTextMap.
    setTransform(AffineTransform) - Method in interface org.openscience.cdk.renderer.elements.IRenderingVisitor
    Sets the affine transformations used.
    setTransform(AffineTransform) - Method in class org.openscience.cdk.renderer.visitor.AbstractAWTDrawVisitor
    Sets a new affine transformation to convert world coordinates into screen coordinates.
    setType(CTFileQueryBond.Type) - Method in class org.openscience.cdk.isomorphism.matchers.CTFileQueryBond
    Getter for bond type
    setType(SgroupType) - Method in class org.openscience.cdk.sgroup.Sgroup
    Set the type of the Sgroup.
    setUnspecified(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom
     
    setup() - Method in class org.openscience.cdk.renderer.AbstractRenderer
    Creates the transform using the scale, zoom, drawCenter, and modelCenter.
    setup(IAtomContainer, Rectangle) - Method in class org.openscience.cdk.renderer.AtomContainerRenderer
    Setup the transformations necessary to draw this Atom Container.
    setup(IChemModel, Rectangle) - Method in class org.openscience.cdk.renderer.ChemModelRenderer
    Setup the transformations necessary to draw this Chem Model.
    setup(T, Rectangle) - Method in interface org.openscience.cdk.renderer.IRenderer
    Setup the transformations necessary to draw the IChemObject matching this IRenderer implementation.
    setup(IAtomContainerSet, Rectangle) - Method in class org.openscience.cdk.renderer.MoleculeSetRenderer
    Setup the transformations necessary to draw this IAtomContainerSet.
    setup(IReaction, Rectangle) - Method in class org.openscience.cdk.renderer.ReactionRenderer
    Setup the transformations necessary to draw this Reaction.
    setup(IReactionSet, Rectangle) - Method in class org.openscience.cdk.renderer.ReactionSetRenderer
    Setup the transformations necessary to draw this Reaction Set.
    setupTransformNatural(Rectangle2D) - Method in class org.openscience.cdk.renderer.AbstractRenderer
    Set the transform for a non-fit to screen paint.
    setupTransformToFit(Rectangle2D, Rectangle2D, double, boolean) - Method in class org.openscience.cdk.renderer.AbstractRenderer
    Sets the transformation needed to draw the model on the canvas when the diagram needs to fit the screen.
    setUseAromaticityFlag(boolean) - Method in class org.openscience.cdk.smiles.SmilesGenerator
    Deprecated.
    since 1.5.6, use SmilesGenerator.aromatic() - invoking this method does nothing
    setUseIdentityTemplates(boolean) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
    Set whether identity templates are used.
    setUseTemplates(boolean) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
    Deprecated.
    always false, substructure templates are not used anymore
    setValency(Integer) - Method in class org.openscience.cdk.AtomType
    Sets the the exact electron valency of the AtomType object.
    setValency(Integer) - Method in class org.openscience.cdk.debug.DebugAtom
    Sets the the exact electron valency of the AtomType object.
    setValency(Integer) - Method in class org.openscience.cdk.debug.DebugAtomType
    Sets the the exact electron valency of the AtomType object.
    setValency(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
    Sets the the exact electron valency of the AtomType object.
    setValency(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
    Sets the the exact electron valency of the AtomType object.
    setValency(Integer) - Method in interface org.openscience.cdk.interfaces.IAtomType
    Sets the the exact electron valency of the AtomType object.
    setValency(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
    Sets the the exact electron valency of the AtomType object.
    setValency(Integer) - Method in class org.openscience.cdk.silent.AtomType
    Sets the the exact electron valency of the AtomType object.
    setValue(Object) - Method in interface org.openscience.cdk.reaction.type.parameters.IParameterReact
    Set the value of the parameter.
    setValue(Object) - Method in class org.openscience.cdk.reaction.type.parameters.ParameterReact
    Set the value of the parameter.
    setValue(T) - Method in interface org.openscience.cdk.renderer.generators.IGeneratorParameter
    Sets the value for this parameter.
    setValue(T) - Method in class org.openscience.cdk.renderer.generators.parameter.AbstractGeneratorParameter
    Sets the value for this parameter.
    setValueAt(int, int, double) - Method in class org.openscience.cdk.graph.invariant.GIMatrix
    Sets the value of the element at the given index.
    setVanDerWaalsFile(String) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
     
    setWriteAromaticBondTypes(boolean) - Method in class org.openscience.cdk.io.MDLV2000Writer
    Convenience method to set the option for writing aromatic bond types.
    setWriter(Writer) - Method in class org.openscience.cdk.io.CDKSourceCodeWriter
     
    setWriter(OutputStream) - Method in class org.openscience.cdk.io.CDKSourceCodeWriter
     
    setWriter(Writer) - Method in class org.openscience.cdk.io.CMLWriter
     
    setWriter(OutputStream) - Method in class org.openscience.cdk.io.CMLWriter
     
    setWriter(Writer) - Method in class org.openscience.cdk.io.CrystClustWriter
     
    setWriter(OutputStream) - Method in class org.openscience.cdk.io.CrystClustWriter
     
    setWriter(Writer) - Method in class org.openscience.cdk.io.HINWriter
     
    setWriter(OutputStream) - Method in class org.openscience.cdk.io.HINWriter
     
    setWriter(Writer) - Method in interface org.openscience.cdk.io.IChemObjectWriter
    Sets the Writer from which this ChemObjectWriter should write the contents.
    setWriter(OutputStream) - Method in interface org.openscience.cdk.io.IChemObjectWriter
    Sets the OutputStream from which this ChemObjectWriter should write the contents.
    setWriter(Writer) - Method in class org.openscience.cdk.io.MDLRXNWriter
     
    setWriter(OutputStream) - Method in class org.openscience.cdk.io.MDLRXNWriter
     
    setWriter(Writer) - Method in class org.openscience.cdk.io.MDLV2000Writer
     
    setWriter(OutputStream) - Method in class org.openscience.cdk.io.MDLV2000Writer
     
    setWriter(Writer) - Method in class org.openscience.cdk.io.MDLV3000Writer
    Sets the Writer from which this ChemObjectWriter should write the contents.
    setWriter(OutputStream) - Method in class org.openscience.cdk.io.MDLV3000Writer
    Sets the OutputStream from which this ChemObjectWriter should write the contents.
    setWriter(Writer) - Method in class org.openscience.cdk.io.Mol2Writer
     
    setWriter(OutputStream) - Method in class org.openscience.cdk.io.Mol2Writer
     
    setWriter(Writer) - Method in class org.openscience.cdk.io.PDBWriter
     
    setWriter(OutputStream) - Method in class org.openscience.cdk.io.PDBWriter
     
    setWriter(Writer) - Method in class org.openscience.cdk.io.program.GaussianInputWriter
     
    setWriter(OutputStream) - Method in class org.openscience.cdk.io.program.GaussianInputWriter
     
    setWriter(OutputStream) - Method in class org.openscience.cdk.io.program.Mopac7Writer
     
    setWriter(Writer) - Method in class org.openscience.cdk.io.program.Mopac7Writer
     
    setWriter(Writer) - Method in class org.openscience.cdk.io.rdf.CDKOWLWriter
    Sets the Writer from which this ChemObjectWriter should write the contents.
    setWriter(OutputStream) - Method in class org.openscience.cdk.io.rdf.CDKOWLWriter
    Sets the OutputStream from which this ChemObjectWriter should write the contents.
    setWriter(OutputStream) - Method in class org.openscience.cdk.io.RGroupQueryWriter
    Sets the writer to given output stream.
    setWriter(Writer) - Method in class org.openscience.cdk.io.RGroupQueryWriter
    Sets the writer.
    setWriter(Writer) - Method in class org.openscience.cdk.io.RssWriter
     
    setWriter(OutputStream) - Method in class org.openscience.cdk.io.RssWriter
     
    setWriter(Writer) - Method in class org.openscience.cdk.io.SDFWriter
     
    setWriter(OutputStream) - Method in class org.openscience.cdk.io.SDFWriter
     
    setWriter(Writer) - Method in class org.openscience.cdk.io.ShelXWriter
     
    setWriter(OutputStream) - Method in class org.openscience.cdk.io.ShelXWriter
     
    setWriter(Writer) - Method in class org.openscience.cdk.io.SMILESWriter
     
    setWriter(OutputStream) - Method in class org.openscience.cdk.io.SMILESWriter
     
    setWriter(Writer) - Method in class org.openscience.cdk.io.XYZWriter
     
    setWriter(OutputStream) - Method in class org.openscience.cdk.io.XYZWriter
     
    setX(double, double) - Method in class org.openscience.cdk.renderer.GraphRendererModel
    Sets the function area, which will painted
    setXTitle(String) - Method in class org.openscience.cdk.renderer.GraphRendererModel
    Set the title of the x axis
    setY(double, double) - Method in class org.openscience.cdk.renderer.GraphRendererModel
    Sets the function area, which will painted
    setYTitle(String) - Method in class org.openscience.cdk.renderer.GraphRendererModel
    Set the title of the y axis
    setZ(Integer) - Method in class org.openscience.cdk.Crystal
    Sets the number of asymmetric parts in the unit cell.
    setZ(Integer) - Method in class org.openscience.cdk.debug.DebugCrystal
    Sets the number of asymmetric parts in the unit cell.
    setZ(Integer) - Method in interface org.openscience.cdk.interfaces.ICrystal
    Sets the number of assymmetric parts in the unit cell.
    setZ(Integer) - Method in class org.openscience.cdk.silent.Crystal
    Sets the number of asymmetric parts in the unit cell.
    setZoom(double) - Method in class org.openscience.cdk.renderer.AbstractRenderer
    Set the zoom, where 1.0 is 100% zoom.
    setZoom(double) - Method in interface org.openscience.cdk.renderer.IRenderer
    Set a new zoom factor.
    setZoomToFit(double, double, double, double) - Method in class org.openscience.cdk.renderer.AbstractRenderer
    Calculate and set the zoom factor needed to completely fit the diagram onto the screen bounds.
    Sgroup - Class in org.openscience.cdk.sgroup
    Generic CTab Sgroup (substructure group) that stores all other types of group.
    Sgroup() - Constructor for class org.openscience.cdk.sgroup.Sgroup
    Create a new generic Sgroup.
    SgroupBracket - Class in org.openscience.cdk.sgroup
    Representation of an Sgroup bracket.
    SgroupBracket(double, double, double, double) - Constructor for class org.openscience.cdk.sgroup.SgroupBracket
    Create an Sgroup bracket.
    SgroupKey - Enum in org.openscience.cdk.sgroup
    Keys for indexing common Sgroup attributes.
    SgroupType - Enum in org.openscience.cdk.sgroup
    Enumeration of Ctab Sgroup types.
    shallowCopy() - Method in class org.openscience.cdk.ChemObject
    Clones this IChemObject, but preserves references to Objects.
    shallowCopy() - Method in class org.openscience.cdk.silent.ChemObject
    Clones this IChemObject, but preserves references to Objects.
    shapeOf(Shape, Color) - Static method in class org.openscience.cdk.renderer.elements.GeneralPath
    Create a filled path of the specified Java 2D Shape and color.
    SharingAnionReaction - Class in org.openscience.cdk.reaction.type
    IReactionProcess which participate in movement resonance.
    SharingAnionReaction() - Constructor for class org.openscience.cdk.reaction.type.SharingAnionReaction
    Constructor of the SharingAnionReaction object.
    SharingChargeDBReaction - Class in org.openscience.cdk.reaction.type
    IReactionProcess which participate in movement resonance.
    SharingChargeDBReaction() - Constructor for class org.openscience.cdk.reaction.type.SharingChargeDBReaction
    Constructor of the SharingChargeDBReaction object.
    SharingChargeSBReaction - Class in org.openscience.cdk.reaction.type
    IReactionProcess which participate in movement resonance.
    SharingChargeSBReaction() - Constructor for class org.openscience.cdk.reaction.type.SharingChargeSBReaction
    Constructor of the SharingChargeSBReaction object.
    SharingElectronMechanism - Class in org.openscience.cdk.reaction.mechanism
    This mechanism displaces the charge (lonePair) because of deficiency of charge.
    SharingElectronMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.SharingElectronMechanism
     
    SharingLonePairReaction - Class in org.openscience.cdk.reaction.type
    IReactionProcess which participate in movement resonance.
    SharingLonePairReaction() - Constructor for class org.openscience.cdk.reaction.type.SharingLonePairReaction
    Constructor of the SharingLonePairReaction object.
    SHEET - Static variable in class org.openscience.cdk.protein.data.PDBStructure
     
    SHEET - Static variable in class org.openscience.cdk.silent.PDBStructure
     
    ShelXFormat - Class in org.openscience.cdk.io.formats
    See here.
    ShelXFormat() - Constructor for class org.openscience.cdk.io.formats.ShelXFormat
     
    ShelXReader - Class in org.openscience.cdk.io
    A reader for ShelX output (RES) files.
    ShelXReader(Reader) - Constructor for class org.openscience.cdk.io.ShelXReader
    Create an ShelX file reader.
    ShelXReader(InputStream) - Constructor for class org.openscience.cdk.io.ShelXReader
     
    ShelXReader() - Constructor for class org.openscience.cdk.io.ShelXReader
     
    ShelXWriter - Class in org.openscience.cdk.io
    Serializes a MoleculeSet or a Molecule object to ShelX code.
    ShelXWriter(Writer) - Constructor for class org.openscience.cdk.io.ShelXWriter
    Constructs a new ShelXWriter class.
    ShelXWriter(OutputStream) - Constructor for class org.openscience.cdk.io.ShelXWriter
     
    ShelXWriter() - Constructor for class org.openscience.cdk.io.ShelXWriter
     
    shift(Rectangle, Rectangle) - Method in class org.openscience.cdk.renderer.AbstractRenderer
    Determine the overlap of the diagram with the screen, and shift (if necessary) the diagram draw center.
    shift(Rectangle, Rectangle) - Method in class org.openscience.cdk.renderer.MoleculeSetRenderer
    Determine the overlap of the diagram with the screen, and shift (if necessary) the diagram draw center.
    shiftContainer(IAtomContainer, Rectangle2D, Rectangle2D, double) - Static method in class org.openscience.cdk.geometry.GeometryTools
    Shift the container horizontally to the right to make its bounds not overlap with the other bounds.
    shiftContainer(IAtomContainer, double[], double[], double) - Static method in class org.openscience.cdk.geometry.GeometryUtil
    Shift the container horizontally to the right to make its bounds not overlap with the other bounds.
    shiftDrawCenter(double, double) - Method in class org.openscience.cdk.renderer.AbstractRenderer
    Move the draw center by dx and dy.
    shiftDrawCenter(double, double) - Method in interface org.openscience.cdk.renderer.IRenderer
    Set a new drawing center in screen coordinates.
    shiftReactionVertical(IReaction, Rectangle2D, Rectangle2D, double) - Static method in class org.openscience.cdk.geometry.GeometryTools
    Shift the containers in a reaction vertically upwards to not overlap with the reference Rectangle2D.
    shiftReactionVertical(IReaction, double[], double[], double) - Static method in class org.openscience.cdk.geometry.GeometryUtil
    Shift the containers in a reaction vertically upwards to not overlap with the reference rectangle.
    ShortestPathFingerprinter - Class in org.openscience.cdk.fingerprint
    Generates a fingerprint for a given IAtomContainer.
    ShortestPathFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.ShortestPathFingerprinter
    Creates a fingerprint generator of length DEFAULT_SIZE
    ShortestPathFingerprinter(int) - Constructor for class org.openscience.cdk.fingerprint.ShortestPathFingerprinter
    Constructs a fingerprint generator that creates fingerprints of the given fingerprintLength, using a generation algorithm with shortest paths.
    ShortestPaths - Class in org.openscience.cdk.graph
    Find and reconstruct the shortest paths from a given start atom to any other connected atom.
    ShortestPaths(IAtomContainer, IAtom) - Constructor for class org.openscience.cdk.graph.ShortestPaths
    Create a new shortest paths tool for a single start atom.
    ShortestPathWalker - Class in org.openscience.cdk.fingerprint
     
    ShortestPathWalker(IAtomContainer) - Constructor for class org.openscience.cdk.fingerprint.ShortestPathWalker
    Create a new shortest path walker for a given container.
    shouldBeLinear(IAtom, IAtomContainer) - Static method in class org.openscience.cdk.layout.AtomPlacer
    Deprecated.
    showCarbon(IAtom, IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.AtomMassGenerator
    Returns true if the mass number of this element is set and not equal the mass number of the most abundant isotope of this element.
    showCarbon(IAtom, IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator
    Checks a carbon atom to see if it should be shown.
    SI - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    SigmaElectronegativityDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
    Atomic descriptor that reflects that Gasteiger-Marsili sigma electronegativity.
    SigmaElectronegativityDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor
    Constructor for the SigmaElectronegativityDescriptor object
    SignatureFingerprinter - Class in org.openscience.cdk.fingerprint
    An implementation of a AtomSignature-based fingerprint.
    SignatureFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.SignatureFingerprinter
    Initialize the fingerprinter with a default signature depth of 1.
    SignatureFingerprinter(int) - Constructor for class org.openscience.cdk.fingerprint.SignatureFingerprinter
    Initialize the fingerprinter with a certain signature depth.
    signatureForVertex(int) - Method in class org.openscience.cdk.signature.MoleculeSignature
     
    SignatureQuotientGraph - Class in org.openscience.cdk.signature
    A signature quotient graph has a vertex for every signature symmetry class and an edge for each bond in the molecule between atoms in their class.
    SignatureQuotientGraph(IAtomContainer) - Constructor for class org.openscience.cdk.signature.SignatureQuotientGraph
    Construct a quotient graph from the symmetry classes generated from the atom container.
    SignatureQuotientGraph(IAtomContainer, int) - Constructor for class org.openscience.cdk.signature.SignatureQuotientGraph
    Construct a quotient graph using symmetry classes defined by signatures of height height.
    SignatureReactionCanoniser - Class in org.openscience.cdk.smsd.labelling
    Deprecated.
    This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    SignatureReactionCanoniser() - Constructor for class org.openscience.cdk.smsd.labelling.SignatureReactionCanoniser
    Deprecated.
     
    signatureStringForVertex(int) - Method in class org.openscience.cdk.signature.MoleculeSignature
     
    signatureStringForVertex(int, int) - Method in class org.openscience.cdk.signature.MoleculeSignature
     
    signedDistanceToPlane(Vector3d, Point3d, Point3d) - Static method in class org.openscience.cdk.stereo.StereoTool
    Given a normalized normal for a plane, any point in that plane, and a point, will return the distance between the plane and that point.
    SilentChemObjectBuilder - Class in org.openscience.cdk.silent
    A factory class to provide implementation independent ICDKObjects.
    SILICON - Static variable in enum org.openscience.cdk.config.Elements
     
    SILVER - Static variable in enum org.openscience.cdk.config.Elements
     
    SILVER - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    similar(IMatrix) - Method in class org.openscience.cdk.math.IMatrix
    Similar transformation Ut * M * U
    similar(IMatrix, IMatrix) - Method in class org.openscience.cdk.math.IMatrix
    Similar transformation Ut * M * U
    similar(Matrix) - Method in class org.openscience.cdk.math.Matrix
    Similar transformation Ut * M * U
    SimpleAtomCanonicalizer - Class in org.openscience.cdk.fingerprint
    This code returns a sorted set of atoms for a container according to its symbol and hybridization states.
    SimpleAtomCanonicalizer() - Constructor for class org.openscience.cdk.fingerprint.SimpleAtomCanonicalizer
     
    SimpleAtomComparator - Class in org.openscience.cdk.fingerprint
    This code returns a sorted set of atoms for a container according to its symbol and hybridization states.
    SimpleAtomComparator() - Constructor for class org.openscience.cdk.fingerprint.SimpleAtomComparator
     
    SimpleBasisSet - Class in org.openscience.cdk.math.qm
    This class will generate a simple base set for a atom container.
    SimpleBasisSet(IAtom[]) - Constructor for class org.openscience.cdk.math.qm.SimpleBasisSet
    Create a base set
    SimpleBond() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
     
    SimpleCharStream - Class in org.openscience.cdk.iupac.parser
    An implementation of interface CharStream, where the stream is assumed to contain only ASCII characters (without unicode processing).
    SimpleCharStream(Reader, int, int, int) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream
    Constructor.
    SimpleCharStream(Reader, int, int) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream
    Constructor.
    SimpleCharStream(Reader) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream
    Constructor.
    SimpleCharStream(InputStream, String, int, int, int) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream
    Constructor.
    SimpleCharStream(InputStream, int, int, int) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream
    Constructor.
    SimpleCharStream(InputStream, String, int, int) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream
    Constructor.
    SimpleCharStream(InputStream, int, int) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream
    Constructor.
    SimpleCharStream(InputStream, String) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream
    Constructor.
    SimpleCharStream(InputStream) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream
    Constructor.
    SimpleCharStream - Class in org.openscience.cdk.smiles.smarts.parser
    An implementation of interface CharStream, where the stream is assumed to contain only ASCII characters (without unicode processing).
    SimpleCharStream(Reader, int, int, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
    Constructor.
    SimpleCharStream(Reader, int, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
    Constructor.
    SimpleCharStream(Reader) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
    Constructor.
    SimpleCharStream(InputStream, String, int, int, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
    Constructor.
    SimpleCharStream(InputStream, int, int, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
    Constructor.
    SimpleCharStream(InputStream, String, int, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
    Constructor.
    SimpleCharStream(InputStream, int, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
    Constructor.
    SimpleCharStream(InputStream, String) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
    Constructor.
    SimpleCharStream(InputStream) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
    Constructor.
    SimpleCycle - Class in org.openscience.cdk.ringsearch.cyclebasis
    Deprecated.
    internal implemenation detail from SSSRFinder, do not use
    SimpleCycle(UndirectedGraph, Collection) - Constructor for class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycle
    Deprecated.
    Constructs a cycle in a graph consisting of the specified edges.
    SimpleCycle(UndirectedGraph, Set) - Constructor for class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycle
    Deprecated.
    Constructs a cycle in a graph consisting of the specified edges.
    SimpleCycleBasis - Class in org.openscience.cdk.ringsearch.cyclebasis
    Deprecated.
    internal implemenation detail from SSSRFinder, do not use
    SimpleCycleBasis(List<SimpleCycle>, List, UndirectedGraph) - Constructor for class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis
    Deprecated.
     
    SimpleCycleBasis(UndirectedGraph) - Constructor for class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis
    Deprecated.
     
    simplifyMolecularFormula(String) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
    Simplify the molecular formula.
    SINGLE_ELECTRON_COUNT - Static variable in class org.openscience.cdk.CDKConstants
    Used as property key for indicating the number of single electrons on the atom type.
    SINGLE_OR_DOUBLE - Static variable in class org.openscience.cdk.CDKConstants
    Flag used for marking uncertainty of the bond order.
    SINGLEBOND - Static variable in class org.openscience.cdk.libio.jena.CDK
     
    SingleElectron - Class in org.openscience.cdk.silent
    A Single Electron is an orbital which is occupied by only one electron.
    SingleElectron(IAtom) - Constructor for class org.openscience.cdk.silent.SingleElectron
    Constructs an single electron orbital on an Atom.
    SingleElectron() - Constructor for class org.openscience.cdk.silent.SingleElectron
    Constructs an single electron orbital with an associated Atom.
    SingleElectron - Class in org.openscience.cdk
    A Single Electron is an orbital which is occupied by only one electron.
    SingleElectron(IAtom) - Constructor for class org.openscience.cdk.SingleElectron
    Constructs an single electron orbital on an Atom.
    SingleElectron() - Constructor for class org.openscience.cdk.SingleElectron
    Constructs an single electron orbital with an associated Atom.
    singleElectronCount - Variable in class org.openscience.cdk.AtomContainer
    Number of single electrons contained by this object.
    singleElectronCount - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
    Number of single electrons contained by this object.
    singleElectronCount - Variable in class org.openscience.cdk.silent.AtomContainer
    Number of single electrons contained by this object.
    SingleElectronDiff - Class in org.openscience.cdk.tools.diff
    Compares two ISingleElectron classes.
    singleElectrons - Variable in class org.openscience.cdk.AtomContainer
    Internal array of single electrons.
    singleElectrons() - Method in class org.openscience.cdk.AtomContainer
    Returns an Iterable for looping over all single electrons in this container.
    singleElectrons() - Method in class org.openscience.cdk.debug.DebugAminoAcid
    Returns an Iterable for looping over all single electrons in this container.
    singleElectrons() - Method in class org.openscience.cdk.debug.DebugAtomContainer
    Returns an Iterable for looping over all single electrons in this container.
    singleElectrons() - Method in class org.openscience.cdk.debug.DebugBioPolymer
    Returns an Iterable for looping over all single electrons in this container.
    singleElectrons() - Method in class org.openscience.cdk.debug.DebugCrystal
    Returns an Iterable for looping over all single electrons in this container.
    singleElectrons() - Method in class org.openscience.cdk.debug.DebugMonomer
    Returns an Iterable for looping over all single electrons in this container.
    singleElectrons() - Method in class org.openscience.cdk.debug.DebugPolymer
    Returns an Iterable for looping over all single electrons in this container.
    singleElectrons() - Method in class org.openscience.cdk.debug.DebugRing
    Returns an Iterable for looping over all single electrons in this container.
    singleElectrons() - Method in class org.openscience.cdk.debug.DebugStrand
    Returns an Iterable for looping over all single electrons in this container.
    singleElectrons() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
    Returns an Iterable for looping over all single electrons in this container.
    singleElectrons - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
    Internal array of single electrons.
    singleElectrons() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
    Returns an Iterable for looping over all single electrons in this container.
    singleElectrons - Variable in class org.openscience.cdk.silent.AtomContainer
    Internal array of single electrons.
    singleElectrons() - Method in class org.openscience.cdk.silent.AtomContainer
    Returns an Iterable for looping over all single electrons in this container.
    SingleMapping - Class in org.openscience.cdk.smsd.algorithm.single
    Deprecated.
    This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    SingleMapping() - Constructor for class org.openscience.cdk.smsd.algorithm.single.SingleMapping
    Deprecated.
    Default
    SingleMappingHandler - Class in org.openscience.cdk.smsd.algorithm.single
    Deprecated.
    This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    SingleMappingHandler(boolean) - Constructor for class org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler
    Deprecated.
     
    SingleStructureRandomGenerator - Class in org.openscience.cdk.structgen
    Randomly generates a single, connected, correctly bonded structure for a given molecular formula.
    SingleStructureRandomGenerator(long) - Constructor for class org.openscience.cdk.structgen.SingleStructureRandomGenerator
    Constructor for the SingleStructureRandomGenerator object.
    SingleStructureRandomGenerator() - Constructor for class org.openscience.cdk.structgen.SingleStructureRandomGenerator
    Constructor for the SingleStructureRandomGenerator object.
    sitefinder() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
    Main method which calls the methods: assignProteinToGrid, GridScan, and FindPockets.
    size() - Method in class org.openscience.cdk.ConformerContainer
    Get the number of conformers stored.
    size() - Method in class org.openscience.cdk.debug.DebugAdductFormula
    Returns the number of MolecularFormulas in this AdductFormula.
    size() - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet
    Returns the number of MolecularFormulas in this MolecularFormulaSet.
    size() - Method in class org.openscience.cdk.dict.Dictionary
     
    size() - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
     
    size() - Method in interface org.openscience.cdk.fingerprint.IBitFingerprint
    Returns the size of the fingerprint, i.e., the number of hash bins.
    size() - Method in interface org.openscience.cdk.fingerprint.ICountFingerprint
    Returns the number of bits of this fingerprint.
    size() - Method in class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
     
    size() - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
     
    size() - Method in class org.openscience.cdk.formula.AdductFormula
    Returns the number of MolecularFormulas in this AdductFormula.
    size() - Method in class org.openscience.cdk.formula.MolecularFormulaSet
    Returns the number of MolecularFormulas in this MolecularFormulaSet.
    size() - Method in class org.openscience.cdk.graph.AllCycles
    Cardinality of the set.
    size() - Method in class org.openscience.cdk.graph.EssentialCycles
    Number of essential cycles.
    size() - Method in class org.openscience.cdk.graph.MinimumCycleBasis
    The number of the cycles in the minimum cycle basis.
    size() - Method in class org.openscience.cdk.graph.RelevantCycles
    The number of the relevant cycles.
    size() - Method in class org.openscience.cdk.graph.TripletShortCycles
    Size of the cycle basis, cardinality of the ESSSR.
    size() - Method in class org.openscience.cdk.group.Partition
    Gets the size of the partition, in terms of the number of cells.
    size() - Method in class org.openscience.cdk.group.Permutation
    Get the number of elements in the permutation.
    size() - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet
    Returns the number of MolecularFormulas in this IMolecularFormulaSet.
    size() - Method in interface org.openscience.cdk.io.random.IRandomAccessChemObjectReader
     
    size() - Method in class org.openscience.cdk.io.random.RandomAccessReader
     
    size - Variable in class org.openscience.cdk.math.IVector
    Size of this vector
    size - Variable in class org.openscience.cdk.math.Vector
    The size of this vector
    size() - Method in class org.openscience.cdk.silent.AdductFormula
    Returns the number of MolecularFormulas in this AdductFormula.
    size() - Method in class org.openscience.cdk.silent.MolecularFormulaSet
    Returns the number of MolecularFormulas in this MolecularFormulaSet.
    skeleton(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
    Create a skeleton copy of the provided structure.
    SM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    SMALL_FIRST - Static variable in class org.openscience.cdk.silent.RingSet
    Flag to denote that the set is order with the smallest ring first?
    SMALL_FIRST - Static variable in class org.openscience.cdk.tools.manipulator.RingSizeComparator
    Flag to denote that the set is order with the smallest ring first
    SMALLEST_RINGS - Static variable in class org.openscience.cdk.CDKConstants
    A smallest set of smallest rings computed for this molecule.
    SmallestRingAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
    Match an atom in a specific size ring.
    SmallestRingAtom(int, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.SmallestRingAtom
    Creates a matcher for specified ring size.
    SmallestRingSize() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
     
    SmallRingDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
    Small ring descriptors: these are based on enumeration of all the small rings (sizes 3 to 9) in a molecule, which can be obtained quickly and deterministically.
    SmallRingDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor
     
    Smarts2MQLVisitor - Class in org.openscience.cdk.smiles.smarts.parser
    An AST tree visitor.
    Smarts2MQLVisitor() - Constructor for class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    SMARTSAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
    Abstract smarts atom.
    SMARTSAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom
     
    SMARTSBond - Class in org.openscience.cdk.isomorphism.matchers.smarts
    Abstract smarts bond.
    SMARTSBond(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.SMARTSBond
     
    SMARTSBond(IQueryAtom, IQueryAtom, IBond.Order, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.SMARTSBond
     
    SmartsDumpVisitor - Class in org.openscience.cdk.smiles.smarts.parser
    An AST Tree visitor.
    SmartsDumpVisitor() - Constructor for class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    SmartsExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
     
    SMARTSFormat - Class in org.openscience.cdk.io.formats
    See here.
    SMARTSFormat() - Constructor for class org.openscience.cdk.io.formats.SMARTSFormat
     
    SmartsFragmentExtractor - Class in org.openscience.cdk.smarts
    Utility class to create SMARTS that match part (substructure) of a molecule.
    SmartsFragmentExtractor(IAtomContainer) - Constructor for class org.openscience.cdk.smarts.SmartsFragmentExtractor
    Create a new instance over the provided molecule.
    SmartsMatchers - Class in org.openscience.cdk.isomorphism.matchers.smarts
    Bridging class between the SMARTS matcher and the parser/query tool.
    SmartsMatchers() - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.SmartsMatchers
     
    SMARTSParser - Class in org.openscience.cdk.smiles.smarts.parser
    This parser implements a nearly complete subset of the SMARTS syntax as defined on the Daylight website.
    SMARTSParser(InputStream) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
    Constructor with InputStream.
    SMARTSParser(InputStream, String) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
    Constructor with InputStream and supplied encoding
    SMARTSParser(Reader) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
    Constructor.
    SMARTSParser(SMARTSParserTokenManager) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
    Constructor with generated Token Manager.
    SMARTSParserConstants - Interface in org.openscience.cdk.smiles.smarts.parser
    Token literal values and constants.
    SMARTSParserTokenManager - Class in org.openscience.cdk.smiles.smarts.parser
    Token Manager.
    SMARTSParserTokenManager(SimpleCharStream) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager
    Constructor.
    SMARTSParserTokenManager(SimpleCharStream, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager
    Constructor.
    SMARTSParserTreeConstants - Interface in org.openscience.cdk.smiles.smarts.parser
     
    SMARTSParserVisitor - Interface in org.openscience.cdk.smiles.smarts.parser
     
    SmartsPattern - Class in org.openscience.cdk.smiles.smarts
    A Pattern for matching a single SMARTS query against multiple target compounds.
    SMARTSQueryTool - Class in org.openscience.cdk.smiles.smarts
    This class provides a easy to use wrapper around SMARTS matching functionality.
    SMARTSQueryTool(String, IChemObjectBuilder) - Constructor for class org.openscience.cdk.smiles.smarts.SMARTSQueryTool
    Create a new SMARTS query tool for the specified SMARTS string.
    SmartsQueryVisitor - Class in org.openscience.cdk.smiles.smarts.parser
    An AST tree visitor.
    SmartsQueryVisitor(IChemObjectBuilder) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    SmartsStereoMatch - Class in org.openscience.cdk.isomorphism
    Filters SMARTS matches for those that have valid stereochemistry configuration.
    SmartsStereoMatch(IAtomContainer, IAtomContainer) - Constructor for class org.openscience.cdk.isomorphism.SmartsStereoMatch
    Create a predicate for checking mappings between a provided query and target.
    SmiFlavor - Class in org.openscience.cdk.smiles
    Flags for customising SMILES generation.
    SMILES - Static variable in class org.openscience.cdk.CDKConstants
    The Daylight SMILES.
    SMILESFIXFormat - Class in org.openscience.cdk.io.formats
     
    SMILESFIXFormat() - Constructor for class org.openscience.cdk.io.formats.SMILESFIXFormat
     
    SMILESFormat - Class in org.openscience.cdk.io.formats
    See here.
    SMILESFormat() - Constructor for class org.openscience.cdk.io.formats.SMILESFormat
     
    SmilesGenerator - Class in org.openscience.cdk.smiles
    SMILES [Weininger, David, SMILES, a Chemical Language and Information System. 1. Introduction to Methodology and Encoding Rules, Journal of Chemical Information and Computer Sciences, 1988, 28:31-36, Weininger, David and Weininger, Arthur and Weininger, Joseph L., SMILES 2. Algorithm for Generation of Unique SMILES Notation, Journal of Chemical Information and Computer Sciences, 1989, 29:97-101] provides a compact representation of chemical structures and reactions.
    SmilesGenerator() - Constructor for class org.openscience.cdk.smiles.SmilesGenerator
    Deprecated.
    SmilesGenerator(int) - Constructor for class org.openscience.cdk.smiles.SmilesGenerator
    Create a SMILES generator with the specified SmiFlavor.
    SmilesParser - Class in org.openscience.cdk.smiles
    Read molecules and reactions from a SMILES [?Authors?, SMILES Tutorial] string.
    SmilesParser(IChemObjectBuilder) - Constructor for class org.openscience.cdk.smiles.SmilesParser
    Create a new SMILES parser which will create IAtomContainers with the specified builder.
    SmilesReactionCanoniser - Class in org.openscience.cdk.smsd.labelling
    Deprecated.
    This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    SmilesReactionCanoniser() - Constructor for class org.openscience.cdk.smsd.labelling.SmilesReactionCanoniser
    Deprecated.
     
    SMILESReader - Class in org.openscience.cdk.io
    This Reader reads files which has one SMILES string on each line, where the format is given as below:
    SMILESReader(Reader) - Constructor for class org.openscience.cdk.io.SMILESReader
    Construct a new reader from a Reader and a specified builder object.
    SMILESReader(InputStream) - Constructor for class org.openscience.cdk.io.SMILESReader
     
    SMILESReader() - Constructor for class org.openscience.cdk.io.SMILESReader
     
    SmilesValencyChecker - Class in org.openscience.cdk.tools
    Small customization of ValencyHybridChecker suggested by Todd Martin specially tuned for SMILES parsing.
    SmilesValencyChecker() - Constructor for class org.openscience.cdk.tools.SmilesValencyChecker
     
    SmilesValencyChecker(String) - Constructor for class org.openscience.cdk.tools.SmilesValencyChecker
     
    SMILESWriter - Class in org.openscience.cdk.io
    Writes the SMILES strings to a plain text file.
    SMILESWriter(Writer) - Constructor for class org.openscience.cdk.io.SMILESWriter
    Constructs a new SMILESWriter that can write a list of SMILES to a Writer
    SMILESWriter(OutputStream) - Constructor for class org.openscience.cdk.io.SMILESWriter
     
    SMILESWriter() - Constructor for class org.openscience.cdk.io.SMILESWriter
     
    SMILESWriter(FileOutputStream) - Constructor for class org.openscience.cdk.io.SMILESWriter
    Constructs a new SMILESWriter that can write an list of SMILES to a given OutputStream
    SMSDNormalizer - Class in org.openscience.cdk.normalize
    Deprecated.
    This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    SMSDNormalizer() - Constructor for class org.openscience.cdk.normalize.SMSDNormalizer
    Deprecated.
     
    SN - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    SODIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    SODIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    sort() - Method in class org.openscience.cdk.signature.Orbit
    Sorts the atom indices in this orbit.
    sort(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
    Sorts the IAtomContainers in the given IAtomContainerSet by the following criteria with decreasing priority:
    sort(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator
    Sorts the rings in the set by size.
    sortAndNormalizedByIntensity(IsotopePattern) - Static method in class org.openscience.cdk.formula.IsotopePatternManipulator
    Return the isotope pattern sorted and normalized by intensity to the highest abundance.
    sortAtomContainers(Comparator<IAtomContainer>) - Method in class org.openscience.cdk.AtomContainerSet
    Sort the AtomContainers and multipliers using a provided Comparator.
    sortAtomContainers(Comparator<IAtomContainer>) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
    Sort the AtomContainers using a provided Comparator.
    sortAtomContainers(Comparator<IAtomContainer>) - Method in class org.openscience.cdk.silent.AtomContainerSet
    Sort the AtomContainers and multipliers using a provided Comparator
    sortBy2DDistance(IAtom[], Point2d) - Static method in class org.openscience.cdk.geometry.GeometryTools
    Sorts a Vector of atoms such that the 2D distances of the atom locations from a given point are smallest for the first atoms in the vector.
    sortBy2DDistance(IAtom[], Point2d) - Static method in class org.openscience.cdk.geometry.GeometryUtil
    Sorts a Vector of atoms such that the 2D distances of the atom locations from a given point are smallest for the first atoms in the vector.
    sortByIntensity(IsotopePattern) - Static method in class org.openscience.cdk.formula.IsotopePatternManipulator
    Return the isotope pattern sorted by intensity to the highest abundance.
    sortByMass(IsotopePattern) - Static method in class org.openscience.cdk.formula.IsotopePatternManipulator
    Return the isotope pattern sorted by mass to the highest abundance.
    sortResultsByEnergies() - Method in class org.openscience.cdk.smsd.filters.ChemicalFilters
    Deprecated.
    Sort MCS solution by bond breaking energy.
    sortResultsByFragments() - Method in class org.openscience.cdk.smsd.filters.ChemicalFilters
    Deprecated.
    Sort solution by ascending order of the fragment count.
    sortResultsByStereoAndBondMatch() - Method in class org.openscience.cdk.smsd.filters.ChemicalFilters
    Deprecated.
    Sort MCS solution by stereo and bond type matches.
    SPACE - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    SpanningTree - Class in org.openscience.cdk.graph
    Spanning tree of a molecule.
    SpanningTree(IAtomContainer) - Constructor for class org.openscience.cdk.graph.SpanningTree
    Create a new spanning tree for the provided molecule.
    SpartanFormat - Class in org.openscience.cdk.io.formats
     
    SpartanFormat() - Constructor for class org.openscience.cdk.io.formats.SpartanFormat
     
    specialCase() - Method in class org.openscience.cdk.iupac.parser.NomParser
    Deprecated.
    Deal with special cases where the rules don't apply.
    specialToken - Variable in class org.openscience.cdk.iupac.parser.Token
    This field is used to access special tokens that occur prior to this token, but after the immediately preceding regular (non-special) token.
    specialToken - Variable in class org.openscience.cdk.smiles.smarts.parser.Token
    This field is used to access special tokens that occur prior to this token, but after the immediately preceding regular (non-special) token.
    sphere - Variable in class org.openscience.cdk.tools.HOSECodeGenerator
    Counter for the sphere in which we currently work.
    sphereDelimiters - Variable in class org.openscience.cdk.tools.HOSECodeGenerator
    Delimiters used to separate spheres in the output string.
    sphereNodes - Variable in class org.openscience.cdk.tools.HOSECodeGenerator
    Container for the nodes in a sphere.
    sphereNodesWithAtoms - Variable in class org.openscience.cdk.tools.HOSECodeGenerator
     
    spheres - Variable in class org.openscience.cdk.tools.HOSECodeGenerator
    Here we store the spheres that we assemble, in order to parse them into a code later.
    spheresWithAtoms - Variable in class org.openscience.cdk.tools.HOSECodeGenerator
     
    SPHERICAL_MATCHER - Static variable in class org.openscience.cdk.CDKConstants
    Used as property key for indicating the HOSE code for a certain atom type.
    spinMultiplicities - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
     
    splice(PathEdge) - Method in class org.openscience.cdk.smsd.ring.PathEdge
    Deprecated.
     
    SPLIT_MODE_BREADTH_FIRST - Static variable in class org.openscience.cdk.structgen.stochastic.operator.CrossoverMachine
    Indicates that crossover is using SPLIT_MODE_BREADTH_FIRST mode.
    SPLIT_MODE_DEPTH_FIRST - Static variable in class org.openscience.cdk.structgen.stochastic.operator.CrossoverMachine
    Indicates that crossover is using SPLIT_MODE_DEPTH_FIRST mode.
    SPLIT_MODE_RADNDOM - Static variable in class org.openscience.cdk.structgen.stochastic.operator.CrossoverMachine
    Indicates that crossover is using SPLIT_MODE_RADNDOM mode.
    splitAfter(int, int) - Method in class org.openscience.cdk.group.Partition
    Splits this partition by taking the cell at cellIndex and making two new cells - the first with the the rest of the elements from that cell and the second with the singleton splitElement.
    splitBefore(int, int) - Method in class org.openscience.cdk.group.Partition
    Splits this partition by taking the cell at cellIndex and making two new cells - the first with the singleton splitElement and the second with the rest of the elements from that cell.
    splitMolecule(IAtomContainer, IBond) - Static method in class org.openscience.cdk.fragment.FragmentUtils
    Non destructively split a molecule into two parts at the specified bond.
    sqrt() - Method in class org.openscience.cdk.math.Quaternion
     
    SR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    sssr(IAtomContainer) - Static method in class org.openscience.cdk.graph.Cycles
    Find the smallest set of smallest rings (SSSR) - aka minimum cycle basis (MCB) of a molecule.
    SSSRFinder - Class in org.openscience.cdk.ringsearch
    Deprecated.
    SSSRFinder(IAtomContainer) - Constructor for class org.openscience.cdk.ringsearch.SSSRFinder
    Deprecated.
    Constructs a SSSRFinder for a specified molecule.
    st - Variable in class org.openscience.cdk.io.VASPReader
     
    StabilizationCharges - Class in org.openscience.cdk.charges
    The stabilization of the positive and the negative charge obtained (e.g in the polar breaking of a bond) is calculated from the sigma- and lone pair-electronegativity values of the atoms that are in conjugation to the atoms obtaining the charges.
    StabilizationCharges() - Constructor for class org.openscience.cdk.charges.StabilizationCharges
    Constructor for the StabilizationCharges object.
    StabilizationPlusChargeDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
    The stabilization of the positive charge (e.g.) obtained in the polar breaking of a bond is calculated from the sigma- and lone pair-electronegativity values of the atoms that are in conjugation to the atoms obtaining the charges.
    StabilizationPlusChargeDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor
    Constructor for the StabilizationPlusChargeDescriptor object
    StandardGenerator - Class in org.openscience.cdk.renderer.generators.standard
    The standard generator creates IRenderingElements for the atoms and bonds of a structure diagram.
    StandardGenerator(Font) - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator
    Create a new standard generator that utilises the specified font to display atom symbols.
    StandardGenerator.AnnotationColor - Class in org.openscience.cdk.renderer.generators.standard
    The color of the atom numbers.
    StandardGenerator.AnnotationColor() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.AnnotationColor
     
    StandardGenerator.AnnotationDistance - Class in org.openscience.cdk.renderer.generators.standard
    The distance of atom numbers from their parent atom as a percentage of bond length, default value is 0.25 (25%)
    StandardGenerator.AnnotationDistance() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.AnnotationDistance
     
    StandardGenerator.AnnotationFontScale - Class in org.openscience.cdk.renderer.generators.standard
    Annotation font size relative to element symbols, default = 0.4 (40%).
    StandardGenerator.AnnotationFontScale() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.AnnotationFontScale
     
    StandardGenerator.AtomColor - Class in org.openscience.cdk.renderer.generators.standard
    Defines the color of unselected atoms (and bonds).
    StandardGenerator.AtomColor() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.AtomColor
     
    StandardGenerator.BondSeparation - Class in org.openscience.cdk.renderer.generators.standard
    Defines the ratio of the separation between lines in double bonds as a percentage of length (BasicSceneGenerator.BondLength).
    StandardGenerator.BondSeparation() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.BondSeparation
     
    StandardGenerator.DashSection - Class in org.openscience.cdk.renderer.generators.standard
    The number of sections to render in a dashed 'unknown' bond, default = 4;
    StandardGenerator.DashSection() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.DashSection
     
    StandardGenerator.FancyBoldWedges - Class in org.openscience.cdk.renderer.generators.standard
    Modify bold wedges to be flush with adjacent bonds, default = true.
    StandardGenerator.FancyBoldWedges() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.FancyBoldWedges
     
    StandardGenerator.FancyHashedWedges - Class in org.openscience.cdk.renderer.generators.standard
    Modify hashed wedges to be flush when there is a single adjacent bond, default = true.
    StandardGenerator.FancyHashedWedges() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.FancyHashedWedges
     
    StandardGenerator.HashSpacing - Class in org.openscience.cdk.renderer.generators.standard
    The preferred spacing between lines in hashed bonds.
    StandardGenerator.HashSpacing() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.HashSpacing
     
    StandardGenerator.Highlighting - Class in org.openscience.cdk.renderer.generators.standard
    Parameter defines the style of highlight used to emphasis atoms and bonds.
    StandardGenerator.Highlighting() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.Highlighting
     
    StandardGenerator.HighlightStyle - Enum in org.openscience.cdk.renderer.generators.standard
    Enumeration of highlight style.
    StandardGenerator.OuterGlowWidth - Class in org.openscience.cdk.renderer.generators.standard
    The width of outer glow as a percentage of stroke width.
    StandardGenerator.OuterGlowWidth() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.OuterGlowWidth
     
    StandardGenerator.SgroupBracketDepth - Class in org.openscience.cdk.renderer.generators.standard
    How "deep" are brackets drawn.
    StandardGenerator.SgroupBracketDepth() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.SgroupBracketDepth
     
    StandardGenerator.SgroupFontScale - Class in org.openscience.cdk.renderer.generators.standard
    Scale Sgroup annotations relative to the normal font size (atom symbol).
    StandardGenerator.SgroupFontScale() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.SgroupFontScale
     
    StandardGenerator.StrokeRatio - Class in org.openscience.cdk.renderer.generators.standard
    Defines the ratio of the stroke to the width of the stroke of the font used to depict atom symbols.
    StandardGenerator.StrokeRatio() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.StrokeRatio
     
    StandardGenerator.SymbolMarginRatio - Class in org.openscience.cdk.renderer.generators.standard
    Defines the margin between an atom symbol and a connected bond based on the stroke width.
    StandardGenerator.SymbolMarginRatio() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.SymbolMarginRatio
     
    StandardGenerator.Visibility - Class in org.openscience.cdk.renderer.generators.standard
    Defines which atoms have their symbol displayed.
    StandardGenerator.Visibility() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.Visibility
     
    StandardGenerator.WaveSpacing - Class in org.openscience.cdk.renderer.generators.standard
    The spacing of waves (semi circles) drawn in wavy bonds with.
    StandardGenerator.WaveSpacing() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.WaveSpacing
     
    StandardGenerator.WedgeRatio - Class in org.openscience.cdk.renderer.generators.standard
    Ratio of the wide end of wedge compared to the narrow end (stroke width).
    StandardGenerator.WedgeRatio() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.WedgeRatio
     
    StandardSubstructureSets - Class in org.openscience.cdk.fingerprint
    Default sets of atom containers aimed for use with the substructure.
    StandardSubstructureSets() - Constructor for class org.openscience.cdk.fingerprint.StandardSubstructureSets
     
    Start() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
    Start ::= <ReactionExpression> <#_WS> ReactionExpression ::= <GroupExpression>? (">" <GroupExpression>? ">" <GroupExpression>?)? GroupExpression ::= ["("] <SmartsExpresion> [")"] ( "." ["("] <SmartsExpression> [")"] )* SmartsExpression ::= <AtomExpression> ( ( [ <LowAndBond> ] ( <Digit> | <AtomExpression> ) ) | ( "(" [ <LowAndBond> ] <SmartsExpression> ")" ) )* AtomExpression ::= ( "[" [ <AtomicMass> ] <LowAndExpression> [:<Digit>+] "]" ) | <ExplicitAtomExpression> LowAndBond ::= <OrBond> [ ";" <AndBond> ] OrBond ::= <ExplicitHighAndBond> [ "," <OrBond> ] ExplicitHighAndBond ::= <ImplicitHighAndBond> [ "&" <ExplicitHighAndBond> ] ImplicitHighAndBond ::= <NotBond> [ <ImplicitHighAndBond> ] NotBond ::= [ "!" ] <SimpleBond> SimpleBond ::= "/" | "\\" | "/?" | "\\?" | "=" | "#" | "~" | "@" ExplicitAtomExpression ::= [ "B" | "C" | "N" | "O" | "P" | "S" | "F" | "CL" | "BR" | "I" | "c" | "o" | "n" | "*" | "A" | "a" | "p" | "as" | "se" ] LowAndExpression ::= <OrExpression> ( ";" <LowAndExpression> )? OrExpression ::= <ExplicitHighAndExpression> ( "," <OrExpression> ) ? ExplicitHighAndExpression ::= <ImplicitHighAndExpression> ( "&" <ExplicitHighAndExpression> )? ImplicitHighAndExpression ::= <NotExpression> ( <ImplicitHighAndExpression> ) ? NotExpression ::= "!" ( <PrimitiveAtomExpression> | <RecursiveSmartsExpression> ) RecursiveSmartsExpression ::= "$" "(" <SmartsExpression> ")" PrimitiveAtomExpression ::= <NonHydrogenElement> | "*" | "A" | "a" | "D" (<Digits>)? | "H" (<Digits>)? | "h" (<Digits>)? | "R" (<Digit>+)? | "r" (<Digit>+)? | "v" (<Digit>+)? | "#X" | "G" (<DIGIT>+) | "X" (<Digit>+)? | "x" (<Digit>+)? | "^" (<DIGIT>) | ("+" | "-") (<Digit>+)? | "#" (<Digit>+) | "@" | "@@" | <Digit>+ Digit ::= ( "0" - "9") NonHydrogenElement ::= [ "HE" | "LI" | "BE" | "NE" | "NA" | "MG" | "AL" | "SI" | "AR" | "CA" | "SC" | "TI" | "CR" | "MN" | "FE" | "CO" | "NI" | "CU" | "ZN" | "GA" | "GE" | "AS" | "SE" | "BR" | "KR" | "RB" | "SR" | "ZR" | "NB" | "MO" | "TC" | "RU" | "RH" | "PD" | "AG" | "CD" | "IN" | "SN" | "SB" | "TE" | "XE" | "CS" | "BA" | "LA" | "HF" | "TA" | "RE" | "OS" | "IR" | "PT" | "AU" | "HG" | "TL" | "PB" | "BI" | "PO" | "AT" | "RN" | "FR" | "RA" | "AC" | "TH" | "PA" | "B" | "C" | "N" | "O" | "F" | "P" | "S" | "K" | "V" | "Y" | "I" | "U" | "c" | "o" | "n" | "p" | "as" | "se" ]
    startDocument() - Method in class org.openscience.cdk.config.atomtypes.AtomTypeHandler
    startDocument() - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeHandler
    startDocument() - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingHandler
    startDocument() - Method in class org.openscience.cdk.config.isotopes.IsotopeHandler
    startDocument() - Method in class org.openscience.cdk.dict.DictionaryHandler
     
    startDocument() - Method in class org.openscience.cdk.io.cml.CDKConvention
     
    startDocument() - Method in class org.openscience.cdk.io.cml.CMLCoreModule
     
    startDocument() - Method in class org.openscience.cdk.io.cml.CMLHandler
     
    startDocument() - Method in interface org.openscience.cdk.io.cml.ICMLModule
     
    startDocument() - Method in class org.openscience.cdk.io.cml.MDLMolConvention
     
    startDocument() - Method in class org.openscience.cdk.io.cml.PMPConvention
     
    startDocument() - Method in class org.openscience.cdk.io.inchi.INChIHandler
     
    startDocument() - Method in class org.openscience.cdk.io.iterator.event.EventCMLHandler
    Procedure required by the CDOInterface.
    startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.config.atomtypes.AtomTypeHandler
    startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeHandler
    startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingHandler
    startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.config.isotopes.IsotopeHandler
    startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.dict.DictionaryHandler
     
    startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.CDKConvention
     
    startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.CMLCoreModule
     
    startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.CMLHandler
     
    startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.CMLReactionModule
     
    startElement(CMLStack, String, String, String, Attributes) - Method in interface org.openscience.cdk.io.cml.ICMLModule
     
    startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.JMOLANIMATIONConvention
     
    startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.MDLMolConvention
     
    startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.MDMoleculeConvention
    Add parsing of elements in mdmolecule: mdmolecule chargeGroup id cgNumber atomArray switchingAtom residue id title resNumber atomArray
    startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.PDBConvention
     
    startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.PMPConvention
     
    startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.QSARConvention
     
    startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.io.inchi.INChIHandler
    Implementation of the startElement() procedure overwriting the DefaultHandler interface.
    startMcGregorIteration(int, Map<Integer, Integer>) - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregor
    Deprecated.
    Start McGregor search and extend the mappings if possible.
    startMcGregorIteration(int, List<Integer>, List<Integer>) - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregor
    Deprecated.
    Start McGregor search and extend the mappings if possible.
    startObject(String) - Method in class org.openscience.cdk.io.iterator.event.EventCMLHandler
    Procedure required by the CDOInterface.
    startX - Variable in class org.openscience.cdk.renderer.elements.ArrowElement
    X coordinate of the point where the arrow starts.
    startY - Variable in class org.openscience.cdk.renderer.elements.ArrowElement
    Y coordinate of the point where the arrow starts.
    stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.AtomContainer
    Called by objects to which this object has registered as a listener.
    stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.AtomContainerSet
    Called by objects to which this object has registered as a listener.
    stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.ChemFile
    Called by objects to which this object has registered as a listener.
    stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.ChemModel
    Called by objects to which this object has registered as a listener.
    stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.ChemSequence
    Called by objects to which this object has registered as a listener.
    stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugAminoAcid
    Called by objects to which this object has registered as a listener.
    stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugBioPolymer
    Called by objects to which this object has registered as a listener.
    stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugCrystal
    Called by objects to which this object has registered as a listener.
    stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugMonomer
    Called by objects to which this object has registered as a listener.
    stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugPolymer
    Called by objects to which this object has registered as a listener.
    stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugRing
    Called by objects to which this object has registered as a listener.
    stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugStrand
    Called by objects to which this object has registered as a listener.
    stateChanged(EventObject) - Method in interface org.openscience.cdk.event.ICDKChangeListener
    Invoked when the target of the listener has changed its state.
    stateChanged(EventObject) - Method in interface org.openscience.cdk.event.ICDKSelectionChangeListener
    Invoked when the target of the listener has changed its state.
    stateChanged(IChemObjectChangeEvent) - Method in interface org.openscience.cdk.interfaces.IChemObjectListener
    Called by objects to notify objects that implemented this interface and registered with them as ChemObjectListeners.
    stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
    Called by objects to which this object has registered as a listener.
    stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.ReactionSet
     
    stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.AtomContainer
    Called by objects to which this object has registered as a listener.
    stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.AtomContainerSet
    Called by objects to which this object has registered as a listener.
    stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.ChemFile
    Called by objects to which this object has registered as a listener.
    stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.ChemModel
    Called by objects to which this object has registered as a listener.
    stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.ChemSequence
    Called by objects to which this object has registered as a listener.
    stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.ReactionSet
     
    stateChanged(List) - Method in interface org.openscience.cdk.structgen.IStructureGenerationListener
     
    staticFlag - Static variable in class org.openscience.cdk.iupac.parser.SimpleCharStream
    Whether parser is static.
    staticFlag - Static variable in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
    Whether parser is static.
    STDOUT_LOGGING_TOOL_CLASS - Static variable in class org.openscience.cdk.tools.LoggingToolFactory
    Back-up logging tool.
    stereo - Variable in class org.openscience.cdk.Bond
    A descriptor the stereochemical orientation of this bond.
    stereo - Variable in class org.openscience.cdk.isomorphism.matchers.QueryBond
    A descriptor the stereochemical orientation of this query bond.
    stereo - Variable in class org.openscience.cdk.silent.Bond
    A descriptor the stereochemical orientation of this bond.
    Stereo - Static variable in class org.openscience.cdk.smiles.SmiFlavor
    Output supported stereochemistry types.
    STEREO_ATOM_PARITY_MINUS - Static variable in class org.openscience.cdk.CDKConstants
    A negative atom parity.
    STEREO_ATOM_PARITY_PLUS - Static variable in class org.openscience.cdk.CDKConstants
    A positive atom parity.
    STEREO_ATOM_PARITY_UNDEFINED - Static variable in class org.openscience.cdk.CDKConstants
    A undefined atom parity.
    StereoBond - Class in org.openscience.cdk.isomorphism.matchers.smarts
    This query bond indicates a particular geometric stereo configuration.
    StereoBond(IChemObjectBuilder, StereoBond.Direction, boolean) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.StereoBond
     
    StereoBond.Direction - Enum in org.openscience.cdk.isomorphism.matchers.smarts
     
    Stereocenters - Class in org.openscience.cdk.stereo
    Find atoms which can support stereo chemistry based on the connectivity.
    Stereocenters.Stereocenter - Enum in org.openscience.cdk.stereo
    Defines the type of a stereocenter.
    Stereocenters.Type - Enum in org.openscience.cdk.stereo
     
    stereocenterType(int) - Method in class org.openscience.cdk.stereo.Stereocenters
    Determine the type of stereocenter is the atom at index v.
    stereochemistry() - Method in class org.openscience.cdk.isomorphism.Mappings
    Filter the mappings for those which preserve stereochemistry specified in the query.
    StereoCisTrans - Static variable in class org.openscience.cdk.smiles.SmiFlavor
    Output cis-trans stereochemistry specified by directional \ of / bonds.
    StereoElementFactory - Class in org.openscience.cdk.stereo
    Create stereo elements for a structure with 2D and 3D coordinates.
    StereoElementFactory(IAtomContainer, int[][], GraphUtil.EdgeToBondMap) - Constructor for class org.openscience.cdk.stereo.StereoElementFactory
    Internal constructor.
    stereoElements - Variable in class org.openscience.cdk.AtomContainer
    Internal list of atom parities.
    stereoElements() - Method in class org.openscience.cdk.AtomContainer
    Returns the stereo elements defined for this atom container.
    stereoElements() - Method in class org.openscience.cdk.debug.DebugAminoAcid
    Returns the stereo elements defined for this atom container.
    stereoElements() - Method in class org.openscience.cdk.debug.DebugAtomContainer
    Returns the stereo elements defined for this atom container.
    stereoElements() - Method in class org.openscience.cdk.debug.DebugBioPolymer
    Returns the stereo elements defined for this atom container.
    stereoElements() - Method in class org.openscience.cdk.debug.DebugCrystal
    Returns the stereo elements defined for this atom container.
    stereoElements() - Method in class org.openscience.cdk.debug.DebugMonomer
    Returns the stereo elements defined for this atom container.
    stereoElements() - Method in class org.openscience.cdk.debug.DebugPolymer
    Returns the stereo elements defined for this atom container.
    stereoElements() - Method in class org.openscience.cdk.debug.DebugRing
    Returns the stereo elements defined for this atom container.
    stereoElements() - Method in class org.openscience.cdk.debug.DebugStrand
    Returns the stereo elements defined for this atom container.
    stereoElements() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
    Returns the stereo elements defined for this atom container.
    stereoElements - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
    Internal list of atom parities.
    stereoElements() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
    Returns the stereo elements defined for this atom container.
    stereoElements - Variable in class org.openscience.cdk.silent.AtomContainer
    Internal list of atom parities.
    stereoElements() - Method in class org.openscience.cdk.silent.AtomContainer
    Returns the stereo elements defined for this atom container.
    StereoEncoder - Interface in org.openscience.cdk.hash.stereo
    An encoder for stereo chemistry.
    StereoEncoderFactory - Interface in org.openscience.cdk.hash.stereo
    Describes a factory for stereo elements.
    StereoExTetrahedral - Static variable in class org.openscience.cdk.smiles.SmiFlavor
    Output extended tetrahedral stereochemistry on atoms as @ and @@.
    stereoGiven - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
     
    stereoParity - Variable in class org.openscience.cdk.Atom
    A stereo parity descriptor for the stereochemistry of this atom.
    stereoParity - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom
    A stereo parity descriptor for the stereochemistry of this atom.
    stereoParity - Variable in class org.openscience.cdk.silent.Atom
    A stereo parity descriptor for the stereochemistry of this atom.
    stereosAreOpposite(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.BondTools
    Says if of four atoms connected two one atom the up and down bonds are opposite or not, i.
    StereoTetrahedral - Static variable in class org.openscience.cdk.smiles.SmiFlavor
    Output tetrahedral stereochemistry on atoms as @ and @@.
    StereoTool - Class in org.openscience.cdk.stereo
    Methods to determine or check the stereo class of a set of atoms.
    StereoTool() - Constructor for class org.openscience.cdk.stereo.StereoTool
     
    StereoTool.SquarePlanarShape - Enum in org.openscience.cdk.stereo
    The shape that four atoms take in a plane.
    StereoTool.StereoClass - Enum in org.openscience.cdk.stereo
    Currently unused, but intended for the StereoTool to indicate what it 'means' by an assignment of some atoms to a class.
    StereoTool.TetrahedralSign - Enum in org.openscience.cdk.stereo
    The handedness of a tetrahedron, in terms of the point-plane distance of three of the corners, compared to the fourth.
    storeAtomData() - Method in class org.openscience.cdk.io.cml.CMLCoreModule
     
    storeAtomData() - Method in class org.openscience.cdk.io.cml.PDBConvention
     
    storeBondData() - Method in class org.openscience.cdk.io.cml.CMLCoreModule
     
    storeData() - Method in class org.openscience.cdk.io.cml.CMLCoreModule
     
    storeData() - Method in class org.openscience.cdk.io.cml.PDBConvention
     
    Strand - Class in org.openscience.cdk.silent
    A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms.
    Strand() - Constructor for class org.openscience.cdk.silent.Strand
    Constructs a new Strand.
    Strand - Class in org.openscience.cdk
    A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms.
    Strand() - Constructor for class org.openscience.cdk.Strand
    Constructs a new Strand.
    StringDifference - Class in org.openscience.cdk.tools.diff.tree
    IDifference between two String.
    StringIOSetting - Class in org.openscience.cdk.io.setting
    An class for a reader setting which must be of type String.
    StringIOSetting(String, IOSetting.Importance, String, String) - Constructor for class org.openscience.cdk.io.setting.StringIOSetting
     
    stroke - Variable in class org.openscience.cdk.renderer.elements.GeneralPath
    The width of the stroke.
    STRONTIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    STRONTIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    structgenATF - Variable in class org.openscience.cdk.tools.SmilesValencyChecker
     
    StructGenAtomTypeGuesser - Class in org.openscience.cdk.atomtype
    AtomTypeMatcher that finds an AtomType by matching the Atom's element symbol.
    StructGenAtomTypeGuesser() - Constructor for class org.openscience.cdk.atomtype.StructGenAtomTypeGuesser
    Constructor for the StructGenMatcher object.
    StructGenMatcher - Class in org.openscience.cdk.atomtype
    AtomTypeMatcher that finds an AtomType by matching the Atom's element symbol.
    StructGenMatcher() - Constructor for class org.openscience.cdk.atomtype.StructGenMatcher
    Constructor for the StructGenMatcher object.
    StructureDiagramGenerator - Class in org.openscience.cdk.layout
    Generates 2D coordinates for a molecule for which only connectivity is known or the coordinates have been discarded for some reason.
    StructureDiagramGenerator() - Constructor for class org.openscience.cdk.layout.StructureDiagramGenerator
    The empty constructor.
    StructureDiagramGenerator(IAtomContainer) - Constructor for class org.openscience.cdk.layout.StructureDiagramGenerator
    Creates an instance of this class while assigning a molecule to be layed out.
    StructureResonanceGenerator - Class in org.openscience.cdk.tools
    This class try to generate resonance structure for a determinate molecule.
    StructureResonanceGenerator() - Constructor for class org.openscience.cdk.tools.StructureResonanceGenerator
    Construct an instance of StructureResonanceGenerator.
    StructureResonanceGenerator(boolean) - Constructor for class org.openscience.cdk.tools.StructureResonanceGenerator
    Construct an instance of StructureResonanceGenerator.
    sub(Complex) - Method in class org.openscience.cdk.math.Complex
    Subtracs a complex value
    sub(IMatrix) - Method in class org.openscience.cdk.math.IMatrix
    Subtraktion from two matrices
    sub(IMatrix, IMatrix) - Method in class org.openscience.cdk.math.IMatrix
    Subtraktion from two matrices
    sub(IVector) - Method in class org.openscience.cdk.math.IVector
    Subtraction from two vectors
    sub(IVector, IVector) - Method in class org.openscience.cdk.math.IVector
    Subtraction from two vectors
    sub(Matrix) - Method in class org.openscience.cdk.math.Matrix
    Subtracts from two matrices.
    sub(Quaternion) - Method in class org.openscience.cdk.math.Quaternion
     
    sub(Vector) - Method in class org.openscience.cdk.math.Vector
    Subtraktion from two vectors
    subChain() - Method in class org.openscience.cdk.iupac.parser.NomParser
    Deprecated.
    The substituent part of the prefix
    subgraph(int[][], int[]) - Static method in class org.openscience.cdk.graph.GraphUtil
    Create a subgraph by specifying the vertices from the original graph to include in the subgraph.
    subGraph - Variable in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
     
    subList(int, int) - Method in class org.openscience.cdk.ConformerContainer
     
    subscript - Variable in class org.openscience.cdk.renderer.elements.TextGroupElement.Child
    A subscript (if any) for the child.
    Substance - Class in org.openscience.cdk.silent
    An implementation of the ISubstance interface.
    Substance() - Constructor for class org.openscience.cdk.silent.Substance
     
    Substance - Class in org.openscience.cdk
    An implementation of the ISubstance interface.
    Substance() - Constructor for class org.openscience.cdk.Substance
     
    SubstructureFingerprinter - Class in org.openscience.cdk.fingerprint
    IFingerprinter that gives a bit set which has a size equal to the number of substructures it was constructed from.
    SubstructureFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.SubstructureFingerprinter
    Set up the fingerprinter to use the fragments from StandardSubstructureSets.
    SubstructureFingerprinter(String[]) - Constructor for class org.openscience.cdk.fingerprint.SubstructureFingerprinter
    Set up the fingerprinter to use a user-defined set of fragments.
    suggest(Class<?>) - Method in class org.openscience.cdk.DynamicFactory
    Provides a list of all possible constructor keys for the provided interface.
    SULFUR - Static variable in enum org.openscience.cdk.config.Elements
     
    suppressHydrogens() - Method in class org.openscience.cdk.hash.HashGeneratorMaker
    Suppress any explicit hydrogens in the encoding of hash values.
    suppressHydrogens(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
    Suppress any explicit hydrogens in the provided container.
    SVG_FMT - Static variable in class org.openscience.cdk.depict.Depiction
    Structured Vector Graphics (SVG) format key.
    SVGFormat - Class in org.openscience.cdk.io.formats
     
    SVGFormat() - Constructor for class org.openscience.cdk.io.formats.SVGFormat
     
    svgPrevisit(String, double, SvgDrawVisitor, List<? extends IRenderingElement>) - Method in class org.openscience.cdk.depict.Depiction
     
    SwingEventRelay - Class in org.openscience.cdk.controller
     
    SwingEventRelay(JComponent) - Constructor for class org.openscience.cdk.controller.SwingEventRelay
     
    SwingGUIListener - Class in org.openscience.cdk.io.listener
    Allows processing of IOSetting quesions which are passed to the user by using Swing dialogs.
    SwingGUIListener(Component, IOSetting.Importance) - Constructor for class org.openscience.cdk.io.listener.SwingGUIListener
    0 = ask no questions 3 = ask all questions
    SwingMouseEventRelay - Class in org.openscience.cdk.controller
     
    SwingMouseEventRelay(IMouseEventRelay) - Constructor for class org.openscience.cdk.controller.SwingMouseEventRelay
     
    SwissArmyKnife - Class in org.openscience.cdk.tools
    Deprecated.
    SwissArmyKnife() - Constructor for class org.openscience.cdk.tools.SwissArmyKnife
    Deprecated.
     
    SwitchTo(int) - Method in class org.openscience.cdk.iupac.parser.NomParserTokenManager
    Switch to specified lex state.
    SwitchTo(int) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager
    Switch to specified lex state.
    SybylAtomTypeMatcher - Class in org.openscience.cdk.atomtype
    Atom Type matcher for Sybyl atom types.
    SybylDescriptorFormat - Class in org.openscience.cdk.io.formats
    See here.
    SybylDescriptorFormat() - Constructor for class org.openscience.cdk.io.formats.SybylDescriptorFormat
     
    symbol() - Method in enum org.openscience.cdk.config.Elements
    The element symbol, C for carbon, N for nitrogen, Na for sodium, etc.
    symbol - Variable in class org.openscience.cdk.Element
    The element symbol for this element as listed in the periodic table.
    symbol - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom
    The element symbol for this element as listed in the periodic table.
    SYMBOL - Static variable in class org.openscience.cdk.libio.jena.CDK
     
    symbol - Variable in class org.openscience.cdk.silent.Element
    The element symbol for this element as listed in the periodic table.
    SymbolAndChargeQueryAtom - Class in org.openscience.cdk.isomorphism.matchers
     
    SymbolAndChargeQueryAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolAndChargeQueryAtom
     
    SymbolAndChargeQueryAtom(IAtom) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolAndChargeQueryAtom
     
    SymbolChargeIDQueryAtom - Class in org.openscience.cdk.isomorphism.matchers
     
    SymbolChargeIDQueryAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolChargeIDQueryAtom
     
    SymbolChargeIDQueryAtom(IAtom) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolChargeIDQueryAtom
     
    SymbolQueryAtom - Class in org.openscience.cdk.isomorphism.matchers
     
    SymbolQueryAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom
     
    SymbolQueryAtom(IAtom) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom
     
    SymbolSetQueryAtom - Class in org.openscience.cdk.isomorphism.matchers
    A QueryAtom that matches all symbols in this container.
    SymbolSetQueryAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom
    Constructor for the SymbolSetQueryAtom object
    SymbolVisibility - Class in org.openscience.cdk.renderer
    Predicate that defines whether an atom symbol is displayed in a structure diagram.
    SymbolVisibility() - Constructor for class org.openscience.cdk.renderer.SymbolVisibility
     
    symmetry(IAtomContainer, int[][]) - Static method in class org.openscience.cdk.graph.invariant.Canon
    Compute the symmetry classes for the provided structure.
    SYSTEMID - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
     
    SystemOutLoggingTool - Class in org.openscience.cdk.tools
    Implementation of the ILoggingTool interface that sends output to the System.out channel.
    SystemOutLoggingTool(Class<?>) - Constructor for class org.openscience.cdk.tools.SystemOutLoggingTool
    Constructs a ILoggingTool which produces log lines indicating them to be for the given Class.

    T

    T_BOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    TA - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    tabSize - Variable in class org.openscience.cdk.iupac.parser.SimpleCharStream
     
    tabSize - Variable in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
     
    TaeAminoAcidDescriptor - Class in org.openscience.cdk.qsar.descriptors.protein
    An implementation of the TAE descriptors for amino acids.
    TaeAminoAcidDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor
     
    Tanimoto - Class in org.openscience.cdk.similarity
    Calculates the Tanimoto coefficient for a given pair of two fingerprint bitsets or real valued feature vectors.
    TANTALUM - Static variable in enum org.openscience.cdk.config.Elements
     
    TANTALUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    TargetProcessor - Class in org.openscience.cdk.smsd.algorithm.mcgregor
    Deprecated.
    SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    TargetProcessor(List<String>, List<String>, String[], int, int, List<Integer>, List<String>, int, List<Integer>, List<String>) - Constructor for class org.openscience.cdk.smsd.algorithm.mcgregor.TargetProcessor
    Deprecated.
     
    TargetProperties - Class in org.openscience.cdk.smsd.algorithm.vflib.builder
    Deprecated.
    SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    TargetProperties(IAtomContainer) - Constructor for class org.openscience.cdk.smsd.algorithm.vflib.builder.TargetProperties
    Deprecated.
     
    TautomerizationMechanism - Class in org.openscience.cdk.reaction.mechanism
    This mechanism produces the tautomerization chemical reaction between two tautomers.
    TautomerizationMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.TautomerizationMechanism
     
    TautomerizationReaction - Class in org.openscience.cdk.reaction.type
    IReactionProcess which produces a tautomerization chemical reaction.
    TautomerizationReaction() - Constructor for class org.openscience.cdk.reaction.type.TautomerizationReaction
    Constructor of the TautomerizationReaction object.
    TB - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    TC - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    TE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    TECHNETIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    TECHNETIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    TELLURIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    TELLURIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    TemplateExtractor - Class in org.openscience.cdk.modeling.builder3d
    Helper class that help setup a template library of CDK's Builder3D.
    TemplateExtractor() - Constructor for class org.openscience.cdk.modeling.builder3d.TemplateExtractor
     
    TemplateHandler - Class in org.openscience.cdk.layout
    Helper class for Structure Diagram Generation.
    TemplateHandler(IChemObjectBuilder) - Constructor for class org.openscience.cdk.layout.TemplateHandler
    Creates a new TemplateHandler with default templates loaded.
    TemplateHandler() - Constructor for class org.openscience.cdk.layout.TemplateHandler
    Creates a new TemplateHandler without any default templates.
    TemplateHandler3D - Class in org.openscience.cdk.modeling.builder3d
    Helper class for ModelBuilder3D.
    tensNoUnits() - Method in class org.openscience.cdk.iupac.parser.NomParser
    Deprecated.
    Deal with fragments refering to the positioning of the base numbers (denoting their magnitude)
    tensWithUnits() - Method in class org.openscience.cdk.iupac.parser.NomParser
    Deprecated.
    Deals with numbers above 30 where the base numbers set appear twice.
    TERBIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    TERBIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    Tessellate - Class in org.openscience.cdk.geometry.surface
    Performs a tessellation of the unit sphere.
    Tessellate() - Constructor for class org.openscience.cdk.geometry.surface.Tessellate
     
    Tessellate(String, int) - Constructor for class org.openscience.cdk.geometry.surface.Tessellate
     
    test(Permutation) - Method in class org.openscience.cdk.group.PermutationGroup
    Test a permutation to see if it is in the group.
    TETR - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    TETRAHEDRAL_ANGLE - Static variable in class org.openscience.cdk.geometry.AtomTools
     
    TETRAHEDRAL_ANGLE - Static variable in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
     
    TetrahedralChirality - Class in org.openscience.cdk.stereo
    Stereochemistry specification for quadrivalent atoms.
    TetrahedralChirality(IAtom, IAtom[], ITetrahedralChirality.Stereo) - Constructor for class org.openscience.cdk.stereo.TetrahedralChirality
    Constructor to create a new ITetrahedralChirality implementation instance.
    TetrahedralElementEncoderFactory - Class in org.openscience.cdk.hash.stereo
    Defines a stereo encoder factory for the hash code.
    TetrahedralElementEncoderFactory() - Constructor for class org.openscience.cdk.hash.stereo.TetrahedralElementEncoderFactory
     
    text - Variable in class org.openscience.cdk.renderer.elements.TextElement
    The text to be displayed.
    text - Variable in class org.openscience.cdk.renderer.elements.TextGroupElement.Child
    The text of this child.
    TextElement - Class in org.openscience.cdk.renderer.elements
    Text element as used in the chemical drawing.
    TextElement(double, double, String, Color) - Constructor for class org.openscience.cdk.renderer.elements.TextElement
    Constructs a new TextElement with the content text to be drawn at position (x,y) in the color color.
    TextGroupElement - Class in org.openscience.cdk.renderer.elements
    A group of text elements, particularly the element symbol (eg: "C") surrounded by other annotations such as mass number, charge, etc.
    TextGroupElement(double, double, String, Color) - Constructor for class org.openscience.cdk.renderer.elements.TextGroupElement
    Make a text group at (x, y) with the text and color given.
    TextGroupElement.Child - Class in org.openscience.cdk.renderer.elements
    A string of text that should be shown around the parent.
    TextGroupElement.Child(String, TextGroupElement.Position) - Constructor for class org.openscience.cdk.renderer.elements.TextGroupElement.Child
    Make a child element with the specified text and position.
    TextGroupElement.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.
    TextGroupElement.Position - Enum in org.openscience.cdk.renderer.elements
    Compass-point positions for text element annotation children.
    TextGUIListener - Class in org.openscience.cdk.io.listener
    Allows processing of IOSetting quesions which are passed to the user by using the System.out and System.in by default.
    TextGUIListener(IOSetting.Importance) - Constructor for class org.openscience.cdk.io.listener.TextGUIListener
     
    TH - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    THALLIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    THALLIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    THIOPHENE_RING - Static variable in class org.openscience.cdk.tools.AtomTypeTools
     
    THORIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    THORIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    THULIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    THULIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    TI - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    TimeManager - Class in org.openscience.cdk.smsd.tools
    Deprecated.
    SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    TimeManager() - Constructor for class org.openscience.cdk.smsd.tools.TimeManager
    Deprecated.
    Constructor for storing execution time
    timeout(long) - Static method in exception org.openscience.cdk.exception.Intractable
    Utility for creating a message which indicates an operation timed out after a given time in milliseconds, t.
    timeout(String, long) - Static method in exception org.openscience.cdk.exception.Intractable
    Utility for creating a message which indicates an operation timed out after a given time in milliseconds, t.
    TimeOut - Class in org.openscience.cdk.smsd.global
    Deprecated.
    SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    TimeOut() - Constructor for class org.openscience.cdk.smsd.global.TimeOut
    Deprecated.
     
    TIN - Static variable in enum org.openscience.cdk.config.Elements
     
    TIN - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    TinkerMM2Format - Class in org.openscience.cdk.io.formats
    See here.
    TinkerMM2Format() - Constructor for class org.openscience.cdk.io.formats.TinkerMM2Format
     
    TinkerXYZFormat - Class in org.openscience.cdk.io.formats
    See here.
    TinkerXYZFormat() - Constructor for class org.openscience.cdk.io.formats.TinkerXYZFormat
     
    TITANIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    TITANIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    TITLE - Static variable in class org.openscience.cdk.CDKConstants
    The title for a IChemObject.
    TL - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    TM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    toAdjList(IAtomContainer) - Static method in class org.openscience.cdk.graph.GraphUtil
    Create an adjacent list representation of the container.
    toAdjList(IAtomContainer, GraphUtil.EdgeToBondMap) - Static method in class org.openscience.cdk.graph.GraphUtil
    Create an adjacent list representation of the container and fill in the bondMap for quick lookup.
    toAdjListSubgraph(IAtomContainer, Set<IBond>) - Static method in class org.openscience.cdk.graph.GraphUtil
    Create an adjacent list representation of the container that only includes bonds that are in the set provided as an argument.
    toArray() - Method in class org.openscience.cdk.ConformerContainer
    Returns the conformers in the form of an array of IAtomContainers.
    toArray(IAtomContainer[]) - Method in class org.openscience.cdk.ConformerContainer
     
    toArray(T[]) - Method in class org.openscience.cdk.io.setting.SettingManager
    Compatibility method generates an array of ISetting objects.
    toArray() - Method in class org.openscience.cdk.isomorphism.Mappings
    Mappings are lazily generated and best used in a loop.
    toAtomBondMap() - Method in class org.openscience.cdk.isomorphism.Mappings
    Convert the permutations to an atom-atom bond-bond map.
    toAtomMap() - Method in class org.openscience.cdk.isomorphism.Mappings
    Convert the permutations to a atom-atom map.
    toBondMap() - Method in class org.openscience.cdk.isomorphism.Mappings
    Convert the permutations to a bond-bond map.
    toCanonicalSignatureString(int) - Method in class org.openscience.cdk.signature.MoleculeSignature
    Make a canonical signature string of a given height.
    toChemObjects() - Method in class org.openscience.cdk.isomorphism.Mappings
    Obtain the chem objects (atoms and bonds) that have 'hit' in the target molecule.
    toCycleString() - Method in class org.openscience.cdk.group.Permutation
    An easily-readable version of the permutation as a product of cycles.
    toEpsStr() - Method in class org.openscience.cdk.depict.Depiction
    Render the image to an EPS format string.
    toIElement() - Method in enum org.openscience.cdk.config.Elements
    Access an IElement instance of the chemical element.
    toImg() - Method in class org.openscience.cdk.depict.Depiction
    Render the depiction to a Java AWT BufferedImage.
    token - Variable in class org.openscience.cdk.iupac.parser.NomParser
    Deprecated.
    Current token.
    Token - Class in org.openscience.cdk.iupac.parser
    Describes the input token stream.
    Token() - Constructor for class org.openscience.cdk.iupac.parser.Token
    No-argument constructor
    Token(int) - Constructor for class org.openscience.cdk.iupac.parser.Token
    Constructs a new token for the specified Image.
    Token(int, String) - Constructor for class org.openscience.cdk.iupac.parser.Token
    Constructs a new token for the specified Image and Kind.
    token - Variable in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
    Current token.
    Token - Class in org.openscience.cdk.smiles.smarts.parser
    Describes the input token stream.
    Token() - Constructor for class org.openscience.cdk.smiles.smarts.parser.Token
    No-argument constructor
    Token(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.Token
    Constructs a new token for the specified Image.
    Token(int, String) - Constructor for class org.openscience.cdk.smiles.smarts.parser.Token
    Constructs a new token for the specified Image and Kind.
    token_source - Variable in class org.openscience.cdk.iupac.parser.NomParser
    Deprecated.
    Generated Token Manager.
    token_source - Variable in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
    Generated Token Manager.
    tokenImage - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    Literal token values.
    tokenImage - Variable in exception org.openscience.cdk.iupac.parser.ParseException
    This is a reference to the "tokenImage" array of the generated parser within which the parse error occurred.
    tokenImage - Variable in exception org.openscience.cdk.smiles.smarts.parser.ParseException
    This is a reference to the "tokenImage" array of the generated parser within which the parse error occurred.
    tokenImage - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    Literal token values.
    TokenMgrError - Error in org.openscience.cdk.iupac.parser
    Token Manager Error.
    TokenMgrError() - Constructor for error org.openscience.cdk.iupac.parser.TokenMgrError
    No arg constructor.
    TokenMgrError(String, int) - Constructor for error org.openscience.cdk.iupac.parser.TokenMgrError
    Constructor with message and reason.
    TokenMgrError(boolean, int, int, int, String, char, int) - Constructor for error org.openscience.cdk.iupac.parser.TokenMgrError
    Full Constructor.
    TokenMgrError - Error in org.openscience.cdk.smiles.smarts.parser
    Token Manager Error.
    TokenMgrError() - Constructor for error org.openscience.cdk.smiles.smarts.parser.TokenMgrError
    No arg constructor.
    TokenMgrError(String, int) - Constructor for error org.openscience.cdk.smiles.smarts.parser.TokenMgrError
    Constructor with message and reason.
    TokenMgrError(boolean, int, int, int, String, char, int) - Constructor for error org.openscience.cdk.smiles.smarts.parser.TokenMgrError
    Full Constructor.
    ToleranceRangeRule - Class in org.openscience.cdk.formula.rules
    This class validate if the mass from an IMolecularFormula is between the tolerance range give a experimental mass.
    ToleranceRangeRule() - Constructor for class org.openscience.cdk.formula.rules.ToleranceRangeRule
    Constructor for the ToleranceRangeRule object.
    toMiddle() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
    Set the font size pointer to the middle of the range.
    toModelCoordinates(double, double) - Method in class org.openscience.cdk.renderer.AbstractRenderer
    Convert a point in screen space into a point in model space.
    toModelCoordinates(double, double) - Method in interface org.openscience.cdk.renderer.IRenderer
    Converts screen coordinates into model (or world) coordinates.
    toMolecule(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
    Converts a reaction to an 'inlined' reaction stored as a molecule.
    toPdfStr() - Method in class org.openscience.cdk.depict.Depiction
    Render the image to an PDF format string.
    toPermutation() - Method in class org.openscience.cdk.group.Partition
    Converts the whole partition into a permutation.
    TopologicalMatrix - Class in org.openscience.cdk.graph.matrix
    Calculator for a topological matrix representation of this AtomContainer.
    TopologicalMatrix() - Constructor for class org.openscience.cdk.graph.matrix.TopologicalMatrix
     
    toReaction(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
    Converts an 'inlined' reaction stored in a molecule back to a reaction.
    toRingSet() - Method in class org.openscience.cdk.graph.Cycles
    Convert the cycles to a IRingSet containing the IAtoms and IBonds of the input molecule.
    toRotationMatrix() - Method in class org.openscience.cdk.math.Quaternion
     
    toScreenCoordinates(double, double) - Method in class org.openscience.cdk.renderer.AbstractRenderer
    Convert a point in model space into a point in screen space.
    toScreenCoordinates(double, double) - Method in interface org.openscience.cdk.renderer.IRenderer
    Converts model (or world) coordinates into screen coordinates.
    toString() - Method in class org.openscience.cdk.AminoAcid
     
    toString() - Method in class org.openscience.cdk.Association
    Returns a one line string representation of this Container.
    toString() - Method in class org.openscience.cdk.Atom
    Returns a one line string representation of this Atom.
    toString() - Method in class org.openscience.cdk.AtomContainer
    Returns a one line string representation of this Container.
    toString() - Method in class org.openscience.cdk.AtomContainerSet
    Returns the String representation of this AtomContainerSet.
    toString() - Method in class org.openscience.cdk.AtomType
     
    toString() - Method in class org.openscience.cdk.BioPolymer
     
    toString() - Method in class org.openscience.cdk.Bond
    Returns a one line string representation of this Container.
    toString() - Method in class org.openscience.cdk.ChemFile
    Returns a String representation of this class.
    toString() - Method in class org.openscience.cdk.ChemModel
    Returns a String representation of the contents of this IChemObject.
    toString() - Method in class org.openscience.cdk.ChemSequence
     
    toString() - Method in class org.openscience.cdk.Crystal
    Returns a String representation of this crystal.
    toString() - Method in class org.openscience.cdk.dict.DictRef
     
    toString() - Method in class org.openscience.cdk.dict.Entry
     
    toString() - Method in class org.openscience.cdk.DynamicFactory.ConstructorKey
    toString() - Method in class org.openscience.cdk.ElectronContainer
     
    toString() - Method in class org.openscience.cdk.Element
     
    toString() - Method in class org.openscience.cdk.fingerprint.ShortestPathWalker
    toString() - Method in class org.openscience.cdk.FragmentAtom
     
    toString() - Method in class org.openscience.cdk.graph.Matching
    toString() - Method in class org.openscience.cdk.graph.rebond.Bspt
     
    toString() - Method in class org.openscience.cdk.graph.rebond.Point
     
    toString() - Method in class org.openscience.cdk.group.DisjointSetForest
     
    toString() - Method in class org.openscience.cdk.group.Partition
    toString() - Method in class org.openscience.cdk.group.Permutation
    toString() - Method in class org.openscience.cdk.group.PermutationGroup
    toString() - Method in interface org.openscience.cdk.interfaces.IChemObject
    Returns a one line description of this IChemObject.
    toString() - Method in class org.openscience.cdk.io.cml.CMLModuleStack
    Returns a String representation of the stack.
    toString() - Method in class org.openscience.cdk.io.random.RandomAccessReader
     
    toString() - Method in class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom
    The toString method
    toString() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
     
    toString() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
    Returns a one line string representation of this query bond.
    toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AliphaticAtom
     
    toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AliphaticSymbolAtom
     
    toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AnyAtom
     
    toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AnyOrderQueryBond
     
    toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AromaticAtom
     
    toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AromaticOrSingleQueryBond
     
    toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AromaticQueryBond
     
    toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AromaticSymbolAtom
     
    toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.FormalChargeAtom
     
    toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.HybridizationNumberAtom
     
    toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ImplicitHCountAtom
     
    toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.MassAtom
     
    toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.NonCHHeavyAtom
     
    toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.OrderQueryBond
     
    toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.PeriodicGroupNumberAtom
     
    toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ReactionRoleQueryAtom
     
    toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.TotalHCountAtom
    Returns a one line description of this IChemObject.
    toString() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolAndChargeQueryAtom
     
    toString() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolChargeIDQueryAtom
     
    toString() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom
     
    toString() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom
    The toString method
    toString() - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
    Returns a string representation of the RGraph.
    toString() - Method in class org.openscience.cdk.isomorphism.mcss.RNode
    Returns a string representation of the RNode.
    toString() - Method in class org.openscience.cdk.Isotope
    A string representation of this isotope.
    toString() - Method in class org.openscience.cdk.iupac.parser.AttachedGroup
    A debug string which represents the contents of the class.
    toString() - Method in class org.openscience.cdk.iupac.parser.Token
    Returns the image.
    toString() - Method in class org.openscience.cdk.LonePair
    Returns a one line string representation of this LonePair.
    toString() - Method in class org.openscience.cdk.math.Complex
    Create a string of the content of this class
    toString() - Method in class org.openscience.cdk.math.IMatrix
    Return a matrix as a string
    toString() - Method in class org.openscience.cdk.math.IVector
    Return a vector as a string
    toString() - Method in class org.openscience.cdk.math.Matrix
    Return a matrix as a String.
    toString() - Method in class org.openscience.cdk.math.Quaternion
     
    toString() - Method in class org.openscience.cdk.math.Vector
    Return a vector as a string
    toString() - Method in class org.openscience.cdk.Monomer
     
    toString() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQuery
    String representation of this query.
    toString() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryAngleBond
    String representation of an angle constraint.
    toString() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryAtom
    String representation of this pharmacophore group.
    toString() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryBond
    String representation of a distance constraint.
    toString() - Method in class org.openscience.cdk.Polymer
     
    toString() - Method in class org.openscience.cdk.protein.data.PDBAtom
    Returns a one line string representation of this Atom.
    toString() - Method in class org.openscience.cdk.protein.data.PDBMonomer
    Returns a one line string representation of this Atom.
    toString() - Method in class org.openscience.cdk.protein.data.PDBPolymer
     
    toString() - Method in class org.openscience.cdk.protein.data.PDBStrand
     
    toString() - Method in class org.openscience.cdk.PseudoAtom
    Returns a one line string representation of this Atom.
    toString() - Method in class org.openscience.cdk.qsar.result.BooleanResult
     
    toString() - Method in class org.openscience.cdk.qsar.result.BooleanResultType
     
    toString() - Method in class org.openscience.cdk.qsar.result.DoubleArrayResult
     
    toString() - Method in class org.openscience.cdk.qsar.result.DoubleArrayResultType
     
    toString() - Method in class org.openscience.cdk.qsar.result.DoubleResult
     
    toString() - Method in class org.openscience.cdk.qsar.result.DoubleResultType
     
    toString() - Method in interface org.openscience.cdk.qsar.result.IDescriptorResult
    String representation of the result.
    toString() - Method in class org.openscience.cdk.qsar.result.IntegerArrayResult
     
    toString() - Method in class org.openscience.cdk.qsar.result.IntegerArrayResultType
     
    toString() - Method in class org.openscience.cdk.qsar.result.IntegerResult
     
    toString() - Method in class org.openscience.cdk.qsar.result.IntegerResultType
     
    toString() - Method in class org.openscience.cdk.Reaction
    Returns a one line string representation of this Atom.
    toString() - Method in class org.openscience.cdk.ReactionSet
     
    toString() - Method in class org.openscience.cdk.renderer.elements.Bounds
    toString() - Method in class org.openscience.cdk.Ring
     
    toString() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycle
    Deprecated.
     
    toString() - Method in class org.openscience.cdk.RingSet
    Returns the String representation of this RingSet.
    toString() - Method in class org.openscience.cdk.sgroup.SgroupBracket
     
    toString() - Method in class org.openscience.cdk.signature.Orbit
    toString() - Method in class org.openscience.cdk.silent.AminoAcid
     
    toString() - Method in class org.openscience.cdk.silent.Atom
    Returns a one line string representation of this Atom.
    toString() - Method in class org.openscience.cdk.silent.AtomContainer
    Returns a one line string representation of this Container.
    toString() - Method in class org.openscience.cdk.silent.AtomContainerSet
    Returns the String representation of this AtomContainerSet.
    toString() - Method in class org.openscience.cdk.silent.AtomType
     
    toString() - Method in class org.openscience.cdk.silent.BioPolymer
     
    toString() - Method in class org.openscience.cdk.silent.Bond
    Returns a one line string representation of this Container.
    toString() - Method in class org.openscience.cdk.silent.ChemFile
    Returns a String representation of this class.
    toString() - Method in class org.openscience.cdk.silent.ChemModel
    Returns a String representation of the contents of this IChemObject.
    toString() - Method in class org.openscience.cdk.silent.ChemSequence
     
    toString() - Method in class org.openscience.cdk.silent.Crystal
    Returns a String representation of this crystal.
    toString() - Method in class org.openscience.cdk.silent.ElectronContainer
     
    toString() - Method in class org.openscience.cdk.silent.Element
     
    toString() - Method in class org.openscience.cdk.silent.FragmentAtom
     
    toString() - Method in class org.openscience.cdk.silent.Isotope
    A string representation of this isotope.
    toString() - Method in class org.openscience.cdk.silent.LonePair
    Returns a one line string representation of this LonePair.
    toString() - Method in class org.openscience.cdk.silent.Monomer
     
    toString() - Method in class org.openscience.cdk.silent.PDBAtom
    Returns a one line string representation of this Atom.
    toString() - Method in class org.openscience.cdk.silent.PDBMonomer
    Returns a one line string representation of this Atom.
    toString() - Method in class org.openscience.cdk.silent.PDBPolymer
     
    toString() - Method in class org.openscience.cdk.silent.Polymer
     
    toString() - Method in class org.openscience.cdk.silent.PseudoAtom
    Returns a one line string representation of this Atom.
    toString() - Method in class org.openscience.cdk.silent.Reaction
    Returns a one line string representation of this Atom.
    toString() - Method in class org.openscience.cdk.silent.ReactionSet
     
    toString() - Method in class org.openscience.cdk.silent.Ring
     
    toString() - Method in class org.openscience.cdk.silent.RingSet
    Returns the String representation of this RingSet.
    toString() - Method in class org.openscience.cdk.silent.SingleElectron
    Returns a one line string representation of this SingleElectron.
    toString() - Method in class org.openscience.cdk.silent.Strand
     
    toString() - Method in class org.openscience.cdk.SingleElectron
    Returns a one line string representation of this SingleElectron.
    toString() - Method in class org.openscience.cdk.smiles.InvPair
    String representation.
    toString() - Method in class org.openscience.cdk.smiles.smarts.parser.Token
    Returns the image.
    toString() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
    Deprecated.
    Returns a string representation of the CDKRGraph.
    toString() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode
    Deprecated.
    Returns a string representation of the RNode
    toString(IAtomContainer) - Method in class org.openscience.cdk.smsd.labelling.AtomContainerPrinter
    Deprecated.
     
    toString() - Method in class org.openscience.cdk.stereo.TetrahedralChirality
    Returns a String representation of this chiral element.
    toString() - Method in class org.openscience.cdk.Strand
     
    toString() - Method in class org.openscience.cdk.tools.diff.tree.AtomTypeHybridizationDifference
    Returns a String representation for this IDifference.
    toString() - Method in class org.openscience.cdk.tools.diff.tree.BondOrderDifference
    Returns a String representation for this IDifference.
    toString() - Method in class org.openscience.cdk.tools.diff.tree.BooleanArrayDifference
    Returns a String representation for this IDifference.
    toString() - Method in class org.openscience.cdk.tools.diff.tree.BooleanDifference
    Returns a String representation for this IDifference.
    toString() - Method in class org.openscience.cdk.tools.diff.tree.ChemObjectDifference
    Returns a String representation for this IDifference.
    toString() - Method in class org.openscience.cdk.tools.diff.tree.DoubleDifference
    Returns a String representation for this IDifference.
    toString() - Method in class org.openscience.cdk.tools.diff.tree.IntegerDifference
    Returns a String representation for this IDifference.
    toString() - Method in class org.openscience.cdk.tools.diff.tree.Point2dDifference
    Returns a String representation for this IDifference.
    toString() - Method in class org.openscience.cdk.tools.diff.tree.Point3dDifference
    Returns a String representation for this IDifference.
    toString() - Method in class org.openscience.cdk.tools.diff.tree.StringDifference
    Returns a String representation for this IDifference.
    toString() - Method in class org.openscience.cdk.tools.FormatStringBuffer
    Get the result of the formatting.
    toString() - Method in class org.openscience.cdk.tools.GridGenerator
     
    toSubstructures() - Method in class org.openscience.cdk.isomorphism.Mappings
    Obtain the mapped substructures (atoms/bonds) of the target compound.
    toSvgStr() - Method in class org.openscience.cdk.depict.Depiction
    Render the image to an SVG image.
    TOTAL_CONNECTIONS - Static variable in class org.openscience.cdk.CDKConstants
     
    TOTAL_H_COUNT - Static variable in class org.openscience.cdk.CDKConstants
     
    TotalConnectionAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
    This matches an atom using total number of connections - referred to in SMARTS as the connectivity.
    TotalConnectionAtom(int, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.TotalConnectionAtom
    Creates a new instance.
    TotalConnectivity() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
     
    TotalHCount() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
     
    TotalHCountAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
    SMARTS query atom for matching the total hydrogen count.
    TotalHCountAtom(int, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.TotalHCountAtom
     
    TotalRingConnectionAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
    This matcher checks the number of ring connections of the checked Atom with other Atom's.
    TotalRingConnectionAtom(int, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.TotalRingConnectionAtom
    Create a matcher for the number of rings an atom belongs to.
    TotalValencyAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
    This matcher checks the valence of the Atom.
    TotalValencyAtom(int, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.TotalValencyAtom
    Match the valence of atom.
    TPSADescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
    Calculation of topological polar surface area based on fragment contributions (TPSA) [Ertl, P. and Rohde, B. and Selzer, P., Fast Calculation of Molecular Polar Surface Area as a Sum of Fragment-Based Contributions and Its Application to the Prediction of Drug Transport Properties, J. Med. Chem., 2000, 43:3714-3717, doi:10.1021/jm000942e].
    TPSADescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor
    Constructor for the TPSADescriptor object.
    trace() - Method in class org.openscience.cdk.graph.invariant.GIMatrix
    Returns the trace of this matrix, that is the sum of the elements of its diagonal.
    training - Variable in class org.openscience.cdk.fingerprint.model.Bayesian
     
    trainingActives - Variable in class org.openscience.cdk.fingerprint.model.Bayesian
     
    trainingSize - Variable in class org.openscience.cdk.fingerprint.model.Bayesian
     
    transform - Variable in class org.openscience.cdk.renderer.AbstractRenderer
    Converts between model coordinates and screen coordinates.
    transform - Variable in class org.openscience.cdk.renderer.visitor.AbstractAWTDrawVisitor
    This is initially null, and must be set in the setTransform method!
    transformPoint(double, double) - Method in class org.openscience.cdk.renderer.visitor.AbstractAWTDrawVisitor
    Transforms a point according to the current affine transformation, converting a world coordinate into a screen coordinate.
    transformPoint(double[]) - Method in class org.openscience.cdk.renderer.visitor.AbstractAWTDrawVisitor
     
    translate2D(IAtomContainer, double, double) - Static method in class org.openscience.cdk.geometry.GeometryTools
    Translates the given molecule by the given Vector.
    translate2D(IAtomContainer, Vector2d) - Static method in class org.openscience.cdk.geometry.GeometryTools
    Translates a molecule from the origin to a new point denoted by a vector.
    translate2D(IAtomContainer, double, double) - Static method in class org.openscience.cdk.geometry.GeometryUtil
    Translates the given molecule by the given Vector.
    translate2D(IAtomContainer, Vector2d) - Static method in class org.openscience.cdk.geometry.GeometryUtil
    Translates a molecule from the origin to a new point denoted by a vector.
    translate2DCenterTo(IAtomContainer, Point2d) - Static method in class org.openscience.cdk.geometry.GeometryTools
    Translates the geometric 2DCenter of the given AtomContainer container to the specified Point2d p.
    translate2DCenterTo(IAtomContainer, Point2d) - Static method in class org.openscience.cdk.geometry.GeometryUtil
    Translates the geometric 2DCenter of the given AtomContainer container to the specified Point2d p.
    translate2DCentreOfMassTo(IAtomContainer, Point2d) - Static method in class org.openscience.cdk.geometry.GeometryTools
    Translates a molecule from the origin to a new point denoted by a vector.
    translate2DCentreOfMassTo(IAtomContainer, Point2d) - Static method in class org.openscience.cdk.geometry.GeometryUtil
    Translates a molecule from the origin to a new point denoted by a vector.
    translateAllPositive(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
    Adds an automatically calculated offset to the coordinates of all atoms such that all coordinates are positive and the smallest x or y coordinate is exactly zero.
    translateAllPositive(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
    Adds an automatically calculated offset to the coordinates of all atoms such that all coordinates are positive and the smallest x or y coordinate is exactly zero.
    transpose() - Method in class org.openscience.cdk.graph.invariant.GIMatrix
    Returns the transpose of this matrix.
    transpose() - Method in class org.openscience.cdk.math.IMatrix
    Transpose a matrix
    transpose(IMatrix) - Method in class org.openscience.cdk.math.IMatrix
    Transpose a matrix
    transpose() - Method in class org.openscience.cdk.math.Matrix
    Transposes a matrix.
    transversal(PermutationGroup) - Method in class org.openscience.cdk.group.PermutationGroup
    Generate a transversal of a subgroup in this group.
    traverse(IAtomContainer, IAtom, List<IBond>) - Static method in class org.openscience.cdk.fragment.FragmentUtils
     
    travIndex - Variable in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
     
    TRI - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    Triangle - Class in org.openscience.cdk.geometry.surface
    Representation of a triangle in 3D.
    Triangle(Point3d, Point3d, Point3d) - Constructor for class org.openscience.cdk.geometry.surface.Triangle
     
    TRIPLEBOND - Static variable in class org.openscience.cdk.libio.jena.CDK
     
    tripletShort() - Static method in class org.openscience.cdk.graph.Cycles
    Create a cycle finder which will compute the triplet short cycles of a molecule.
    tripletShort(IAtomContainer) - Static method in class org.openscience.cdk.graph.Cycles
    Find the triplet short cycles of a molecule.
    TripletShortCycles - Class in org.openscience.cdk.graph
    Compute the shortest cycles through each vertex triple.
    TripletShortCycles(MinimumCycleBasis, boolean) - Constructor for class org.openscience.cdk.graph.TripletShortCycles
    Compute the cycles of the extended smallest set of smallest rings (ESSSR) for an existing minimum cycle basis.
    TUNGSTEN - Static variable in enum org.openscience.cdk.config.Elements
     
    TUNGSTEN - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    TurboMoleFormat - Class in org.openscience.cdk.io.formats
    See here.
    TurboMoleFormat() - Constructor for class org.openscience.cdk.io.formats.TurboMoleFormat
     
    TURN - Static variable in class org.openscience.cdk.protein.data.PDBStructure
     
    TURN - Static variable in class org.openscience.cdk.silent.PDBStructure
     
    twoOrThreeAttachLocations() - Method in class org.openscience.cdk.iupac.parser.NomParser
    Deprecated.
    Two or three attach locations specidied, handle the second and if needed, the third one here.
    TXTBasedAtomTypeConfigurator - Class in org.openscience.cdk.config
    AtomType list configurator that uses the AtomTypes originally defined in Jmol v5.
    TXTBasedAtomTypeConfigurator() - Constructor for class org.openscience.cdk.config.TXTBasedAtomTypeConfigurator
     
    type(int) - Method in class org.openscience.cdk.DynamicFactory.ConstructorKey
    Access the type of class at the given parameter index.
    type - Variable in class org.openscience.cdk.isomorphism.matchers.CTFileQueryBond
    The type of this bond.
    type - Variable in class org.openscience.cdk.renderer.elements.path.PathElement
    the type of the path element.
    type() - Method in class org.openscience.cdk.renderer.elements.path.PathElement
    Get the type of the path element.
    Type - Enum in org.openscience.cdk.renderer.elements.path
    The type of the path elements.
    type - Variable in class org.openscience.cdk.renderer.elements.WedgeLineElement
    The type of the bond (dashed, wedged, not defined).
    type() - Method in enum org.openscience.cdk.smsd.interfaces.Algorithm
    Deprecated.
    Returns type of algorithm.

    U

    U - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    Ullmann - Class in org.openscience.cdk.isomorphism
    A structure pattern which utilises the Ullmann algorithm [Ullmann J R, An Algorithm for Subgraph Isomorphism, Journal of the Association for Computing Machinery, 1976, 23:?-?, doi:10.1145/321921.321925].
    unchorded(CycleFinder) - Static method in class org.openscience.cdk.graph.Cycles
    Derive a new cycle finder that only provides cycles without a chord.
    UNDEC - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    undoableEditHappened(UndoableEditEvent) - Method in class org.openscience.cdk.controller.UndoAdapter
     
    UndoAdapter - Class in org.openscience.cdk.controller
    An undo adapter for updating the state of the undo components according to the new state of the undo history list.
    UndoAdapter(UndoManager) - Constructor for class org.openscience.cdk.controller.UndoAdapter
     
    UniChemXYZFormat - Class in org.openscience.cdk.io.formats
     
    UniChemXYZFormat() - Constructor for class org.openscience.cdk.io.formats.UniChemXYZFormat
     
    UniColor - Class in org.openscience.cdk.renderer.color
    Defines an atom color that draws as a single uniform color.
    UniColor(Color) - Constructor for class org.openscience.cdk.renderer.color.UniColor
    Create a uniform atom colorer.
    Unique - Static variable in class org.openscience.cdk.smiles.SmiFlavor
    Output canonical SMILES without stereochemistry, atomic masses.
    unique() - Static method in class org.openscience.cdk.smiles.SmilesGenerator
    Create a unique SMILES generator.
    uniqueAtoms() - Method in class org.openscience.cdk.isomorphism.Mappings
    Filter the mappings for those which cover a unique set of atoms in the target.
    uniqueBonds() - Method in class org.openscience.cdk.isomorphism.Mappings
    Filter the mappings for those which cover a unique set of bonds in the target.
    unit(int) - Static method in class org.openscience.cdk.group.Partition
    Create a unit partition - in other words, the coarsest possible partition where all the elements are in one cell.
    unitcellparams - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
     
    UniversalIsomorphismTester - Class in org.openscience.cdk.isomorphism
    This class implements a multipurpose structure comparison tool.
    UniversalIsomorphismTester() - Constructor for class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
     
    UniversalSmiles - Static variable in class org.openscience.cdk.smiles.SmiFlavor
    Output canonical SMILES with stereochemistry and atomic masses, This output uses the InChI labelling algorithm to generate a 'Universal SMILES' [O’Boyle, Noel, Towards a Universal SMILES representation - A standard method to generate canonical SMILES based on the InChI, Journal of Cheminformatics, 2012, 4:?-?, doi:10.1186/1758-2946-4-22].
    unmark(IChemObject) - Static method in class org.openscience.cdk.validate.ProblemMarker
     
    unmarkWithError(IChemObject) - Static method in class org.openscience.cdk.validate.ProblemMarker
     
    unmarkWithWarning(IChemObject) - Static method in class org.openscience.cdk.validate.ProblemMarker
     
    unmarshal(Reader) - Static method in class org.openscience.cdk.dict.Dictionary
     
    unmarshal(Reader) - Static method in class org.openscience.cdk.dict.OWLFile
     
    unmarshal(Element, String) - Static method in class org.openscience.cdk.dict.OWLFile
     
    unmarshal(Reader) - Static method in class org.openscience.cdk.dict.OWLReact
     
    unmarshal(Element, String) - Static method in class org.openscience.cdk.dict.OWLReact
     
    unmatch(int) - Method in class org.openscience.cdk.graph.Matching
    Remove a matching for the specified vertex.
    unmatched(int) - Method in class org.openscience.cdk.graph.Matching
    Determine if a vertex is not matched.
    unregisterAtomListeners(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
    A method to remove AtomListeners.
    unregisterElectronContainerListeners(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
    A method to remove ElectronContainerListeners.
    unsaturate(IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker
    Resets the bond orders of all atoms to 1.0.
    unsaturateBonds(IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker
    Resets the bond order of the Bond to 1.0.
    unsaturateByDecreasingBondOrder(IBond) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
     
    UNSET - Static variable in class org.openscience.cdk.CDKConstants
     
    unspecified() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.StereoBond
     
    UnsupportedChemObjectException - Exception in org.openscience.cdk.exception
     
    UnsupportedChemObjectException(String) - Constructor for exception org.openscience.cdk.exception.UnsupportedChemObjectException
     
    UNUNBIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    UNUNHEXIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    UNUNPENTIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    UNUNQUADIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    UNUNTRIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    UP_OR_UNSPECIFIED_S_BOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    UP_S_BOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    UpdateLineColumn(char) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
     
    UpdateLineColumn(char) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
     
    updateView() - Method in interface org.openscience.cdk.controller.IViewEventRelay
     
    updateView() - Method in class org.openscience.cdk.controller.SwingEventRelay
     
    updateView() - Method in class org.openscience.cdk.controller.SwingMouseEventRelay
     
    URANIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    URANIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    URI - Static variable in class org.openscience.cdk.libio.jena.CDK
     
    UseAromaticSymbols - Static variable in class org.openscience.cdk.smiles.SmiFlavor
    Writes aromatic atoms as lower case letters.
    useEssentialRings() - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool
    Indicates that ring properties should use the Essential Rings (default).
    useRelevantRings() - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool
    Indicates that ring properties should use the Relevant Rings.
    useSmallestSetOfSmallestRings() - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool
    Indicates that ring properties should use the Smallest Set of Smallest Rings.
    using2DCoordinates(IAtomContainer) - Static method in class org.openscience.cdk.stereo.StereoElementFactory
    Create a stereo element factory for creating stereo elements using 2D coordinates and depiction labels (up/down, wedge/hatch).
    using3DCoordinates(IAtomContainer) - Static method in class org.openscience.cdk.stereo.StereoElementFactory
    Create a stereo element factory for creating stereo elements using 3D coordinates and depiction labels (up/down, wedge/hatch).
    usingThreshold(AllRingsFinder.Threshold) - Static method in class org.openscience.cdk.ringsearch.AllRingsFinder
    Create an AllRingsFinder instance using the given threshold.

    V

    v - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    V - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    VABCDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
    Volume descriptor using the method implemented in the VABCVolume class.
    VABCDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor
     
    VABCVolume - Class in org.openscience.cdk.geometry.volume
    Calculates the Van der Waals volume using the method proposed in [Zhao, Yuan H. and Abraham, Michael H. and Zissimos, Andreas M., Fast Calculation of van der Waals Volume as a Sum of Atomic and Bond Contributions and Its Application to Drug Compounds, The Journal of Organic Chemistry, 2003, 68:7368-7373, doi:10.1021/jo034808o].
    VABCVolume() - Constructor for class org.openscience.cdk.geometry.volume.VABCVolume
     
    VAdjMaDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
    Vertex adjacency information (magnitude): 1 + log2 m where m is the number of heavy-heavy bonds.
    VAdjMaDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor
    Constructor for the VAdjMaDescriptor object
    Valence() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
     
    validate(IMolecularFormula) - Method in class org.openscience.cdk.formula.rules.ChargeRule
    Validate the charge of this IMolecularFormula.
    validate(IMolecularFormula) - Method in class org.openscience.cdk.formula.rules.ElementRule
    Validate the occurrence of this IMolecularFormula.
    validate(IMolecularFormula) - Method in interface org.openscience.cdk.formula.rules.IRule
    Analyze the validity for the given IMolecularFormula.
    validate(IMolecularFormula) - Method in class org.openscience.cdk.formula.rules.IsotopePatternRule
    Validate the isotope pattern of this IMolecularFormula.
    validate(IMolecularFormula) - Method in class org.openscience.cdk.formula.rules.MMElementRule
    Validate the occurrence of this IMolecularFormula.
    validate(IMolecularFormula) - Method in class org.openscience.cdk.formula.rules.NitrogenRule
    Validate the nitrogen rule of this IMolecularFormula.
    validate(IMolecularFormula) - Method in class org.openscience.cdk.formula.rules.RDBERule
    Validate the RDBRule of this IMolecularFormula.
    validate(IMolecularFormula, double) - Method in class org.openscience.cdk.formula.rules.RDBERule
    Validate the ion state.
    validate(IMolecularFormula) - Method in class org.openscience.cdk.formula.rules.ToleranceRangeRule
    Validate the Tolerance Range of this IMolecularFormula.
    validateAtom(IAtom) - Method in class org.openscience.cdk.validate.AbstractValidator
     
    validateAtom(IAtom) - Method in class org.openscience.cdk.validate.BasicValidator
     
    validateAtom(IAtom) - Method in interface org.openscience.cdk.validate.IValidator
     
    validateAtom(IAtom) - Method in class org.openscience.cdk.validate.ValidatorEngine
     
    validateAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.validate.AbstractValidator
     
    validateAtomContainer(IAtomContainer) - Method in interface org.openscience.cdk.validate.IValidator
     
    validateAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.validate.ValidatorEngine
     
    validateAtomType(IAtomType) - Method in class org.openscience.cdk.validate.AbstractValidator
     
    validateAtomType(IAtomType) - Method in interface org.openscience.cdk.validate.IValidator
     
    validateAtomType(IAtomType) - Method in class org.openscience.cdk.validate.ValidatorEngine
     
    validateBond(IBond) - Method in class org.openscience.cdk.validate.AbstractValidator
     
    validateBond(IBond) - Method in class org.openscience.cdk.validate.BasicValidator
     
    validateBond(IBond) - Method in class org.openscience.cdk.validate.Geometry3DValidator
     
    validateBond(IBond) - Method in interface org.openscience.cdk.validate.IValidator
     
    validateBond(IBond) - Method in class org.openscience.cdk.validate.ValidatorEngine
     
    validateChemFile(IChemFile) - Method in class org.openscience.cdk.validate.AbstractValidator
     
    validateChemFile(IChemFile) - Method in class org.openscience.cdk.validate.CDKValidator
     
    validateChemFile(IChemFile) - Method in interface org.openscience.cdk.validate.IValidator
     
    validateChemFile(IChemFile) - Method in class org.openscience.cdk.validate.ValidatorEngine
     
    validateChemModel(IChemModel) - Method in class org.openscience.cdk.validate.AbstractValidator
     
    validateChemModel(IChemModel) - Method in interface org.openscience.cdk.validate.IValidator
     
    validateChemModel(IChemModel) - Method in class org.openscience.cdk.validate.ValidatorEngine
     
    validateChemObject(IChemObject) - Method in class org.openscience.cdk.validate.AbstractValidator
     
    validateChemObject(IChemObject) - Method in class org.openscience.cdk.validate.DictionaryValidator
     
    validateChemObject(IChemObject) - Method in interface org.openscience.cdk.validate.IValidator
     
    validateChemObject(IChemObject) - Method in class org.openscience.cdk.validate.ValidatorEngine
     
    validateChemSequence(IChemSequence) - Method in class org.openscience.cdk.validate.AbstractValidator
     
    validateChemSequence(IChemSequence) - Method in class org.openscience.cdk.validate.CDKValidator
     
    validateChemSequence(IChemSequence) - Method in interface org.openscience.cdk.validate.IValidator
     
    validateChemSequence(IChemSequence) - Method in class org.openscience.cdk.validate.ValidatorEngine
     
    validateCrystal(ICrystal) - Method in class org.openscience.cdk.validate.AbstractValidator
     
    validateCrystal(ICrystal) - Method in interface org.openscience.cdk.validate.IValidator
     
    validateCrystal(ICrystal) - Method in class org.openscience.cdk.validate.ValidatorEngine
     
    validateElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.validate.AbstractValidator
     
    validateElectronContainer(IElectronContainer) - Method in interface org.openscience.cdk.validate.IValidator
     
    validateElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.validate.ValidatorEngine
     
    validateElement(IElement) - Method in class org.openscience.cdk.validate.AbstractValidator
     
    validateElement(IElement) - Method in interface org.openscience.cdk.validate.IValidator
     
    validateElement(IElement) - Method in class org.openscience.cdk.validate.ValidatorEngine
     
    validateFiveFold() - Method in class org.openscience.cdk.fingerprint.model.Bayesian
    Produces a ROC validation set by partitioning the inputs into 5 groups, and performing five separate 80% in/20% out model simulations.
    validateIsotope(IIsotope) - Method in class org.openscience.cdk.validate.AbstractValidator
     
    validateIsotope(IIsotope) - Method in class org.openscience.cdk.validate.BasicValidator
     
    validateIsotope(IIsotope) - Method in interface org.openscience.cdk.validate.IValidator
     
    validateIsotope(IIsotope) - Method in class org.openscience.cdk.validate.ValidatorEngine
     
    validateIsotopeExistence(IIsotope) - Method in class org.openscience.cdk.validate.BasicValidator
     
    validateLeaveOneOut() - Method in class org.openscience.cdk.fingerprint.model.Bayesian
    Produces an ROC validation set, using the inputs provided prior to the model building, using leave-one-out.
    validateMolecule(IAtomContainer) - Method in class org.openscience.cdk.validate.AbstractValidator
     
    validateMolecule(IAtomContainer) - Method in class org.openscience.cdk.validate.BasicValidator
     
    validateMolecule(IAtomContainer) - Method in interface org.openscience.cdk.validate.IValidator
     
    validateMolecule(IAtomContainer) - Method in class org.openscience.cdk.validate.ValidatorEngine
     
    validateMoleculeSet(IAtomContainerSet) - Method in class org.openscience.cdk.validate.AbstractValidator
     
    validateMoleculeSet(IAtomContainerSet) - Method in interface org.openscience.cdk.validate.IValidator
     
    validateMoleculeSet(IAtomContainerSet) - Method in class org.openscience.cdk.validate.ValidatorEngine
     
    validateReaction(IReaction) - Method in class org.openscience.cdk.validate.AbstractValidator
     
    validateReaction(IReaction) - Method in class org.openscience.cdk.validate.BasicValidator
     
    validateReaction(IReaction) - Method in interface org.openscience.cdk.validate.IValidator
     
    validateReaction(IReaction) - Method in class org.openscience.cdk.validate.ValidatorEngine
     
    validateReactionSet(IReactionSet) - Method in class org.openscience.cdk.validate.AbstractValidator
     
    validateReactionSet(IReactionSet) - Method in interface org.openscience.cdk.validate.IValidator
     
    validateReactionSet(IReactionSet) - Method in class org.openscience.cdk.validate.ValidatorEngine
     
    validateThreeFold() - Method in class org.openscience.cdk.fingerprint.model.Bayesian
    Produces a ROC validation set by partitioning the inputs into 3 groups, and performing three separate 66% in/33% out model simulations.
    ValidationReport - Class in org.openscience.cdk.validate
    A report on validation of chemical semantics.
    ValidationReport() - Constructor for class org.openscience.cdk.validate.ValidationReport
    Constructs a new empty ValidationReport.
    ValidationTest - Class in org.openscience.cdk.validate
    Error found during sematical validation of a IChemObject.
    ValidationTest(IChemObject, String) - Constructor for class org.openscience.cdk.validate.ValidationTest
     
    ValidationTest(IChemObject, String, String) - Constructor for class org.openscience.cdk.validate.ValidationTest
     
    ValidatorEngine - Class in org.openscience.cdk.validate
    Engine that performs the validation by traversing the IChemObject hierarchy.
    ValidatorEngine() - Constructor for class org.openscience.cdk.validate.ValidatorEngine
     
    valueOf(String) - Static method in enum org.openscience.cdk.config.Elements
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.formula.rules.MMElementRule.Database
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.formula.rules.MMElementRule.RangeMass
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.geometry.cip.CIPTool.CIP_CHIRALITY
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.geometry.GeometryTools.CoordinateCoverage
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.geometry.GeometryUtil.CoordinateCoverage
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.hash.BasicAtomEncoder
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.interfaces.IAtomType.Hybridization
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.interfaces.IBond.Order
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.interfaces.IBond.Stereo
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.interfaces.IDoubleBondStereochemistry.Conformation
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.interfaces.IReaction.Direction
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.io.IChemObjectReader.Mode
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.io.MDLV2000Writer.SPIN_MULTIPLICITY
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.io.setting.IOSetting.Importance
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.isomorphism.matchers.CTFileQueryBond.Type
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.isomorphism.matchers.smarts.StereoBond.Direction
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.ReactionRole
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.renderer.elements.LineElement.LineType
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.renderer.elements.path.Type
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.renderer.elements.TextGroupElement.Position
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.renderer.elements.WedgeLineElement.Direction
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.renderer.elements.WedgeLineElement.TYPE
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.renderer.font.IFontManager.FontStyle
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.renderer.generators.BasicAtomGenerator.Shape
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.renderer.generators.standard.StandardGenerator.HighlightStyle
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.ringsearch.AllRingsFinder.Threshold
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.sgroup.SgroupKey
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.sgroup.SgroupType
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.smsd.interfaces.Algorithm
    Deprecated.
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.stereo.Projection
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.stereo.Stereocenters.Stereocenter
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.stereo.Stereocenters.Type
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.stereo.StereoTool.SquarePlanarShape
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.stereo.StereoTool.StereoClass
    Returns the enum constant of this type with the specified name.
    valueOf(String) - Static method in enum org.openscience.cdk.stereo.StereoTool.TetrahedralSign
    Returns the enum constant of this type with the specified name.
    values() - Static method in enum org.openscience.cdk.config.Elements
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.formula.rules.MMElementRule.Database
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.formula.rules.MMElementRule.RangeMass
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.geometry.cip.CIPTool.CIP_CHIRALITY
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.geometry.GeometryTools.CoordinateCoverage
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.geometry.GeometryUtil.CoordinateCoverage
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.hash.BasicAtomEncoder
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.interfaces.IAtomType.Hybridization
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.interfaces.IBond.Order
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.interfaces.IBond.Stereo
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.interfaces.IDoubleBondStereochemistry.Conformation
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.interfaces.IReaction.Direction
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.io.IChemObjectReader.Mode
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.io.MDLV2000Writer.SPIN_MULTIPLICITY
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.io.setting.IOSetting.Importance
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.isomorphism.matchers.CTFileQueryBond.Type
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.isomorphism.matchers.smarts.StereoBond.Direction
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.ReactionRole
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.renderer.elements.LineElement.LineType
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.renderer.elements.path.Type
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.renderer.elements.TextGroupElement.Position
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.renderer.elements.WedgeLineElement.Direction
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.renderer.elements.WedgeLineElement.TYPE
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.renderer.font.IFontManager.FontStyle
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.renderer.generators.BasicAtomGenerator.Shape
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.renderer.generators.standard.StandardGenerator.HighlightStyle
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.ringsearch.AllRingsFinder.Threshold
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.sgroup.SgroupKey
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.sgroup.SgroupType
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.smsd.interfaces.Algorithm
    Deprecated.
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.stereo.Projection
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.stereo.Stereocenters.Stereocenter
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.stereo.Stereocenters.Type
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.stereo.StereoTool.SquarePlanarShape
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.stereo.StereoTool.StereoClass
    Returns an array containing the constants of this enum type, in the order they are declared.
    values() - Static method in enum org.openscience.cdk.stereo.StereoTool.TetrahedralSign
    Returns an array containing the constants of this enum type, in the order they are declared.
    VANADIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    VANADIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    VASPFormat - Class in org.openscience.cdk.io.formats
     
    VASPFormat() - Constructor for class org.openscience.cdk.io.formats.VASPFormat
     
    VASPReader - Class in org.openscience.cdk.io
    Read output files generated with the VASP software.
    VASPReader(Reader) - Constructor for class org.openscience.cdk.io.VASPReader
    Creates a new VASPReader instance.
    VASPReader(InputStream) - Constructor for class org.openscience.cdk.io.VASPReader
     
    VASPReader() - Constructor for class org.openscience.cdk.io.VASPReader
     
    vdwRadius() - Method in enum org.openscience.cdk.config.Elements
    The van der Waals radius, rw, of an atom is the radius of an imaginary hard sphere which can be used to model the atom.
    VdWRadiusDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
    This class return the VdW radius of a given atom.
    VdWRadiusDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor
    Constructor for the VdWRadiusDescriptor object.
    Vector - Class in org.openscience.cdk.math
    This class handles vectors.
    Vector(int) - Constructor for class org.openscience.cdk.math.Vector
    Constructs a Vector with "size" elements
    Vector(double[]) - Constructor for class org.openscience.cdk.math.Vector
    Constructs a vector with the content of a array
    Vector(Tuple3d) - Constructor for class org.openscience.cdk.math.Vector
    Constructs a Vector with a Tuple3d, Vector3d or Point3d
    vector - Variable in class org.openscience.cdk.math.Vector
    The content of this vector
    VentoFoggia - Class in org.openscience.cdk.isomorphism
    A structure pattern which utilises the Vento-Foggia (VF) algorithm [Cordella Luigi P and Foggia Pasquale and Carlo Sansone and Vento Mario , A (Sub)Graph Isomorphism Algorithm for Matching Large Graphs, IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE, 2004, 26:10].
    vertexAdded(GraphVertexChangeEvent) - Method in class org.openscience.cdk.graph.BiconnectivityInspector
     
    vertexColor() - Method in interface org.openscience.cdk.ringsearch.CyclicVertexSearch
    Build an indexed lookup of vertex color.
    vertexList() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycle
    Deprecated.
    Returns a list of the vertices contained in this cycle.
    vertexRemoved(GraphVertexChangeEvent) - Method in class org.openscience.cdk.graph.BiconnectivityInspector
     
    vertexShort() - Static method in class org.openscience.cdk.graph.Cycles
    Create a cycle finder which will compute the shortest cycles of each vertex in a molecule.
    vertexShort(IAtomContainer) - Static method in class org.openscience.cdk.graph.Cycles
    Find the vertex short cycles of a molecule.
    VFAtomMatcher - Interface in org.openscience.cdk.smsd.algorithm.matchers
    Deprecated.
    This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    VFBondMatcher - Interface in org.openscience.cdk.smsd.algorithm.matchers
    Deprecated.
    This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    VFlibMCSHandler - Class in org.openscience.cdk.smsd.algorithm.vflib
    Deprecated.
    SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    VFlibMCSHandler() - Constructor for class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler
    Deprecated.
    Constructor for an extended VF Algorithm for the MCS search
    VFlibSubStructureHandler - Class in org.openscience.cdk.smsd.algorithm.vflib
    Deprecated.
    SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    VFlibSubStructureHandler() - Constructor for class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler
    Deprecated.
    Constructor for an extended VF Algorithm for the MCS search
    VFlibTurboHandler - Class in org.openscience.cdk.smsd.algorithm.vflib
    Deprecated.
    SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    VFlibTurboHandler() - Constructor for class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler
    Deprecated.
    Constructor for an extended VF Algorithm for the MCS search
    VFMapper - Class in org.openscience.cdk.smsd.algorithm.vflib.map
    Deprecated.
    SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    VFMapper(IQuery) - Constructor for class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper
    Deprecated.
     
    VFMapper(IAtomContainer, boolean) - Constructor for class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper
    Deprecated.
     
    VFMCSMapper - Class in org.openscience.cdk.smsd.algorithm.vflib.map
    Deprecated.
    SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    VFMCSMapper(IQuery) - Constructor for class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper
    Deprecated.
     
    VFMCSMapper(IAtomContainer, boolean) - Constructor for class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper
    Deprecated.
     
    VFQueryBuilder - Class in org.openscience.cdk.smsd.algorithm.vflib.builder
    Deprecated.
    SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    VFQueryBuilder() - Constructor for class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder
    Deprecated.
    Constructor for VF Query Builder
    VFState - Class in org.openscience.cdk.smsd.algorithm.vflib.map
    Deprecated.
    SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    VFState(IQuery, TargetProperties) - Constructor for class org.openscience.cdk.smsd.algorithm.vflib.map.VFState
    Deprecated.
    Initialise the VFState with query and target
    Vibration - Class in org.openscience.cdk
    A molecular vibration composed of a set of atom vectors.
    Vibration(String) - Constructor for class org.openscience.cdk.Vibration
    Create a vibration identified by the label.
    VicinitySampler - Class in org.openscience.cdk.structgen
    The VicinitySampler is a generator of constitutional isomers.
    VicinitySampler() - Constructor for class org.openscience.cdk.structgen.VicinitySampler
     
    ViewmolFormat - Class in org.openscience.cdk.io.formats
    See here.
    ViewmolFormat() - Constructor for class org.openscience.cdk.io.formats.ViewmolFormat
     
    visible(IAtom, List<IBond>, RendererModel) - Method in class org.openscience.cdk.renderer.generators.standard.SelectionVisibility
    Determine if an atom with the specified bonds is visible.
    visible(IAtom, List<IBond>, RendererModel) - Method in class org.openscience.cdk.renderer.SymbolVisibility
    Determine if an atom with the specified bonds is visible.
    visit(IRenderingElement) - Method in interface org.openscience.cdk.renderer.elements.IRenderingVisitor
    Translates a IRenderingElement into a widget toolkit specific rendering element.
    visit(IRenderingElement) - Method in class org.openscience.cdk.renderer.visitor.AWTDrawVisitor
    Translates a IRenderingElement into a widget toolkit specific rendering element.
    visit(ASTRingIdentifier, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(SimpleNode, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTStart, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTReaction, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTGroup, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTSmarts, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTLowAndBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTOrBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTExplicitHighAndBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTImplicitHighAndBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTNotBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTSimpleBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTExplicitAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTLowAndExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTOrExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTExplicitHighAndExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTImplicitHighAndExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTNotExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTRecursiveSmartsExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTTotalHCount, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTImplicitHCount, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTExplicitConnectivity, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTAtomicNumber, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTHybrdizationNumber, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTCharge, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTRingConnectivity, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTPeriodicGroupNumber, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTTotalConnectivity, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTValence, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTRingMembership, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTSmallestRingSize, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTAliphatic, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTNonCHHeavyAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTAromatic, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTAnyAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTAtomicMass, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTChirality, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTElement, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
     
    visit(ASTRingIdentifier, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(SimpleNode, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTStart, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTReaction, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTGroup, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTSmarts, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTNotBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTSimpleBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTImplicitHighAndBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTLowAndBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTOrBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTExplicitHighAndBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTElement, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTRecursiveSmartsExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTPrimitiveAtomExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTTotalHCount, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTImplicitHCount, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTExplicitConnectivity, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTAtomicNumber, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTHybrdizationNumber, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTCharge, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTRingConnectivity, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTPeriodicGroupNumber, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTTotalConnectivity, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTValence, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTRingMembership, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTSmallestRingSize, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTAliphatic, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTNonCHHeavyAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTAromatic, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTAnyAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTAtomicMass, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTChirality, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTLowAndExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTOrExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTNotExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTExplicitHighAndExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTImplicitHighAndExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(ASTExplicitAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
     
    visit(SimpleNode, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTStart, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTReaction, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTGroup, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTSmarts, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTAtom, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTLowAndBond, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTOrBond, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTExplicitHighAndBond, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTImplicitHighAndBond, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTNotBond, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTSimpleBond, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTExplicitAtom, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTLowAndExpression, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTOrExpression, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTExplicitHighAndExpression, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTImplicitHighAndExpression, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTNotExpression, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTRecursiveSmartsExpression, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTTotalHCount, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTImplicitHCount, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTExplicitConnectivity, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTAtomicNumber, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTHybrdizationNumber, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTCharge, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTRingConnectivity, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTPeriodicGroupNumber, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTTotalConnectivity, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTValence, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTRingMembership, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTSmallestRingSize, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTAliphatic, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTNonCHHeavyAtom, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTAromatic, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTAnyAtom, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTAtomicMass, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTRingIdentifier, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTChirality, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTElement, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
     
    visit(ASTRingIdentifier, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(SimpleNode, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTStart, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTReaction, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTGroup, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTSmarts, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTNotBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTImplicitHighAndBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTLowAndBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTOrBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTExplicitHighAndBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTSimpleBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTRecursiveSmartsExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTElement, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTTotalHCount, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTImplicitHCount, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTExplicitConnectivity, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTAtomicNumber, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTHybrdizationNumber, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTCharge, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTRingConnectivity, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTPeriodicGroupNumber, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTTotalConnectivity, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTValence, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTRingMembership, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTSmallestRingSize, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTAliphatic, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTNonCHHeavyAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTAromatic, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTAnyAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTAtomicMass, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTChirality, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTLowAndExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTOrExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTNotExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTExplicitHighAndExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTImplicitHighAndExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visit(ASTExplicitAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
     
    visitChildren(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.ElementGroup
    Visit the members of the group.
    VISITED - Static variable in class org.openscience.cdk.CDKConstants
    Flag is set if chemobject has been visited.
    visited(IAtom) - Method in class org.openscience.cdk.geometry.cip.VisitedAtoms
    Marks the given atom as visited.
    visited(VisitedAtoms) - Method in class org.openscience.cdk.geometry.cip.VisitedAtoms
    Adds all atoms from the visitedAtoms list to the current list.
    visited - Variable in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
     
    VisitedAtoms - Class in org.openscience.cdk.geometry.cip
    Helper class for the CIPTool to keep track of which atoms have already been visited.
    VisitedAtoms() - Constructor for class org.openscience.cdk.geometry.cip.VisitedAtoms
    Creates a new empty list of visited IAtoms.

    W

    W - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    warn(Object) - Method in interface org.openscience.cdk.tools.ILoggingTool
    Shows WARN output for the Object.
    warn(Object, Object...) - Method in interface org.openscience.cdk.tools.ILoggingTool
    Shows WARN output for the given Object's.
    warn(Object) - Method in class org.openscience.cdk.tools.LoggingTool
    Shows WARN output for the Object.
    warn(Object, Object...) - Method in class org.openscience.cdk.tools.LoggingTool
    Shows WARN output for the given Object's.
    warn(Object) - Method in class org.openscience.cdk.tools.SystemOutLoggingTool
    Shows WARN output for the Object.
    warn(Object, Object...) - Method in class org.openscience.cdk.tools.SystemOutLoggingTool
    Shows WARN output for the given Object's.
    warning(SAXParseException) - Method in class org.openscience.cdk.io.cml.CMLErrorHandler
    Outputs a SAXParseException warning to the logger.
    WARNING_MARKER - Static variable in class org.openscience.cdk.validate.ProblemMarker
     
    WedgeLineElement - Class in org.openscience.cdk.renderer.elements
    A 'wedge' is a triangle aligned along a bond that indicates stereochemistry.
    WedgeLineElement(double, double, double, double, double, WedgeLineElement.TYPE, WedgeLineElement.Direction, Color) - Constructor for class org.openscience.cdk.renderer.elements.WedgeLineElement
    Make a wedge between the points (x1, y1) and (x2, y2) with a certain width, direction, dash, and color.
    WedgeLineElement(LineElement, WedgeLineElement.TYPE, WedgeLineElement.Direction, Color) - Constructor for class org.openscience.cdk.renderer.elements.WedgeLineElement
    Make a wedge along the given line element.
    WedgeLineElement.Direction - Enum in org.openscience.cdk.renderer.elements
    'toFirst' means that the wedge gets thicker in the direction of the first point in the line.
    WedgeLineElement.TYPE - Enum in org.openscience.cdk.renderer.elements
    If the bond is dashed ,wedged, or "up_or_down", i.e., not defined.
    weight() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycle
    Deprecated.
    Returns the sum of the weights of all edges in this cycle.
    WeightDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
    IDescriptor based on the weight of atoms of a certain element type.
    WeightDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor
    Constructor for the WeightDescriptor object.
    WeightedPathDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
    Evaluates the weighted path descriptors.
    WeightedPathDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor
     
    weightVector() - Method in class org.openscience.cdk.ringsearch.cyclebasis.CycleBasis
    Deprecated.
     
    weightVector() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis
    Deprecated.
     
    WHIMDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
    Holistic descriptors described by Todeschini et al [Todeschini, R. and Gramatica, P., New 3D Molecular Descriptors: The WHIM theory and QAR Applications, Persepectives in Drug Discovery and Design, 1998, ?:355-380].
    WHIMDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor
     
    width() - Method in class org.openscience.cdk.graph.invariant.GIMatrix
    Returns the number of columns of the matrix.
    width - Variable in class org.openscience.cdk.renderer.elements.ArrowElement
    Width of the arrow line.
    width() - Method in class org.openscience.cdk.renderer.elements.Bounds
    Specifies the width of the bounding box.
    width - Variable in class org.openscience.cdk.renderer.elements.LineElement
    The width of the line.
    width - Variable in class org.openscience.cdk.renderer.elements.RectangleElement
    The width of the rectangle.
    WienerNumbersDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
    This descriptor calculates the Wiener numbers.
    WienerNumbersDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor
    Constructor for the WienerNumbersDescriptor object.
    WILDCARD - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    WIND_EVEN_ODD - Static variable in class org.openscience.cdk.renderer.elements.GeneralPath
     
    WIND_NON_ZERO - Static variable in class org.openscience.cdk.renderer.elements.GeneralPath
     
    winding - Variable in class org.openscience.cdk.renderer.elements.GeneralPath
    Winding rule for determining path interior.
    winding() - Method in class org.openscience.cdk.stereo.ExtendedTetrahedral
    The winding of the peripherals, when viewed from the first atom.
    withAnnotationColor(Color) - Method in class org.openscience.cdk.depict.DepictionGenerator
    Set the color annotations (e.g.
    withAnnotationScale(double) - Method in class org.openscience.cdk.depict.DepictionGenerator
    Set the size of annotations relative to atom symbols.
    withAtomClasses() - Method in class org.openscience.cdk.smiles.SmilesGenerator
    Deprecated.
    configure with SmiFlavor
    withAtomColors() - Method in class org.openscience.cdk.depict.DepictionGenerator
    Color atom symbols using typical colors, oxygens are red, nitrogens are blue, etc.
    withAtomColors(IAtomColorer) - Method in class org.openscience.cdk.depict.DepictionGenerator
    Color atom symbols using provided colorer.
    withAtomMapHighlight() - Method in class org.openscience.cdk.depict.DepictionGenerator
    Adds to the highlight the coloring of reaction atom-maps.
    withAtomMapHighlight(Color[]) - Method in class org.openscience.cdk.depict.DepictionGenerator
    Adds to the highlight the coloring of reaction atom-maps.
    withAtomMapNumbers() - Method in class org.openscience.cdk.depict.DepictionGenerator
    Display atom-atom mapping numbers on a reaction.
    withAtomNumbers() - Method in class org.openscience.cdk.depict.DepictionGenerator
    Display atom numbers on the molecule or reaction.
    withAtomValues() - Method in class org.openscience.cdk.depict.DepictionGenerator
    Display atom numbers on the molecule or reaction.
    withBackgroundColor(Color) - Method in class org.openscience.cdk.depict.DepictionGenerator
    Change the background color.
    withCapacity(int) - Static method in class org.openscience.cdk.graph.Matching
    Create an empty matching with the specified capacity.
    withCarbonSymbols() - Method in class org.openscience.cdk.depict.DepictionGenerator
    Display atom symbols for all atoms in the molecule.
    withFillToFit() - Method in class org.openscience.cdk.depict.DepictionGenerator
    Resize depictions to fill all available space (only if a size is specified).
    withHighlight(Iterable<? extends IChemObject>, Color) - Method in class org.openscience.cdk.depict.DepictionGenerator
    Highlight the provided set of atoms and bonds in the depiction in the specified color.
    withMappedRxnAlign(boolean) - Method in class org.openscience.cdk.depict.DepictionGenerator
    Specifies that reactions with atom-atom mappings should have their reactants/product coordinates aligned.
    withMargin(double) - Method in class org.openscience.cdk.depict.DepictionGenerator
    Specify a desired size of margin.
    withMolTitle() - Method in class org.openscience.cdk.depict.DepictionGenerator
    Display a molecule title with each depiction.
    withOuterGlowHighlight() - Method in class org.openscience.cdk.depict.DepictionGenerator
    Highlights are shown as an outer glow around the atom symbols and bonds rather than recoloring.
    withOuterGlowHighlight(double) - Method in class org.openscience.cdk.depict.DepictionGenerator
    Highlights are shown as an outer glow around the atom symbols and bonds rather than recoloring.
    withPadding(double) - Method in class org.openscience.cdk.depict.DepictionGenerator
    Specify a desired size of padding for molecule sets and reactions.
    withParam(Class<T>, U) - Method in class org.openscience.cdk.depict.DepictionGenerator
    Low-level option method to set a rendering model parameter.
    withRxnTitle() - Method in class org.openscience.cdk.depict.DepictionGenerator
    Display a reaction title with the depiction.
    withSize(double, double) - Method in class org.openscience.cdk.depict.DepictionGenerator
    Specify a desired size of depiction.
    withSpaceFor(IAtomContainer) - Static method in class org.openscience.cdk.graph.GraphUtil.EdgeToBondMap
    Create a map with enough space for all the bonds in the molecule, container.
    withTerminalCarbons() - Method in class org.openscience.cdk.depict.DepictionGenerator
    Display atom symbols for terminal carbons (i.e.
    withTitleColor(Color) - Method in class org.openscience.cdk.depict.DepictionGenerator
    Set the color titles will appear in.
    withTitleScale(double) - Method in class org.openscience.cdk.depict.DepictionGenerator
    Set the size of titles compared to atom symbols.
    withZoom(double) - Method in class org.openscience.cdk.depict.DepictionGenerator
    Specify a desired zoom factor - this changes the base size of a depiction and is used for uniformly making depictions bigger.
    write(IChemObject) - Method in class org.openscience.cdk.io.CDKSourceCodeWriter
     
    write(IChemObject) - Method in class org.openscience.cdk.io.CMLWriter
    Serializes the IChemObject to CML and redirects it to the output Writer.
    write(IChemObject) - Method in class org.openscience.cdk.io.CrystClustWriter
    Serializes the IChemObject to CrystClust format and redirects it to the output Writer.
    write(IChemObject) - Method in class org.openscience.cdk.io.HINWriter
     
    write(IChemObject) - Method in interface org.openscience.cdk.io.IChemObjectWriter
    Writes the content of "object" to output.
    write(IChemObject) - Method in class org.openscience.cdk.io.MDLRXNWriter
    Writes a IChemObject to the MDL RXN file formated output.
    write(IChemObject) - Method in class org.openscience.cdk.io.MDLV2000Writer
    Writes a IChemObject to the MDL molfile formated output.
    write(IChemObject) - Method in class org.openscience.cdk.io.MDLV3000Writer
    Writes a molecule to the V3000 format.
    write(IChemObject) - Method in class org.openscience.cdk.io.Mol2Writer
     
    write(IChemObject) - Method in class org.openscience.cdk.io.PDBWriter
     
    write(IChemObject) - Method in class org.openscience.cdk.io.program.GaussianInputWriter
     
    write(IChemObject) - Method in class org.openscience.cdk.io.program.Mopac7Writer
    Writes the content of "object" to output.
    write(IChemObject) - Method in class org.openscience.cdk.io.rdf.CDKOWLWriter
    Writes the content of "object" to output.
    write(IChemObject) - Method in class org.openscience.cdk.io.RGroupQueryWriter
    The actual writing of the output.
    write(IChemObject) - Method in class org.openscience.cdk.io.RssWriter
    Writes a IChemObject to the MDL molfile formated output.
    write(IChemObject) - Method in class org.openscience.cdk.io.SDFWriter
    Writes a IChemObject to the MDL SD file formated output.
    write(IChemObject) - Method in class org.openscience.cdk.io.ShelXWriter
    Serializes the IChemObject to ShelX and redirects it to the output Writer.
    write(IChemObject) - Method in class org.openscience.cdk.io.SMILESWriter
    Writes the content from object to output.
    write(IChemObject) - Method in class org.openscience.cdk.io.XYZWriter
     
    writeAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.io.SMILESWriter
    Writes the content from molecule to output.
    writeAtomContainerSet(IAtomContainerSet) - Method in class org.openscience.cdk.io.SMILESWriter
    Writes a list of molecules to an OutputStream.
    writeChemModel(IAtomContainerSet, String, String) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor
     
    writeCrystal(ICrystal) - Method in class org.openscience.cdk.io.PDBWriter
     
    writeGridInPmeshFormat(String) - Method in class org.openscience.cdk.tools.GridGenerator
    Method transforms the grid into pmesh format.
    writeGridInPmeshFormat(String, double) - Method in class org.openscience.cdk.tools.GridGenerator
    Method transforms the grid into pmesh format.
    writeMolecule(IAtomContainer) - Method in class org.openscience.cdk.io.MDLV2000Writer
    Writes a Molecule to an OutputStream in MDL sdf format.
    writeMolecule(IAtomContainer) - Method in class org.openscience.cdk.io.Mol2Writer
    Writes a single frame in XYZ format to the Writer.
    writeMolecule(IAtomContainer) - Method in class org.openscience.cdk.io.PDBWriter
    Writes a single frame in PDB format to the Writer.
    writeMolecule(IAtomContainer) - Method in class org.openscience.cdk.io.program.GaussianInputWriter
    Writes a molecule for input for Gaussian.
    writeMolecule(IAtomContainer) - Method in class org.openscience.cdk.io.XYZWriter
    writes a single frame in XYZ format to the Writer.
    writePharmacophoreDefinition(PharmacophoreQuery, OutputStream) - Static method in class org.openscience.cdk.pharmacophore.PharmacophoreUtils
    Write out one or more pharmacophore queries in the CDK XML format.
    writePharmacophoreDefinition(List<PharmacophoreQuery>, OutputStream) - Static method in class org.openscience.cdk.pharmacophore.PharmacophoreUtils
    Write out one or more pharmacophore queries in the CDK XML format.
    writePharmacophoreDefinition(PharmacophoreQuery[], OutputStream) - Static method in class org.openscience.cdk.pharmacophore.PharmacophoreUtils
    Write out one or more pharmacophore queries in the CDK XML format.
    writePocketsToPMesh(String) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
    Method writes the pockets to pmesh format.
    WriterFactory - Class in org.openscience.cdk.io
    Helper tool to create IChemObjectWriters.
    WriterFactory() - Constructor for class org.openscience.cdk.io.WriterFactory
    Constructs a ChemObjectIOInstantionTests.
    writeTo(String, OutputStream) - Method in class org.openscience.cdk.depict.Depiction
    Write the depiction to the provided output stream.
    writeTo(String, File) - Method in class org.openscience.cdk.depict.Depiction
    Write the depiction to the provided output stream.
    writeTo(String, String) - Method in class org.openscience.cdk.depict.Depiction
    Write the depiction to the provided file path.
    writeTo(String) - Method in class org.openscience.cdk.depict.Depiction
    Write the depiction to the provided file path, the format is determined by the path suffix.
    writeXMLDeclaration() - Method in class org.openscience.cdk.io.cml.CustomSerializer
    Overwrite the Serializer.writeXMLDeclaration() method, and have it not output the XML declaration.
    WS - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.

    X

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

    Y

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

    Z

    z3 - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
     
    ZagrebIndexDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
    Zagreb index: the sum of the squares of atom degree over all heavy atoms i.
    ZagrebIndexDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor
    Constructor for the ZagrebIndexDescriptor object.
    zero(int, int) - Static method in class org.openscience.cdk.graph.invariant.GIMatrix
    Returns a null matrix (with zeros everywhere) of given dimensions.
    zfract - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
     
    ZINC - Static variable in enum org.openscience.cdk.config.Elements
     
    ZINC - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    ZindoFormat - Class in org.openscience.cdk.io.formats
    See here.
    ZindoFormat() - Constructor for class org.openscience.cdk.io.formats.ZindoFormat
     
    ZIRCONIUM - Static variable in enum org.openscience.cdk.config.Elements
     
    ZIRCONIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
    RegularExpression Id.
    zmatrixChainToCartesian(IAtomContainer, boolean) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
    Takes the given Z Matrix coordinates and converts them to cartesian coordinates.
    ZMatrixFormat - Class in org.openscience.cdk.io.formats
     
    ZMatrixFormat() - Constructor for class org.openscience.cdk.io.formats.ZMatrixFormat
     
    ZMatrixReader - Class in org.openscience.cdk.io
    It reads Z matrices like in Gaussian input files.
    ZMatrixReader(Reader) - Constructor for class org.openscience.cdk.io.ZMatrixReader
    Constructs a ZMatrixReader from a Reader that contains the data to be parsed.
    ZMatrixReader(InputStream) - Constructor for class org.openscience.cdk.io.ZMatrixReader
     
    ZMatrixReader() - Constructor for class org.openscience.cdk.io.ZMatrixReader
     
    zmatrixToCartesian(double[], int[], double[], int[], double[], int[]) - Static method in class org.openscience.cdk.geometry.ZMatrixTools
    Takes the given Z Matrix coordinates and converts them to cartesian coordinates.
    ZMatrixTools - Class in org.openscience.cdk.geometry
    A set of static utility classes for dealing with Z matrices.
    ZMatrixTools() - Constructor for class org.openscience.cdk.geometry.ZMatrixTools
     
    ZN - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    ZR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
    RegularExpression Id.
    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 

    Copyright © 2017. All Rights Reserved.

    Parameters for this descriptor: