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

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

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

AbstractRenderer<T extends IChemObject> - Class in org.openscience.cdk.renderer

The base class for all renderers, handling the core aspects of rendering such as the location of the model in 'model space' and the location on the screen to draw the model.

AbstractRenderer(RendererModel) - Constructor for class org.openscience.cdk.renderer.AbstractRenderer

AbstractResourceFormat - Class in org.openscience.cdk.io.formats

An abstract class providing AbstractResourceFormat.hashCode() and AbstractResourceFormat.equals(java.lang.Object) for IResourceFormats.

AbstractResourceFormat() - Constructor for class org.openscience.cdk.io.formats.AbstractResourceFormat

AbstractSelection - Class in org.openscience.cdk.renderer.selection

An abstract selection of IChemObjects.

AbstractSelection() - Constructor for class org.openscience.cdk.renderer.selection.AbstractSelection

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

accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.ArrowElement

Converts this TextElement into widget specific objects.

accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.AtomSymbolElement

Converts this TextElement into widget specific objects.

accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.Bounds

Converts this TextElement into widget specific objects.

accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.ElementGroup

Converts this TextElement into widget specific objects.

accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.GeneralPath

Converts this TextElement into widget specific objects.

accept(IRenderingVisitor) - Method in interface org.openscience.cdk.renderer.elements.IRenderingElement

Converts this TextElement into widget specific objects.

accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.LineElement

Converts this TextElement into widget specific objects.

accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.MarkedElement

Converts this TextElement into widget specific objects.

accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.OvalElement

Converts this TextElement into widget specific objects.

accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.PathElement

Converts this TextElement into widget specific objects.

accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.RectangleElement

Converts this TextElement into widget specific objects.

accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.RingElement

Converts this TextElement into widget specific objects.

accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.TextElement

Converts this TextElement into widget specific objects.

accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.TextGroupElement

Converts this TextElement into widget specific objects.

accept(IRenderingVisitor) - Method in class org.openscience.cdk.renderer.elements.WedgeLineElement

Converts this TextElement into widget specific objects.

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.CDKSourceCodeWriter

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.CIFReader

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.CMLReader

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.CMLWriter

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.CrystClustReader

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.CrystClustWriter

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.CTXReader

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.GamessReader

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.Gaussian03Reader

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.Gaussian98Reader

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.GhemicalMMReader

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.HINReader

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.HINWriter

accepts(Class<? extends IChemObject>) - Method in interface org.openscience.cdk.io.IChemObjectIO

Returns whether the given IChemObject can be read or written.

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.INChIPlainTextReader

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.INChIReader

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader

accepts(IChemObject) - Method in class org.openscience.cdk.io.iterator.event.DefaultEventChemObjectReader

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.iterator.event.DefaultEventChemObjectReader

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MDLReader

Deprecated.

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MDLRXNReader

Deprecated.

accepts(IChemObject) - Method in class org.openscience.cdk.io.MDLRXNReader

Deprecated.

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MDLRXNV2000Reader

accepts(IChemObject) - Method in class org.openscience.cdk.io.MDLRXNV2000Reader

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MDLRXNV3000Reader

accepts(IChemObject) - Method in class org.openscience.cdk.io.MDLRXNV3000Reader

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MDLRXNWriter

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MDLV2000Reader

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MDLV2000Writer

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MDLV3000Reader

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MDLV3000Writer

Returns whether the given IChemObject can be read or written.

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.Mol2Reader

accepts(IChemObject) - Method in class org.openscience.cdk.io.Mol2Reader

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.Mol2Writer

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.Mopac7Reader

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MoSSOutputReader

Returns whether the given IChemObject can be read or written.

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.PCCompoundASNReader

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.PCCompoundXMLReader

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.PCSubstanceXMLReader

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.PDBReader

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.PDBWriter

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.PMPReader

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.program.GaussianInputWriter

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.program.Mopac7Writer

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.random.RandomAccessSDFReader

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.rdf.CDKOWLReader

Returns whether the given IChemObject can be read or written.

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.rdf.CDKOWLWriter

Returns whether the given IChemObject can be read or written.

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.RGroupQueryReader

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.RGroupQueryWriter

Returns true for accepted input types.

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.RssWriter

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.SDFWriter

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.ShelXReader

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.ShelXWriter

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.SMILESReader

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.SMILESWriter

accepts(Class) - Method in class org.openscience.cdk.io.VASPReader

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.XYZReader

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.XYZWriter

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.ZMatrixReader

acceptStructure() - Method in class org.openscience.cdk.structgen.RandomGenerator

Tell the RandomGenerator to accept the last structure that had been proposed.

ACDLABS_LABEL - Static variable in class org.openscience.cdk.CDKConstants

Atom number/label that can be applied using the Manual Numbering Tool in ACD/ChemSketch.

Aces2Format - Class in org.openscience.cdk.io.formats

Aces2Format() - Constructor for class org.openscience.cdk.io.formats.Aces2Format

AcidicGroupCountDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

Returns the number of acidic groups.

AcidicGroupCountDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor

Creates a new AcidicGroupCountDescriptor.

ACTINIUM - Static variable in enum org.openscience.cdk.config.Elements

activity - Variable in class org.openscience.cdk.fingerprint.model.Bayesian

add(IAtomContainer) - Method in class org.openscience.cdk.AtomContainer

Adds all atoms and electronContainers of a given atomcontainer to this container.

add(IAtomContainerSet) - Method in class org.openscience.cdk.AtomContainerSet

Adds all atomContainers in the AtomContainerSet to this container.

add(IIsotope) - Method in class org.openscience.cdk.config.IsotopeFactory

Protected methods only to be used by classes extending this class to add an IIsotope.

add(IAtomContainer) - Method in class org.openscience.cdk.ConformerContainer

Add a conformer to the end of the list.

add(int, IAtomContainer) - Method in class org.openscience.cdk.ConformerContainer

add(IMolecularFormulaSet) - Method in class org.openscience.cdk.debug.DebugAdductFormula

Adds all molecularFormulas in the AdductFormula to this chemObject.

add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Adds all atoms and electronContainers of a given atomcontainer to this container.

add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainer

Adds all atoms and electronContainers of a given atomcontainer to this container.

add(IAtomContainerSet) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet

Adds all atomContainers in the AtomContainerSet to this container.

add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Adds all atoms and electronContainers of a given atomcontainer to this container.

add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugCrystal

Adds all atoms and electronContainers of a given atomcontainer to this container.

add(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugMolecularFormula

Adds an molecularFormula to this MolecularFormula.

add(IMolecularFormulaSet) - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet

Adds all molecularFormulas in the MolecularFormulaSet to this chemObject.

add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugMonomer

Adds all atoms and electronContainers of a given atomcontainer to this container.

add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugPolymer

Adds all atoms and electronContainers of a given atomcontainer to this container.

add(IReactionScheme) - Method in class org.openscience.cdk.debug.DebugReactionScheme

Add a Scheme of Reactions.

add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugRing

Adds all atoms and electronContainers of a given atomcontainer to this container.

add(IRingSet) - Method in class org.openscience.cdk.debug.DebugRingSet

Adds all rings of another RingSet if they are not already part of this ring set.

add(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugStrand

Adds all atoms and electronContainers of a given atomcontainer to this container.

add(IAtomContainerSet) - Method in class org.openscience.cdk.debug.DebugSubstance

Adds all atomContainers in the AtomContainerSet to this container.

add(String) - Method in class org.openscience.cdk.depict.Abbreviations

Convenience method to add an abbreviation from a SMILES string.

add(IAtomContainer, String) - Method in class org.openscience.cdk.depict.Abbreviations

Add an abbreviation to the factory.

add(IMolecularFormulaSet) - Method in class org.openscience.cdk.formula.AdductFormula

Adds all molecularFormulas in the AdductFormula to this chemObject.

add(IMolecularFormula) - Method in class org.openscience.cdk.formula.MolecularFormula

Adds an molecularFormula to this MolecularFormula.

add(IMolecularFormulaSet) - Method in class org.openscience.cdk.formula.MolecularFormulaSet

Adds all molecularFormulas in the MolecularFormulaSet to this chemObject.

add(GIMatrix) - Method in class org.openscience.cdk.graph.invariant.GIMatrix

Addition from two matrices.

add(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Adds all atoms and electronContainers of a given atomcontainer to this container.

add(IAtomContainerSet) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet

Adds all atomContainers in the AtomContainerSet to this container.

add(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.ICrystal

Adds the atoms in the AtomContainer as cell content.

add(IMolecularFormula) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula

Adds an molecularFormula to this MolecularFormula.

add(IMolecularFormulaSet) - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet

Adds all molecularFormulas in the MolecularFormulaSet to this chemObject.

add(IReactionScheme) - Method in interface org.openscience.cdk.interfaces.IReactionScheme

Add a scheme of reactions.

add(IRingSet) - Method in interface org.openscience.cdk.interfaces.IRingSet

Adds all rings of another RingSet if they are not allready part of this ring set.

add(IChemObject) - Method in class org.openscience.cdk.io.random.RandomAccessReader

add(T) - Method in class org.openscience.cdk.io.setting.SettingManager

Add a setting to the manager and return the instance to use.

add(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Adds all atoms and electronContainers of a given atomcontainer to this container.

add(double) - Method in class org.openscience.cdk.qsar.result.DoubleArrayResult

add(int) - Method in class org.openscience.cdk.qsar.result.IntegerArrayResult

add(IReactionScheme) - Method in class org.openscience.cdk.ReactionScheme

Add a Scheme of Reactions.

add(IRenderingElement) - Method in class org.openscience.cdk.renderer.elements.Bounds

Add the specified element bounds.

add(double, double) - Method in class org.openscience.cdk.renderer.elements.Bounds

Ensure the point x,y is included in the bounding box.

add(Bounds) - Method in class org.openscience.cdk.renderer.elements.Bounds

Add one bounds to another.

add(IRenderingElement) - Method in class org.openscience.cdk.renderer.elements.ElementGroup

Add a new element to the group.

add(IRingSet) - Method in class org.openscience.cdk.RingSet

Adds all rings of another RingSet if they are not already part of this ring set.

add(IMolecularFormulaSet) - Method in class org.openscience.cdk.silent.AdductFormula

Adds all molecularFormulas in the AdductFormula to this chemObject.

add(IAtomContainer) - Method in class org.openscience.cdk.silent.AtomContainer

Adds all atoms and electronContainers of a given atomcontainer to this container.

add(IAtomContainerSet) - Method in class org.openscience.cdk.silent.AtomContainerSet

Adds all atomContainers in the AtomContainerSet to this container.

add(IMolecularFormula) - Method in class org.openscience.cdk.silent.MolecularFormula

Adds an molecularFormula to this MolecularFormula.

add(IMolecularFormulaSet) - Method in class org.openscience.cdk.silent.MolecularFormulaSet

Adds all molecularFormulas in the MolecularFormulaSet to this chemObject.

add(IReactionScheme) - Method in class org.openscience.cdk.silent.ReactionScheme

Add a Scheme of Reactions.

add(IRingSet) - Method in class org.openscience.cdk.silent.RingSet

Adds all rings of another RingSet if they are not already part of this ring set.

add3DCoordinates1(IAtomContainer) - Static method in class org.openscience.cdk.geometry.AtomTools

Generate coordinates for all atoms which are singly bonded and have no coordinates.

add3DCoordinatesForSinglyBondedLigands(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

Generate coordinates for all atoms which are singly bonded and have no coordinates.

addAcidicOxygen(IAminoAcid) - Static method in class org.openscience.cdk.tools.manipulator.AminoAcidManipulator

Adds the singly bonded oxygen from the acid group of the AminoAcid.

addAgent(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugReaction

Adds an agent to this reaction.

addAgent(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IReaction

Adds an agent to this reaction.

addAgent(IAtomContainer) - Method in class org.openscience.cdk.Reaction

Adds an agent to this reaction.

addAgent(IAtomContainer) - Method in class org.openscience.cdk.silent.Reaction

Adds an agent to this reaction.

addAll(Collection<? extends IAtomContainer>) - Method in class org.openscience.cdk.ConformerContainer

addAll(int, Collection<? extends IAtomContainer>) - Method in class org.openscience.cdk.ConformerContainer

addAminoAcidAtCTerminus(IBioPolymer, IAminoAcid, IStrand, IAminoAcid) - Static method in class org.openscience.cdk.tools.ProteinBuilderTool

Builds a protein by connecting a new amino acid at the C-terminus of the given strand.

addAminoAcidAtNTerminus(IBioPolymer, IAminoAcid, IStrand, IAminoAcid) - Static method in class org.openscience.cdk.tools.ProteinBuilderTool

Builds a protein by connecting a new amino acid at the N-terminus of the given strand.

addArrayElementsTo(List<String>, String) - Method in class org.openscience.cdk.io.cml.CMLCoreModule

addAtom(IAtom) - Method in class org.openscience.cdk.AtomContainer

Adds an atom to this container.

addAtom(IAtom, IStrand) - Method in class org.openscience.cdk.BioPolymer

Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.

addAtom(IAtom, IMonomer, IStrand) - Method in class org.openscience.cdk.BioPolymer

Adds the atom to a specified Strand and a specified Monomer.

addAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Adds an atom to this container.

addAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer

Adds an atom to this container.

addAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Adds an atom to this container.

addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Adds the atom oAtom to a specified Monomer.

addAtom(IAtom, IStrand) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.

addAtom(IAtom, IMonomer, IStrand) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Adds the atom to a specified Strand and a specified Monomer.

addAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal

Adds an atom to this container.

addAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer

Adds an atom to this container.

addAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer

Adds an atom to this container.

addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.debug.DebugPolymer

Adds the atom oAtom to a specified Monomer.

addAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugRing

Adds an atom to this container.

addAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand

Adds the atom oAtom without specifying a Monomer or a Strand.

addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.debug.DebugStrand

Adds the atom oAtom to a specific Monomer.

addAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Adds an atom to this container.

addAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.IBioPolymer

Adds the atom oAtom without specifying a Monomer or a Strand.

addAtom(IAtom, IStrand) - Method in interface org.openscience.cdk.interfaces.IBioPolymer

Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.

addAtom(IAtom, IMonomer, IStrand) - Method in interface org.openscience.cdk.interfaces.IBioPolymer

Adds the atom to a specified Strand and a specified Monomer.

addAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.ICrystal

Adds the atom to the crystal.

addAtom(IPDBAtom) - Method in interface org.openscience.cdk.interfaces.IPDBPolymer

Adds the atom oAtom without specifying a Monomer or a Strand.

addAtom(IPDBAtom, IMonomer, IStrand) - Method in interface org.openscience.cdk.interfaces.IPDBPolymer

Adds the atom to a specified Strand and a specified Monomer.

addAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.IPolymer

Adds the atom oAtom without specifying a Monomer.

addAtom(IAtom, IMonomer) - Method in interface org.openscience.cdk.interfaces.IPolymer

Adds the atom oAtom to a specified Monomer.

addAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.IStrand

Adds the atom oAtom without specifying a Monomer or a Strand.

addAtom(IAtom, IMonomer) - Method in interface org.openscience.cdk.interfaces.IStrand

Adds the atom oAtom to a specific Monomer.

addAtom(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Adds an atom to this container.

addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.Polymer

Adds the atom oAtom to a specified Monomer.

addAtom(IPDBAtom) - Method in class org.openscience.cdk.protein.data.PDBPolymer

Adds the atom oAtom without specifying a IMonomer or a Strand.

addAtom(IPDBAtom, IMonomer) - Method in class org.openscience.cdk.protein.data.PDBPolymer

Adds the atom oAtom to a specified Monomer.

addAtom(IPDBAtom, IMonomer, IStrand) - Method in class org.openscience.cdk.protein.data.PDBPolymer

Adds the IPDBAtom oAtom to a specified Monomer of a specified Strand.

addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.protein.data.PDBStrand

Adds the atom oAtom to a specified Monomer.

addAtom(IAtom) - Method in class org.openscience.cdk.sgroup.Sgroup

Add an atom to this Sgroup.

addAtom(int) - Method in class org.openscience.cdk.signature.Orbit

Adds an atom index to the orbit.

addAtom(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer

Adds an atom to this container.

addAtom(IAtom, IStrand) - Method in class org.openscience.cdk.silent.BioPolymer

Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.

addAtom(IAtom, IMonomer, IStrand) - Method in class org.openscience.cdk.silent.BioPolymer

Adds the atom to a specified Strand and a specified Monomer.

addAtom(IPDBAtom) - Method in class org.openscience.cdk.silent.PDBPolymer

Adds the atom oAtom without specifying a IMonomer or a Strand.

addAtom(IPDBAtom, IMonomer) - Method in class org.openscience.cdk.silent.PDBPolymer

Adds the atom oAtom to a specified Monomer.

addAtom(IPDBAtom, IMonomer, IStrand) - Method in class org.openscience.cdk.silent.PDBPolymer

Adds the IPDBAtom oAtom to a specified Monomer of a specified Strand.

addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.silent.Polymer

Adds the atom oAtom to a specified Monomer.

addAtom(IAtom) - Method in class org.openscience.cdk.silent.Strand

Adds the atom oAtom without specifying a Monomer or a Strand.

addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.silent.Strand

Adds the atom oAtom to a specific Monomer.

addAtom(IAtom) - Method in class org.openscience.cdk.Strand

Adds the atom oAtom without specifying a Monomer or a Strand.

addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.Strand

Adds the atom oAtom to a specific Monomer.

addAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.AtomContainerSet

Adds an atomContainer to this container.

addAtomContainer(IAtomContainer, double) - Method in class org.openscience.cdk.AtomContainerSet

Adds an atomContainer to this container with the given multiplier.

addAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet

Adds an atomContainer to this container.

addAtomContainer(IAtomContainer, double) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet

Adds an atomContainer to this container with the given multiplier.

addAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugSubstance

Adds an atomContainer to this container.

addAtomContainer(IAtomContainer, double) - Method in class org.openscience.cdk.debug.DebugSubstance

Adds an atomContainer to this container with the given multiplier.

addAtomContainer(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet

Adds an atomContainer to this container.

addAtomContainer(IAtomContainer, double) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet

Adds an atomContainer to this container with the given multiplier.

addAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.silent.AtomContainerSet

Adds an atomContainer to this container.

addAtomContainer(IAtomContainer, double) - Method in class org.openscience.cdk.silent.AtomContainerSet

Adds an atomContainer to this container with the given multiplier.

addAtomVector(double[]) - Method in class org.openscience.cdk.Vibration

Adds a atom vector to the vibration.

addBond(IBond) - Method in class org.openscience.cdk.AtomContainer

Adds a Bond to this AtomContainer.

addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.AtomContainer

Adds a bond to this container.

addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.AtomContainer

Adds a bond to this container.

addBond(IBond) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Adds a Bond to this AtomContainer.

addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Adds a bond to this container.

addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Adds a bond to this container.

addBond(IBond) - Method in class org.openscience.cdk.debug.DebugAtomContainer

Adds a Bond to this AtomContainer.

addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugAtomContainer

Adds a bond to this container.

addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugAtomContainer

Adds a bond to this container.

addBond(IBond) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Adds a Bond to this AtomContainer.

addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Adds a bond to this container.

addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Adds a bond to this container.

addBond(IBond) - Method in class org.openscience.cdk.debug.DebugCrystal

Adds a Bond to this AtomContainer.

addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugCrystal

Adds a bond to this container.

addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugCrystal

Adds a bond to this container.

addBond(IBond) - Method in class org.openscience.cdk.debug.DebugMonomer

Adds a Bond to this AtomContainer.

addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugMonomer

Adds a bond to this container.

addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugMonomer

Adds a bond to this container.

addBond(IBond) - Method in class org.openscience.cdk.debug.DebugPolymer

Adds a Bond to this AtomContainer.

addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugPolymer

Adds a bond to this container.

addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugPolymer

Adds a bond to this container.

addBond(IBond) - Method in class org.openscience.cdk.debug.DebugRing

Adds a Bond to this AtomContainer.

addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugRing

Adds a bond to this container.

addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugRing

Adds a bond to this container.

addBond(IBond) - Method in class org.openscience.cdk.debug.DebugStrand

Adds a Bond to this AtomContainer.

addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugStrand

Adds a bond to this container.

addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.debug.DebugStrand

Adds a bond to this container.

addBond(IBond) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Adds a Bond to this AtomContainer.

addBond(int, int, IBond.Order, IBond.Stereo) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Adds a bond to this container.

addBond(int, int, IBond.Order) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Adds a bond to this container.

addBond(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Adds a Bond to this AtomContainer.

addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Adds a bond to this container.

addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Adds a bond to this container.

addBond(IBond) - Method in class org.openscience.cdk.sgroup.Sgroup

Add a bond to this Sgroup.

addBond(IBond) - Method in class org.openscience.cdk.silent.AtomContainer

Adds a Bond to this AtomContainer.

addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.silent.AtomContainer

Adds a bond to this container.

addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.silent.AtomContainer

Adds a bond to this container.

addBracket(SgroupBracket) - Method in class org.openscience.cdk.sgroup.Sgroup

Add a bracket for this Sgroup.

addCDKChangeListener(ICDKChangeListener) - Method in class org.openscience.cdk.renderer.RendererModel

Adds a change listener to the list of listeners.

addCDKError(ValidationTest) - Method in class org.openscience.cdk.validate.ValidationReport

Adds a CDK problem.

addCell(int...) - Method in class org.openscience.cdk.group.Partition

Adds a new cell to the end of the partition containing these elements.

addCell(Collection<Integer>) - Method in class org.openscience.cdk.group.Partition

Adds a new cell to the end of the partition.

addChargeGroup(ChargeGroup) - Method in class org.openscience.cdk.libio.md.MDMolecule

Add a ChargeGroup to the MDMolecule if not already present.

addChemModel(IChemModel) - Method in class org.openscience.cdk.ChemSequence

Adds an chemModel to this container.

addChemModel(IChemModel) - Method in class org.openscience.cdk.debug.DebugChemSequence

Adds an chemModel to this container.

addChemModel(IChemModel) - Method in interface org.openscience.cdk.interfaces.IChemSequence

Adds an chemModel to this container.

addChemModel(IChemModel) - Method in class org.openscience.cdk.silent.ChemSequence

Adds an chemModel to this container.

addChemObjectIOListener(IChemObjectIOListener) - Method in class org.openscience.cdk.io.ChemObjectIO

Adds a IChemObjectIOListener to this IChemObjectIO.

addChemObjectIOListener(IChemObjectIOListener) - Method in interface org.openscience.cdk.io.IChemObjectIO

Adds a IChemObjectIOListener to this IChemObjectIO.

addChemObjectIOListener(IChemObjectIOListener) - Method in class org.openscience.cdk.io.random.DefaultRandomAccessChemObjectReader

addChemObjectIOListener(IChemObjectIOListener) - Method in class org.openscience.cdk.io.random.RandomAccessReader

addChemSequence(IChemSequence) - Method in class org.openscience.cdk.ChemFile

Adds a ChemSequence to this container.

addChemSequence(IChemSequence) - Method in class org.openscience.cdk.debug.DebugChemFile

Adds a ChemSequence to this container.

addChemSequence(IChemSequence) - Method in interface org.openscience.cdk.interfaces.IChemFile

Adds an IChemSequence to this container.

addChemSequence(IChemSequence) - Method in class org.openscience.cdk.silent.ChemFile

Adds a ChemSequence to this container.

addChild(String, TextGroupElement.Position) - Method in class org.openscience.cdk.renderer.elements.TextGroupElement

Add a child text element.

addChild(String, String, TextGroupElement.Position) - Method in class org.openscience.cdk.renderer.elements.TextGroupElement

Add a child text element with a subscript.

addChild(IDifference) - Method in class org.openscience.cdk.tools.diff.tree.AbstractDifferenceList

Adds a new IDifference as child to this tree.

addChild(IDifference) - Method in interface org.openscience.cdk.tools.diff.tree.IDifferenceList

Adds a new IDifference as child to this tree.

addChildren(List<IDifference>) - Method in class org.openscience.cdk.tools.diff.tree.AbstractDifferenceList

Adds multiple IDifferences as child to this tree.

addChildren(List<IDifference>) - Method in interface org.openscience.cdk.tools.diff.tree.IDifferenceList

Adds multiple IDifferences as child to this tree.

addCTerminus(IAtom) - Method in class org.openscience.cdk.AminoAcid

Add an Atom and makes it the C-terminus atom.

addCTerminus(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Add an Atom and makes it the C-terminus atom.

addCTerminus(IAtom) - Method in interface org.openscience.cdk.interfaces.IAminoAcid

Add an Atom and makes it the C-terminus atom.

addCTerminus(IAtom) - Method in class org.openscience.cdk.silent.AminoAcid

Add an Atom and makes it the C-terminus atom.

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.

addExampleReaction(String) - Method in class org.openscience.cdk.dict.EntryReact

add a example for this reaction.

addFormula(IMolecularFormula) - Method in class org.openscience.cdk.formula.IsotopeContainer

Add a formula to this isotope container.

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.

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.

addNode(RNode) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph

Adds a new node to the RGraph.

addNTerminus(IAtom) - Method in class org.openscience.cdk.AminoAcid

Add an Atom and makes it the N-terminus atom.

addNTerminus(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Add an Atom and makes it the N-terminus atom.

addNTerminus(IAtom) - Method in interface org.openscience.cdk.interfaces.IAminoAcid

Add an Atom and makes it the N-terminus atom.

addNTerminus(IAtom) - Method in class org.openscience.cdk.silent.AminoAcid

Add an Atom and makes it the N-terminus atom.

addOK(ValidationTest) - Method in class org.openscience.cdk.validate.ValidationReport

Adds a validation test which did not find a problem.

addParameter(List<String>) - Method in class org.openscience.cdk.dict.EntryReact

Add a IParameterReact's of the reaction.

addParent(Sgroup) - Method in class org.openscience.cdk.sgroup.Sgroup

Add a parent Sgroup.

addProduct(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugReaction

Adds a product to this reaction.

addProduct(IAtomContainer, Double) - Method in class org.openscience.cdk.debug.DebugReaction

Adds a product to this reaction.

addProduct(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IReaction

Adds a product to this reaction.

addProduct(IAtomContainer, Double) - Method in interface org.openscience.cdk.interfaces.IReaction

Adds a product to this reaction.

addProduct(IAtomContainer) - Method in class org.openscience.cdk.Reaction

Adds a product to this reaction.

addProduct(IAtomContainer, Double) - Method in class org.openscience.cdk.Reaction

Adds a product to this reaction.

addProduct(IAtomContainer) - Method in class org.openscience.cdk.silent.Reaction

Adds a product to this reaction.

addProduct(IAtomContainer, Double) - Method in class org.openscience.cdk.silent.Reaction

Adds a product to this reaction.

addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.ChemObject

Sets the properties of this object.

addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Sets the properties of this object.

addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugAtom

Sets the properties of this object.

addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugAtomContainer

Sets the properties of this object.

addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet

Sets the properties of this object.

addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugAtomType

Sets the properties of this object.

addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Sets the properties of this object.

addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugBond

Sets the properties of this object.

addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugChemFile

Sets the properties of this object.

addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugChemModel

Sets the properties of this object.

addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugChemObject

Sets the properties of this object.

addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugChemSequence

Sets the properties of this object.

addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugCrystal

Sets the properties of this object.

addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugElectronContainer

Sets the properties of this object.

addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugElement

Sets the properties of this object.

addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Sets the properties of this object.

addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugIsotope

Sets the properties of this object.

addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugLonePair

Sets the properties of this object.

addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugMapping

Sets the properties of this object.

addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugMonomer

Sets the properties of this object.

addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugPolymer

Sets the properties of this object.

addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Sets the properties of this object.

addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugReaction

Sets the properties of this object.

addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugReactionScheme

Sets the properties of this object.

addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugReactionSet

Sets the properties of this object.

addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugRing

Sets the properties of this object.

addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugSingleElectron

Sets the properties of this object.

addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugStrand

Sets the properties of this object.

addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugSubstance

Sets the properties of this object.

addProperties(Map<Object, Object>) - Method in interface org.openscience.cdk.interfaces.IChemObject

Add properties to this object, duplicate keys will replace any existing value.

addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject

Sets the properties of this object.

addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.silent.ChemObject

Sets the properties of this object.

addReactant(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugReaction

Adds a reactant to this reaction.

addReactant(IAtomContainer, Double) - Method in class org.openscience.cdk.debug.DebugReaction

Adds a reactant to this reaction with a stoichiometry coefficient.

addReactant(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IReaction

Adds a reactant to this reaction.

addReactant(IAtomContainer, Double) - Method in interface org.openscience.cdk.interfaces.IReaction

Adds a reactant to this reaction with a stoichiometry coefficient.

addReactant(IAtomContainer) - Method in class org.openscience.cdk.Reaction

Adds a reactant to this reaction.

addReactant(IAtomContainer, Double) - Method in class org.openscience.cdk.Reaction

Adds a reactant to this reaction with a stoichiometry coefficient.

addReactant(IAtomContainer) - Method in class org.openscience.cdk.silent.Reaction

Adds a reactant to this reaction.

addReactant(IAtomContainer, Double) - Method in class org.openscience.cdk.silent.Reaction

Adds a reactant to this reaction with a stoichiometry coefficient.

addReaction(IReaction) - Method in class org.openscience.cdk.debug.DebugReactionSet

Adds an reaction to this container.

addReaction(IReaction) - Method in interface org.openscience.cdk.interfaces.IReactionSet

Adds an reaction to this container.

addReaction(IReaction, int) - Method in class org.openscience.cdk.reaction.ReactionChain

Added a IReaction for this chain in position.

addReaction(IReaction) - Method in class org.openscience.cdk.ReactionSet

Adds an reaction to this container.

addReaction(IReaction) - Method in class org.openscience.cdk.silent.ReactionSet

Adds an reaction to this container.

addReport(ValidationReport) - Method in class org.openscience.cdk.validate.ValidationReport

Merges the tests with the tests in this ValidationReport.

addResidue(Residue) - Method in class org.openscience.cdk.libio.md.MDMolecule

Add a Residue to the MDMolecule if not already present.

addSetting(IOSetting) - Method in class org.openscience.cdk.io.ChemObjectIO

Add an IOSetting to the reader/writer.

addSetting(IOSetting) - Method in interface org.openscience.cdk.io.IChemObjectIO

Add an IOSetting to the reader/writer.

addSettings(Collection<IOSetting>) - Method in class org.openscience.cdk.io.ChemObjectIO

Adds a collection of IOSettings to the reader/writer.

addSettings(Collection<IOSetting>) - Method in interface org.openscience.cdk.io.IChemObjectIO

Adds a collection of IOSettings to the reader/writer.

addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.AtomContainer

Adds a single electron to this AtomContainer.

addSingleElectron(int) - Method in class org.openscience.cdk.AtomContainer

Adds a SingleElectron to this Atom.

addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Adds a single electron to this AtomContainer.

addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Adds a SingleElectron to this Atom.

addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAtomContainer

Adds a single electron to this AtomContainer.

addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer

Adds a SingleElectron to this Atom.

addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Adds a single electron to this AtomContainer.

addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Adds a SingleElectron to this Atom.

addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugCrystal

Adds a single electron to this AtomContainer.

addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugCrystal

Adds a SingleElectron to this Atom.

addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugMonomer

Adds a single electron to this AtomContainer.

addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugMonomer

Adds a SingleElectron to this Atom.

addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugPolymer

Adds a single electron to this AtomContainer.

addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugPolymer

Adds a SingleElectron to this Atom.

addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugRing

Adds a single electron to this AtomContainer.

addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugRing

Adds a SingleElectron to this Atom.

addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugStrand

Adds a single electron to this AtomContainer.

addSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugStrand

Adds a SingleElectron to this Atom.

addSingleElectron(ISingleElectron) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Adds a single electron to this AtomContainer.

addSingleElectron(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Adds a SingleElectron to this Atom.

addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Adds a single electron to this AtomContainer.

addSingleElectron(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Adds a LonePair to this Atom.

addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.silent.AtomContainer

Adds a single electron to this AtomContainer.

addSingleElectron(int) - Method in class org.openscience.cdk.silent.AtomContainer

Adds a SingleElectron to this Atom.

addSingletonCell(int) - Method in class org.openscience.cdk.group.Partition

Add a new singleton cell to the end of the partition containing only this element.

addStereoElement(IStereoElement) - Method in class org.openscience.cdk.AtomContainer

Adds a stereo element to this container.

addStereoElement(IStereoElement) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Adds a stereo element to this container.

addStereoElement(IStereoElement) - Method in class org.openscience.cdk.debug.DebugAtomContainer

Adds a stereo element to this container.

addStereoElement(IStereoElement) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Adds a stereo element to this container.

addStereoElement(IStereoElement) - Method in class org.openscience.cdk.debug.DebugCrystal

Adds a stereo element to this container.

addStereoElement(IStereoElement) - Method in class org.openscience.cdk.debug.DebugMonomer

Adds a stereo element to this container.

addStereoElement(IStereoElement) - Method in class org.openscience.cdk.debug.DebugPolymer

Adds a stereo element to this container.

addStereoElement(IStereoElement) - Method in class org.openscience.cdk.debug.DebugRing

Adds a stereo element to this container.

addStereoElement(IStereoElement) - Method in class org.openscience.cdk.debug.DebugStrand

Adds a stereo element to this container.

addStereoElement(IStereoElement) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Adds a stereo element to this container.

addStereoElement(IStereoElement) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Adds a stereo element to this container.

addStereoElement(IStereoElement) - Method in class org.openscience.cdk.silent.AtomContainer

Adds a stereo element to this container.

addStructure(IPDBStructure) - Method in class org.openscience.cdk.debug.DebugPDBPolymer

Adds the PDBStructure structure a this PDBPolymer.

addStructure(IPDBStructure) - Method in interface org.openscience.cdk.interfaces.IPDBPolymer

Adds the PDBStructure structure a this PDBPolymer.

addStructure(IPDBStructure) - Method in class org.openscience.cdk.protein.data.PDBPolymer

addStructure(IPDBStructure) - Method in class org.openscience.cdk.silent.PDBPolymer

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

adjustProtonation(IMolecularFormula, int) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator

Adjust the protonation of a molecular formula.

agents - Variable in class org.openscience.cdk.Reaction

These are the used solvent, catalysts etc that normally appear above the reaction arrow

agents - Variable in class org.openscience.cdk.silent.Reaction

These are the used solvent, catalysts etc that normally appear above the reaction arrow

AL - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

ExtendedTetrahedral a.k.a.

AlchemyFormat - Class in org.openscience.cdk.io.formats

AlchemyFormat() - Constructor for class org.openscience.cdk.io.formats.AlchemyFormat

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.

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.

allCoplanar(Vector3d, Point3d, Point3d...) - Static method in class org.openscience.cdk.stereo.StereoTool

Check that all the points in the list are coplanar (in the same plane) as the plane defined by the planeNormal and the pointInPlane.

AllCycles - Class in org.openscience.cdk.graph

Compute all simple cycles (rings) in a graph.

AllCycles(int[][], int, int) - Constructor for class org.openscience.cdk.graph.AllCycles

Compute all simple cycles up to given maxCycleSize in the provided graph.

Allenal - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

ExtendedTetrahedral (e.g.

allHeavyAtomsPlaced(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D

True is all the atoms in the given AtomContainer have been placed.

allOrVertexShort() - Static method in class org.openscience.cdk.graph.Cycles

Deprecated.

use Cycles.or(org.openscience.cdk.graph.CycleFinder, org.openscience.cdk.graph.CycleFinder) to define a custom fall-back

AllPairsShortestPaths - Class in org.openscience.cdk.graph

Utility to determine the shortest paths between all pairs of atoms in a molecule.

AllPairsShortestPaths(IAtomContainer) - Constructor for class org.openscience.cdk.graph.AllPairsShortestPaths

Create a new all shortest paths utility for an IAtomContainer.

allPlaced(IAtomContainer) - Static method in class org.openscience.cdk.layout.AtomPlacer

True is all the atoms in the given AtomContainer have been placed

allPlaced(IRingSet) - Method in class org.openscience.cdk.layout.RingPlacer

True if coordinates have been assigned to all atoms in all rings.

AllRingsFinder - Class in org.openscience.cdk.ringsearch

Compute the set of all rings in a molecule.

AllRingsFinder(boolean) - Constructor for class org.openscience.cdk.ringsearch.AllRingsFinder

Deprecated.

turn logging off by setting the level in the logger implementation

AllRingsFinder() - Constructor for class org.openscience.cdk.ringsearch.AllRingsFinder

Default constructor using a threshold of AllRingsFinder.Threshold.PubChem_99.

AllRingsFinder.Threshold - Enum in org.openscience.cdk.ringsearch

The threshold values provide a limit at which the computation stops.

allSaturated(IAtomContainer) - Method in class org.openscience.cdk.tools.LonePairElectronChecker

Determines of all atoms on the AtomContainer have the right number the lone pair electrons.

allSaturated(IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker

allSaturated(IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker

ALOGPDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

This class calculates ALOGP (Ghose-Crippen LogKow) and the Ghose-Crippen molar refractivity (Ghose, A.K. and Crippen, G.M. . Journal of Computational Chemistry. 1986. 7, Ghose, A.K. and Crippen, G.M. . Journal of Chemical Information and Computer Science. 1987. 27).

ALOGPDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor

alogpfrag - Variable in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor

ALUMINIUM - Static variable in enum org.openscience.cdk.config.Elements

AMERICIUM - Static variable in enum org.openscience.cdk.config.Elements

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

and(IBitFingerprint) - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint

and(IBitFingerprint) - Method in interface org.openscience.cdk.fingerprint.IBitFingerprint

Performs a logical AND of the bits in this target bit set with the bits in the argument fingerprint.

and(IBitFingerprint) - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint

and(IntArrayFingerprint) - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint

and(Expr) - Method in class org.openscience.cdk.isomorphism.matchers.Expr

Utility, combine this expression with another, using conjunction.

ANGSTROM_UNIT - Static variable in class org.openscience.cdk.io.GamessReader

Boolean constant used to specify that the coordinates are given in Ångstrom units.

ANNOTATION_LABEL - Static variable in class org.openscience.cdk.renderer.generators.standard.StandardGenerator

Defines the annotation label(s) of a chem object in a depiction.

AnnotationColor() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.AnnotationColor

AnnotationDistance() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.AnnotationDistance

AnnotationFontScale() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.AnnotationFontScale

ANNOTATIONS - Static variable in class org.openscience.cdk.CDKConstants

A List of annotation remarks.

anonymise(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator

Anonymise the provided container to single-bonded carbon atoms.

ANTIMONY - Static variable in enum org.openscience.cdk.config.Elements

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.

applyTo(Permutation) - Method in interface org.openscience.cdk.group.PermutationGroup.Backtracker

Do something to the permutation

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.SmilesGenerator

Deprecated.

configure with SmiFlavor

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.

ArrowElement - Class in org.openscience.cdk.renderer.elements

IRenderingElement for linear arrows.

ArrowElement(double, double, double, double, double, boolean, Color) - Constructor for class org.openscience.cdk.renderer.elements.ArrowElement

Constructor for an arrow element, based on starting point, end point, width, direction, and color.

ArrowHeadWidth() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ArrowHeadWidth

ArrowHeadWidth() - Constructor for class org.openscience.cdk.renderer.generators.ReactionSceneGenerator.ArrowHeadWidth

ARSENIC - Static variable in enum org.openscience.cdk.config.Elements

asBitSet() - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint

asBitSet() - Method in interface org.openscience.cdk.fingerprint.IBitFingerprint

Returns a BitSet representation of the fingerprint.

asBitSet() - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint

assignAtomTypePropertiesToAtom(IAtomContainer) - Method in class org.openscience.cdk.tools.AtomTypeTools

assignAtomTypePropertiesToAtom(IAtomContainer, boolean) - Method in class org.openscience.cdk.tools.AtomTypeTools

Method assigns certain properties to an atom.

assignAtomTypes(IAtomContainer) - Method in class org.openscience.cdk.forcefield.mmff.Mmff

Assign MMFF Symbolic atom types.

assignAtomTyps(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator

Method assigns atom types to atoms (calculates sssr and aromaticity)

assignGasteigerMarsiliSigmaPartialCharges(IAtomContainer, boolean) - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges

Main method which assigns Gasteiger Marisili partial sigma charges.

assignGasteigerPiPartialCharges(IAtomContainer, boolean) - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges

Main method which assigns Gasteiger partial pi charges.

assignGasteigerSigmaMarsiliFactors(IAtomContainer) - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges

Method which stores and assigns the factors a,b,c and CHI+.

assignInductivePartialCharges(IAtomContainer) - Method in class org.openscience.cdk.charges.InductivePartialCharges

Main method, set charge as atom properties.

assignMMFF94PartialCharges(IAtomContainer) - Method in class org.openscience.cdk.charges.MMFF94PartialCharges

Main method which assigns MMFF94 partial charges

assignProteinToGrid() - Method in class org.openscience.cdk.protein.ProteinPocketFinder

Method assigns the atoms of a biopolymer to the grid.

assignrPiMarsilliFactors(IAtomContainerSet) - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges

Method which stores and assigns the factors a,b,c and CHI+.

assignVdWRadiiToProtein() - Method in class org.openscience.cdk.protein.ProteinPocketFinder

Method which assigns van der Waals radii to the biopolymer default org/openscience/cdk/config/data/pdb_atomtypes.xml stored in the variable String vanDerWaalsFile.

Association - Class in org.openscience.cdk

Base class for storing interactions like hydrogen bonds and ionic interactions.

Association(IAtom, IAtom) - Constructor for class org.openscience.cdk.Association

Constructs an association between two Atom's.

Association() - Constructor for class org.openscience.cdk.Association

Constructs an empty association.

ASTATINE - Static variable in enum org.openscience.cdk.config.Elements

AT - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Atropisomeric (e.g.

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_NAME_FORMAT - Variable in class org.openscience.cdk.io.PDBWriter

atomAromaticities - Variable in class org.openscience.cdk.io.cml.CMLCoreModule

AtomAtomMap - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Output atom-atom mapping for reactions and atom classes for molecules.

AtomAtomMappingLineColor() - Constructor for class org.openscience.cdk.renderer.generators.MappingGenerator.AtomAtomMappingLineColor

AtomAtomMapRenumber - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Renumber AtomAtomMaps during canonical generation

AtomColor() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.AtomColor

AtomColor() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.AtomColor

AtomColorer() - Constructor for class org.openscience.cdk.renderer.generators.AtomNumberGenerator.AtomColorer

AtomColorer() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.AtomColorer

AtomContainer - Class in org.openscience.cdk

Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.

AtomContainer() - Constructor for class org.openscience.cdk.AtomContainer

Constructs an empty AtomContainer.

AtomContainer(IAtomContainer) - Constructor for class org.openscience.cdk.AtomContainer

Constructs an AtomContainer with a copy of the atoms and electronContainers of another AtomContainer (A shallow copy, i.e., with the same objects as in the original AtomContainer).

AtomContainer(int, int, int, int) - Constructor for class org.openscience.cdk.AtomContainer

Constructs an empty AtomContainer that will contain a certain number of atoms and electronContainers.

atomContainer - Variable in class org.openscience.cdk.graph.AtomContainerPermutor

The atom container that is permuted at each step.

atomContainer - Variable in class org.openscience.cdk.inchi.InChIGenerator

AtomContainer instance refers to.

AtomContainer - Class in org.openscience.cdk.silent

Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.

AtomContainer() - Constructor for class org.openscience.cdk.silent.AtomContainer

Constructs an empty AtomContainer.

AtomContainer(IAtomContainer) - Constructor for class org.openscience.cdk.silent.AtomContainer

Constructs an AtomContainer with a copy of the atoms and electronContainers of another AtomContainer (A shallow copy, i.e., with the same objects as in the original AtomContainer).

AtomContainer(int, int, int, int) - Constructor for class org.openscience.cdk.silent.AtomContainer

Constructs an empty AtomContainer that will contain a certain number of atoms and electronContainers.

atomContainer - Variable in class org.openscience.cdk.tools.HOSECodeGenerator

The molecular structure on which we work

AtomContainerAtomPermutor - Class in org.openscience.cdk.graph

An atom container atom permutor that uses ranking and unranking to calculate the next permutation in the series.

AtomContainerAtomPermutor(IAtomContainer) - Constructor for class org.openscience.cdk.graph.AtomContainerAtomPermutor

A permutor wraps the original atom container, and produces cloned (and permuted!) copies on demand.

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.

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

AtomHashGenerator - Interface in org.openscience.cdk.hash

A hash function which generates 64-bit hash codes for the atoms of a molecule.

AtomHybridizationDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic

This class returns the hybridization of an atom.

AtomHybridizationDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor

AtomHybridizationVSEPRDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic

This class returns the hybridization of an atom.

AtomHybridizationVSEPRDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor

Constructor for the AtomHybridizationVSEPRDescriptor object

atomic() - Method in class org.openscience.cdk.hash.HashGeneratorMaker

Given the current configuration create an AtomHashGenerator.

AtomicMass - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Output atomic mass on atoms.

AtomicMassStrict - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Deprecated.

no longer needed, default CDK behaviour is now to pass through mass numbers if non-null

atomicNumber - Variable in class org.openscience.cdk.Element

The atomic number for this element giving their position in the periodic table.

atomicNumber - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom

The atomic number for this element giving their position in the periodic table.

atomicNumber - Variable in class org.openscience.cdk.silent.Element

The atomic number for this element giving their position in the periodic table.

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

AtomNumberGenerator - Class in org.openscience.cdk.renderer.generators

IGenerator for IAtomContainers that will draw atom numbers for the atoms.

AtomNumberGenerator() - Constructor for class org.openscience.cdk.renderer.generators.AtomNumberGenerator

AtomNumberGenerator.AtomColorer - Class in org.openscience.cdk.renderer.generators

The color scheme by which to color the atom numbers, if the AtomNumberGenerator.ColorByType boolean is true.

AtomNumberGenerator.AtomNumberTextColor - Class in org.openscience.cdk.renderer.generators

Color to draw the atom numbers with.

AtomNumberGenerator.ColorByType - Class in org.openscience.cdk.renderer.generators

Boolean to indicate of the AtomNumberGenerator.AtomColorer scheme will be used.

AtomNumberGenerator.Offset - Class in org.openscience.cdk.renderer.generators

Offset vector in screen space coordinates where the atom number label will be placed.

AtomNumberGenerator.WillDrawAtomNumbers - Class in org.openscience.cdk.renderer.generators

Boolean parameter indicating if atom numbers should be drawn, allowing this feature to be disabled temporarily.

AtomNumberTextColor() - Constructor for class org.openscience.cdk.renderer.generators.AtomNumberGenerator.AtomNumberTextColor

AtomPairs2DFingerprinter - Class in org.openscience.cdk.fingerprint

Generates an atom pair 2D fingerprint as implemented in PaDEL given an IAtomContainer, that extends the Fingerprinter.

AtomPairs2DFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.AtomPairs2DFingerprinter

atomParities - Variable in class org.openscience.cdk.io.cml.CMLCoreModule

AtomPlacer - Class in org.openscience.cdk.layout

Methods for generating coordinates for atoms in various situations.

AtomPlacer() - Constructor for class org.openscience.cdk.layout.AtomPlacer

Constructor for the AtomPlacer object

AtomPlacer3D - Class in org.openscience.cdk.modeling.builder3d

Place aliphatic chains with Z matrix method.

AtomRadius() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.AtomRadius

AtomRef - Class in org.openscience.cdk

An atom ref, references a CDK IAtom indirectly.

AtomRef(IAtom) - Constructor for class org.openscience.cdk.AtomRef

Create a pointer for the provided atom.

AtomRefinerBuilder() - Constructor for class org.openscience.cdk.group.PartitionRefinement.AtomRefinerBuilder

atoms - Variable in class org.openscience.cdk.Association

The atoms which take part in the association.

atoms - Variable in class org.openscience.cdk.AtomContainer

Internal array of atoms.

atoms() - Method in class org.openscience.cdk.AtomContainer

Returns an Iterable for looping over all atoms in this container.

atoms - Variable in class org.openscience.cdk.Bond

A list of atoms participating in this bond.

atoms() - Method in class org.openscience.cdk.Bond

Returns the Iterator to atoms making up this bond.

atoms() - Method in class org.openscience.cdk.BondRef

Returns the Iterable to atoms making up this bond.

atoms() - Method in class org.openscience.cdk.debug.DebugAminoAcid

Returns an Iterable for looping over all atoms in this container.

atoms() - Method in class org.openscience.cdk.debug.DebugAtomContainer

Returns an Iterable for looping over all atoms in this container.

atoms() - Method in class org.openscience.cdk.debug.DebugBioPolymer

Returns an Iterable for looping over all atoms in this container.

atoms() - Method in class org.openscience.cdk.debug.DebugBond

Returns the Iterator to atoms making up this bond.

atoms() - Method in class org.openscience.cdk.debug.DebugCrystal

Returns an Iterable for looping over all atoms in this container.

atoms() - Method in class org.openscience.cdk.debug.DebugMonomer

Returns an Iterable for looping over all atoms in this container.

atoms() - Method in class org.openscience.cdk.debug.DebugPolymer

Returns an Iterable for looping over all atoms in this container.

atoms() - Method in class org.openscience.cdk.debug.DebugRing

Returns an Iterable for looping over all atoms in this container.

atoms() - Method in class org.openscience.cdk.debug.DebugStrand

Returns an Iterable for looping over all atoms in this container.

atoms - Variable in class org.openscience.cdk.fingerprint.CircularFingerprinter.FP

atoms() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns an Iterable for looping over all atoms in this container.

atoms() - Method in interface org.openscience.cdk.interfaces.IBond

Returns the Iterable to atoms making up this bond.

atoms - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Internal array of atoms.

atoms() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Returns an Iterable for looping over all atoms in this container.

atoms - Variable in class org.openscience.cdk.isomorphism.matchers.QueryBond

A list of atoms participating in this query bond.

atoms() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond

Returns the Iterator to atoms making up this query bond.

atoms - Variable in class org.openscience.cdk.silent.AtomContainer

Internal array of atoms.

atoms() - Method in class org.openscience.cdk.silent.AtomContainer

Returns an Iterable for looping over all atoms in this container.

atoms - Variable in class org.openscience.cdk.silent.Bond

A list of atoms participating in this bond.

atoms() - Method in class org.openscience.cdk.silent.Bond

Returns the Iterator to atoms making up this bond.

AtomSignature - Class in org.openscience.cdk.signature

The signature (Faulon, J. L., Visco, D. P., and Pophale, R. S.. Journal of Chemical Information and Computer Sciences. 2003. 43, Faulon, J. L., Collins, M. J., and Carr, R. D.. Journal of Chemical Information and Computer Sciences. 2004. 44) for a molecule rooted at a particular atom.

AtomSignature(int, IAtomContainer) - Constructor for class org.openscience.cdk.signature.AtomSignature

Create an atom signature starting at atomIndex.

AtomSignature(IAtom, IAtomContainer) - Constructor for class org.openscience.cdk.signature.AtomSignature

Create an atom signature for the atom atom.

AtomSignature(int, int, IAtomContainer) - Constructor for class org.openscience.cdk.signature.AtomSignature

Create an atom signature starting at atomIndex and with a maximum height of height.

AtomSignature(IAtom, int, IAtomContainer) - Constructor for class org.openscience.cdk.signature.AtomSignature

Create an atom signature for the atom atom and with a maximum height of height.

AtomSignature(int, int, AbstractVertexSignature.InvariantType, IAtomContainer) - Constructor for class org.openscience.cdk.signature.AtomSignature

Create an atom signature starting at atomIndex, with maximum height of height, and using a particular invariant type.

AtomSignature(IAtom, int, AbstractVertexSignature.InvariantType, IAtomContainer) - Constructor for class org.openscience.cdk.signature.AtomSignature

Create an atom signature for the atom atom, with maximum height of height, and using a particular invariant type.

atomsTo(int) - Method in class org.openscience.cdk.graph.ShortestPaths

Reconstruct a shortest path to the provided end vertex.

atomsTo(IAtom) - Method in class org.openscience.cdk.graph.ShortestPaths

Reconstruct a shortest path to the provided end atom.

AtomSymbolElement - Class in org.openscience.cdk.renderer.elements

A text element with added information.

AtomSymbolElement(double, double, String, Integer, Integer, int, Color) - Constructor for class org.openscience.cdk.renderer.elements.AtomSymbolElement

AtomTetrahedralLigandPlacer3D - Class in org.openscience.cdk.modeling.builder3d

A set of static utility classes for geometric calculations on Atoms.

AtomTools - Class in org.openscience.cdk.geometry

A set of static utility classes for geometric calculations on Atoms.

AtomTools() - Constructor for class org.openscience.cdk.geometry.AtomTools

AtomType - Class in org.openscience.cdk

The base class for atom types.

AtomType(String) - Constructor for class org.openscience.cdk.AtomType

Constructor for the AtomType object.

AtomType(String, String) - Constructor for class org.openscience.cdk.AtomType

Constructor for the AtomType object.

AtomType(IElement) - Constructor for class org.openscience.cdk.AtomType

Constructs an isotope by copying the symbol, atomic number, flags, identifier, exact mass, natural abundance and mass number from the given IIsotope.

ATOMTYPE - Static variable in class org.openscience.cdk.libio.jena.CDK

AtomType - Class in org.openscience.cdk.silent

The base class for atom types.

AtomType(String) - Constructor for class org.openscience.cdk.silent.AtomType

Constructor for the AtomType object.

AtomType(String, String) - Constructor for class org.openscience.cdk.silent.AtomType

Constructor for the AtomType object.

AtomType(IElement) - Constructor for class org.openscience.cdk.silent.AtomType

Constructs an isotope by copying the symbol, atomic number, flags, identifier, exact mass, natural abundance and mass number from the given IIsotope.

ATOMTYPE_ID_JMOL - Static variable in class org.openscience.cdk.config.AtomTypeFactory

Used as an ID to describe the atom type.

ATOMTYPE_ID_MODELING - Static variable in class org.openscience.cdk.config.AtomTypeFactory

Used as an ID to describe the atom type.

ATOMTYPE_ID_STRUCTGEN - Static variable in class org.openscience.cdk.config.AtomTypeFactory

Used as an ID to describe the atom type.

AtomTypeAwareSaturationChecker - Class in org.openscience.cdk.tools

This class tries to figure out the bond order of the bonds that has the flag SINGLE_OR_DOUBLE raised (i.e.

AtomTypeAwareSaturationChecker() - Constructor for class org.openscience.cdk.tools.AtomTypeAwareSaturationChecker

Constructs an AtomTypeAwareSaturationChecker checker.

AtomTypeCharges - Class in org.openscience.cdk.charges

Assigns charges to atom types.

AtomTypeDiff - Class in org.openscience.cdk.tools.diff

Compares two IAtomType classes.

AtomTypeFactory - Class in org.openscience.cdk.config

General class for defining AtomTypes.

AtomTypeHandler - Class in org.openscience.cdk.config.atomtypes

SAX Handler for the AtomTypeReader.

AtomTypeHandler(IChemObjectBuilder) - Constructor for class org.openscience.cdk.config.atomtypes.AtomTypeHandler

Constructs a new AtomTypeHandler and will create IAtomType implementations using the given IChemObjectBuilder.

AtomTypeHybridizationDifference - Class in org.openscience.cdk.tools.diff.tree

IDifference between two IAtomType.Hybridizations.

AtomTypeManipulator - Class in org.openscience.cdk.tools.manipulator

Class with utilities for the IAtomType class.

AtomTypeManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.AtomTypeManipulator

AtomTypeMapper - Class in org.openscience.cdk.atomtype.mapper

An AtomTypeMapper allows the mapping of atom types between atom type schemes.

AtomTypeReader - Class in org.openscience.cdk.config.atomtypes

XML Reader for the CDKBasedAtomTypeConfigurator.

AtomTypeReader(Reader) - Constructor for class org.openscience.cdk.config.atomtypes.AtomTypeReader

Instantiates the XML based AtomTypeReader.

AtomTypeTools - Class in org.openscience.cdk.tools

AtomTypeTools is a helper class for assigning atom types to an atom.

AtomTypeTools() - Constructor for class org.openscience.cdk.tools.AtomTypeTools

Constructor for the MMFF94AtomTypeMatcher object.

AtomValenceDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic

This class returns the valence of an atom.

AtomValenceDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor

Constructor for the AtomValenceDescriptor object

AtomValenceTool - Class in org.openscience.cdk.qsar

This class returns the valence of an atom.

AtomValenceTool() - Constructor for class org.openscience.cdk.qsar.AtomValenceTool

Atropisomeric - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Atropisomeric (e.g.

Atropisomeric - Class in org.openscience.cdk.stereo

Restricted axial rotation around Aryl-Aryl bonds.

Atropisomeric(IBond, IAtom[], int) - Constructor for class org.openscience.cdk.stereo.Atropisomeric

Define a new atropisomer using the focus bond and the carrier atoms.

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).

AutocorrelationDescriptorCharge - Class in org.openscience.cdk.qsar.descriptors.molecular

This class calculates ATS autocorrelation descriptor, where the weight equal to the charges.

AutocorrelationDescriptorCharge() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge

AutocorrelationDescriptorMass - Class in org.openscience.cdk.qsar.descriptors.molecular

This class calculates ATS autocorrelation descriptor, where the weight equal to the scaled atomic mass (Moreau G. and Broto P.. Nouveau Journal de Chimie. 1980. null).

AutocorrelationDescriptorMass() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass

AutocorrelationDescriptorPolarizability - Class in org.openscience.cdk.qsar.descriptors.molecular

This class calculates ATS autocorrelation descriptor, where the weight equal to the charges.

AutocorrelationDescriptorPolarizability() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability

AUTOMATIC - Static variable in class org.openscience.cdk.depict.DepictionGenerator

Magic value for indicating automatic parameters.

AUTONOMNAME - Static variable in class org.openscience.cdk.CDKConstants

The IUPAC compatible name generated with AutoNom.

AverageBondLengthCalculator - Class in org.openscience.cdk.renderer

Utility class for calculating the average bond length for various IChemObject subtypes : IReaction, IAtomContainerSet, IChemModel, and IReactionSet.

AverageBondLengthCalculator() - Constructor for class org.openscience.cdk.renderer.AverageBondLengthCalculator

AWTDrawVisitor - Class in org.openscience.cdk.renderer.visitor

Implementation of the IDrawVisitor interface for the AWT widget toolkit, allowing molecules to be rendered with toolkits based on AWT, like the Java reference graphics platform Swing.

AWTDrawVisitor(Graphics2D) - Constructor for class org.openscience.cdk.renderer.visitor.AWTDrawVisitor

Constructs a new IDrawVisitor using the AWT widget toolkit, taking a Graphics2D object to which the chemical content is drawn.

AWTFontManager - Class in org.openscience.cdk.renderer.font

AWT-specific font manager.

AWTFontManager() - Constructor for class org.openscience.cdk.renderer.font.AWTFontManager

Make a manager for fonts in AWT, with a minimum font size of 9.

axisScanX(int, int, int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder

Method performs a scan; works only for cubic grids!

axisScanY(int, int, int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder

Method performs a scan; works only for cubic grids!

axisScanZ(int, int, int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder

Method performs a scan; works only for cubic grids!

B

b - Variable in class org.openscience.cdk.io.random.RandomAccessReader

BackgroundColor() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.BackgroundColor

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

BasicAtomEncoder - Enum in org.openscience.cdk.hash

Enumeration of atom encoders for seeding atomic hash codes.

BasicAtomGenerator - Class in org.openscience.cdk.renderer.generators

Generates basic IRenderingElements for atoms in an atom container.

BasicAtomGenerator() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator

An empty constructor necessary for reflection.

BasicAtomGenerator.AtomColor - Class in org.openscience.cdk.renderer.generators

Class to hold the color by which atom labels are drawn.

BasicAtomGenerator.AtomColorer - Class in org.openscience.cdk.renderer.generators

IAtomColorer used to draw elements.

BasicAtomGenerator.AtomRadius - Class in org.openscience.cdk.renderer.generators

Magic number with unknown units that defines the radius around an atom, e.g.

BasicAtomGenerator.ColorByType - Class in org.openscience.cdk.renderer.generators

Boolean property that triggers atoms to be colored by type when set to true.

BasicAtomGenerator.CompactAtom - Class in org.openscience.cdk.renderer.generators

Boolean parameters that will cause atoms to be drawn as filled shapes when set to true.

BasicAtomGenerator.CompactShape - Class in org.openscience.cdk.renderer.generators

Shape to be used when drawing atoms in compact mode, as defined by the BasicAtomGenerator.CompactAtom parameter.

BasicAtomGenerator.KekuleStructure - Class in org.openscience.cdk.renderer.generators

Determines whether structures should be drawn as Kekule structures, thus giving each carbon element explicitly, instead of not displaying the element symbol.

BasicAtomGenerator.Shape - Enum in org.openscience.cdk.renderer.generators

When atoms are selected or in compact mode, they will be covered by a shape determined by this enumeration.

BasicAtomGenerator.ShowEndCarbons - Class in org.openscience.cdk.renderer.generators

Boolean parameters that will show carbons with only one (non-hydrogen) neighbor to be drawn with an element symbol.

BasicAtomGenerator.ShowExplicitHydrogens - Class in org.openscience.cdk.renderer.generators

Boolean property that triggers explicit hydrogens to be drawn if set to true.

BasicBondGenerator - Class in org.openscience.cdk.renderer.generators

Generator for elements from bonds.

BasicBondGenerator() - Constructor for class org.openscience.cdk.renderer.generators.BasicBondGenerator

An empty constructor necessary for reflection.

BasicBondGenerator.BondDistance - Class in org.openscience.cdk.renderer.generators

The gap between double and triple bond lines on the screen.

BasicBondGenerator.BondWidth - Class in org.openscience.cdk.renderer.generators

The width on screen of a bond.

BasicBondGenerator.DefaultBondColor - Class in org.openscience.cdk.renderer.generators

The color to draw bonds if not other color is given.

BasicBondGenerator.TowardsRingCenterProportion - Class in org.openscience.cdk.renderer.generators

The proportion to move in towards the ring center.

BasicBondGenerator.WedgeWidth - Class in org.openscience.cdk.renderer.generators

The width on screen of the fat end of a wedge bond.

BasicCreator(Class<T>) - Constructor for class org.openscience.cdk.DynamicFactory.BasicCreator

Create a basic constructor with a given declaring class.

BasicGenerator - Class in org.openscience.cdk.renderer.generators

Combination generator for basic drawing of molecules.

BasicGenerator() - Constructor for class org.openscience.cdk.renderer.generators.BasicGenerator

Make a basic generator that creates elements for atoms and bonds.

BasicGroupCountDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

Returns the number of basic groups.

BasicGroupCountDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor

Creates a new BasicGroupCountDescriptor.

basicInvariants(IAtomContainer, int[][]) - Static method in class org.openscience.cdk.graph.invariant.Canon

Generate the initial invariants for each atom in the container.

BasicSceneGenerator - Class in org.openscience.cdk.renderer.generators

This generator does not create any elements, but acts as a holding place for various generator parameters used by most drawings, such as the zoom, background color, margin, etc.

BasicSceneGenerator() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator

An empty constructor necessary for reflection.

BasicSceneGenerator.ArrowHeadWidth - Class in org.openscience.cdk.renderer.generators

The width of the head of arrows.

BasicSceneGenerator.BackgroundColor - Class in org.openscience.cdk.renderer.generators

The background color of the drawn image.

BasicSceneGenerator.BondLength - Class in org.openscience.cdk.renderer.generators

The length on the screen of a typical bond.

BasicSceneGenerator.FitToScreen - Class in org.openscience.cdk.renderer.generators

If true, the scale is set such that the diagram fills the whole screen.

BasicSceneGenerator.FontName - Class in org.openscience.cdk.renderer.generators

Font to use for text.

BasicSceneGenerator.ForegroundColor - Class in org.openscience.cdk.renderer.generators

The foreground color, with which objects are drawn.

BasicSceneGenerator.Margin - Class in org.openscience.cdk.renderer.generators

Area on each of the four margins to keep empty.

BasicSceneGenerator.Scale - Class in org.openscience.cdk.renderer.generators

The scale is the factor to multiply model coordinates by to convert the coordinates to screen space coordinate, such that the entire structure fits the visible screen dimension.

BasicSceneGenerator.ShowMoleculeTitle - Class in org.openscience.cdk.renderer.generators

Determines if the molecule's title is depicted.

BasicSceneGenerator.ShowReactionTitle - Class in org.openscience.cdk.renderer.generators

Determines if the reaction's title is depicted.

BasicSceneGenerator.ShowTooltip - Class in org.openscience.cdk.renderer.generators

Determines if tooltips are to be shown.

BasicSceneGenerator.UseAntiAliasing - Class in org.openscience.cdk.renderer.generators

If set to true, uses anti-aliasing for drawing.

BasicSceneGenerator.UsedFontStyle - Class in org.openscience.cdk.renderer.generators

The font style to use for text.

BasicSceneGenerator.ZoomFactor - Class in org.openscience.cdk.renderer.generators

The zoom factor which is a user oriented parameter allowing the user to zoom in on parts of the molecule.

BasicValidator - Class in org.openscience.cdk.validate

Validator which tests a number of basic chemical semantics.

BasicValidator() - Constructor for class org.openscience.cdk.validate.BasicValidator

Bayesian - Class in org.openscience.cdk.fingerprint.model

Bayesian models using fingerprints: provides model creation, analysis, prediction and serialisation. Uses a variation of the classic Bayesian model, using a Laplacian correction, which sums log values of ratios rather than multiplying them together.

Bayesian(int) - Constructor for class org.openscience.cdk.fingerprint.model.Bayesian

Instantiate a Bayesian model with no data.

Bayesian(int, int) - Constructor for class org.openscience.cdk.fingerprint.model.Bayesian

Instantiate a Bayesian model with no data.

BCUTDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

Eigenvalue based descriptor noted for its utility in chemical diversity.

BCUTDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor

BEILSTEINRN - Static variable in class org.openscience.cdk.CDKConstants

The Beilstein Registry Number.

BENZENE_RING - Static variable in class org.openscience.cdk.tools.AtomTypeTools

BERKELIUM - Static variable in enum org.openscience.cdk.config.Elements

BERYLLIUM - Static variable in enum org.openscience.cdk.config.Elements

BGFFormat - Class in org.openscience.cdk.io.formats

BGFFormat() - Constructor for class org.openscience.cdk.io.formats.BGFFormat

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

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).

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

Bond - Class in org.openscience.cdk

Implements the concept of a covalent bond between two or more atoms.

Bond() - Constructor for class org.openscience.cdk.Bond

Constructs an empty bond.

Bond(IAtom, IAtom) - Constructor for class org.openscience.cdk.Bond

Constructs a bond with a single bond order..

Bond(IAtom, IAtom, IBond.Order) - Constructor for class org.openscience.cdk.Bond

Constructs a bond with a given order.

Bond(IAtom[]) - Constructor for class org.openscience.cdk.Bond

Constructs a multi-center bond, with undefined order and no stereo information.

Bond(IAtom[], IBond.Order) - Constructor for class org.openscience.cdk.Bond

Constructs a multi-center bond, with a specified order and no stereo information.

Bond(IAtom, IAtom, IBond.Order, IBond.Stereo) - Constructor for class org.openscience.cdk.Bond

Constructs a bond with a given order and stereo orientation from an array of atoms.

BOND - Static variable in class org.openscience.cdk.libio.jena.CDK

Bond - Class in org.openscience.cdk.silent

Implements the concept of a covalent bond between two or more atoms.

Bond() - Constructor for class org.openscience.cdk.silent.Bond

Constructs an empty bond.

Bond(IAtom, IAtom) - Constructor for class org.openscience.cdk.silent.Bond

Constructs a bond with a single bond order..

Bond(IAtom, IAtom, IBond.Order) - Constructor for class org.openscience.cdk.silent.Bond

Constructs a bond with a given order.

Bond(IAtom[]) - Constructor for class org.openscience.cdk.silent.Bond

Constructs a multi-center bond, with undefined order and no stereo information.

Bond(IAtom[], IBond.Order) - Constructor for class org.openscience.cdk.silent.Bond

Constructs a multi-center bond, with a specified order and no stereo information.

Bond(IAtom, IAtom, IBond.Order, IBond.Stereo) - Constructor for class org.openscience.cdk.silent.Bond

Constructs a bond with a given order and stereo orientation from an array of atoms.

bondARef1 - Variable in class org.openscience.cdk.io.cml.CMLCoreModule

bondARef2 - Variable in class org.openscience.cdk.io.cml.CMLCoreModule

bondAromaticity - Variable in class org.openscience.cdk.io.cml.CMLCoreModule

bondCount - Variable in class org.openscience.cdk.AtomContainer

Number of bonds contained by this object.

bondCount - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Number of bonds contained by this object.

bondCount - Variable in class org.openscience.cdk.silent.AtomContainer

Number of bonds contained by this object.

BondCountDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

IDescriptor based on the number of bonds of a certain bond order.

BondCountDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor

Constructor for the BondCountDescriptor object

bondCounter - Variable in class org.openscience.cdk.io.cml.CMLCoreModule

bondCustomProperty - Variable in class org.openscience.cdk.io.cml.CMLCoreModule

bondDictRefs - Variable in class org.openscience.cdk.io.cml.CMLCoreModule

BondDiff - Class in org.openscience.cdk.tools.diff

Compares two IBond classes.

BondDistance() - Constructor for class org.openscience.cdk.renderer.generators.BasicBondGenerator.BondDistance

bondElid - Variable in class org.openscience.cdk.io.cml.CMLCoreModule

bondid - Variable in class org.openscience.cdk.io.cml.CMLCoreModule

BondLength() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.BondLength

BondManipulator - Class in org.openscience.cdk.tools.manipulator

Class with convenience methods that provide methods to manipulate AtomContainer's.

BondManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.BondManipulator

bondMap - Variable in class org.openscience.cdk.stereo.StereoElementFactory

A bond map for fast access to bond labels between two atom indices.

BondMatcher - Class in org.openscience.cdk.isomorphism

Defines compatibility checking of bonds for (subgraph)-isomorphism mapping.

BondMatcher() - Constructor for class org.openscience.cdk.isomorphism.BondMatcher

BONDORDER_DOUBLE - Static variable in class org.openscience.cdk.CDKConstants

Deprecated.

Use IBond.Order DOUBLE directly.

BONDORDER_QUADRUPLE - Static variable in class org.openscience.cdk.CDKConstants

Deprecated.

Use IBond.Order QUADRUPLE directly.

BONDORDER_SINGLE - Static variable in class org.openscience.cdk.CDKConstants

Deprecated.

Use IBond.Order SINGLE directly.

BONDORDER_TRIPLE - Static variable in class org.openscience.cdk.CDKConstants

Deprecated.

Use IBond.Order TRIPLE directly.

bondOrderCanBeIncreased(IBond, IAtomContainer) - Method in class org.openscience.cdk.tools.AtomTypeAwareSaturationChecker

Check if the bond order can be increased.

BondOrderDifference - Class in org.openscience.cdk.tools.diff.tree

IDifference between two IBond.Orders.

BondPartialPiChargeDescriptor - Class in org.openscience.cdk.qsar.descriptors.bond

The calculation of bond-pi Partial charge is calculated determining the difference the Partial Pi Charge on atoms A and B of a bond.

BondPartialPiChargeDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor

Constructor for the BondPartialPiChargeDescriptor object.

BondPartialSigmaChargeDescriptor - Class in org.openscience.cdk.qsar.descriptors.bond

The calculation of bond-sigma Partial charge is calculated determining the difference the Partial Sigma Charge on atoms A and B of a bond.

BondPartialSigmaChargeDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor

Constructor for the BondPartialSigmaChargeDescriptor object.

BondPartialTChargeDescriptor - Class in org.openscience.cdk.qsar.descriptors.bond

The calculation of bond total Partial charge is calculated determining the difference the Partial Total Charge on atoms A and B of a bond.

BondPartialTChargeDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor

Constructor for the BondPartialTChargeDescriptor object.

BondRef - Class in org.openscience.cdk

A bond ref, references a CDK IBond indirectly.

BondRef(IBond) - Constructor for class org.openscience.cdk.BondRef

Create a pointer for the provided bond.

BondRefinerBuilder() - Constructor for class org.openscience.cdk.group.PartitionRefinement.BondRefinerBuilder

bonds() - Method in class org.openscience.cdk.Atom

Returns the bonds connected to this atom.

bonds - Variable in class org.openscience.cdk.AtomContainer

Internal array of bonds.

bonds() - Method in class org.openscience.cdk.AtomContainer

Returns an Iterable for looping over all bonds in this container.

bonds() - Method in class org.openscience.cdk.AtomRef

bonds() - Method in class org.openscience.cdk.debug.DebugAminoAcid

Returns an Iterable for looping over all bonds in this container.

bonds() - Method in class org.openscience.cdk.debug.DebugAtom

Returns the bonds connected to this atom.

bonds() - Method in class org.openscience.cdk.debug.DebugAtomContainer

Returns an Iterable for looping over all bonds in this container.

bonds() - Method in class org.openscience.cdk.debug.DebugBioPolymer

Returns an Iterable for looping over all bonds in this container.

bonds() - Method in class org.openscience.cdk.debug.DebugCrystal

Returns an Iterable for looping over all bonds in this container.

bonds() - Method in class org.openscience.cdk.debug.DebugMonomer

Returns an Iterable for looping over all bonds in this container.

bonds() - Method in class org.openscience.cdk.debug.DebugPolymer

Returns an Iterable for looping over all bonds in this container.

bonds() - Method in class org.openscience.cdk.debug.DebugRing

Returns an Iterable for looping over all bonds in this container.

bonds() - Method in class org.openscience.cdk.debug.DebugStrand

Returns an Iterable for looping over all bonds in this container.

bonds() - Method in interface org.openscience.cdk.interfaces.IAtom

Returns the bonds connected to this atom.

bonds() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns an Iterable for looping over all bonds in this container.

bonds() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Returns the bonds connected to this atom.

bonds - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Internal array of bonds.

bonds() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Returns an Iterable for looping over all bonds in this container.

bonds() - Method in class org.openscience.cdk.silent.Atom

Returns the bonds connected to this atom.

bonds - Variable in class org.openscience.cdk.silent.AtomContainer

Internal array of bonds.

bonds() - Method in class org.openscience.cdk.silent.AtomContainer

Returns an Iterable for looping over all bonds in this container.

BondSeparation() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.BondSeparation

BondSigmaElectronegativityDescriptor - Class in org.openscience.cdk.qsar.descriptors.bond

The calculation of bond-Polarizability is calculated determining the difference the Sigma electronegativity on atoms A and B of a bond.

BondSigmaElectronegativityDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor

Constructor for the BondSigmaElectronegativityDescriptor object.

bondsInTree - Variable in class org.openscience.cdk.graph.SpanningTree

bondStereo - Variable in class org.openscience.cdk.io.cml.CMLCoreModule

BondsToAtomDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic

This class returns the number of bonds on the shortest path between two atoms.

BondsToAtomDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor

Constructor for the BondsToAtomDescriptor object

bondSymbols - Variable in class org.openscience.cdk.tools.HOSECodeGenerator

The bond symbols used for bond orders "single", "double", "triple" and "aromatic"

BondTools - Class in org.openscience.cdk.geometry

A set of static utility classes for geometric calculations on IBonds.

BondTools() - Constructor for class org.openscience.cdk.geometry.BondTools

BondWidth() - Constructor for class org.openscience.cdk.renderer.generators.BasicBondGenerator.BondWidth

BooleanArrayDifference - Class in org.openscience.cdk.tools.diff.tree

Difference between two boolean[]'s.

BooleanDifference - Class in org.openscience.cdk.tools.diff.tree

IDifference between two Booleans.

BooleanIOSetting - Class in org.openscience.cdk.io.setting

An class for a reader setting which must be of type String.

BooleanIOSetting(String, IOSetting.Importance, String, String) - Constructor for class org.openscience.cdk.io.setting.BooleanIOSetting

BooleanResult - Class in org.openscience.cdk.qsar.result

Object that provides access to the calculated descriptor value.

BooleanResult(boolean) - Constructor for class org.openscience.cdk.qsar.result.BooleanResult

BooleanResultType - Class in org.openscience.cdk.qsar.result

IDescriptorResult type for boolean.

BooleanResultType() - Constructor for class org.openscience.cdk.qsar.result.BooleanResultType

booleanValue() - Method in class org.openscience.cdk.qsar.result.BooleanResult

BORON - Static variable in enum org.openscience.cdk.config.Elements

Bounds - Class in org.openscience.cdk.renderer.elements

Defines a bounding box element which the renderer can use to determine the true drawing limits.

Bounds(double, double, double, double) - Constructor for class org.openscience.cdk.renderer.elements.Bounds

Specify the min/max coordinates of the bounding box.

Bounds() - Constructor for class org.openscience.cdk.renderer.elements.Bounds

An empty bounding box.

Bounds(IRenderingElement) - Constructor for class org.openscience.cdk.renderer.elements.Bounds

An bounding box around the specified element.

BoundsCalculator - Class in org.openscience.cdk.renderer

Utility class for calculating the 2D bounding rectangles (bounds) of various IChemObject subtypes - IChemModel, IReactionSet, IReaction, IAtomContainerSet, and IAtomContainer.

BoundsCalculator() - Constructor for class org.openscience.cdk.renderer.BoundsCalculator

BoundsColor() - Constructor for class org.openscience.cdk.renderer.generators.BoundsGenerator.BoundsColor

BoundsGenerator - Class in org.openscience.cdk.renderer.generators

Produce a bounding rectangle for various chem objects.

BoundsGenerator() - Constructor for class org.openscience.cdk.renderer.generators.BoundsGenerator

BoundsGenerator.BoundsColor - Class in org.openscience.cdk.renderer.generators

The color of the box drawn at the bounds of a molecule, molecule set, or reaction.

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

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

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

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

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.

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

C

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

CAESIUM - Static variable in enum org.openscience.cdk.config.Elements

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

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(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.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(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor

Calculates the descriptor value for the given IAtomContainer.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor

The AlogP descriptor.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor

Determine the number of amino acids groups the supplied IAtomContainer.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor

Calculate the sum of atomic polarizabilities in an IAtomContainer.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor

Calculate the count of aromatic atoms in the supplied IAtomContainer.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor

Calculate the count of aromatic atoms in the supplied IAtomContainer.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor

This method calculate the number of atoms of a given type in an IAtomContainer.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass

This method calculate the ATS Autocorrelation descriptor.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability

This method calculate the ATS Autocorrelation descriptor.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor

Calculates the descriptor value for the given IAtomContainer.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor

Calculates the three classes of BCUT descriptors.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor

This method calculate the number of bonds of a given type in an atomContainer

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor

This method calculate the sum of the absolute value of the difference between atomic polarizabilities of all bonded atoms in the molecule

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor

Calculates the 9 carbon types descriptors

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor

Evaluates the 29 CPSA descriptors using Gasteiger-Marsilli charges.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor

Calculates the eccentric connectivity

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor

Calculates the FMF descriptor value for the given IAtomContainer.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalCSP3Descriptor

Calculates the Fsp³ descriptor value for the given IAtomContainer.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor

Calculates the topological polar surface area and expresses it as a ratio to molecule size.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor

Calculate the complexity in the supplied IAtomContainer.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor

Calculates the 9 gravitational indices.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor

Calculates the number of H bond acceptors.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor

Calculates the number of H bond donors.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor

Calculate sp3/sp2 hybridization ratio in the supplied IAtomContainer.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor

calculates the kier shape indices for an atom container

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor

This method calculates occurrences of the Kier & Hall E-state fragments.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor

Calculate the count of atoms of the largest chain in the supplied IAtomContainer.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor

Calculate the count of atoms of the largest pi system in the supplied IAtomContainer.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor

Evaluate the descriptor for the molecule.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor

Calculate the count of atoms of the longest aliphatic chain in the supplied IAtomContainer.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor

Calculates the Mannhold LogP for an atom container.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

Calculate the weight of specified element type in the supplied IAtomContainer.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor

Calculates the 3 MI's, 3 ration and the R_gyr value.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor

Evaluate the descriptor for the molecule.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor

Calculates the two Petitjean shape indices.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor

The method calculates the number of rotatable bonds of an atom container.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor

the method take a boolean checkAromaticity: if the boolean is true, it means that aromaticity has to be checked.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor

Performs the calculation: the graph will be analyzed and ring information will be determined and wrapped up into descriptors.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.SpiroAtomCountDescriptor

Calculates the descriptor value for the given IAtomContainer.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor

Calculates the TPSA for an atom container.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor

Calculates the descriptor value using the VABCVolume class.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor

calculates the VAdjMa descriptor for an atom container

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor

Calculate the 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.

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.

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.

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.

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.

calculateSurface() - Method in class org.openscience.cdk.geometry.surface.NumericalSurface

Evaluate the surface.

CALIFORNIUM - Static variable in enum org.openscience.cdk.config.Elements

cancel() - Method in class org.openscience.cdk.formula.MolecularFormulaGenerator

Cancel the current search.

canDraw(IAtom, IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator

Checks an atom to see if it should be drawn.

Canon - Class in org.openscience.cdk.graph.invariant

An implementation based on the canon algorithm (Weininger, David et. al.. Journal of Chemical Information and Computer Sciences. 1989. 29).

Canonical - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Output SMILES in a canonical order.

CANONICAL_LABEL - Static variable in class org.openscience.cdk.smiles.InvPair

canonicalizeAtoms(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.SimpleAtomCanonicalizer

CanonicalLabeler - Class in org.openscience.cdk.graph.invariant

Deprecated.

this labeller uses slow data structures and has been replaced - Canon

CanonicalLabeler() - Constructor for class org.openscience.cdk.graph.invariant.CanonicalLabeler

Deprecated.

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

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

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.

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.

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.

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

CDKSourceCodeFormat - Class in org.openscience.cdk.io.formats

CDKSourceCodeFormat() - Constructor for class org.openscience.cdk.io.formats.CDKSourceCodeFormat

CDKSourceCodeWriter - Class in org.openscience.cdk.io

Converts a Molecule into CDK source code that would build the same molecule.

CDKSourceCodeWriter(Writer) - Constructor for class org.openscience.cdk.io.CDKSourceCodeWriter

Constructs a new CDKSourceCodeWriter.

CDKSourceCodeWriter(OutputStream) - Constructor for class org.openscience.cdk.io.CDKSourceCodeWriter

CDKSourceCodeWriter() - Constructor for class org.openscience.cdk.io.CDKSourceCodeWriter

CDKStyleAromaticity() - Constructor for class org.openscience.cdk.renderer.generators.RingGenerator.CDKStyleAromaticity

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

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

CFG_MASK - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

changeBase(Permutation) - Method in class org.openscience.cdk.group.PermutationGroup

Change the base of the group to the new base newBase.

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.

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.

charged() - Method in class org.openscience.cdk.hash.HashGeneratorMaker

Discriminate protonation states.

ChargeGroup - Class in org.openscience.cdk.libio.md

A ChargeGroup (CG) is a numbered collection of atoms in an MDMolecule.

ChargeGroup() - Constructor for class org.openscience.cdk.libio.md.ChargeGroup

Empty constructor.

ChargeGroup(IAtomContainer, int, MDMolecule) - Constructor for class org.openscience.cdk.libio.md.ChargeGroup

Constructor to create a ChargeGroup based on an AC, a number, and a MDMolecule.

ChargeRule - Class in org.openscience.cdk.formula.rules

This class validate if the charge in the IMolecularFormula correspond with a specific value.

ChargeRule() - Constructor for class org.openscience.cdk.formula.rules.ChargeRule

Constructor for the ChargeRule object.

CHECK_RING_SYSTEM - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor

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.

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.

checkSymmetry(boolean) - Method in class org.openscience.cdk.stereo.StereoElementFactory

checkTimeout() - Method in class org.openscience.cdk.ringsearch.AllRingsFinder

Deprecated.

timeout not used

Chem3D_Cartesian_1Format - Class in org.openscience.cdk.io.formats

Chem3D_Cartesian_1Format() - Constructor for class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format

Chem3D_Cartesian_2Format - Class in org.openscience.cdk.io.formats

Chem3D_Cartesian_2Format() - Constructor for class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format

ChemDrawFormat - Class in org.openscience.cdk.io.formats

ChemDrawFormat() - Constructor for class org.openscience.cdk.io.formats.ChemDrawFormat

ChemFile - Class in org.openscience.cdk

A Object containing a number of ChemSequences.

ChemFile() - Constructor for class org.openscience.cdk.ChemFile

Constructs an empty ChemFile.

ChemFile - Class in org.openscience.cdk.silent

A Object containing a number of ChemSequences.

ChemFile() - Constructor for class org.openscience.cdk.silent.ChemFile

Constructs an empty ChemFile.

ChemFileManipulator - Class in org.openscience.cdk.tools.manipulator

Class with convenience methods that provide methods from methods from ChemObjects within the ChemFile.

ChemFileManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.ChemFileManipulator

ChemGraph - Class in org.openscience.cdk.structgen.stochastic.operator

ChemGraph(IAtomContainer) - Constructor for class org.openscience.cdk.structgen.stochastic.operator.ChemGraph

CHEMICAL_GROUP_CONSTANT - Static variable in class org.openscience.cdk.CDKConstants

Used as property key for indicating the chemical group of a certain atom type.

ChemModel - Class in org.openscience.cdk

An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.

ChemModel() - Constructor for class org.openscience.cdk.ChemModel

Constructs an new ChemModel with a null setOfMolecules.

ChemModel - Class in org.openscience.cdk.silent

An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.

ChemModel() - Constructor for class org.openscience.cdk.silent.ChemModel

Constructs an new ChemModel with a null setOfMolecules.

chemModelCount - Variable in class org.openscience.cdk.ChemSequence

Number of ChemModels contained by this container.

chemModelCount - Variable in class org.openscience.cdk.silent.ChemSequence

Number of ChemModels contained by this container.

ChemModelManipulator - Class in org.openscience.cdk.tools.manipulator

Class with convenience methods that provide methods from methods from ChemObjects within the ChemModel.

ChemModelManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.ChemModelManipulator

ChemModelRenderer - Class in org.openscience.cdk.renderer

A general renderer for IChemModels, IReactions, and IAtomContainers.

ChemModelRenderer(List<IGenerator<IAtomContainer>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.ChemModelRenderer

A renderer that generates diagrams using the specified generators and manages fonts with the supplied font manager.

ChemModelRenderer(List<IGenerator<IAtomContainer>>, List<IGenerator<IReaction>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.ChemModelRenderer

chemModels - Variable in class org.openscience.cdk.ChemSequence

Array of ChemModels.

chemModels() - Method in class org.openscience.cdk.ChemSequence

Returns an Iterable to ChemModels in this container.

chemModels() - Method in class org.openscience.cdk.debug.DebugChemSequence

Returns an Iterable to ChemModels in this container.

chemModels() - Method in interface org.openscience.cdk.interfaces.IChemSequence

Returns an Iterable to ChemModels in this container.

chemModels - Variable in class org.openscience.cdk.silent.ChemSequence

Array of ChemModels.

chemModels() - Method in class org.openscience.cdk.silent.ChemSequence

Returns an Iterable to ChemModels in this container.

ChemObject - Class in org.openscience.cdk

The base class for all chemical objects in this cdk.

ChemObject() - Constructor for class org.openscience.cdk.ChemObject

Constructs a new IChemObject.

ChemObject(IChemObject) - Constructor for class org.openscience.cdk.ChemObject

Constructs a new IChemObject by copying the flags, and the identifier.

CHEMOBJECT - Static variable in class org.openscience.cdk.libio.jena.CDK

ChemObject - Class in org.openscience.cdk.silent

The base class for all chemical objects in this cdk.

ChemObject() - Constructor for class org.openscience.cdk.silent.ChemObject

Constructs a new IChemObject.

ChemObject(IChemObject) - Constructor for class org.openscience.cdk.silent.ChemObject

Constructs a new IChemObject by copying the flags, and the identifier.

ChemObjectChangeEvent - Class in org.openscience.cdk.event

Event fired by cdk classes to their registered listeners in case something changes within them.

ChemObjectChangeEvent(Object) - Constructor for class org.openscience.cdk.event.ChemObjectChangeEvent

Constructs a ChemObjectChangeEvent with a reference to the object where it originated.

ChemObjectDiff - Class in org.openscience.cdk.tools.diff

Compares two IChemObject classes.

ChemObjectDifference - Class in org.openscience.cdk.tools.diff.tree

IDifference between two IChemObjects.

ChemObjectDifference(String) - Constructor for class org.openscience.cdk.tools.diff.tree.ChemObjectDifference

ChemObjectIO - Class in org.openscience.cdk.io

Provides some basic functionality for readers and writers.

ChemObjectIO() - Constructor for class org.openscience.cdk.io.ChemObjectIO

chemObjectReader - Variable in class org.openscience.cdk.io.random.RandomAccessReader

ChemSequence - Class in org.openscience.cdk

A sequence of ChemModels, which can, for example, be used to store the course of a reaction.

ChemSequence() - Constructor for class org.openscience.cdk.ChemSequence

Constructs an empty ChemSequence.

ChemSequence - Class in org.openscience.cdk.silent

A sequence of ChemModels, which can, for example, be used to store the course of a reaction.

ChemSequence() - Constructor for class org.openscience.cdk.silent.ChemSequence

Constructs an empty ChemSequence.

chemSequenceCount - Variable in class org.openscience.cdk.ChemFile

Number of ChemSequences contained by this container.

chemSequenceCount - Variable in class org.openscience.cdk.silent.ChemFile

Number of ChemSequences contained by this container.

ChemSequenceManipulator - Class in org.openscience.cdk.tools.manipulator

Class with convenience methods that provide methods from methods from ChemObjects within the ChemSequence.

ChemSequenceManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.ChemSequenceManipulator

chemSequences - Variable in class org.openscience.cdk.ChemFile

Array of ChemSquences.

chemSequences() - Method in class org.openscience.cdk.ChemFile

Returns the Iterable to ChemSequences of this container.

chemSequences() - Method in class org.openscience.cdk.debug.DebugChemFile

Returns the Iterable to ChemSequences of this container.

chemSequences() - Method in interface org.openscience.cdk.interfaces.IChemFile

Returns the Iterable to ChemSequences of this container.

chemSequences - Variable in class org.openscience.cdk.silent.ChemFile

Array of ChemSquences.

chemSequences() - Method in class org.openscience.cdk.silent.ChemFile

Returns the Iterable to ChemSequences of this container.

ChemtoolFormat - Class in org.openscience.cdk.io.formats

See here.

ChemtoolFormat() - Constructor for class org.openscience.cdk.io.formats.ChemtoolFormat

ChiChainDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

Evaluates chi chain descriptors.

ChiChainDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor

ChiClusterDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

Evaluates chi cluster descriptors.

ChiClusterDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor

Child(String, TextGroupElement.Position) - Constructor for class org.openscience.cdk.renderer.elements.TextGroupElement.Child

Make a child element with the specified text and position.

Child(String, String, TextGroupElement.Position) - Constructor for class org.openscience.cdk.renderer.elements.TextGroupElement.Child

Make a child element with the specified text, subscript, and position.

childCount() - Method in class org.openscience.cdk.tools.diff.tree.AbstractDifferenceList

Returns the number of children of this IDifference.

childCount() - Method in interface org.openscience.cdk.tools.diff.tree.IDifferenceList

Returns the number of children of this IDifference.

children - Variable in class org.openscience.cdk.renderer.elements.TextGroupElement

The child text elements.

ChiPathClusterDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

Evaluates chi path cluster descriptors.

ChiPathClusterDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor

ChiPathDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

Evaluates chi path descriptors.

ChiPathDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor

chiral() - Method in class org.openscience.cdk.hash.HashGeneratorMaker

Generate different hash codes for stereoisomers.

CHLORINE - Static variable in enum org.openscience.cdk.config.Elements

CHROMIUM - Static variable in enum org.openscience.cdk.config.Elements

CIFFormat - Class in org.openscience.cdk.io.formats

CIFFormat() - Constructor for class org.openscience.cdk.io.formats.CIFFormat

CIFReader - Class in org.openscience.cdk.io

This is not a reader for the CIF and mmCIF crystallographic formats.

CIFReader(Reader) - Constructor for class org.openscience.cdk.io.CIFReader

Create an CIF like file reader.

CIFReader(InputStream) - Constructor for class org.openscience.cdk.io.CIFReader

CIFReader() - Constructor for class org.openscience.cdk.io.CIFReader

CIP_DESCRIPTOR - Static variable in class org.openscience.cdk.CDKConstants

Property key to store the CIP descriptor label for an atom / bond.

CIPLigandRule - Class in org.openscience.cdk.geometry.cip.rules

Compares to ILigands based on CIP sequences sub rules.

CIPLigandRule() - Constructor for class org.openscience.cdk.geometry.cip.rules.CIPLigandRule

CIPTool - Class in org.openscience.cdk.geometry.cip

Tool to help determine the R,S and stereochemistry definitions of a subset of the CIP rules (Cahn, R.S. et. al.. Angew. Chem. Int. Ed.. 1966. 5).

CIPTool() - Constructor for class org.openscience.cdk.geometry.cip.CIPTool

CIPTool.CIP_CHIRALITY - Enum in org.openscience.cdk.geometry.cip

Enumeration with the two tetrahedral chiralities defined by the CIP schema.

CircularFingerprinter - Class in org.openscience.cdk.fingerprint

Circular fingerprints: for generating fingerprints that are functionally equivalent to ECFP-2/4/6 and FCFP-2/4/6 fingerprints, which are partially described by Rogers et al.

CircularFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.CircularFingerprinter

Default constructor: uses the ECFP6 type.

CircularFingerprinter(int) - Constructor for class org.openscience.cdk.fingerprint.CircularFingerprinter

Specific constructor: initializes with descriptor class type, one of ECFP_{p} or FCFP_{p}, where ECFP is for the extended-connectivity fingerprints, FCFP is for the functional class version, and {p} is the path diameter, and may be 0, 2, 4 or 6.

CircularFingerprinter(int, int) - Constructor for class org.openscience.cdk.fingerprint.CircularFingerprinter

Specific constructor: initializes with descriptor class type, one of ECFP_{p} or FCFP_{p}, where ECFP is for the extended-connectivity fingerprints, FCFP is for the functional class version, and {p} is the path diameter, and may be 0, 2, 4 or 6.

CircularFingerprinter.FP - Class in org.openscience.cdk.fingerprint

CisTrans - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Geometric CisTrans (e.g.

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.

clearAtomConfigurations(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator

This method will reset all atom configuration to UNSET.

clearMajorIsotopes(IAtomContainer) - Static method in class org.openscience.cdk.config.Isotopes

Clear the isotope information from atoms that are major isotopes (e.g.

clearMajorIsotopes(IMolecularFormula) - Static method in class org.openscience.cdk.config.Isotopes

Clear the isotope information from istopes that are major (e.g.

clearProps(IAtomContainer) - Method in class org.openscience.cdk.forcefield.mmff.Mmff

Clear all transient properties assigned by this class.

clearTraining() - Method in class org.openscience.cdk.fingerprint.model.Bayesian

Clears out the training set, to free up memory.

clone() - Method in class org.openscience.cdk.AminoAcid

Clones this AminoAcid object.

clone() - Method in class org.openscience.cdk.Atom

Clones this atom object and its content.

clone() - Method in class org.openscience.cdk.AtomContainer

Clones this IChemObject.

clone() - Method in class org.openscience.cdk.AtomContainerSet

Clones this AtomContainerSet and its content.

clone() - Method in class org.openscience.cdk.AtomRef

Returns a deep clone of this IChemObject.

clone() - Method in class org.openscience.cdk.AtomType

clone() - Method in class org.openscience.cdk.BioPolymer

clone() - Method in class org.openscience.cdk.Bond

Clones this bond object, including clones of the atoms between which the bond is defined.

clone() - Method in class org.openscience.cdk.BondRef

Returns a deep clone of this IChemObject.

clone() - Method in class org.openscience.cdk.ChemFile

Allows for getting an clone of this object.

clone() - Method in class org.openscience.cdk.ChemModel

Clones this ChemModel and its content.

clone() - Method in class org.openscience.cdk.ChemObject

Clones this IChemObject.

clone() - Method in class org.openscience.cdk.ChemSequence

clone() - Method in class org.openscience.cdk.Crystal

Makes a clone of this crystal.

clone() - Method in class org.openscience.cdk.debug.DebugAminoAcid

Clones this AminoAcid object.

clone() - Method in class org.openscience.cdk.debug.DebugAtom

Clones this atom object and its content.

clone() - Method in class org.openscience.cdk.debug.DebugAtomContainer

Clones this IChemObject.

clone() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet

Clones this AtomContainerSet and its content.

clone() - Method in class org.openscience.cdk.debug.DebugAtomType

Clones this IChemObject.

clone() - Method in class org.openscience.cdk.debug.DebugBioPolymer

Clones this IChemObject.

clone() - Method in class org.openscience.cdk.debug.DebugBond

Clones this bond object, including clones of the atoms between which the bond is defined.

clone() - Method in class org.openscience.cdk.debug.DebugChemFile

Allows for getting an clone of this object.

clone() - Method in class org.openscience.cdk.debug.DebugChemModel

Clones this ChemModel and its content.

clone() - Method in class org.openscience.cdk.debug.DebugChemObject

Clones this IChemObject.

clone() - Method in class org.openscience.cdk.debug.DebugChemSequence

Clones this IChemObject.

clone() - Method in class org.openscience.cdk.debug.DebugCrystal

Makes a clone of this crystal.

clone() - Method in class org.openscience.cdk.debug.DebugElectronContainer

Clones this IChemObject.

clone() - Method in class org.openscience.cdk.debug.DebugElement

Clones this IChemObject.

clone() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Clones this atom object and its content.

clone() - Method in class org.openscience.cdk.debug.DebugIsotope

Clones this IChemObject.

clone() - Method in class org.openscience.cdk.debug.DebugLonePair

Clones this LonePair object, including a clone of the atom for which the lone pair is defined.

clone() - Method in class org.openscience.cdk.debug.DebugMapping

Clones this Mapping and the mapped IChemObjects.

clone() - Method in class org.openscience.cdk.debug.DebugMonomer

Clones this IChemObject.

clone() - Method in class org.openscience.cdk.debug.DebugPolymer

Clones this IChemObject.

clone() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Clones this atom object and its content.

clone() - Method in class org.openscience.cdk.debug.DebugReaction

Clones this Reaction and its content.

clone() - Method in class org.openscience.cdk.debug.DebugReactionScheme

Clones this ReactionScheme object and its content.

clone() - Method in class org.openscience.cdk.debug.DebugReactionSet

Clones this ReactionSet and the contained Reactions too.

clone() - Method in class org.openscience.cdk.debug.DebugRing

Clones this IChemObject.

clone() - Method in class org.openscience.cdk.debug.DebugSingleElectron

Clones this SingleElectron object, including a clone of the atom for which the SingleElectron is defined.

clone() - Method in class org.openscience.cdk.debug.DebugStrand

Clones this IChemObject.

clone() - Method in class org.openscience.cdk.debug.DebugSubstance

Clones this AtomContainerSet and its content.

clone() - Method in class org.openscience.cdk.ElectronContainer

clone() - Method in class org.openscience.cdk.Element

clone() - Method in class org.openscience.cdk.formula.AdductFormula

Clones this AdductFormula object and its content.

clone() - Method in class org.openscience.cdk.formula.IsotopeContainer

Clones this IsotopeContainer object and its content.

clone() - Method in class org.openscience.cdk.formula.IsotopePattern

Clones this IsotopePattern object and its content.

clone() - Method in class org.openscience.cdk.formula.MolecularFormula

Clones this MolecularFormula object and its content.

clone() - Method in class org.openscience.cdk.formula.MolecularFormulaRange

Clones this MolecularFormulaExpand object and its content.

clone() - Method in class org.openscience.cdk.formula.MolecularFormulaSet

Clones this MolecularFormulaSet object and its content.

clone() - Method in class org.openscience.cdk.FragmentAtom

clone() - Method in interface org.openscience.cdk.interfaces.IAdductFormula

Clones this IAdductFormula object and its content.

clone() - Method in interface org.openscience.cdk.interfaces.IAminoAcid

Returns a deep clone of this IChemObject.

clone() - Method in interface org.openscience.cdk.interfaces.IAtom

Returns a deep clone of this IChemObject.

clone() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns a deep clone of this IChemObject.

clone() - Method in interface org.openscience.cdk.interfaces.IBioPolymer

Returns a deep clone of this IChemObject.

clone() - Method in interface org.openscience.cdk.interfaces.IBond

Returns a deep clone of this IChemObject.

clone() - Method in interface org.openscience.cdk.interfaces.IChemObject

Returns a deep clone of this IChemObject.

clone() - Method in interface org.openscience.cdk.interfaces.ICrystal

Returns a deep clone of this IChemObject.

clone() - Method in interface org.openscience.cdk.interfaces.IMolecularFormula

Clones this MolecularFormula object and its content.

clone() - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet

Clones this IMolecularFormulaSet object and its content.

clone() - Method in interface org.openscience.cdk.interfaces.IMonomer

Returns a deep clone of this IChemObject.

clone() - Method in interface org.openscience.cdk.interfaces.IPDBMonomer

Returns a deep clone of this IChemObject.

clone() - Method in interface org.openscience.cdk.interfaces.IPDBPolymer

Returns a deep clone of this IChemObject.

clone() - Method in interface org.openscience.cdk.interfaces.IPolymer

Returns a deep clone of this IChemObject.

clone() - Method in interface org.openscience.cdk.interfaces.IPseudoAtom

Returns a deep clone of this IChemObject.

clone() - Method in interface org.openscience.cdk.interfaces.IReactionScheme

Clones this IReactionScheme object and its content.

clone() - Method in interface org.openscience.cdk.interfaces.IRing

Returns a deep clone of this IChemObject.

clone() - Method in interface org.openscience.cdk.interfaces.IStrand

Returns a deep clone of this IChemObject.

clone() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

clone() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Clones this AtomContainer object and its content.

clone() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond

Clones this query bond object, including clones of the atoms between which the query bond is defined.

clone() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject

clone() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolChargeIDQueryAtom

clone() - Method in class org.openscience.cdk.Isotope

clone() - Method in class org.openscience.cdk.LonePair

Clones this LonePair object, including a clone of the atom for which the lone pair is defined.

clone() - Method in class org.openscience.cdk.Mapping

Clones this Mapping and the mapped IChemObjects.

clone() - Method in class org.openscience.cdk.Monomer

Clones this IChemObject.

clone() - Method in class org.openscience.cdk.Polymer

clone() - Method in class org.openscience.cdk.protein.data.PDBMonomer

Clones this IChemObject.

clone() - Method in class org.openscience.cdk.protein.data.PDBPolymer

Clones this IChemObject.

clone() - Method in class org.openscience.cdk.PseudoAtom

clone(IAtomContainer) - Static method in class org.openscience.cdk.qsar.AbstractMolecularDescriptor

clone() - Method in class org.openscience.cdk.Reaction

Clones this Reaction and its content.

clone() - Method in class org.openscience.cdk.ReactionScheme

Clones this ReactionScheme object and its content.

clone() - Method in class org.openscience.cdk.ReactionSet

Clones this ReactionSet and the contained Reactions too.

clone() - Method in class org.openscience.cdk.Ring

Clones this IChemObject.

clone() - Method in class org.openscience.cdk.RingSet

Clones this RingSet including the Rings.

clone() - Method in class org.openscience.cdk.signature.Orbit

clone() - Method in class org.openscience.cdk.silent.AdductFormula

Clones this AdductFormula object and its content.

clone() - Method in class org.openscience.cdk.silent.AminoAcid

Clones this AminoAcid object.

clone() - Method in class org.openscience.cdk.silent.Atom

Clones this atom object and its content.

clone() - Method in class org.openscience.cdk.silent.AtomContainer

Clones this IChemObject.

clone() - Method in class org.openscience.cdk.silent.AtomContainerSet

Clones this AtomContainerSet and its content.

clone() - Method in class org.openscience.cdk.silent.AtomType

clone() - Method in class org.openscience.cdk.silent.BioPolymer

clone() - Method in class org.openscience.cdk.silent.Bond

Clones this bond object, including clones of the atoms between which the bond is defined.

clone() - Method in class org.openscience.cdk.silent.ChemFile

Allows for getting an clone of this object.

clone() - Method in class org.openscience.cdk.silent.ChemModel

Clones this ChemModel and its content.

clone() - Method in class org.openscience.cdk.silent.ChemObject

Clones this IChemObject.

clone() - Method in class org.openscience.cdk.silent.ChemSequence

clone() - Method in class org.openscience.cdk.silent.Crystal

Makes a clone of this crystal.

clone() - Method in class org.openscience.cdk.silent.ElectronContainer

clone() - Method in class org.openscience.cdk.silent.Element

clone() - Method in class org.openscience.cdk.silent.FragmentAtom

clone() - Method in class org.openscience.cdk.silent.Isotope

clone() - Method in class org.openscience.cdk.silent.LonePair

Clones this LonePair object, including a clone of the atom for which the lone pair is defined.

clone() - Method in class org.openscience.cdk.silent.Mapping

Clones this Mapping and the mapped IChemObjects.

clone() - Method in class org.openscience.cdk.silent.MolecularFormula

Clones this MolecularFormula object and its content.

clone() - Method in class org.openscience.cdk.silent.MolecularFormulaSet

Clones this MolecularFormulaSet object and its content.

clone() - Method in class org.openscience.cdk.silent.Monomer

Clones this IChemObject.

clone() - Method in class org.openscience.cdk.silent.PDBMonomer

Clones this IChemObject.

clone() - Method in class org.openscience.cdk.silent.PDBPolymer

Clones this IChemObject.

clone() - Method in class org.openscience.cdk.silent.Polymer

clone() - Method in class org.openscience.cdk.silent.PseudoAtom

clone() - Method in class org.openscience.cdk.silent.Reaction

Clones this Reaction and its content.

clone() - Method in class org.openscience.cdk.silent.ReactionScheme

Clones this ReactionScheme object and its content.

clone() - Method in class org.openscience.cdk.silent.ReactionSet

Clones this ReactionSet and the contained Reactions too.

clone() - Method in class org.openscience.cdk.silent.Ring

Clones this IChemObject.

clone() - Method in class org.openscience.cdk.silent.RingSet

Clones this RingSet including the Rings.

clone() - Method in class org.openscience.cdk.silent.SingleElectron

Clones this SingleElectron object, including a clone of the atom for which the SingleElectron is defined.

clone() - Method in class org.openscience.cdk.silent.Strand

clone() - Method in class org.openscience.cdk.SingleElectron

Clones this SingleElectron object, including a clone of the atom for which the SingleElectron is defined.

clone() - Method in class org.openscience.cdk.Strand

close() - Method in class org.openscience.cdk.io.CDKSourceCodeWriter

Flushes the output and closes this object.

close() - Method in class org.openscience.cdk.io.CIFReader

close() - Method in class org.openscience.cdk.io.CMLReader

close() - Method in class org.openscience.cdk.io.CMLWriter

Flushes the output and closes this object.

close() - Method in class org.openscience.cdk.io.CrystClustReader

close() - Method in class org.openscience.cdk.io.CrystClustWriter

Flushes the output and closes this object.

close() - Method in class org.openscience.cdk.io.CTXReader

close() - Method in class org.openscience.cdk.io.GamessReader

close() - Method in class org.openscience.cdk.io.Gaussian03Reader

close() - Method in class org.openscience.cdk.io.Gaussian98Reader

close() - Method in class org.openscience.cdk.io.GhemicalMMReader

close() - Method in class org.openscience.cdk.io.HINReader

close() - Method in class org.openscience.cdk.io.HINWriter

Flushes the output and closes this object.

close() - Method in interface org.openscience.cdk.io.IChemObjectIO

Closes this IChemObjectIO's resources.

close() - Method in class org.openscience.cdk.io.INChIPlainTextReader

close() - Method in class org.openscience.cdk.io.INChIReader

close() - Method in class org.openscience.cdk.io.iterator.event.EventCMLReader

close() - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundASNReader

close() - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader

close() - Method in class org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader

close() - Method in class org.openscience.cdk.io.iterator.IteratingSDFReader

close() - Method in class org.openscience.cdk.io.iterator.IteratingSMILESReader

Close the reader.

close() - Method in class org.openscience.cdk.io.MDLReader

Deprecated.

close() - Method in class org.openscience.cdk.io.MDLRXNReader

Deprecated.

close() - Method in class org.openscience.cdk.io.MDLRXNV2000Reader

close() - Method in class org.openscience.cdk.io.MDLRXNV3000Reader

close() - Method in class org.openscience.cdk.io.MDLRXNWriter

Flushes the output and closes this object.

close() - Method in class org.openscience.cdk.io.MDLV2000Reader

close() - Method in class org.openscience.cdk.io.MDLV2000Writer

Flushes the output and closes this object.

close() - Method in class org.openscience.cdk.io.MDLV3000Reader

close() - Method in class org.openscience.cdk.io.MDLV3000Writer

Closes this IChemObjectIO's resources.

close() - Method in class org.openscience.cdk.io.Mol2Reader

close() - Method in class org.openscience.cdk.io.Mol2Writer

Flushes the output and closes this object.

close() - Method in class org.openscience.cdk.io.Mopac7Reader

close() - Method in class org.openscience.cdk.io.MoSSOutputReader

Closes this IChemObjectIO's resources.

close() - Method in class org.openscience.cdk.io.PCCompoundASNReader

close() - Method in class org.openscience.cdk.io.PCCompoundXMLReader

close() - Method in class org.openscience.cdk.io.PCSubstanceXMLReader

close() - Method in class org.openscience.cdk.io.PDBReader

close() - Method in class org.openscience.cdk.io.PDBWriter

Flushes the output and closes this object.

close() - Method in class org.openscience.cdk.io.PMPReader

close() - Method in class org.openscience.cdk.io.program.GaussianInputWriter

close() - Method in class org.openscience.cdk.io.program.Mopac7Writer

close() - Method in class org.openscience.cdk.io.random.RandomAccessReader

close() - Method in class org.openscience.cdk.io.rdf.CDKOWLReader

Closes this IChemObjectIO's resources.

close() - Method in class org.openscience.cdk.io.rdf.CDKOWLWriter

Closes this IChemObjectIO's resources.

close() - Method in class org.openscience.cdk.io.RGroupQueryReader

close() - Method in class org.openscience.cdk.io.RGroupQueryWriter

Flushes the output and closes this object.

close() - Method in class org.openscience.cdk.io.RssWriter

Flushes the output and closes this object.

close() - Method in class org.openscience.cdk.io.SDFWriter

Flushes the output and closes this object.

close() - Method in class org.openscience.cdk.io.ShelXReader

close() - Method in class org.openscience.cdk.io.ShelXWriter

Flushes the output and closes this object.

close() - Method in class org.openscience.cdk.io.SMILESReader

close() - Method in class org.openscience.cdk.io.SMILESWriter

Flushes the output and closes this object.

close() - Method in class org.openscience.cdk.io.VASPReader

close() - Method in class org.openscience.cdk.io.XYZReader

close() - Method in class org.openscience.cdk.io.XYZWriter

Flushes the output and closes this object.

close() - Method in class org.openscience.cdk.io.ZMatrixReader

Close - Class in org.openscience.cdk.renderer.elements.path

Indicates the closing point of the path.

Close() - Constructor for class org.openscience.cdk.renderer.elements.path.Close

Make a Close PathElement.

close() - Method in class org.openscience.cdk.renderer.elements.path.PathBuilder

Close the path.

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.

CLS_MASK - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

clusterPSPPocket(Point3d, List<Point3d>, int[]) - Method in class org.openscience.cdk.protein.ProteinPocketFinder

Method performs the clustering, is called by findPockets().

CMLCoreModule - Class in org.openscience.cdk.io.cml

Core CML 1.x and 2.x elements are parsed by this class (see (Willighagen, E.L.. Internet Journal of Chemistry. 2001. 4)).

CMLCoreModule(IChemFile) - Constructor for class org.openscience.cdk.io.cml.CMLCoreModule

CMLCoreModule(ICMLModule) - Constructor for class org.openscience.cdk.io.cml.CMLCoreModule

CMLErrorHandler - Class in org.openscience.cdk.io.cml

CDK's SAX2 ErrorHandler for giving feedback on XML errors in the CML document.

CMLErrorHandler() - Constructor for class org.openscience.cdk.io.cml.CMLErrorHandler

Constructor a SAX2 ErrorHandler that uses the cdk.tools.LoggingTool class to output errors and warnings to.

CMLFormat - Class in org.openscience.cdk.io.formats

See here.

CMLFormat() - Constructor for class org.openscience.cdk.io.formats.CMLFormat

CMLHandler - Class in org.openscience.cdk.io.cml

SAX2 implementation for CML XML fragment reading.

CMLHandler(IChemFile) - Constructor for class org.openscience.cdk.io.cml.CMLHandler

Constructor for the CMLHandler.

CMLModuleStack - Class in org.openscience.cdk.io.cml

Low weight alternative to Sun's Stack class.

CMLModuleStack() - Constructor for class org.openscience.cdk.io.cml.CMLModuleStack

CMLReactionModule - Class in org.openscience.cdk.io.cml

CMLReactionModule(IChemFile) - Constructor for class org.openscience.cdk.io.cml.CMLReactionModule

CMLReactionModule(ICMLModule) - Constructor for class org.openscience.cdk.io.cml.CMLReactionModule

CMLReader - Class in org.openscience.cdk.io

Reads a molecule in CML 1.x and 2.0 format.

CMLReader(InputStream) - Constructor for class org.openscience.cdk.io.CMLReader

Reads CML from an java.io.InputStream, for example the FileInputStream.

CMLReader() - Constructor for class org.openscience.cdk.io.CMLReader

CMLReader(String) - Constructor for class org.openscience.cdk.io.CMLReader

Define this CMLReader to take the input from a java.io.Reader class.

CMLResolver - Class in org.openscience.cdk.io.cml

This class resolves DOCTYPE declaration for Chemical Markup Language (CML) files and uses a local version for validation.

CMLResolver() - Constructor for class org.openscience.cdk.io.cml.CMLResolver

CMLRSSFormat - Class in org.openscience.cdk.io.formats

CMLRSSFormat() - Constructor for class org.openscience.cdk.io.formats.CMLRSSFormat

CMLWriter - Class in org.openscience.cdk.io

Serializes a IAtomContainerSet or a IAtomContainer object to CML 2 code.

CMLWriter(Writer) - Constructor for class org.openscience.cdk.io.CMLWriter

Constructs a new CMLWriter class.

CMLWriter(OutputStream) - Constructor for class org.openscience.cdk.io.CMLWriter

CMLWriter() - Constructor for class org.openscience.cdk.io.CMLWriter

COBALT - Static variable in enum org.openscience.cdk.config.Elements

color - Variable in class org.openscience.cdk.renderer.elements.ArrowElement

Color of the arrow.

color - Variable in class org.openscience.cdk.renderer.elements.GeneralPath

The color of the path.

color - Variable in class org.openscience.cdk.renderer.elements.LineElement

The color of the line.

color - Variable in class org.openscience.cdk.renderer.elements.OvalElement

The color to draw the oval.

color(Color) - Method in class org.openscience.cdk.renderer.elements.path.PathBuilder

Sets the color if this path.

color - Variable in class org.openscience.cdk.renderer.elements.PathElement

The color of the path.

color - Variable in class org.openscience.cdk.renderer.elements.RectangleElement

The color of the rectangle.

color - Variable in class org.openscience.cdk.renderer.elements.TextElement

The color of the text.

color(int) - Method in interface org.openscience.cdk.renderer.generators.HighlightGenerator.Palette

Obtain the color in index, id.

ColorByType() - Constructor for class org.openscience.cdk.renderer.generators.AtomNumberGenerator.ColorByType

ColorByType() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.ColorByType

ColorHash() - Constructor for class org.openscience.cdk.renderer.RendererModel.ColorHash

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.

COMMENT - Static variable in class org.openscience.cdk.CDKConstants

A String comment.

commit() - Method in class org.openscience.cdk.smiles.InvPair

CompactAtom() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.CompactAtom

CompactShape() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.CompactShape

compare(Object) - Method in class org.openscience.cdk.Atom

Compares a atom with this atom.

compare(Object) - Method in class org.openscience.cdk.AtomType

Compares a atom type with this atom type.

compare(Object) - Method in class org.openscience.cdk.Bond

Compares a bond with this bond.

compare(Object) - Method in class org.openscience.cdk.BondRef

Compares a bond with this bond.

compare(Object) - Method in class org.openscience.cdk.ChemObject

Compares a IChemObject with this IChemObject.

compare(Object) - Method in class org.openscience.cdk.debug.DebugBond

Compares a bond with this bond.

compare(Object) - Method in class org.openscience.cdk.Element

Compares an Element with this Element.

compare(IAtom, IAtom) - Method in class org.openscience.cdk.fingerprint.SimpleAtomComparator

compare(IsotopePattern, IsotopePattern) - Method in class org.openscience.cdk.formula.IsotopePatternSimilarity

Compare the IMolecularFormula with a isotope abundance pattern.

compare(ILigand, ILigand) - Method in class org.openscience.cdk.geometry.cip.rules.CIPLigandRule

Compares two ligands according to the particular sequence sub rule.

compare(ILigand, ILigand) - Method in interface org.openscience.cdk.geometry.cip.rules.ISequenceSubRule

Compares two ligands according to the particular sequence sub rule.

compare(Object) - Method in interface org.openscience.cdk.interfaces.IBond

Compares a bond with this bond.

compare(Object) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond

Compares a query bond with this query bond.

compare(Object) - Method in class org.openscience.cdk.Isotope

Compares a atom type with this atom type.

compare(Object) - Method in class org.openscience.cdk.silent.Atom

Compares a atom with this atom.

compare(Object) - Method in class org.openscience.cdk.silent.AtomType

Compares a atom type with this atom type.

compare(Object) - Method in class org.openscience.cdk.silent.Bond

Compares a bond with this bond.

compare(Object) - Method in class org.openscience.cdk.silent.ChemObject

Compares a IChemObject with this IChemObject.

compare(Object) - Method in class org.openscience.cdk.silent.Element

Compares an Element with this Element.

compare(Object) - Method in class org.openscience.cdk.silent.Isotope

Compares an isotope with this isotope.

compare(String, String) - Method in class org.openscience.cdk.tools.ElementComparator

Returns a negative if o1 comes before o2 in a molecular formula, returns zero if they are identical, and positive if o1 comes after o2 in the formula.

compare(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.tools.manipulator.AtomContainerComparator

compare(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.tools.manipulator.AtomContainerComparatorBy2DCenter

Compare two AtomContainers based on their 2D position.

compare(IMolecularFormula, IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator

Compare two IMolecularFormula looking at type and number of IIsotope and charge of the formula.

compare(IRing, IRing) - Method in class org.openscience.cdk.tools.manipulator.RingSizeComparator

compareTo(DynamicFactory.ConstructorKey) - Method in class org.openscience.cdk.DynamicFactory.ConstructorKey

Orders constructor keys by the number of parameters and then this name.

compareTo(IChemFormatMatcher.MatchResult) - Method in class org.openscience.cdk.io.formats.IChemFormatMatcher.MatchResult

Compares the match result with another, results with lower position are ordered before those with higher position.

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.

components() - Method in class org.openscience.cdk.graph.ConnectedComponents

Access the components each vertex belongs to.

computeFloydAPSP(int[][]) - Static method in class org.openscience.cdk.graph.PathTools

All-Pairs-Shortest-Path computation based on Floyd's algorithm (Floyd, R.W.. Commun. ACM. 1962. 5).

computeFloydAPSP(double[][]) - Static method in class org.openscience.cdk.graph.PathTools

All-Pairs-Shortest-Path computation based on Floyd's algorithm (Floyd, R.W.. Commun. ACM. 1962. 5).

configure(IAtom) - Method in class org.openscience.cdk.config.AtomTypeFactory

Configures an atom.

configure(IAtom) - Method in class org.openscience.cdk.config.IsotopeFactory

Configures an atom.

configure(IAtom, IIsotope) - Method in class org.openscience.cdk.config.IsotopeFactory

Configures an atom to have all the data of the given isotope.

configure(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

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.

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

construct(String, IAtomType.Hybridization, IAtomType.Hybridization) - Static method in class org.openscience.cdk.tools.diff.tree.AtomTypeHybridizationDifference

Constructs a new IDifference object.

construct(String, IBond.Order, IBond.Order) - Static method in class org.openscience.cdk.tools.diff.tree.BondOrderDifference

Constructs a new IDifference object.

construct(String, boolean[], boolean[]) - Static method in class org.openscience.cdk.tools.diff.tree.BooleanArrayDifference

Constructs a new IDifference object.

construct(String, Boolean, Boolean) - Static method in class org.openscience.cdk.tools.diff.tree.BooleanDifference

Constructs a new IDifference object.

construct(String, Double, Double) - Static method in class org.openscience.cdk.tools.diff.tree.DoubleDifference

Constructs a new IDifference object.

construct(String, Integer, Integer) - Static method in class org.openscience.cdk.tools.diff.tree.IntegerDifference

Constructs a new IDifference object.

construct(String, Point2d, Point2d) - Static method in class org.openscience.cdk.tools.diff.tree.Point2dDifference

Constructs a new IDifference object.

construct(String, Point3d, Point3d) - Static method in class org.openscience.cdk.tools.diff.tree.Point3dDifference

Constructs a new IDifference object.

construct(String, String, String) - Static method in class org.openscience.cdk.tools.diff.tree.StringDifference

Constructs a new IDifference object.

ConstructorKey() - Constructor for class org.openscience.cdk.DynamicFactory.ConstructorKey

contab - Variable in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph

container - Variable in class org.openscience.cdk.stereo.StereoElementFactory

Native CDK structure representation.

containerFromPermutation(int[]) - Method in class org.openscience.cdk.graph.AtomContainerAtomPermutor

Generate the atom container with this permutation of the atoms.

containerFromPermutation(int[]) - Method in class org.openscience.cdk.graph.AtomContainerBondPermutor

containerFromPermutation(int[]) - Method in class org.openscience.cdk.graph.AtomContainerPermutor

Convert a permutation (expressed as a list of numbers) into a permuted atom container.

contains(IAtom) - Method in class org.openscience.cdk.Association

Returns true if the given atom participates in this Association.

contains(IAtom) - Method in class org.openscience.cdk.AtomContainer

True, if the AtomContainer contains the given atom object.

contains(IBond) - Method in class org.openscience.cdk.AtomContainer

True, if the AtomContainer contains the given bond object.

contains(ILonePair) - Method in class org.openscience.cdk.AtomContainer

True, if the AtomContainer contains the given LonePair object.

contains(ISingleElectron) - Method in class org.openscience.cdk.AtomContainer

True, if the AtomContainer contains the given SingleElectron object.

contains(IElectronContainer) - Method in class org.openscience.cdk.AtomContainer

True, if the AtomContainer contains the given ElectronContainer object.

contains(IAtom) - Method in class org.openscience.cdk.Bond

Returns true if the given atom participates in this bond.

contains(IAtom) - Method in class org.openscience.cdk.BondRef

Returns true if the given atom participates in this bond.

contains(Object) - Method in class org.openscience.cdk.ConformerContainer

Checks to see whether the specified conformer is currently stored.

contains(IIsotope) - Method in class org.openscience.cdk.debug.DebugAdductFormula

True, if the AdductFormula contains the given IIsotope object and not the instance.

contains(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugAdductFormula

True, if the AdductFormula contains the given IMolecularFormula object.

contains(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid

True, if the AtomContainer contains the given atom object.

contains(IBond) - Method in class org.openscience.cdk.debug.DebugAminoAcid

True, if the AtomContainer contains the given bond object.

contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugAminoAcid

True, if the AtomContainer contains the given LonePair object.

contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAminoAcid

True, if the AtomContainer contains the given SingleElectron object.

contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugAminoAcid

True, if the AtomContainer contains the given ElectronContainer object.

contains(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer

True, if the AtomContainer contains the given atom object.

contains(IBond) - Method in class org.openscience.cdk.debug.DebugAtomContainer

True, if the AtomContainer contains the given bond object.

contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugAtomContainer

True, if the AtomContainer contains the given LonePair object.

contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAtomContainer

True, if the AtomContainer contains the given SingleElectron object.

contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainer

True, if the AtomContainer contains the given ElectronContainer object.

contains(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer

True, if the AtomContainer contains the given atom object.

contains(IBond) - Method in class org.openscience.cdk.debug.DebugBioPolymer

True, if the AtomContainer contains the given bond object.

contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugBioPolymer

True, if the AtomContainer contains the given LonePair object.

contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugBioPolymer

True, if the AtomContainer contains the given SingleElectron object.

contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugBioPolymer

True, if the AtomContainer contains the given ElectronContainer object.

contains(IAtom) - Method in class org.openscience.cdk.debug.DebugBond

Returns true if the given atom participates in this bond.

contains(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal

True, if the AtomContainer contains the given atom object.

contains(IBond) - Method in class org.openscience.cdk.debug.DebugCrystal

True, if the AtomContainer contains the given bond object.

contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugCrystal

True, if the AtomContainer contains the given LonePair object.

contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugCrystal

True, if the AtomContainer contains the given SingleElectron object.

contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugCrystal

True, if the AtomContainer contains the given ElectronContainer object.

contains(IAtom) - Method in class org.openscience.cdk.debug.DebugLonePair

Returns true if the given atom participates in this lone pair.

contains(IIsotope) - Method in class org.openscience.cdk.debug.DebugMolecularFormula

True, if the MolecularFormula contains the given IIsotope object and not the instance.

contains(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet

True, if the MolecularFormulaSet contains the given IMolecularFormula object.

contains(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer

True, if the AtomContainer contains the given atom object.

contains(IBond) - Method in class org.openscience.cdk.debug.DebugMonomer

True, if the AtomContainer contains the given bond object.

contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugMonomer

True, if the AtomContainer contains the given LonePair object.

contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugMonomer

True, if the AtomContainer contains the given SingleElectron object.

contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugMonomer

True, if the AtomContainer contains the given ElectronContainer object.

contains(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer

True, if the AtomContainer contains the given atom object.

contains(IBond) - Method in class org.openscience.cdk.debug.DebugPolymer

True, if the AtomContainer contains the given bond object.

contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugPolymer

True, if the AtomContainer contains the given LonePair object.

contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugPolymer

True, if the AtomContainer contains the given SingleElectron object.

contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugPolymer

True, if the AtomContainer contains the given ElectronContainer object.

contains(IAtom) - Method in class org.openscience.cdk.debug.DebugRing

True, if the AtomContainer contains the given atom object.

contains(IBond) - Method in class org.openscience.cdk.debug.DebugRing

True, if the AtomContainer contains the given bond object.

contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugRing

True, if the AtomContainer contains the given LonePair object.

contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugRing

True, if the AtomContainer contains the given SingleElectron object.

contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugRing

True, if the AtomContainer contains the given ElectronContainer object.

contains(IAtom) - Method in class org.openscience.cdk.debug.DebugRingSet

True, if at least one of the rings in the ringset contains the given atom.

contains(IAtom) - Method in class org.openscience.cdk.debug.DebugSingleElectron

Returns true if the given atom participates in this SingleElectron.

contains(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand

True, if the AtomContainer contains the given atom object.

contains(IBond) - Method in class org.openscience.cdk.debug.DebugStrand

True, if the AtomContainer contains the given bond object.

contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugStrand

True, if the AtomContainer contains the given LonePair object.

contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugStrand

True, if the AtomContainer contains the given SingleElectron object.

contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugStrand

True, if the AtomContainer contains the given ElectronContainer object.

contains(IIsotope) - Method in class org.openscience.cdk.formula.AdductFormula

True, if the AdductFormula contains the given IIsotope object and not the instance.

contains(IMolecularFormula) - Method in class org.openscience.cdk.formula.AdductFormula

True, if the AdductFormula contains the given IMolecularFormula object.

contains(IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormula

True, if the MolecularFormula contains the given IIsotope object and not the instance.

contains(IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormulaRange

True, if the MolecularFormulaExpand contains the given IIsotope.

contains(IMolecularFormula) - Method in class org.openscience.cdk.formula.MolecularFormulaSet

True, if the MolecularFormulaSet contains the given IMolecularFormula object.

contains(IIsotope) - Method in interface org.openscience.cdk.interfaces.IAdductFormula

True, if the AdductFormula contains the given IIsotope object.

contains(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

True, if the AtomContainer contains the given atom object.

contains(IBond) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

True, if the AtomContainer contains the given bond object.

contains(ILonePair) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

True, if the AtomContainer contains the given LonePair object.

contains(ISingleElectron) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

True, if the AtomContainer contains the given SingleElectron object.

contains(IElectronContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

True, if the AtomContainer contains the given ElectronContainer object.

contains(IAtom) - Method in interface org.openscience.cdk.interfaces.IBond

Returns true if the given atom participates in this bond.

contains(IAtom) - Method in interface org.openscience.cdk.interfaces.ILonePair

Returns true if the given atom participates in this lone pair.

contains(IIsotope) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula

True, if the MolecularFormula contains the given IIsotope object.

contains(IMolecularFormula) - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet

True, if the IMolecularFormulaSet contains the given IMolecularFormula object.

contains(IAtom) - Method in interface org.openscience.cdk.interfaces.IRingSet

True, if at least one of the rings in the ringset contains the given atom.

contains(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IRingSet

True, if this set contains the IAtomContainer.

contains(IAtom) - Method in interface org.openscience.cdk.interfaces.ISingleElectron

Returns true if the given atom participates in this SingleElectron.

contains(IAtom) - Method in interface org.openscience.cdk.interfaces.IStereoElement

Does the stereo element contain the provided atom.

contains(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

True, if the AtomContainer contains the given atom object.

contains(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

True, if the AtomContainer contains the given bond object.

contains(ILonePair) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

True, if the AtomContainer contains the given LonePair object.

contains(ISingleElectron) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

True, if the AtomContainer contains the given SingleElectron object.

contains(IElectronContainer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

True, if the AtomContainer contains the given ElectronContainer object.

contains(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond

Returns true if the given atom participates in this query bond.

contains(IAtom) - Method in class org.openscience.cdk.LonePair

Returns true if the given atom participates in this lone pair.

contains(IChemObject) - Method in interface org.openscience.cdk.renderer.selection.IChemObjectSelection

Determines if the IChemObject is part of the current selection.

contains(IAtom) - Method in class org.openscience.cdk.RingSet

True, if at least one of the rings in the ringset contains the given atom.

contains(IAtomContainer) - Method in class org.openscience.cdk.RingSet

Checks for presence of a ring in this RingSet.

contains(int) - Method in class org.openscience.cdk.signature.Orbit

Checks to see if the orbit contains this atom index.

contains(IIsotope) - Method in class org.openscience.cdk.silent.AdductFormula

True, if the AdductFormula contains the given IIsotope object and not the instance.

contains(IMolecularFormula) - Method in class org.openscience.cdk.silent.AdductFormula

True, if the AdductFormula contains the given IMolecularFormula object.

contains(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer

True, if the AtomContainer contains the given atom object.

contains(IBond) - Method in class org.openscience.cdk.silent.AtomContainer

True, if the AtomContainer contains the given bond object.

contains(ILonePair) - Method in class org.openscience.cdk.silent.AtomContainer

True, if the AtomContainer contains the given LonePair object.

contains(ISingleElectron) - Method in class org.openscience.cdk.silent.AtomContainer

True, if the AtomContainer contains the given SingleElectron object.

contains(IElectronContainer) - Method in class org.openscience.cdk.silent.AtomContainer

True, if the AtomContainer contains the given ElectronContainer object.

contains(IAtom) - Method in class org.openscience.cdk.silent.Bond

Returns true if the given atom participates in this bond.

contains(IAtom) - Method in class org.openscience.cdk.silent.LonePair

Returns true if the given atom participates in this lone pair.

contains(IIsotope) - Method in class org.openscience.cdk.silent.MolecularFormula

True, if the MolecularFormula contains the given IIsotope object and not the instance.

contains(IMolecularFormula) - Method in class org.openscience.cdk.silent.MolecularFormulaSet

True, if the MolecularFormulaSet contains the given IMolecularFormula object.

contains(IAtom) - Method in class org.openscience.cdk.silent.RingSet

True, if at least one of the rings in the ringset contains the given atom.

contains(IAtomContainer) - Method in class org.openscience.cdk.silent.RingSet

Checks for presence of a ring in this RingSet.

contains(IAtom) - Method in class org.openscience.cdk.silent.SingleElectron

Returns true if the given atom participates in this SingleElectron.

contains(IAtom) - Method in class org.openscience.cdk.SingleElectron

Returns true if the given atom participates in this SingleElectron.

contains(IMolecularFormulaSet, IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaSetManipulator

True, if the IMolecularFormulaSet contains the given IMolecularFormula but not as object.

containsAll(Collection<?>) - Method in class org.openscience.cdk.ConformerContainer

containsByID(IAtomContainerSet, String) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator

Tells if an AtomContainerSet contains at least one AtomContainer with the same ID as atomContainer.

containsElement(IMolecularFormula, IElement) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator

True, if the MolecularFormula contains the given element as IIsotope object.

contribs - Variable in class org.openscience.cdk.fingerprint.model.Bayesian

convertEdgeLabelToColor(String) - Method in class org.openscience.cdk.signature.AtomSignature

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

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

copy(Collection<Sgroup>, Map<? extends IChemObject, ? extends IChemObject>) - Static method in class org.openscience.cdk.tools.manipulator.SgroupManipulator

Copy a collection of Sgroups, replacing any IAtom/IBond references with those present in the provided 'replace' map.

copyAndSuppressedHydrogens(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator

Copy the input container and suppress any explicit hydrogens.

copyBlock(int) - Method in class org.openscience.cdk.group.Partition

Creates and returns a copy of the cell at cell index.

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.

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

countUnique() - Method in class org.openscience.cdk.isomorphism.Mappings

Convenience method to count the number of unique atom mappings.

covalentRadius() - Method in enum org.openscience.cdk.config.Elements

The covalent radius, r_cov, is a measure of the size of an atom that forms part of one covalent bond.

CovalentRadiusDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic

This class returns the covalent radius of a given atom.

CovalentRadiusDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor

Constructor for the CovalentRadiusDescriptor object.

CPKAtomColors - Class in org.openscience.cdk.renderer.color

Deprecated.

JmolColors provides more comprehensive CPK color pallet

CPKAtomColors() - Constructor for class org.openscience.cdk.renderer.color.CPKAtomColors

Deprecated.

CPSADescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

Calculates 29 Charged Partial Surface Area (CPSA) descriptors.

CPSADescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor

create(Object[]) - Method in interface org.openscience.cdk.DynamicFactory.Creator

Create a new instance with the provided object parameters.

create() - Method in class org.openscience.cdk.group.PartitionRefinement.AtomRefinerBuilder

create() - Method in class org.openscience.cdk.group.PartitionRefinement.BondRefinerBuilder

create(IAtomContainer, int[][]) - Method in class org.openscience.cdk.hash.stereo.DoubleBondElementEncoderFactory

Create a stereo-encoder for possible stereo-chemical configurations.

create(IAtomContainer, int[][]) - Method in class org.openscience.cdk.hash.stereo.GeometricCumulativeDoubleBondFactory

Create a stereo encoder for cumulative double bonds.

create(IAtomContainer, int[][]) - Method in class org.openscience.cdk.hash.stereo.GeometricDoubleBondEncoderFactory

Create a stereo encoder for all potential 2D and 3D double bond stereo configurations.

create(IAtomContainer, int[][]) - Method in class org.openscience.cdk.hash.stereo.GeometricTetrahedralEncoderFactory

Create a stereo encoder for all potential 2D and 3D tetrahedral elements.

create(IAtomContainer, int[][]) - Method in interface org.openscience.cdk.hash.stereo.StereoEncoderFactory

Create a stereo-encoder for possible stereo-chemical configurations.

create(IAtomContainer, int[][]) - Method in class org.openscience.cdk.hash.stereo.TetrahedralElementEncoderFactory

Create a stereo-encoder for possible stereo-chemical configurations.

create(IAtomContainer, Expr.Type...) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Create a query from a molecule and a provided set of expressions.

create(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.smarts.SmartsPattern

Create a Pattern that will match the given smarts query.

create(String) - Static method in class org.openscience.cdk.smarts.SmartsPattern

Default SMARTS pattern constructor, passes in a null chem object builder.

create(IAtomContainer) - Method in class org.openscience.cdk.smiles.SmilesGenerator

Generate SMILES for the provided molecule.

create(IAtomContainer, int[]) - Method in class org.openscience.cdk.smiles.SmilesGenerator

Creates a SMILES string of the flavour specified in the constructor and write the output order to the provided array.

create(IAtomContainer, int, int[]) - Static method in class org.openscience.cdk.smiles.SmilesGenerator

Creates a SMILES string of the flavour specified as a parameter and write the output order to the provided array.

create(IReaction) - Method in class org.openscience.cdk.smiles.SmilesGenerator

Create a SMILES for a reaction of the flavour specified in the constructor.

create(IReaction, int[]) - Method in class org.openscience.cdk.smiles.SmilesGenerator

Create a SMILES for a reaction of the flavour specified in the constructor and write the output order to the provided array.

create(IBond, List<IAtom>, int) - Method in class org.openscience.cdk.stereo.Atropisomeric

create(IBond, List<IBond>, int) - Method in class org.openscience.cdk.stereo.DoubleBondStereochemistry

create(IBond, List<IBond>, int) - Method in class org.openscience.cdk.stereo.ExtendedCisTrans

create(IAtom, List<IAtom>, int) - Method in class org.openscience.cdk.stereo.ExtendedTetrahedral

create(IAtom, List<IAtom>, int) - Method in class org.openscience.cdk.stereo.Octahedral

create(IAtom, List<IAtom>, int) - Method in class org.openscience.cdk.stereo.SquarePlanar

create(IAtom, List<IAtom>, int) - Method in class org.openscience.cdk.stereo.TetrahedralChirality

create(IAtom, List<IAtom>, int) - Method in class org.openscience.cdk.stereo.TrigonalBipyramidal

create(Class<?>) - Static method in class org.openscience.cdk.tools.LoggingTool

Creates a new LoggingTool for the given class.

create(Class<?>) - Static method in class org.openscience.cdk.tools.SystemOutLoggingTool

Creates a new SystemOutLoggingTool for the given class.

createAAs() - Static method in class org.openscience.cdk.templates.AminoAcids

Creates amino acid AminoAcid objects.

createAll() - Method in class org.openscience.cdk.stereo.StereoElementFactory

Creates all stereo elements found by Stereocenters using the or 2D/3D coordinates to specify the configuration (clockwise/anticlockwise).

createAllCarbonAllSingleNonAromaticBondAtomContainer(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator

Deprecated.

not all attributes are removed producing unexpected results, use AtomContainerManipulator.anonymise(org.openscience.cdk.interfaces.IAtomContainer)

createAnyAtomAnyBondContainer(IAtomContainer, boolean) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator

Creates a QueryAtomContainer with the following settings:

createAnyAtomAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor

createAnyAtomContainer(IAtomContainer, boolean) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator

Creates a QueryAtomContainer with the following settings:

createAnyAtomForPseudoAtomQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator

Creates a QueryAtomContainer with the following settings:

createAutoGenPalette(float, float, boolean) - Static method in class org.openscience.cdk.renderer.generators.HighlightGenerator

Create an auto generating palette which will generate colors using the provided parameters.

createAutoGenPalette(boolean) - Static method in class org.openscience.cdk.renderer.generators.HighlightGenerator

Create an auto generating palette which will generate colors using the provided parameters.

createAutoPalette(float, float, int) - Static method in class org.openscience.cdk.renderer.generators.HighlightGenerator

Create an auto generating palette which will generate colors using the provided parameters.

createBasicQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator

Creates a QueryAtomContainer with the following settings:

createBondOrder(double) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator

Convenience method to convert a double into an IBond.Order.

createChemObjectReader() - Method in class org.openscience.cdk.io.random.RandomAccessReader

createChemObjectReader() - Method in class org.openscience.cdk.io.random.RandomAccessSDFReader

createComparator(IAtomContainer, int) - Static method in class org.openscience.cdk.smiles.SmilesGenerator

createCubicGrid() - Method in class org.openscience.cdk.protein.ProteinPocketFinder

Method creates a cubic grid with the grid generator class.

createFromSubstructure(Pattern, Iterable<IAtomContainer>) - Static method in class org.openscience.cdk.layout.TemplateHandler

Create a template from a substructure pattern.

createFromSubstructure(Pattern, IAtomContainer) - Static method in class org.openscience.cdk.layout.TemplateHandler

Create a template from a substructure pattern.

createIDs(IChemObject) - Static method in class org.openscience.cdk.tools.IDCreator

Labels the Atom's and Bond's in the AtomContainer using the a1, a2, b1, b2 scheme often used in CML.

createLoggingTool(Class<?>) - Static method in class org.openscience.cdk.tools.LoggingToolFactory

Dynamically create a ILoggingTool for the given sourceClass.

createNewMolecule(IChemModel) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator

Adds a new Molecule to the MoleculeSet inside a given ChemModel.

createPalette(Color[]) - Static method in class org.openscience.cdk.renderer.generators.HighlightGenerator

Create a palette which uses the provided colors.

createPalette(Color, Color...) - Static method in class org.openscience.cdk.renderer.generators.HighlightGenerator

Create a palette which uses the provided colors.

createPath() - Method in class org.openscience.cdk.renderer.elements.path.PathBuilder

Create and return the final path.

createProtein(String) - Static method in class org.openscience.cdk.tools.ProteinBuilderTool

Creates a BioPolymer from a sequence of amino acid as identified by a the sequence of their one letter codes.

createProtein(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.ProteinBuilderTool

Creates a BioPolymer from a sequence of amino acid as identified by a the sequence of their one letter codes.

createReactionScheme(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator

Create a IReactionScheme give a IReactionSet object.

createReactionSMILES(IReaction) - Method in class org.openscience.cdk.smiles.SmilesGenerator

Deprecated.

use SmilesGenerator.create(IAtomContainer)

createReader(InputStream) - Method in class org.openscience.cdk.io.ReaderFactory

Detects the format of the Reader input, and if known, it will return a CDK Reader to read the format, or null when the reader is not implemented.

createReader(IChemFormat) - Method in class org.openscience.cdk.io.ReaderFactory

Creates a new IChemObjectReader based on the given IChemFormat.

createReader(Reader) - Method in class org.openscience.cdk.io.ReaderFactory

Detects the format of the Reader input, and if known, it will return a CDK Reader to read the format.

createSingleton(IAtomContainer) - Static method in class org.openscience.cdk.layout.TemplateHandler

Singleton template instance, mainly useful for aligning molecules.

createSMILES(IAtomContainer) - Method in class org.openscience.cdk.smiles.SmilesGenerator

Deprecated.

use #create

createSMILES(IReaction) - Method in class org.openscience.cdk.smiles.SmilesGenerator

Deprecated.

use #createReactionSMILES

createSymbolAndBondOrderQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator

Creates a QueryAtomContainer with the following settings:

createSymbolAndChargeQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator

Creates a QueryAtomContainer with the following settings:

createSymbolChargeIDQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator

createWriter(IChemFormat) - Method in class org.openscience.cdk.io.WriterFactory

Creates a new IChemObjectWriter based on the given IChemFormat.

CRK2DFormat - Class in org.openscience.cdk.io.formats

See here.

CRK2DFormat() - Constructor for class org.openscience.cdk.io.formats.CRK2DFormat

CRK3DFormat - Class in org.openscience.cdk.io.formats

See here.

CRK3DFormat() - Constructor for class org.openscience.cdk.io.formats.CRK3DFormat

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

CT - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Geometric CisTrans (e.g.

CTAB_SGROUPS - Static variable in class org.openscience.cdk.CDKConstants

Key to store/fetch CTab Sgroups from Molfiles.

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.interfaces.IStereoElement

ExtendedCisTrans a.k.a.

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.

Cumulene - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Cumulene

CURIUM - Static variable in enum org.openscience.cdk.config.Elements

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

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 the property CDKConstants.COMMENT using IChemObject.setProperty(Object, Object)

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.

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.

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.

D

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

DashSection() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.DashSection

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.

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 - Static variable in interface org.openscience.cdk.tools.ILoggingTool

Debug, Info, Warn, Error, and Fatal messages will be emitted.

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(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

DebugSubstance - Class in org.openscience.cdk.debug

Debugging data class.

DebugSubstance() - Constructor for class org.openscience.cdk.debug.DebugSubstance

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.

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.

DefaultBondColor() - Constructor for class org.openscience.cdk.renderer.generators.BasicBondGenerator.DefaultBondColor

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

DefaultInterfaceProvider() - Constructor for class org.openscience.cdk.DynamicFactory.DefaultInterfaceProvider

DefaultIteratingChemObjectReader<T extends IChemObject> - Class in org.openscience.cdk.io.iterator

Abstract class that IteratingChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners.

DefaultIteratingChemObjectReader() - Constructor for class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader

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

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.

deref(IAtom) - Static method in class org.openscience.cdk.AtomRef

Utility method to dereference an atom.

deref() - Method in class org.openscience.cdk.AtomRef

Dereference the atom pointer once providing access to the base atom.

deref(IBond) - Static method in class org.openscience.cdk.BondRef

Utility method to dereference an bond pointer.

deref() - Method in class org.openscience.cdk.BondRef

Dereference the bond pointer once providing access to the base bond.

DESCRIPTION - Static variable in class org.openscience.cdk.CDKConstants

A description for a IChemObject.

DescriptorEngine - Class in org.openscience.cdk.qsar

A class that provides access to automatic descriptor calculation and more.

DescriptorEngine(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.

determinant() - Method in class org.openscience.cdk.graph.invariant.GIMatrix

Returns the determinant of this matrix.

DfPattern - Class in org.openscience.cdk.isomorphism

The depth-first (DF) backtracking sub-structure matching algorithm so named because it matches the molecule in a depth-first manner (bond by bond).

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!

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

dim - Variable in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph

direction - Variable in class org.openscience.cdk.renderer.elements.ArrowElement

Boolean that is true if the arrow points from start to end, false if from end to start.

direction - Variable in class org.openscience.cdk.renderer.elements.WedgeLineElement

The direction indicates which way the wedge gets thicker.

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.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.

DMol3Format - Class in org.openscience.cdk.io.formats

DMol3Format() - Constructor for class org.openscience.cdk.io.formats.DMol3Format

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

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 doubles.

DoubleArrayResultType(int) - Constructor for class org.openscience.cdk.qsar.result.DoubleArrayResultType

DOUBLEBOND - Static variable in class org.openscience.cdk.libio.jena.CDK

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.

DoubleBondStereochemistry(IBond, IBond[], int) - Constructor for class org.openscience.cdk.stereo.DoubleBondStereochemistry

DoubleDifference - Class in org.openscience.cdk.tools.diff.tree

IDifference between two Double.

DoubleResult - Class in org.openscience.cdk.qsar.result

DoubleResult(double) - Constructor for class org.openscience.cdk.qsar.result.DoubleResult

DoubleResultType - Class in org.openscience.cdk.qsar.result

IDescriptorResult type for double.

DoubleResultType() - Constructor for class org.openscience.cdk.qsar.result.DoubleResultType

doubleValue() - Method in class org.openscience.cdk.qsar.result.DoubleResult

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

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.

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.ConstructorKey - Class in org.openscience.cdk

A class which encapsulates the information about an interface (of this implementation) and the parameter types of the constructor.

DynamicFactory.CreationModifier<T> - Interface in org.openscience.cdk

An interface that allows posterior modification of an instance after it has been created.

DynamicFactory.Creator<T> - Interface in org.openscience.cdk

An interface that wraps object creation via the DynamicFactory.Creator.create(Object[]) method.

DynamicFactory.DefaultInterfaceProvider - Class in org.openscience.cdk

A default interface provider implementation that simply returns the classes from Class.getInterfaces().

DynamicFactory.InterfaceProvider - Interface in org.openscience.cdk

An interface that can provide which interfaces the given class implements.

DYSPROSIUM - Static variable in enum org.openscience.cdk.config.Elements

E

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

edgeShort() - Static method in class org.openscience.cdk.graph.Cycles

Create a cycle finder which will compute the shortest cycles of each vertex in a molecule.

edgeShort(IAtomContainer) - Static method in class org.openscience.cdk.graph.Cycles

Find the edge short cycles of a molecule.

EffectiveAtomPolarizabilityDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic

Effective polarizability of a heavy atom Parameters for this descriptor: Name Default Description no parameters

EffectiveAtomPolarizabilityDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor

Constructor for the EffectiveAtomPolarizabilityDescriptor object

effectiveCharges(IAtomContainer) - Method in class org.openscience.cdk.forcefield.mmff.Mmff

Assign the effective formal charges used by MMFF in calculating the final partial charge values.

EINSTEINIUM - Static variable in enum org.openscience.cdk.config.Elements

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

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_ISOTOPE_ARRAY - Static variable in class org.openscience.cdk.config.IsotopeFactory

EMPTY_SELECTION - Static variable in class org.openscience.cdk.renderer.selection.AbstractSelection

Static implementation of an empty selection.

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

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.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

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.

EPS_FMT - Static variable in class org.openscience.cdk.depict.Depiction

Encapsulated PostScript (EPS) format key.

equals(Object) - Method in class org.openscience.cdk.Atom

equals(Object) - Method in class org.openscience.cdk.AtomRef

equals(Object) - Method in class org.openscience.cdk.Bond

equals(Object) - Method in class org.openscience.cdk.BondRef

equals(Object) - Method in class org.openscience.cdk.DynamicFactory.ConstructorKey

equals(Object) - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint

equals(Object) - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint

equals(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.Expr

equals(Object) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

equals(Object) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond

equals(Object) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList

equals(Object) - Method in class org.openscience.cdk.isomorphism.mcss.RMap

The equals method.

equals(Object) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom

equals(Object) - Method in class org.openscience.cdk.silent.Atom

equals(Object) - Method in class org.openscience.cdk.silent.Bond

equals(Object) - Method in class org.openscience.cdk.smiles.InvPair

Check whether this instance equals another instance.

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.

ERBIUM - Static variable in enum org.openscience.cdk.config.Elements

error(SAXParseException) - Method in class org.openscience.cdk.io.cml.CMLErrorHandler

Outputs a SAXParseException error to the logger.

ERROR - Static variable in interface org.openscience.cdk.tools.ILoggingTool

Error, and Fatal messages will be emitted.

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

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.

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

EUROPIUM - Static variable in enum org.openscience.cdk.config.Elements

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.

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

exponentialDouble(double) - Static method in class org.openscience.cdk.math.RandomNumbersTool

Generates a random double from an Exponential distribution with the specified mean value.

Expr - Class in org.openscience.cdk.isomorphism.matchers

A expression stores a predicate tree for checking properties of atoms and bonds.

Expr() - Constructor for class org.openscience.cdk.isomorphism.matchers.Expr

Creates an atom expression that will always match (Expr.Type.TRUE).

Expr(Expr.Type) - Constructor for class org.openscience.cdk.isomorphism.matchers.Expr

Creates an atom expression for the specified primitive.

Expr(Expr.Type, int) - Constructor for class org.openscience.cdk.isomorphism.matchers.Expr

Creates an atom expression for the specified primitive and 'value'.

Expr(Expr.Type, Expr, Expr) - Constructor for class org.openscience.cdk.isomorphism.matchers.Expr

Creates a logical atom expression for the specified.

Expr(Expr.Type, IAtomContainer) - Constructor for class org.openscience.cdk.isomorphism.matchers.Expr

Creates a recursive atom expression.

Expr(Expr) - Constructor for class org.openscience.cdk.isomorphism.matchers.Expr

Copy-constructor, creates a shallow copy of the provided expression.

Expr.Type - Enum in org.openscience.cdk.isomorphism.matchers

Types of expression, for use in the Expr tree object.

ExtendedAtomGenerator - Class in org.openscience.cdk.renderer.generators

A generator for atoms with mass, charge, etc.

ExtendedAtomGenerator() - Constructor for class org.openscience.cdk.renderer.generators.ExtendedAtomGenerator

ExtendedAtomGenerator.ShowAtomTypeNames - Class in org.openscience.cdk.renderer.generators

Boolean that indicates if atom type names should be given instead of element symbols.

ExtendedAtomGenerator.ShowImplicitHydrogens - Class in org.openscience.cdk.renderer.generators

Boolean that indicates if implicit hydrogens should be depicted.

ExtendedCisTrans - Class in org.openscience.cdk.stereo

Extended Cis/Trans double bond configuration.

ExtendedCisTrans(IBond, IBond[], int) - Constructor for class org.openscience.cdk.stereo.ExtendedCisTrans

ExtendedFingerprinter - Class in org.openscience.cdk.fingerprint

Generates an extended fingerprint for a given IAtomContainer, that extends the Fingerprinter with additional 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'.

ExtendedTetrahedral(IAtom, IAtom[], int) - Constructor for class org.openscience.cdk.stereo.ExtendedTetrahedral

ExternalHighlightColor() - Constructor for class org.openscience.cdk.renderer.RendererModel.ExternalHighlightColor

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

F

FancyBoldWedges() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.FancyBoldWedges

FancyHashedWedges() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.FancyHashedWedges

FATAL - Static variable in interface org.openscience.cdk.tools.ILoggingTool

Only Fatal messages will be emitted.

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.

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

fieldVal - Variable in class org.openscience.cdk.io.VASPReader

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.

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).

finalize() - Method in class org.openscience.cdk.io.random.RandomAccessReader

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.GeometryUtil

Returns the atoms which are closes to an atom in an AtomContainer by distance in 3d.

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.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.StructGenMatcher

findMatchingAtomTypes(IAtomContainer) - Method in class org.openscience.cdk.atomtype.SybylAtomTypeMatcher

Method that assigns atom types to atoms in the given atom container.

findPathes(IAtomContainer, int) - Method in class org.openscience.cdk.fingerprint.Fingerprinter

Deprecated.

Use Fingerprinter.encodePaths(IAtomContainer, int, BitSet, int)

findSubstructure(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.DfPattern

Create a pattern which can be used to find molecules which contain the query structure.

findSubstructure(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.Pattern

Create a pattern which can be used to find molecules which contain the query structure.

findSubstructure(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.Ullmann

Create a pattern which can be used to find molecules which contain the query structure.

findSubstructure(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.VentoFoggia

Create a pattern which can be used to find molecules which contain the query structure.

findSubstructure(IAtomContainer, AtomMatcher, BondMatcher) - Static method in class org.openscience.cdk.isomorphism.VentoFoggia

Create a pattern which can be used to find molecules which contain the query structure.

findTerminalAtoms(IAtomContainer, IBond) - Static method in class org.openscience.cdk.stereo.ExtendedCisTrans

Helper method to locate two terminal atoms in a container for this extended Cis/Trans element.

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

Fires IChemObjectIOListener.processIOSettingQuestion(org.openscience.cdk.io.setting.IOSetting) for all managed listeners.

fireIOSettingQuestion(IOSetting) - Method in class org.openscience.cdk.io.random.DefaultRandomAccessChemObjectReader

first() - Method in interface org.openscience.cdk.io.random.IRandomAccessChemObjectReader

first() - Method in class org.openscience.cdk.io.random.RandomAccessReader

first() - Method in class org.openscience.cdk.isomorphism.Mappings

Obtain the first match - if there is no first match an empty array is returned.

firstIndexOfDifference(Permutation) - Method in class org.openscience.cdk.group.Permutation

Find an r such that this[r] != other[r].

firstIsIdentity() - Method in interface org.openscience.cdk.group.DiscretePartitionRefiner

Check that the first refined partition is the identity.

firstPointX - Variable in class org.openscience.cdk.renderer.elements.LineElement

The x-coordinate of the first point.

firstPointY - Variable in class org.openscience.cdk.renderer.elements.LineElement

The y-coordinate of the first point.

FitToScreen() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.FitToScreen

FIVE_SECOND_TIMEOUT - Static variable in class org.openscience.cdk.inchi.JniInChIInputAdapter

FLAG_MASKS - Static variable in class org.openscience.cdk.CDKConstants

FLAVOR_CACTVS - Static variable in class org.openscience.cdk.smarts.Smarts

FLAVOR_CDK - Static variable in class org.openscience.cdk.smarts.Smarts

FLAVOR_CDK_LEGACY - Static variable in class org.openscience.cdk.smarts.Smarts

FLAVOR_DAYLIGHT - Static variable in class org.openscience.cdk.smarts.Smarts

FLAVOR_LOOSE - Static variable in class org.openscience.cdk.smarts.Smarts

FLAVOR_MOE - Static variable in class org.openscience.cdk.smarts.Smarts

FLAVOR_OECHEM - Static variable in class org.openscience.cdk.smarts.Smarts

FLEROVIUM - 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

FMFDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

An implementation of the FMF descriptor characterizing complexity of a molecule.

FMFDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor

focus() - Method in class org.openscience.cdk.stereo.ExtendedTetrahedral

The central atom in the cumulated system.

fontManager - Variable in class org.openscience.cdk.renderer.AbstractRenderer

Font managers change the font size depending on the zoom.

FontName() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.FontName

forAny() - Static method in class org.openscience.cdk.isomorphism.AtomMatcher

Atoms are always compatible.

forAny() - Static method in class org.openscience.cdk.isomorphism.BondMatcher

All bonds are compatible.

forAtoms() - Static method in class org.openscience.cdk.group.PartitionRefinement

forBonds() - Method in class org.openscience.cdk.group.PartitionRefinement

ForceDelocalisedBondDisplay() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.ForceDelocalisedBondDisplay

ForceFieldConfigurator - Class in org.openscience.cdk.modeling.builder3d

Reads in a force field configuration file, set the atom types into a vector, and the data into a hashtable Therefore, it uses the class MM2BasedParameterSetReader.

ForceFieldConfigurator() - Constructor for class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator

Constructor for the ForceFieldConfigurator object

ForegroundColor() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ForegroundColor

forElement() - Static method in class org.openscience.cdk.isomorphism.AtomMatcher

Atoms are compatible if they are the same element.

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.

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.

FP(int, int, int[]) - Constructor for class org.openscience.cdk.fingerprint.CircularFingerprinter.FP

FP_SIZE - Static variable in class org.openscience.cdk.fingerprint.PubchemFingerprinter

Number of bits in this fingerprint.

FractionalCSP3Descriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

An implementation of the Fractional CSP3 descriptor described in (Lovering, Frank et. al.. J. Med. Chem.. 2009. 52).

FractionalCSP3Descriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.FractionalCSP3Descriptor

fractionalPoint3d - Variable in class org.openscience.cdk.Atom

A 3 point specifying the location of this atom in a crystal unit cell.

fractionalPoint3d - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom

A 3 point specifying the location of this atom in a crystal unit cell.

fractionalPoint3d - Variable in class org.openscience.cdk.silent.Atom

A 3 point specifying the location of this atom in a crystal unit cell.

FractionalPSADescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

Polar surface area expressed as a ratio to molecular size.

FractionalPSADescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor

fractionalToCartesian(Vector3d, Vector3d, Vector3d, Point3d) - Static method in class org.openscience.cdk.geometry.CrystalGeometryTools

fractionalToCartesian(ICrystal) - Static method in class org.openscience.cdk.geometry.CrystalGeometryTools

Creates Cartesian coordinates for all Atoms in the Crystal.

FragmentAtom - Class in org.openscience.cdk

Class to represent an IPseudoAtom which embeds an IAtomContainer.

FragmentAtom() - 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

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.

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.

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

GADOLINIUM - Static variable in enum org.openscience.cdk.config.Elements

GALLIUM - Static variable in enum org.openscience.cdk.config.Elements

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.. Tetrahedron. 1980. 36).

GasteigerMarsiliPartialCharges() - Constructor for class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges

Constructor for the GasteigerMarsiliPartialCharges object.

GasteigerPEPEPartialCharges - Class in org.openscience.cdk.charges

The calculation of the Gasteiger (PEPE) partial charges is based on (Saller, H., Quantitative Emperische Modelle fur Elektronische Effekte in Pi-Systemen und fur die Chemische Reaktivitat, 1985, ?Institute?).

GasteigerPEPEPartialCharges() - Constructor for class org.openscience.cdk.charges.GasteigerPEPEPartialCharges

Constructor for the GasteigerPEPEPartialCharges object.

Gaussian03Format - Class in org.openscience.cdk.io.formats

See here.

Gaussian03Format() - Constructor for class org.openscience.cdk.io.formats.Gaussian03Format

Gaussian03Reader - Class in org.openscience.cdk.io

A reader for Gaussian03 output.

Gaussian03Reader(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

GaussJordan() - Method in class org.openscience.cdk.graph.invariant.GIMatrix

Gauss-Jordan algorithm.

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(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(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(IAtomContainer) - Static method in class org.openscience.cdk.smarts.Smarts

Generate a SMARTS string from the provided molecule.

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.

generateAtom(Expr) - Static method in class org.openscience.cdk.smarts.Smarts

Utility to generate an atom expression.

generateAtomContainerFromInchi(IChemObjectBuilder) - Method in class org.openscience.cdk.inchi.InChIToStructure

Gets structure from InChI, and converts InChI library data structure into an IAtomContainer.

generateBond(IBond, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator

Generate stereo or bond elements for this bond.

generateBond(Expr) - Static method in class org.openscience.cdk.smarts.Smarts

Utility to generate a bond expression.

generateBondElement(IBond, 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.

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.

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

Deprecated.

use StructureDiagramGenerator.generateCoordinates()

generateExperimentalCoordinates(Vector2d) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

Deprecated.

use StructureDiagramGenerator.generateCoordinates()

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.

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

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.

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(IAtom) - Static method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom

get(IBond) - Static method in class org.openscience.cdk.pharmacophore.PharmacophoreBond

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.BondRef

Returns the geometric 2D center of the bond.

get2DCenter() - Method in class org.openscience.cdk.debug.DebugBond

Returns the geometric 2D center of the bond.

get2DCenter(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.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.GeometryUtil

Determines the coverage of this IAtomContainer's 2D coordinates.

get2DDimension(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil

Returns the dimension of a molecule (width/height).

get3DCenter() - Method in class org.openscience.cdk.Bond

Returns the geometric 3D center of the bond.

get3DCenter() - Method in class org.openscience.cdk.BondRef

Returns the geometric 3D center of the bond.

get3DCenter() - Method in class org.openscience.cdk.debug.DebugBond

Returns the geometric 3D center of the bond.

get3DCenter(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.GeometryUtil

Calculates the center of mass for the Atoms in the AtomContainer.

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.

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.

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

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.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.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 the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().

getAtom(int) - Method in class org.openscience.cdk.Bond

Returns an Atom from this bond.

getAtom(int) - Method in class org.openscience.cdk.BondRef

Returns an Atom from this bond.

getAtom(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().

getAtom(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer

Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().

getAtom(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().

getAtom(int) - Method in class org.openscience.cdk.debug.DebugBond

Returns an Atom from this bond.

getAtom(int) - Method in class org.openscience.cdk.debug.DebugCrystal

Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().

getAtom() - 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 the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().

getAtom(int) - Method in class org.openscience.cdk.debug.DebugPolymer

Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().

getAtom(int) - Method in class org.openscience.cdk.debug.DebugRing

Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().

getAtom() - 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 the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().

getAtom(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().

getAtom(int) - Method in interface org.openscience.cdk.interfaces.IBond

Returns an Atom from this bond.

getAtom() - 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 the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().

getAtom(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond

Returns an Atom from this query bond.

getAtom() - 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 the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().

getAtom(int) - Method in class org.openscience.cdk.silent.Bond

Returns an Atom from this bond.

getAtom() - 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

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.BondRef

Returns the number of Atoms in this Bond.

getAtomCount() - Method in class org.openscience.cdk.debug.DebugAminoAcid

Returns the number of Atoms in this Container.

getAtomCount() - Method in class org.openscience.cdk.debug.DebugAtomContainer

Returns the number of Atoms in this Container.

getAtomCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer

Returns the number of Atoms in this Container.

getAtomCount() - Method in class org.openscience.cdk.debug.DebugBond

Returns the number of Atoms in this Bond.

getAtomCount() - Method in class org.openscience.cdk.debug.DebugCrystal

Returns the number of Atoms in this Container.

getAtomCount() - Method in class org.openscience.cdk.debug.DebugMonomer

Returns the number of Atoms in this Container.

getAtomCount() - Method in class org.openscience.cdk.debug.DebugPolymer

Returns the number of Atoms in this Container.

getAtomCount() - Method in class org.openscience.cdk.debug.DebugRing

Returns the number of Atoms in this Container.

getAtomCount() - Method in class org.openscience.cdk.debug.DebugStrand

Returns the number of Atoms in this Container.

getAtomCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the number of Atoms in this Container.

getAtomCount() - Method in interface org.openscience.cdk.interfaces.IBond

Returns the number of Atoms in this Bond.

getAtomCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Returns the number of Atoms in this Container.

getAtomCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond

Returns the number of Atoms in this Bond.

getAtomCount() - Method in class org.openscience.cdk.silent.AtomContainer

Returns the number of Atoms in this Container.

getAtomCount() - Method in class org.openscience.cdk.silent.Bond

Returns the number of Atoms in this Bond.

getAtomCount(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.AtomRef

Returns the atomic number of this element.

getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugAtom

Returns the atomic number of this element.

getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugAtomType

Returns the atomic number of this element.

getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugElement

Returns the atomic number of this element.

getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Returns the atomic number of this element.

getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugIsotope

Returns the atomic number of this element.

getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Returns the atomic number of this element.

getAtomicNumber() - Method in class org.openscience.cdk.Element

Returns the atomic number of this element.

getAtomicNumber() - Method in interface org.openscience.cdk.interfaces.IElement

Returns the atomic number of this element.

getAtomicNumber() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Returns the atomic number of this element.

getAtomicNumber() - Method in class org.openscience.cdk.silent.Element

Returns the atomic number of this element.

getAtomicNumber(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable

Get the atomic number of the element.

getAtomicSoftnessCore(IAtomContainer, int) - Method in class org.openscience.cdk.charges.InductivePartialCharges

Gets the atomicSoftnessCore attribute of the InductivePartialCharges object.

getAtomIndices() - Method in class org.openscience.cdk.signature.Orbit

Gets all the atom indices as a list.

getAtomLayers(int[][]) - Static method in class org.openscience.cdk.graph.invariant.HuLuIndexTool

getAtomNumber(IAtom) - Method in class org.openscience.cdk.AtomContainer

Returns the position of a given atom in the atoms array.

getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Returns the position of a given atom in the atoms array.

getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Returns the position of a given atom in the atoms array.

getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal

Returns the position of a given atom in the atoms array.

getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer

Returns the position of a given atom in the atoms array.

getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer

Returns the position of a given atom in the atoms array.

getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugRing

Returns the position of a given atom in the atoms array.

getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand

Returns the position of a given atom in the atoms array.

getAtomNumber(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Deprecated.

use IAtomContainer.indexOf(IAtom)

getAtomNumber(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Returns the position of a given atom in the atoms array.

getAtomNumber(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer

Returns the position of a given atom in the atoms array.

getAtomOverlapScore(IAtomContainer, Vector) - Method in class org.openscience.cdk.layout.OverlapResolver

Deprecated.

Calculates a score based on the overlap of atoms.

getAtomPlacer() - Method in class org.openscience.cdk.layout.RingPlacer

getAtoms() - Method in class org.openscience.cdk.Association

Returns the array of atoms making up this Association.

getAtoms() - Method in class org.openscience.cdk.sgroup.Sgroup

Access the atoms of this substructure group.

getAtomType(String) - Method in class org.openscience.cdk.config.AtomTypeFactory

Get an AtomType with the given ID.

getAtomTypeFactory(IChemObjectBuilder) - Method in class org.openscience.cdk.tools.SaturationChecker

getAtomTypeFactory(IChemObjectBuilder) - Method in class org.openscience.cdk.tools.SmilesValencyChecker

getAtomTypeMappings() - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingHandler

Returns a Map with atom type mappings.

getAtomTypeName() - Method in class org.openscience.cdk.AtomRef

Gets the id attribute of the AtomType object.

getAtomTypeName() - Method in class org.openscience.cdk.AtomType

Gets the id attribute of the AtomType object.

getAtomTypeName() - Method in class org.openscience.cdk.debug.DebugAtom

Gets the id attribute of the AtomType object.

getAtomTypeName() - Method in class org.openscience.cdk.debug.DebugAtomType

Gets the id attribute of the AtomType object.

getAtomTypeName() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Gets the id attribute of the AtomType object.

getAtomTypeName() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Gets the id attribute of the AtomType object.

getAtomTypeName() - Method in interface org.openscience.cdk.interfaces.IAtomType

Gets the id attribute of the AtomType object.

getAtomTypeName() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Gets the id attribute of the AtomType object.

getAtomTypeName() - Method in class org.openscience.cdk.silent.AtomType

Gets the id attribute of the AtomType object.

getAtomTypePatterns() - Method in class org.openscience.cdk.modeling.builder3d.MM2BasedAtomTypePattern

Gets the atomTypePatterns attribute of the MM2BasedAtomTypePattern object

getAtomTypePatterns() - Method in class org.openscience.cdk.modeling.builder3d.MMFF94BasedAtomTypePattern

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(IAtomContainer) - 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.

getBegin() - Method in class org.openscience.cdk.Bond

Access the begin (or first) atom of the bond.

getBegin() - Method in class org.openscience.cdk.BondRef

Access the begin (or first) atom of the bond.

getBegin() - Method in class org.openscience.cdk.debug.DebugBond

Access the begin (or first) atom of the bond.

getBegin() - Method in interface org.openscience.cdk.interfaces.IBond

Access the begin (or first) atom of the bond.

getBegin() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond

Access the begin (or first) atom of the bond.

getBegin() - Method in class org.openscience.cdk.silent.Bond

Access the begin (or first) atom of the bond.

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.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.GeometryUtil

Determines the best alignment for the label of an atom in 2D space.

getBibData() - Method in class org.openscience.cdk.tools.BremserOneSphereHOSECodePredictor

getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.AtomPairs2DFingerprinter

getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter

Calculates the circular fingerprint for the given IAtomContainer, and folds the result into a single bitset (see getSize()).

getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.EStateFingerprinter

Returns the bit fingerprint for the given IAtomContainer.

getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter

Generates a fingerprint of the default size for the given AtomContainer, using path and ring metrics.

getBitFingerprint(IAtomContainer, 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).

getBitSetFromFile(StringTokenizer) - Static method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D

getBond(IAtom) - Method in class org.openscience.cdk.Atom

Returns the bond connecting 'this' atom to the provided atom.

getBond(int) - Method in class org.openscience.cdk.AtomContainer

Get the bond at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getBondCount().

getBond(IAtom, IAtom) - Method in class org.openscience.cdk.AtomContainer

Returns the bond that connects the two given atoms.

getBond(IAtom) - Method in class org.openscience.cdk.AtomRef

Returns the bond connecting 'this' atom to the provided atom.

getBond(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Get the bond at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getBondCount().

getBond(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 the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getBondCount().

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 the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getBondCount().

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 the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getBondCount().

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 the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getBondCount().

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 the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getBondCount().

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 the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getBondCount().

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 the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getBondCount().

getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugStrand

Returns the bond that connects the two given atoms.

getBond(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtom

Returns the bond connecting 'this' atom to the provided atom.

getBond(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Get the bond at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getBondCount().

getBond(IAtom, IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the bond that connects the two given atoms.

getBond(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Returns the bond connecting 'this' atom to the provided atom.

getBond(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Get the bond at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getBondCount().

getBond(IAtom, IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Returns the bond that connects the two given atoms.

getBond(IAtom) - Method in class org.openscience.cdk.silent.Atom

Returns the bond connecting 'this' atom to the provided atom.

getBond(int) - Method in class org.openscience.cdk.silent.AtomContainer

Get the bond at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getBondCount().

getBond(IAtom, IAtom) - Method in class org.openscience.cdk.silent.AtomContainer

Returns the bond that connects the two given atoms.

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.GeometryUtil

Writes the coordinates of the atoms participating the given bond into an array.

getBondCount() - Method in class org.openscience.cdk.Atom

Get the number of explicit bonds connected to this atom.

getBondCount() - Method in class org.openscience.cdk.AtomContainer

Returns the number of Bonds in this Container.

getBondCount() - Method in class org.openscience.cdk.AtomRef

getBondCount() - Method in class org.openscience.cdk.debug.DebugAminoAcid

Returns the number of Bonds in this Container.

getBondCount() - Method in class org.openscience.cdk.debug.DebugAtomContainer

Returns the number of Bonds in this Container.

getBondCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer

Returns the number of Bonds in this Container.

getBondCount() - Method in class org.openscience.cdk.debug.DebugCrystal

Returns the number of Bonds in this Container.

getBondCount() - Method in class org.openscience.cdk.debug.DebugMonomer

Returns the number of Bonds in this Container.

getBondCount() - Method in class org.openscience.cdk.debug.DebugPolymer

Returns the number of Bonds in this Container.

getBondCount() - Method in class org.openscience.cdk.debug.DebugRing

Returns the number of Bonds in this Container.

getBondCount() - Method in class org.openscience.cdk.debug.DebugStrand

Returns the number of Bonds in this Container.

getBondCount() - Method in interface org.openscience.cdk.interfaces.IAtom

Get the number of explicit bonds connected to this atom.

getBondCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the number of Bonds in this Container.

getBondCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Get the number of explicit bonds connected to this atom.

getBondCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Returns the number of Bonds in this Container.

getBondCount() - Method in class org.openscience.cdk.silent.Atom

Get the number of explicit bonds connected to this atom.

getBondCount() - Method in class org.openscience.cdk.silent.AtomContainer

Returns the number of Bonds in this Container.

getBondCount(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator

getBondCount(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.

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.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.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.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.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.

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

Deprecated.

use IAtomContainer.indexOf(IBond)

getBondNumber(IBond) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Deprecated.

use IAtomContainer.indexOf(IBond)

getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Returns the position of the bond between two given atoms in the electronContainers array.

getBondNumber(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.

getBondOrderSum(IAtom) - Method in class org.openscience.cdk.AtomContainer

Returns the sum of the bond orders for a given Atom.

getBondOrderSum() - Method in class org.openscience.cdk.AtomRef

Gets the bondOrderSum attribute of the AtomType object.

getBondOrderSum() - Method in class org.openscience.cdk.AtomType

Gets the bondOrderSum attribute of the AtomType object.

getBondOrderSum(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

Returns the sum of the bond orders for a given Atom.

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.

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

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.

getCarriers() - Method in interface org.openscience.cdk.interfaces.IStereoElement

The carriers of the stereochemistry

getCASId(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable

Get the CAS ID for an element.

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.

getCell(int) - Method in class org.openscience.cdk.group.Partition

Gets the cell at this index.

getCenterOfMass() - Method in class org.openscience.cdk.geometry.alignment.KabschAlignment

Returns the center of mass for the first molecule or fragment used in the calculation.

getCentralAtom() - Method in interface org.openscience.cdk.geometry.cip.ILigand

The central IAtom to which this ligand is connected via one IBond.

getCentralAtom() - Method in class org.openscience.cdk.geometry.cip.Ligand

The central IAtom to which this ligand is connected via one IBond.

getChainID() - Method in class org.openscience.cdk.debug.DebugPDBAtom

get the Chain identifier of this atom.

getChainID() - Method in class org.openscience.cdk.debug.DebugPDBMonomer

Gets the Chain ID of this monomer.

getChainID() - Method in interface org.openscience.cdk.interfaces.IPDBAtom

get the Chain identifier of this atom.

getChainID() - Method in interface org.openscience.cdk.interfaces.IPDBMonomer

Gets the Chain ID of this monomer.

getChainID() - Method in class org.openscience.cdk.protein.data.PDBAtom

get the Chain identifier of this atom.

getChainID() - Method in class org.openscience.cdk.protein.data.PDBMonomer

getChainID() - Method in class org.openscience.cdk.silent.PDBAtom

get the Chain identifier of this atom.

getChainID() - Method in class org.openscience.cdk.silent.PDBMonomer

getCharge() - Method in class org.openscience.cdk.Atom

Returns the partial charge of this atom.

getCharge() - Method in class org.openscience.cdk.AtomRef

Returns the partial charge of this atom.

getCharge() - Method in class org.openscience.cdk.debug.DebugAdductFormula

Returns the partial charge of this Adduct.

getCharge() - Method in class org.openscience.cdk.debug.DebugAtom

Returns the partial charge of this atom.

getCharge() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Returns the partial charge of this atom.

getCharge() - Method in class org.openscience.cdk.debug.DebugMolecularFormula

Access the charge of this IMolecularFormula.

getCharge() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Returns the partial charge of this atom.

getCharge() - Method in class org.openscience.cdk.formula.AdductFormula

Returns the partial charge of this Adduct.

getCharge() - Method in class org.openscience.cdk.formula.IsotopePattern

Get the charge in this pattern.

getCharge() - Method in class org.openscience.cdk.formula.MolecularFormula

Access the charge of this IMolecularFormula.

getCharge() - Method in interface org.openscience.cdk.interfaces.IAdductFormula

Returns the partial charge of this Adduct.

getCharge() - Method in interface org.openscience.cdk.interfaces.IAtom

Returns the partial charge of this atom.

getCharge() - Method in interface org.openscience.cdk.interfaces.IMolecularFormula

Access the charge of this IMolecularFormula.

getCharge() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Returns the partial charge of this atom.

getCharge() - Method in class org.openscience.cdk.silent.AdductFormula

Returns the partial charge of this Adduct.

getCharge() - Method in class org.openscience.cdk.silent.Atom

Returns the partial charge of this atom.

getCharge() - Method in class org.openscience.cdk.silent.MolecularFormula

Access the charge of this IMolecularFormula.

getChargeGroups() - Method in class org.openscience.cdk.libio.md.MDMolecule

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

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.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.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.

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.

getConfidenceLimit(String) - Method in class org.openscience.cdk.tools.BremserOneSphereHOSECodePredictor

getConfig() - Method in interface org.openscience.cdk.interfaces.IStereoElement

Access the configuration order and class of the stereochemistry.

getConfigClass() - Method in interface org.openscience.cdk.interfaces.IStereoElement

The configuration class of the stereochemistry.

getConfigOrder() - Method in interface org.openscience.cdk.interfaces.IStereoElement

The configuration order of the stereochemistry.

getConnected(int) - Method in class org.openscience.cdk.signature.AtomSignature

getConnectedAtom(IAtom) - Method in class org.openscience.cdk.Bond

Returns the other atom in the bond, the atom is connected to the given atom.

getConnectedAtom(IAtom) - Method in class org.openscience.cdk.BondRef

Returns the other atom in the bond, the atom is connected to the given atom.

getConnectedAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.IBond

Deprecated.

use the method IBond.getOther(IAtom)

getConnectedAtom(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond

Returns the other atom in the bond, the atom is connected to the given atom.

getConnectedAtom(IAtom) - Method in class org.openscience.cdk.silent.Bond

Returns the other atom in the bond, the atom is connected to the given atom.

getConnectedAtomContainer() - Method in interface org.openscience.cdk.renderer.selection.IChemObjectSelection

Make an IAtomContainer where all the bonds only have atoms that are in the selection.

getConnectedAtoms(IAtom) - Method in class org.openscience.cdk.Bond

Returns all the atoms in the bond connected to the given atom.

getConnectedAtoms(IAtom) - Method in class org.openscience.cdk.BondRef

Returns all the atoms in the bond connected to the given atom.

getConnectedAtoms(IAtom) - Method in interface org.openscience.cdk.interfaces.IBond

Returns all the atoms in the bond connected to the given atom.

getConnectedAtoms(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond

Returns all the atoms in the bond connected to the given atom.

getConnectedAtoms(IAtom) - Method in class org.openscience.cdk.silent.Bond

Returns all the atoms in the bond connected to the given atom.

getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.AtomContainer

Returns the number of connected atoms (explicit degree) to the specified atom.

getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Returns the number of connected atoms (explicit degree) to the specified atom.

getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer

Returns the number of connected atoms (explicit degree) to the specified atom.

getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Returns the number of connected atoms (explicit degree) to the specified atom.

getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal

Returns the number of connected atoms (explicit degree) to the specified atom.

getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer

Returns the number of connected atoms (explicit degree) to the specified atom.

getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer

Returns the number of connected atoms (explicit degree) to the specified atom.

getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugRing

Returns the number of connected atoms (explicit degree) to the specified atom.

getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand

Returns the number of connected atoms (explicit degree) to the specified atom.

getConnectedAtomsCount(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Deprecated.

use IAtomContainer.getConnectedBondsCount(IAtom)

getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Returns the number of atoms connected to the given atom.

getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer

Returns the number of connected atoms (explicit degree) to the specified atom.

getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.AtomContainer

Returns the atoms connected connected to the specified atom by a bond.

getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Returns the atoms connected connected to the specified atom by a bond.

getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer

Returns the atoms connected connected to the specified atom by a bond.

getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Returns the atoms connected connected to the specified atom by a bond.

getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal

Returns the atoms connected connected to the specified atom by a bond.

getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer

Returns the atoms connected connected to the specified atom by a bond.

getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer

Returns the atoms connected connected to the specified atom by a bond.

getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugRing

Returns the atoms connected connected to the specified atom by a bond.

getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand

Returns the atoms connected connected to the specified atom by a bond.

getConnectedAtomsList(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the atoms connected connected to the specified atom by a bond.

getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Returns an ArrayList of all atoms connected to the given atom.

getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer

Returns the atoms connected connected to the specified atom by a bond.

getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.AtomContainer

Returns the number of connected bonds (explicit degree) to the specified atom.

getConnectedBondsCount(int) - Method in class org.openscience.cdk.AtomContainer

Returns the number of connected bonds (explicit degree) to atom at the specified index.

getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Returns the number of connected bonds (explicit degree) to the specified atom.

getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer

Returns the number of connected bonds (explicit degree) to the specified atom.

getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Returns the number of connected bonds (explicit degree) to the specified atom.

getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal

Returns the number of connected bonds (explicit degree) to the specified atom.

getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer

Returns the number of connected bonds (explicit degree) to the specified atom.

getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer

Returns the number of connected bonds (explicit degree) to the specified atom.

getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugRing

Returns the number of connected bonds (explicit degree) to the specified atom.

getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand

Returns the number of connected bonds (explicit degree) to the specified atom.

getConnectedBondsCount(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the number of connected bonds (explicit degree) to the specified atom.

getConnectedBondsCount(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the number of connected bonds (explicit degree) to atom at the specified index.

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 connected bonds (explicit degree) to the specified atom.

getConnectedBondsCount(int) - Method in class org.openscience.cdk.silent.AtomContainer

Returns the number of connected bonds (explicit degree) to atom at the specified index.

getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.AtomContainer

Returns the bonds connected connected to the specified atom.

getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Returns the bonds connected connected to the specified atom.

getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer

Returns the bonds connected connected to the specified atom.

getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Returns the bonds connected connected to the specified atom.

getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal

Returns the bonds connected connected to the specified atom.

getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer

Returns the bonds connected connected to the specified atom.

getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer

Returns the bonds connected connected to the specified atom.

getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugRing

Returns the bonds connected connected to the specified atom.

getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand

Returns the bonds connected connected to the specified atom.

getConnectedBondsList(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the bonds connected connected to the specified atom.

getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Returns an ArrayList of all Bonds connected to the given atom.

getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer

Returns the bonds connected connected to the specified atom.

getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.AtomContainer

Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.

getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.

getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer

Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.

getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.

getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal

Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.

getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer

Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.

getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer

Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.

getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugRing

Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.

getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand

Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.

getConnectedElectronContainersList(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.

getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Returns an ArrayList of all electronContainers connected to the given atom.

getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer

Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.

getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.AtomContainer

Returns the number of lone pairs connected to the specified atom.

getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Returns the number of lone pairs connected to the specified atom.

getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer

Returns the number of lone pairs connected to the specified atom.

getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Returns the number of lone pairs connected to the specified atom.

getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal

Returns the number of lone pairs connected to the specified atom.

getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer

Returns the number of lone pairs connected to the specified atom.

getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer

Returns the number of lone pairs connected to the specified atom.

getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugRing

Returns the number of lone pairs connected to the specified atom.

getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand

Returns the number of lone pairs connected to the specified atom.

getConnectedLonePairsCount(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the number of lone pairs connected to the specified atom.

getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Returns the number of LonePairs for a given Atom.

getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer

Returns the number of lone pairs connected to the specified atom.

getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.AtomContainer

Returns the lone pairs connected connected to the specified atom.

getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Returns the lone pairs connected connected to the specified atom.

getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer

Returns the lone pairs connected connected to the specified atom.

getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Returns the lone pairs connected connected to the specified atom.

getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal

Returns the lone pairs connected connected to the specified atom.

getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer

Returns the lone pairs connected connected to the specified atom.

getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer

Returns the lone pairs connected connected to the specified atom.

getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugRing

Returns the lone pairs connected connected to the specified atom.

getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand

Returns the lone pairs connected connected to the specified atom.

getConnectedLonePairsList(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the lone pairs connected connected to the specified atom.

getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Returns the array of lone pairs connected to an atom.

getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer

Returns the lone pairs connected connected to the specified atom.

getConnectedRings(IRing) - Method in class org.openscience.cdk.debug.DebugRingSet

Returns all the rings in the RingSet that share one or more atoms with a given ring.

getConnectedRings(IRing) - Method in interface org.openscience.cdk.interfaces.IRingSet

Returns all the rings in the RingSet that share one or more atoms with a given ring.

getConnectedRings(IRing) - Method in class org.openscience.cdk.RingSet

Returns all the rings in the RingSet that share one or more atoms with a given ring.

getConnectedRings(IRing) - Method in class org.openscience.cdk.silent.RingSet

Returns all the rings in the RingSet that share one or more atoms with a given ring.

getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.AtomContainer

Returns the number of single electrons connected to the specified atom.

getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Returns the number of single electrons connected to the specified atom.

getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer

Returns the number of single electrons connected to the specified atom.

getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Returns the number of single electrons connected to the specified atom.

getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal

Returns the number of single electrons connected to the specified atom.

getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer

Returns the number of single electrons connected to the specified atom.

getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer

Returns the number of single electrons connected to the specified atom.

getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugRing

Returns the number of single electrons connected to the specified atom.

getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand

Returns the number of single electrons connected to the specified atom.

getConnectedSingleElectronsCount(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the number of single electrons connected to the specified atom.

getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Returns the sum of the SingleElectron for a given Atom.

getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer

Returns the number of single electrons connected to the specified atom.

getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.AtomContainer

Returns the single electrons connected connected to the specified atom.

getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Returns the single electrons connected connected to the specified atom.

getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer

Returns the single electrons connected connected to the specified atom.

getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Returns the single electrons connected connected to the specified atom.

getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal

Returns the single electrons connected connected to the specified atom.

getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer

Returns the single electrons connected connected to the specified atom.

getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer

Returns the single electrons connected connected to the specified atom.

getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugRing

Returns the single electrons connected connected to the specified atom.

getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand

Returns the single electrons connected connected to the specified atom.

getConnectedSingleElectronsList(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the single electrons connected connected to the specified atom.

getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Returns an array of all SingleElectron connected to the given atom.

getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer

Returns the single electrons connected connected to the specified atom.

getConnectivity(int, int) - Method in interface org.openscience.cdk.group.Refinable

Get the connectivity between two vertices as an integer, to allow for multigraphs : so a single edge is 1, a double edge 2, etc.

getContainer() - Method in class org.openscience.cdk.Atom

Access the IAtomContainer of which this atom is a member of.

getContainer() - Method in class org.openscience.cdk.AtomRef

Access the IAtomContainer of which this atom is a member of.

getContainer() - Method in class org.openscience.cdk.Bond

getContainer() - Method in class org.openscience.cdk.BondRef

getContainer() - Method in class org.openscience.cdk.debug.DebugAtom

Access the IAtomContainer of which this atom is a member of.

getContainer() - Method in interface org.openscience.cdk.interfaces.IAtom

Access the IAtomContainer of which this atom is a member of.

getContainer() - Method in interface org.openscience.cdk.interfaces.IBond

getContainer() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Access the IAtomContainer of which this atom is a member of.

getContainer() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond

getContainer() - Method in class org.openscience.cdk.silent.Atom

Access the IAtomContainer of which this atom is a member of.

getContainer() - Method in class org.openscience.cdk.silent.Bond

getContainer(IAtomContainer, IAtom) - Method in class org.openscience.cdk.tools.StructureResonanceGenerator

Get the container which the atom is found on resonance from a IAtomContainer.

getContainer(IAtomContainer, IBond) - Method in class org.openscience.cdk.tools.StructureResonanceGenerator

Get the container which the bond is found on resonance from a IAtomContainer.

getContainers(IAtomContainer) - Method in class org.openscience.cdk.tools.StructureResonanceGenerator

Get the container which is found resonance from a IAtomContainer.

getCoordinatesFromGridPoint(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.

getCountableMACCSSMARTS() - Static method in class org.openscience.cdk.fingerprint.StandardSubstructureSets

Subset of the MACCS fingerprint definitions.

getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.AtomPairs2DFingerprinter

getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter

Calculates the circular fingerprint for the given IAtomContainer, and returns a datastructure that enumerates all of the fingerprints, and their counts (i.e.

getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.EStateFingerprinter

Returns the count fingerprint for the given IAtomContainer.

getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter

Returns the count fingerprint for the given IAtomContainer.

getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.Fingerprinter

getCountFingerprint(IAtomContainer) - Method in interface org.openscience.cdk.fingerprint.IFingerprinter

Returns the count fingerprint for the given IAtomContainer.

getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.LingoFingerprinter

getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.MACCSFingerprinter

Returns the count fingerprint for the given IAtomContainer.

getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.PubchemFingerprinter

Returns the count fingerprint for the given IAtomContainer.

getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.ShortestPathFingerprinter

getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.SignatureFingerprinter

getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.SubstructureFingerprinter

Returns the count fingerprint for the given IAtomContainer.

getCountForHash(int) - Method in interface org.openscience.cdk.fingerprint.ICountFingerprint

Get the number of times a certain hash exists in the fingerprint.

getCountForHash(int) - Method in class org.openscience.cdk.fingerprint.IntArrayCountFingerprint

getCovalentRadius() - Method in class org.openscience.cdk.AtomRef

Returns the covalent radius for this AtomType.

getCovalentRadius() - Method in class org.openscience.cdk.AtomType

Returns the covalent radius for this AtomType.

getCovalentRadius() - Method in class org.openscience.cdk.debug.DebugAtom

Returns the covalent radius for this AtomType.

getCovalentRadius() - Method in class org.openscience.cdk.debug.DebugAtomType

Returns the covalent radius for this AtomType.

getCovalentRadius() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Returns the covalent radius for this AtomType.

getCovalentRadius() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Returns the covalent radius for this AtomType.

getCovalentRadius() - Method in interface org.openscience.cdk.interfaces.IAtomType

Returns the covalent radius for this AtomType.

getCovalentRadius() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Returns the covalent radius for this AtomType.

getCovalentRadius() - Method in class org.openscience.cdk.silent.AtomType

Returns the covalent radius for this AtomType.

getCovalentRadius(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable

Get the covalent radius for an element.

getCreatormap() - Method in class org.openscience.cdk.io.RssWriter

getCrystal() - Method in class org.openscience.cdk.ChemModel

Gets the Crystal contained in this ChemModel.

getCrystal() - Method in class org.openscience.cdk.debug.DebugChemModel

Gets the Crystal contained in this ChemModel.

getCrystal() - Method in interface org.openscience.cdk.interfaces.IChemModel

Gets the Crystal contained in this ChemModel.

getCrystal() - Method in class org.openscience.cdk.silent.ChemModel

Gets the Crystal contained in this ChemModel.

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.

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.

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.ForceDelocalisedBondDisplay

Gets the default value for this parameter.

getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.HashSpacing

Gets the default value for this parameter.

getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.Highlighting

Gets the default value for this parameter.

getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.OmitMajorIsotopes

Gets the default value for this parameter.

getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.OuterGlowWidth

Gets the default value for this parameter.

getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.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

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.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.molecular.AcidicGroupCountDescriptor

Returns an array of names for each descriptor value calculated.

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor

Returns an array of names for each descriptor value calculated.

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor

Returns an array of names for each descriptor value calculated.

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalCSP3Descriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor

Returns the names of the descriptors made available by this class.

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.SpiroAtomCountDescriptor

Returns an array of names for each descriptor value calculated.

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.substance.OxygenAtomCountDescriptor

Returns an array of names for each descriptor value calculated.

getDescriptorNames() - Method in interface org.openscience.cdk.qsar.IDescriptor

Returns an array of names for each descriptor value calculated.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor

Returns the specific type of the FMF descriptor value.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalCSP3Descriptor

Returns the specific type of the Fsp3 descriptor value.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor

Returns a type of return value calculated by this descriptor.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor

Returns a placeholder with the descriptor size and type.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.SpiroAtomCountDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in interface org.openscience.cdk.qsar.descriptors.substance.ISubstanceDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.substance.OxygenAtomCountDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorResultType() - Method in interface org.openscience.cdk.qsar.IMolecularDescriptor

Returns the specific type of the DescriptorResult object.

getDescriptorSpecifications() - Method in class org.openscience.cdk.qsar.DescriptorEngine

Returns the DescriptorSpecification objects for all available descriptors.

getDetails() - Method in class org.openscience.cdk.validate.ValidationTest

getDictionary(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.

getDrawCenter() - Method in class org.openscience.cdk.renderer.AbstractRenderer

Get the position on screen that the diagram will be drawn.

getEAIDNumber(IAtomContainer) - Static method in class org.openscience.cdk.graph.invariant.HuLuIndexTool

Calculates the extended adjacency matrix index.

getEdgeLabel(int, int) - Method in class org.openscience.cdk.signature.AtomSignature

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.BondRef

Returns the number of electrons in this electron container.

getElectronCount() - Method in class org.openscience.cdk.debug.DebugBond

Returns the number of electrons in this electron container.

getElectronCount() - Method in class org.openscience.cdk.debug.DebugElectronContainer

Returns the number of electrons in this electron container.

getElectronCount() - Method in class org.openscience.cdk.debug.DebugLonePair

Returns the number of electrons in a LonePair.

getElectronCount() - Method in class org.openscience.cdk.debug.DebugSingleElectron

Returns the number of electrons in this SingleElectron.

getElectronCount() - Method in class org.openscience.cdk.ElectronContainer

Returns the number of electrons in this electron container.

getElectronCount() - Method in interface org.openscience.cdk.interfaces.IElectronContainer

Returns the number of electrons in this electron container.

getElectronCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond

Returns the number of electrons in this bond

getElectronCount() - Method in class org.openscience.cdk.LonePair

Returns the number of electrons in a LonePair.

getElectronCount() - Method in class org.openscience.cdk.silent.ElectronContainer

Returns the number of electrons in this electron container.

getElectronCount() - Method in class org.openscience.cdk.silent.LonePair

Returns the number of electrons in a LonePair.

getElectronCount() - Method in class org.openscience.cdk.silent.SingleElectron

Returns the number of electrons in this SingleElectron.

getElectronCount() - Method in class org.openscience.cdk.SingleElectron

Returns the number of electrons in this SingleElectron.

getElectronegativity(String) - Method in class org.openscience.cdk.tools.AtomicProperties

getElement(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.BondRef

Access the end (or second) atom of the bond.

getEnd() - Method in class org.openscience.cdk.debug.DebugBond

Access the end (or second) atom of the bond.

getEnd() - Method in interface org.openscience.cdk.interfaces.IBond

Access the end (or second) atom of the bond.

getEnd() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond

Access the end (or second) atom of the bond.

getEnd() - Method in class org.openscience.cdk.silent.Bond

Access the end (or second) atom of the bond.

getEndChainID() - Method in class org.openscience.cdk.debug.DebugPDBStructure

get the ending Chain identifier of this structure.

getEndChainID() - Method in interface org.openscience.cdk.interfaces.IPDBStructure

get the ending Chain identifier of this structure.

getEndChainID() - Method in class org.openscience.cdk.protein.data.PDBStructure

get the ending Chain identifier of this structure.

getEndChainID() - Method in class org.openscience.cdk.silent.PDBStructure

get the ending Chain identifier of this structure.

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.

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.

getEntries() - Method in class org.openscience.cdk.dict.Dictionary

getEntry(String) - Method in class org.openscience.cdk.dict.Dictionary

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.

getExactMass() - Method in class org.openscience.cdk.AtomRef

Gets the ExactMass attribute of the Isotope object.

getExactMass() - Method in class org.openscience.cdk.debug.DebugAtom

Gets the ExactMass attribute of the Isotope object.

getExactMass() - Method in class org.openscience.cdk.debug.DebugAtomType

Gets the ExactMass attribute of the Isotope object.

getExactMass() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

The exact mass of an FragmentAtom is defined as the sum of exact masses of the IAtom's in the fragment.

getExactMass() - Method in class org.openscience.cdk.debug.DebugIsotope

Gets the ExactMass attribute of the Isotope object.

getExactMass() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Gets the ExactMass attribute of the Isotope object.

getExactMass() - Method in class org.openscience.cdk.FragmentAtom

The exact mass of an FragmentAtom is defined as the sum of exact masses of the IAtom's in the fragment.

getExactMass() - Method in interface org.openscience.cdk.interfaces.IIsotope

Gets the ExactMass attribute of the Isotope object.

getExactMass() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Gets the ExactMass attribute of the Isotope object.

getExactMass() - Method in class org.openscience.cdk.Isotope

Gets the ExactMass attribute of the Isotope object.

getExactMass() - Method in class org.openscience.cdk.silent.FragmentAtom

The exact mass of an FragmentAtom is defined as the sum of exact masses of the IAtom's in the fragment.

getExactMass() - Method in class org.openscience.cdk.silent.Isotope

Gets the ExactMass attribute of the Isotope object.

getExampleReactions() - Method in class org.openscience.cdk.dict.EntryReact

getException() - Method in class org.openscience.cdk.qsar.DescriptorValue

getExpression() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Get the atom-expression predicate for this query atom.

getExpression() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond

Access the bond expression predicate associated with this query bond.

getExtendedAdjacenyMatrix(IAtomContainer) - 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.

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.

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

Deprecated.

use IAtomContainer.getAtom(int)

getFirstAtom() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Returns the atom at position 0 in the container.

getFirstAtom() - Method in class org.openscience.cdk.signature.Orbit

Gets the first atom index of the orbit.

getFirstAtom() - Method in class org.openscience.cdk.silent.AtomContainer

Returns the atom at position 0 in the container.

getFirstAttachmentPoint() - Method in class org.openscience.cdk.isomorphism.matchers.RGroup

getFirstGraphSize() - Method in class org.openscience.cdk.isomorphism.mcss.RGraph

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.

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.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.

getFocus() - Method in interface org.openscience.cdk.interfaces.IStereoElement

The focus atom or bond at the 'centre' of the stereo-configuration.

getFolding() - Method in class org.openscience.cdk.fingerprint.model.Bayesian

Access to the fingerprint folding extent.

getFont() - Method in class org.openscience.cdk.renderer.font.AWTFontManager

Get the current font.

getFontName() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager

Get the font family name used in this font manager.

getFontSizeForZoom(double) - Method in class org.openscience.cdk.renderer.font.AbstractFontManager

For a particular zoom, get the appropriate font size.

getFontStyle() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager

Get the font style, defined in the IFontManager interface.

getForbidden() - Method in class org.openscience.cdk.isomorphism.mcss.RNode

Gets the forbidden attribute of the RNode object.

getFormalCharge() - Method in class org.openscience.cdk.AtomRef

Returns the formal charge of this atom.

getFormalCharge() - Method in class org.openscience.cdk.AtomType

Returns the formal charge of this atom.

getFormalCharge() - Method in class org.openscience.cdk.debug.DebugAtom

Returns the formal charge of this atom.

getFormalCharge() - Method in class org.openscience.cdk.debug.DebugAtomType

Returns the formal charge of this atom.

getFormalCharge() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Returns the formal charge of this atom.

getFormalCharge() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Returns the formal charge of this atom.

getFormalCharge() - Method in interface org.openscience.cdk.interfaces.IAtomType

Returns the formal charge of this atom.

getFormalCharge() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Returns the formal charge of this atom.

getFormalCharge() - Method in class org.openscience.cdk.silent.AtomType

Returns the formal charge of this atom.

getFormalNeighbourCount() - Method in class org.openscience.cdk.AtomRef

Returns the formal neighbour count of this atom.

getFormalNeighbourCount() - Method in class org.openscience.cdk.AtomType

Returns the formal neighbour count of this atom.

getFormalNeighbourCount() - Method in class org.openscience.cdk.debug.DebugAtom

Returns the formal neighbour count of this atom.

getFormalNeighbourCount() - Method in class org.openscience.cdk.debug.DebugAtomType

Returns the formal neighbour count of this atom.

getFormalNeighbourCount() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Returns the formal neighbour count of this atom.

getFormalNeighbourCount() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Returns the formal neighbour count of this atom.

getFormalNeighbourCount() - Method in interface org.openscience.cdk.interfaces.IAtomType

Returns the formal neighbour count of this atom.

getFormalNeighbourCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Returns the formal neighbour count of this atom.

getFormalNeighbourCount() - Method in class org.openscience.cdk.silent.AtomType

Returns the formal neighbour count of this atom.

getFormat() - Method in class org.openscience.cdk.io.CDKSourceCodeWriter

getFormat() - Method in class org.openscience.cdk.io.CIFReader

getFormat() - Method in class org.openscience.cdk.io.CMLReader

getFormat() - Method in class org.openscience.cdk.io.CMLWriter

getFormat() - Method in class org.openscience.cdk.io.CrystClustReader

getFormat() - Method in class org.openscience.cdk.io.CrystClustWriter

getFormat() - Method in class org.openscience.cdk.io.CTXReader

getFormat() - Method in class org.openscience.cdk.io.GamessReader

getFormat() - Method in class org.openscience.cdk.io.Gaussian03Reader

getFormat() - Method in class org.openscience.cdk.io.Gaussian98Reader

getFormat() - Method in class org.openscience.cdk.io.GhemicalMMReader

getFormat() - Method in class org.openscience.cdk.io.HINReader

getFormat() - Method in class org.openscience.cdk.io.HINWriter

getFormat() - Method in interface org.openscience.cdk.io.IChemObjectIO

Returns the IResourceFormat class for this IO class.

getFormat() - Method in class org.openscience.cdk.io.INChIPlainTextReader

getFormat() - Method in class org.openscience.cdk.io.INChIReader

getFormat() - Method in class org.openscience.cdk.io.iterator.event.EventCMLReader

getFormat() - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundASNReader

getFormat() - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader

getFormat() - Method in class org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader

getFormat() - Method in class org.openscience.cdk.io.iterator.IteratingSDFReader

getFormat() - Method in class org.openscience.cdk.io.iterator.IteratingSMILESReader

Get the format for this reader.

getFormat() - Method in class org.openscience.cdk.io.MDLReader

Deprecated.

getFormat() - Method in class org.openscience.cdk.io.MDLRXNReader

Deprecated.

getFormat() - Method in class org.openscience.cdk.io.MDLRXNV2000Reader

getFormat() - Method in class org.openscience.cdk.io.MDLRXNV3000Reader

getFormat() - Method in class org.openscience.cdk.io.MDLRXNWriter

getFormat() - Method in class org.openscience.cdk.io.MDLV2000Reader

getFormat() - Method in class org.openscience.cdk.io.MDLV2000Writer

getFormat() - Method in class org.openscience.cdk.io.MDLV3000Reader

getFormat() - Method in class org.openscience.cdk.io.MDLV3000Writer

Returns the IResourceFormat class for this IO class.

getFormat() - Method in class org.openscience.cdk.io.Mol2Reader

getFormat() - Method in class org.openscience.cdk.io.Mol2Writer

getFormat() - Method in class org.openscience.cdk.io.Mopac7Reader

getFormat() - Method in class org.openscience.cdk.io.MoSSOutputReader

Returns the IResourceFormat class for this IO class.

getFormat() - Method in class org.openscience.cdk.io.PCCompoundASNReader

getFormat() - Method in class org.openscience.cdk.io.PCCompoundXMLReader

getFormat() - Method in class org.openscience.cdk.io.PCSubstanceXMLReader

getFormat() - Method in class org.openscience.cdk.io.PDBReader

getFormat() - Method in class org.openscience.cdk.io.PDBWriter

getFormat() - Method in class org.openscience.cdk.io.PMPReader

getFormat() - Method in class org.openscience.cdk.io.program.GaussianInputWriter

getFormat() - Method in class org.openscience.cdk.io.program.Mopac7Writer

getFormat() - Method in class org.openscience.cdk.io.random.RandomAccessSDFReader

getFormat() - Method in class org.openscience.cdk.io.rdf.CDKOWLReader

Returns the IResourceFormat for this reader.

getFormat() - Method in class org.openscience.cdk.io.rdf.CDKOWLWriter

Returns the IResourceFormat for this writer.

getFormat() - Method in class org.openscience.cdk.io.RGroupQueryReader

getFormat() - Method in class org.openscience.cdk.io.RGroupQueryWriter

Returns output format.

getFormat() - Method in class org.openscience.cdk.io.RssWriter

getFormat() - Method in class org.openscience.cdk.io.SDFWriter

getFormat() - Method in class org.openscience.cdk.io.ShelXReader

getFormat() - Method in class org.openscience.cdk.io.ShelXWriter

getFormat() - Method in class org.openscience.cdk.io.SMILESReader

getFormat() - Method in class org.openscience.cdk.io.SMILESWriter

getFormat() - Method in class org.openscience.cdk.io.VASPReader

getFormat() - Method in class org.openscience.cdk.io.XYZReader

getFormat() - Method in class org.openscience.cdk.io.XYZWriter

getFormat() - Method in class org.openscience.cdk.io.ZMatrixReader

getFormatName() - Method in class org.openscience.cdk.io.formats.ABINITFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.Aces2Format

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.ADFFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.AlchemyFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.BGFFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.BSFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.CACheFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format

getFormatName() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.CIFFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.CMLFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.CRK2DFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.CRK3DFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.CrystClustFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.CTXFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.DaltonFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.DMol3Format

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.DOCK5Format

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.FingerprintFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.GamessFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian03Format

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian90Format

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian92Format

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian94Format

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian95Format

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian98Format

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.GROMOS96Format

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.HINFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.INChIFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat

Returns a one-lined format name of the format.

getFormatName() - Method in interface org.openscience.cdk.io.formats.IResourceFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.JaguarFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.JMEFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.MacroModelFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.MDLFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.MDLRXNV2000Format

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.MDLV2000Format

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.MDLV3000Format

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.MMODFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.Mol2Format

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC7Format

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC93Format

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC97Format

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.MPQCFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.NWChemFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.PCModelFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.PDBFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.PDBMLFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.PMPFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.POVRayFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.PQSChemFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.QChemFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.RawCopyFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.SDFFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.ShelXFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.SMARTSFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.SMILESFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.SpartanFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.SVGFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.VASPFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.ViewmolFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.XEDFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.XYZFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.YasaraFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.ZindoFormat

Returns a one-lined format name of the format.

getFormatName() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat

Returns a one-lined format name of the format.

getFormats() - Method in class org.openscience.cdk.io.FormatFactory

Returns the list of recognizable formats.

getFormats() - Method in class org.openscience.cdk.io.ReaderFactory

getFormula() - Method in class org.openscience.cdk.formula.IsotopeContainer

Get the IMolecularFormula object of this container.

getFormulas() - Method in class org.openscience.cdk.formula.IsotopeContainer

Access the formulas of this isotope container.

getFP(int) - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter

Returns the requested fingerprint.

getFPCount() - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter

Returns the number of fingerprints generated.

getFractionalPoint3d() - Method in class org.openscience.cdk.Atom

Returns a point specifying the location of this atom in a Crystal unit cell.

getFractionalPoint3d() - Method in class org.openscience.cdk.AtomRef

Returns a point specifying the location of this atom in a Crystal unit cell.

getFractionalPoint3d() - Method in class org.openscience.cdk.debug.DebugAtom

Returns a point specifying the location of this atom in a Crystal unit cell.

getFractionalPoint3d() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Returns a point specifying the location of this atom in a Crystal unit cell.

getFractionalPoint3d() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Returns a point specifying the location of this atom in a Crystal unit cell.

getFractionalPoint3d() - Method in interface org.openscience.cdk.interfaces.IAtom

Returns a point specifying the location of this atom in a Crystal unit cell.

getFractionalPoint3d() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Returns a point specifying the location of this atom in a Crystal unit cell.

getFractionalPoint3d() - Method in class org.openscience.cdk.silent.Atom

Returns a point specifying the location of this atom in a Crystal unit cell.

getFragment() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Returns the fully expended form of the IFragmentAtom.

getFragment() - Method in class org.openscience.cdk.FragmentAtom

getFragment() - Method in interface org.openscience.cdk.interfaces.IFragmentAtom

Returns the fully expended form of the IFragmentAtom.

getFragment() - Method in class org.openscience.cdk.silent.FragmentAtom

getFragments() - Method in class org.openscience.cdk.fragment.ExhaustiveFragmenter

Get the fragments generated as SMILES strings.

getFragments() - Method in interface org.openscience.cdk.fragment.IFragmenter

Get the fragments generated as SMILES strings.

getFragments() - Method in class org.openscience.cdk.fragment.MurckoFragmenter

This returns the frameworks and ring systems from a Murcko fragmentation.

getFragmentsAsContainers() - Method in class org.openscience.cdk.fragment.ExhaustiveFragmenter

Get the fragments generated as IAtomContainer objects..

getFragmentsAsContainers() - Method in interface org.openscience.cdk.fragment.IFragmenter

Get fragments generated as IAtomContainer objects.

getFragmentsAsContainers() - Method in class org.openscience.cdk.fragment.MurckoFragmenter

Get all frameworks and ring systems as IAtomContainer objects.

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.

getFunctionalGroupSMARTS() - Static method in class org.openscience.cdk.fingerprint.StandardSubstructureSets

The functional groups.

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.

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.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

Deprecated.

Use MolecularFormulaManipulator.getString(org.openscience.cdk.interfaces.IMolecularFormula)

getHOSECode(IAtomContainer, IAtom, int) - Method in class org.openscience.cdk.tools.HOSECodeGenerator

Produces a HOSE code for Atom root in the IAtomContainer ac.

getHOSECode(IAtomContainer, IAtom, int, boolean) - Method in class org.openscience.cdk.tools.HOSECodeGenerator

Produces a HOSE code for Atom root in the IAtomContainer ac.

getHTML(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator

Returns the string representation of the molecule formula based on Hill System with numbers wrapped in  tags.

getHTML(IMolecularFormula, boolean, boolean) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator

Returns the string representation of the molecule formula based on Hill System with numbers wrapped in  tags and the isotope of each Element in  tags and the total charge of IMolecularFormula in  tags.

getHTML(IMolecularFormula, String[], boolean, boolean) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator

Returns the string representation of the molecule formula with numbers wrapped in  tags and the isotope of each Element in  tags and the total showCharge of IMolecularFormula in  tags.

getHybridization() - Method in class org.openscience.cdk.AtomRef

Returns the hybridization of this atom.

getHybridization() - Method in class org.openscience.cdk.AtomType

Returns the hybridization of this atom.

getHybridization() - Method in class org.openscience.cdk.debug.DebugAtom

Returns the hybridization of this atom.

getHybridization() - Method in class org.openscience.cdk.debug.DebugAtomType

Returns the hybridization of this atom.

getHybridization() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Returns the hybridization of this atom.

getHybridization() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Returns the hybridization of this atom.

getHybridization() - Method in interface org.openscience.cdk.interfaces.IAtomType

Returns the hybridization of this atom.

getHybridization() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Returns the hybridization of this atom.

getHybridization() - Method in class org.openscience.cdk.silent.AtomType

Returns the hybridization of this atom.

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.

getId2() - Method in class org.openscience.cdk.isomorphism.mcss.RMap

Gets the id2 attribute of the RMap object.

getIgnoreAromaticBonds() - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory

Deprecated.

getImplementationIdentifier() - Method in interface org.openscience.cdk.IImplementationSpecification

Identifier for this implementation which must include version information.

getImplementationIdentifier() - Method in class org.openscience.cdk.qsar.DescriptorSpecification

getImplementationIdentifier() - Method in class org.openscience.cdk.reaction.ReactionSpecification

getImplementationTitle() - Method in interface org.openscience.cdk.IImplementationSpecification

Human-readable name for the implementation for the algorithm specified by the reference.

getImplementationTitle() - Method in class org.openscience.cdk.qsar.DescriptorSpecification

getImplementationTitle() - Method in class org.openscience.cdk.reaction.ReactionSpecification

getImplementationVendor() - Method in interface org.openscience.cdk.IImplementationSpecification

Human-readable name for the vendor that holds copyright for this implementation.

getImplementationVendor() - Method in class org.openscience.cdk.qsar.DescriptorSpecification

getImplementationVendor() - Method in class org.openscience.cdk.reaction.ReactionSpecification

getImplicitHydrogenCount() - Method in class org.openscience.cdk.Atom

Returns the hydrogen count of this atom.

getImplicitHydrogenCount() - Method in class org.openscience.cdk.AtomRef

Returns the implicit hydrogen count of this atom.

getImplicitHydrogenCount() - Method in class org.openscience.cdk.debug.DebugAtom

Returns the hydrogen count of this atom.

getImplicitHydrogenCount() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Returns the hydrogen count of this atom.

getImplicitHydrogenCount() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Returns the hydrogen count of this atom.

getImplicitHydrogenCount() - Method in interface org.openscience.cdk.interfaces.IAtom

Returns the implicit hydrogen count of this atom.

getImplicitHydrogenCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Returns the hydrogen count of this atom.

getImplicitHydrogenCount() - Method in class org.openscience.cdk.silent.Atom

Returns the hydrogen count of this atom.

getImplicitHydrogenCount(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.

getIndex() - Method in class org.openscience.cdk.Atom

Acces the index of an atom in the context of an IAtomContainer.

getIndex() - Method in class org.openscience.cdk.AtomRef

Acces the index of an atom in the context of an IAtomContainer.

getIndex() - Method in class org.openscience.cdk.Bond

getIndex() - Method in class org.openscience.cdk.BondRef

getIndex() - Method in class org.openscience.cdk.debug.DebugAtom

Acces the index of an atom in the context of an IAtomContainer.

getIndex() - Method in interface org.openscience.cdk.interfaces.IAtom

Acces the index of an atom in the context of an IAtomContainer.

getIndex() - Method in interface org.openscience.cdk.interfaces.IBond

getIndex() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Acces the index of an atom in the context of an IAtomContainer.

getIndex() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond

getIndex() - Method in class org.openscience.cdk.silent.Atom

Acces the index of an atom in the context of an IAtomContainer.

getIndex() - Method in class org.openscience.cdk.silent.Bond

getIndexFile(String) - Static method in class org.openscience.cdk.io.random.RandomAccessReader

Opens the file index file _cdk.index in a temporary folder, as specified by "java.io.tmpdir" property.

getIndexOfFirstNonDiscreteCell() - Method in class org.openscience.cdk.group.Partition

Gets the index of the first cell in the partition that is discrete.

getInitialLongestChain(IAtomContainer) - Static method in class org.openscience.cdk.layout.AtomPlacer

Search an aliphatic molecule for the longest chain.

getInitialPartition() - Method in interface org.openscience.cdk.group.Refinable

Get an initial partition of the vertices of the refinable - for example, by color.

getInstance(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.MDLRXNV2000Format

getInstance() - Static method in class org.openscience.cdk.io.formats.MDLRXNV3000Format

getInstance() - Static method in class org.openscience.cdk.io.formats.MDLV2000Format

getInstance() - Static method in class org.openscience.cdk.io.formats.MDLV3000Format

getInstance() - Static method in class org.openscience.cdk.io.formats.MMODFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.Mol2Format

getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC2002Format

getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC2007Format

getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC2009Format

getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC2012Format

getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC7Format

getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC7InputFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC93Format

getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC97Format

getInstance() - Static method in class org.openscience.cdk.io.formats.MoSSOutputFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.MPQCFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.NWChemFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.PCModelFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.PDBFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.PDBMLFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.PMPFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.POVRayFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.PQSChemFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemASNFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.QChemFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.RawCopyFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.RGroupQueryFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.SDFFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.ShelXFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.SMARTSFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.SMILESFIXFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.SMILESFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.SpartanFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.SVGFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.SybylDescriptorFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.TinkerMM2Format

getInstance() - Static method in class org.openscience.cdk.io.formats.TinkerXYZFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.TurboMoleFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.UniChemXYZFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.VASPFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.ViewmolFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.XEDFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.XYZFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.YasaraFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.ZindoFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.ZMatrixFormat

getInstance(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.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

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.

getIsomorphMap(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester

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.

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(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() - 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.

getKey() - Method in enum org.openscience.cdk.sgroup.SgroupType

getLabel() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Returns the label of this PseudoAtom.

getLabel() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Returns the label of this PseudoAtom.

getLabel() - Method in class org.openscience.cdk.dict.Entry

getLabel() - Method in interface org.openscience.cdk.interfaces.IPseudoAtom

Returns the label of this PseudoAtom.

getLabel() - Method in class org.openscience.cdk.PseudoAtom

Returns the label of this PseudoAtom.

getLabel() - Method in class org.openscience.cdk.signature.Orbit

Gets the label of the orbit.

getLabel() - Method in class org.openscience.cdk.silent.PseudoAtom

Returns the label of this PseudoAtom.

getLabel() - Method in class org.openscience.cdk.Vibration

Gets the label identifying this vibration.

getLargestRingSet(List<IRingSet>) - Method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D

Returns the largest (number of atoms) ring set in a molecule.

getLargestRingSet(List<IRingSet>) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator

Returns the largest (number of atoms) ring set in a molecule

getLast() - Method in class org.openscience.cdk.smiles.InvPair

getLastAtom() - Method in class org.openscience.cdk.AtomContainer

Returns the atom at the last position in the container.

getLastAtom() - Method in class org.openscience.cdk.debug.DebugAminoAcid

Returns the atom at the last position in the container.

getLastAtom() - Method in class org.openscience.cdk.debug.DebugAtomContainer

Returns the atom at the last position in the container.

getLastAtom() - Method in class org.openscience.cdk.debug.DebugBioPolymer

Returns the atom at the last position in the container.

getLastAtom() - Method in class org.openscience.cdk.debug.DebugCrystal

Returns the atom at the last position in the container.

getLastAtom() - Method in class org.openscience.cdk.debug.DebugMonomer

Returns the atom at the last position in the container.

getLastAtom() - Method in class org.openscience.cdk.debug.DebugPolymer

Returns the atom at the last position in the container.

getLastAtom() - Method in class org.openscience.cdk.debug.DebugRing

Returns the atom at the last position in the container.

getLastAtom() - Method in class org.openscience.cdk.debug.DebugStrand

Returns the atom at the last position in the container.

getLastAtom() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Deprecated.

use IAtomContainer.getAtom(int)

getLastAtom() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Returns the atom at the last position in the container.

getLastAtom() - Method in class org.openscience.cdk.silent.AtomContainer

Returns the atom at the last position in the container.

getLastErrorLocation() - Static method in class org.openscience.cdk.smarts.Smarts

Access a display of the error position from previously parsed SMARTS (when Smarts.parse(org.openscience.cdk.interfaces.IAtomContainer, java.lang.String, int)=false)

getLastErrorMesg() - Static method in class org.openscience.cdk.smarts.Smarts

Access the error message from previously parsed SMARTS (when Smarts.parse(org.openscience.cdk.interfaces.IAtomContainer, java.lang.String, int)=false).

getLatticeConstant() - Method in class org.openscience.cdk.protein.ProteinPocketFinder

getLatticeConstant() - Method in class org.openscience.cdk.tools.GridGenerator

getLeftTransversal(int) - Method in class org.openscience.cdk.group.PermutationGroup

Get the traversal U_i from the list of transversals.

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

getLevel() - Method in interface org.openscience.cdk.tools.ILoggingTool

Get the current level of this logger.

getLevel() - Method in class org.openscience.cdk.tools.LoggingTool

Get the current level of this logger.

getLevel() - Method in class org.openscience.cdk.tools.SystemOutLoggingTool

Get the current level of this logger.

getLigandAtom() - Method in interface org.openscience.cdk.geometry.cip.ILigand

IAtom of the ligand that is connected to the central IAtom via one IBond.

getLigandAtom() - Method in class org.openscience.cdk.geometry.cip.Ligand

IAtom of the ligand that is connected to the chiral IAtom via one IBond.

getLigandLigands(ILigand) - Static method in class org.openscience.cdk.geometry.cip.CIPTool

Returns a CIP-expanded array of side chains of a ligand.

getLigands() - Method in interface org.openscience.cdk.interfaces.ITetrahedralChirality

Returns an array of ligand atoms around the chiral atom.

getLigands() - Method in class org.openscience.cdk.stereo.TetrahedralChirality

getLimitedPathsOfLengthUpto(IAtomContainer, IAtom, int, int) - Static method in class org.openscience.cdk.graph.PathTools

Get all the paths starting from an atom of length 0 up to the specified length.

getLine(int) - Method in class org.openscience.cdk.graph.invariant.GIMatrix

Returns the line-matrix at the given line index.

getLinkageRadius() - Method in class org.openscience.cdk.protein.ProteinPocketFinder

getLinkmap() - Method in class org.openscience.cdk.io.RssWriter

getListenerCount() - Method in class org.openscience.cdk.ChemObject

Returns the number of ChemObjectListeners registered with this object.

getListenerCount() - Method in class org.openscience.cdk.debug.DebugAminoAcid

Returns the number of ChemObjectListeners registered with this object.

getListenerCount() - Method in class org.openscience.cdk.debug.DebugAtom

Returns the number of ChemObjectListeners registered with this object.

getListenerCount() - Method in class org.openscience.cdk.debug.DebugAtomContainer

Returns the number of ChemObjectListeners registered with this object.

getListenerCount() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet

Returns the number of ChemObjectListeners registered with this object.

getListenerCount() - Method in class org.openscience.cdk.debug.DebugAtomType

Returns the number of ChemObjectListeners registered with this object.

getListenerCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer

Returns the number of ChemObjectListeners registered with this object.

getListenerCount() - Method in class org.openscience.cdk.debug.DebugBond

Returns the number of ChemObjectListeners registered with this object.

getListenerCount() - Method in class org.openscience.cdk.debug.DebugChemFile

Returns the number of ChemObjectListeners registered with this object.

getListenerCount() - Method in class org.openscience.cdk.debug.DebugChemModel

Returns the number of ChemObjectListeners registered with this object.

getListenerCount() - Method in class org.openscience.cdk.debug.DebugChemObject

Returns the number of ChemObjectListeners registered with this object.

getListenerCount() - Method in class org.openscience.cdk.debug.DebugChemSequence

Returns the number of ChemObjectListeners registered with this object.

getListenerCount() - Method in class org.openscience.cdk.debug.DebugCrystal

Returns the number of ChemObjectListeners registered with this object.

getListenerCount() - Method in class org.openscience.cdk.debug.DebugElectronContainer

Returns the number of ChemObjectListeners registered with this object.

getListenerCount() - Method in class org.openscience.cdk.debug.DebugElement

Returns the number of ChemObjectListeners registered with this object.

getListenerCount() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Returns the number of ChemObjectListeners registered with this object.

getListenerCount() - Method in class org.openscience.cdk.debug.DebugIsotope

Returns the number of ChemObjectListeners registered with this object.

getListenerCount() - Method in class org.openscience.cdk.debug.DebugLonePair

Returns the number of ChemObjectListeners registered with this object.

getListenerCount() - Method in class org.openscience.cdk.debug.DebugMapping

Returns the number of ChemObjectListeners registered with this object.

getListenerCount() - Method in class org.openscience.cdk.debug.DebugMonomer

Returns the number of ChemObjectListeners registered with this object.

getListenerCount() - Method in class org.openscience.cdk.debug.DebugPolymer

Returns the number of ChemObjectListeners registered with this object.

getListenerCount() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Returns the number of ChemObjectListeners registered with this object.

getListenerCount() - Method in class org.openscience.cdk.debug.DebugReaction

Returns the number of ChemObjectListeners registered with this object.

getListenerCount() - Method in class org.openscience.cdk.debug.DebugReactionScheme

Returns the number of ChemObjectListeners registered with this object.

getListenerCount() - Method in class org.openscience.cdk.debug.DebugReactionSet

Returns the number of ChemObjectListeners registered with this object.

getListenerCount() - Method in class org.openscience.cdk.debug.DebugRing

Returns the number of ChemObjectListeners registered with this object.

getListenerCount() - Method in class org.openscience.cdk.debug.DebugSingleElectron

Returns the number of ChemObjectListeners registered with this object.

getListenerCount() - Method in class org.openscience.cdk.debug.DebugStrand

Returns the number of ChemObjectListeners registered with this object.

getListenerCount() - Method in class org.openscience.cdk.debug.DebugSubstance

Returns the number of ChemObjectListeners registered with this object.

getListenerCount() - Method in interface org.openscience.cdk.interfaces.IChemObject

Returns the number of ChemObjectListeners registered with this object.

getListenerCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject

Returns the number of ChemObjectListeners registered with this object.

getListenerCount() - Method in class org.openscience.cdk.silent.ChemObject

Returns the number of ChemObjectListeners registered with this object.

getListeners() - Method in class org.openscience.cdk.io.ChemObjectIO

Access all the listeners for this ChemObject Reader or Writer.

getListeners() - Method in interface org.openscience.cdk.io.IChemObjectIO

Access all the listeners for this ChemObject Reader or Writer.

getLog() - Method in class org.openscience.cdk.inchi.InChIGenerator

Gets generated log.

getLog() - Method in class org.openscience.cdk.inchi.InChIToStructure

Gets generated log.

getLoggingToolClass() - Static method in class org.openscience.cdk.tools.LoggingToolFactory

Gets the currently used ILoggingTool implementation.

getLonePair(int) - Method in class org.openscience.cdk.AtomContainer

Get the lone pair at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getLonePairCount().

getLonePair(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Get the lone pair at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getLonePairCount().

getLonePair(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer

Get the lone pair at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getLonePairCount().

getLonePair(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Get the lone pair at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getLonePairCount().

getLonePair(int) - Method in class org.openscience.cdk.debug.DebugCrystal

Get the lone pair at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getLonePairCount().

getLonePair(int) - Method in class org.openscience.cdk.debug.DebugMonomer

Get the lone pair at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getLonePairCount().

getLonePair(int) - Method in class org.openscience.cdk.debug.DebugPolymer

Get the lone pair at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getLonePairCount().

getLonePair(int) - Method in class org.openscience.cdk.debug.DebugRing

Get the lone pair at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getLonePairCount().

getLonePair(int) - Method in class org.openscience.cdk.debug.DebugStrand

Get the lone pair at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getLonePairCount().

getLonePair(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Get the lone pair at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getLonePairCount().

getLonePair(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Get the lone pair at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getLonePairCount().

getLonePair(int) - Method in class org.openscience.cdk.silent.AtomContainer

Get the lone pair at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getLonePairCount().

getLonePairCount() - Method in class org.openscience.cdk.AtomContainer

Returns the number of LonePairs in this Container.

getLonePairCount() - Method in class org.openscience.cdk.debug.DebugAminoAcid

Returns the number of LonePairs in this Container.

getLonePairCount() - Method in class org.openscience.cdk.debug.DebugAtomContainer

Returns the number of LonePairs in this Container.

getLonePairCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer

Returns the number of LonePairs in this Container.

getLonePairCount() - Method in class org.openscience.cdk.debug.DebugCrystal

Returns the number of LonePairs in this Container.

getLonePairCount() - Method in class org.openscience.cdk.debug.DebugMonomer

Returns the number of LonePairs in this Container.

getLonePairCount() - Method in class org.openscience.cdk.debug.DebugPolymer

Returns the number of LonePairs in this Container.

getLonePairCount() - Method in class org.openscience.cdk.debug.DebugRing

Returns the number of LonePairs in this Container.

getLonePairCount() - Method in class org.openscience.cdk.debug.DebugStrand

Returns the number of LonePairs in this Container.

getLonePairCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the number of LonePairs in this Container.

getLonePairCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Returns the number of LonePairs in this Container.

getLonePairCount() - Method in class org.openscience.cdk.silent.AtomContainer

Returns the number of LonePairs in this Container.

getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.AtomContainer

Returns the position of a given lone pair in the lone pair array.

getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Returns the position of a given lone pair in the lone pair array.

getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Returns the position of a given lone pair in the lone pair array.

getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugCrystal

Returns the position of a given lone pair in the lone pair array.

getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugMonomer

Returns the position of a given lone pair in the lone pair array.

getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugPolymer

Returns the position of a given lone pair in the lone pair array.

getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugRing

Returns the position of a given lone pair in the lone pair array.

getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugStrand

Returns the position of a given lone pair in the lone pair array.

getLonePairNumber(ILonePair) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Deprecated.

use IAtomContainer.indexOf(ILonePair)

getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Returns the position of a given lone pair in the lone pair array.

getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.silent.AtomContainer

Returns the position of a given lone pair in the lone pair array.

getLongestUnplacedChain(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.layout.AtomPlacer

Search a molecule for the longest unplaced, aliphatic chain in it.

getLower() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryAngleBond

getLower() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryBond

getMajorIsotope(int) - Method in class org.openscience.cdk.config.IsotopeFactory

Returns the most abundant (major) isotope with a given atomic number.

getMajorIsotope(String) - Method in class org.openscience.cdk.config.IsotopeFactory

Returns the most abundant (major) isotope whose symbol equals element.

getMajorIsotopeMass(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.

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.

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.AtomRef

Returns the atomic mass of this element.

getMassNumber() - Method in class org.openscience.cdk.debug.DebugAtom

Returns the atomic mass of this element.

getMassNumber() - Method in class org.openscience.cdk.debug.DebugAtomType

Returns the atomic mass of this element.

getMassNumber() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Returns the atomic mass of this element.

getMassNumber() - Method in class org.openscience.cdk.debug.DebugIsotope

Returns the atomic mass of this element.

getMassNumber() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Returns the atomic mass of this element.

getMassNumber() - Method in interface org.openscience.cdk.interfaces.IIsotope

Returns the atomic mass of this element.

getMassNumber() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Returns the atomic mass of this element.

getMassNumber() - Method in class org.openscience.cdk.Isotope

Returns the atomic mass of this element.

getMassNumber() - Method in class org.openscience.cdk.silent.Isotope

Returns the atomic mass of this element.

getMatchingAtoms() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom

Get the atoms of a target molecule that correspond to this group.

getMatchingPharmacophoreAtoms() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher

Get the matching pharmacophore groups.

getMatchingPharmacophoreBonds() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher

Get the matching pharmacophore constraints.

getMatrix(IAtomContainer) - Static method in class org.openscience.cdk.graph.matrix.AdjacencyMatrix

Returns the adjacency matrix for the given AtomContainer.

getMatrix(IAtomContainer) - Static method in class org.openscience.cdk.graph.matrix.ConnectionMatrix

Returns the connection matrix representation of this AtomContainer.

getMatrix(IAtomContainer) - Static method in class org.openscience.cdk.graph.matrix.TopologicalMatrix

Returns the topological matrix for the given AtomContainer.

getMaxBondOrder() - Method in class org.openscience.cdk.AtomRef

Gets the MaxBondOrder attribute of the AtomType object.

getMaxBondOrder() - Method in class org.openscience.cdk.AtomType

Gets the MaxBondOrder attribute of the AtomType object.

getMaxBondOrder() - Method in class org.openscience.cdk.debug.DebugAtom

Gets the MaxBondOrder attribute of the AtomType object.

getMaxBondOrder() - Method in class org.openscience.cdk.debug.DebugAtomType

Gets the MaxBondOrder attribute of the AtomType object.

getMaxBondOrder() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Gets the MaxBondOrder attribute of the AtomType object.

getMaxBondOrder() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Gets the MaxBondOrder attribute of the AtomType object.

getMaxBondOrder() - Method in interface org.openscience.cdk.interfaces.IAtomType

Gets the MaxBondOrder attribute of the AtomType object.

getMaxBondOrder() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Gets the MaxBondOrder attribute of the AtomType object.

getMaxBondOrder() - Method in class org.openscience.cdk.silent.AtomType

Gets the MaxBondOrder attribute of the AtomType object.

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.

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.tools.GridGenerator

getMaxy() - Method in class org.openscience.cdk.tools.GridGenerator

getMaxz() - Method in class org.openscience.cdk.tools.GridGenerator

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.

getMIMEType() - Method in class org.openscience.cdk.io.formats.ABINITFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.Aces2Format

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.ADFFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.AlchemyFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.BGFFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.BSFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.CACheFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format

getMIMEType() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.CIFFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.CMLFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.CRK2DFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.CRK3DFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.CrystClustFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.CTXFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.DaltonFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.DMol3Format

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.DOCK5Format

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.FingerprintFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.GamessFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian03Format

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian90Format

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian92Format

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian94Format

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian95Format

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian98Format

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.GROMOS96Format

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.HINFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.INChIFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in interface org.openscience.cdk.io.formats.IResourceFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.JaguarFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.JMEFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.MacroModelFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.MDLFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.MDLRXNV2000Format

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.MDLV2000Format

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.MDLV3000Format

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.MMODFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.Mol2Format

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC7Format

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC93Format

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC97Format

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.MPQCFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.NWChemFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.PCModelFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.PDBFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.PDBMLFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.PMPFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.POVRayFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.PQSChemFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.QChemFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.RawCopyFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.SDFFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.ShelXFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.SMARTSFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.SMILESFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.SpartanFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.SVGFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.VASPFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.ViewmolFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.XEDFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.XYZFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.YasaraFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.ZindoFormat

Returns the accepted MIME type for this format.

getMIMEType() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat

Returns the accepted MIME type for this format.

getMinimalFormula(MolecularFormulaRange, IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaRangeManipulator

Returns the minimal occurrence of the IIsotope into IMolecularFormula from this MolelecularFormulaRange.

getMinimumBondOrder(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.GeometryUtil

Returns the minimum and maximum X and Y coordinates of the atoms in the AtomContainer.

getMinOccurrenceElements(IMolecularFormulaSet) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaSetManipulator

Extract from a set of MolecularFormula the minimal occurrence of each element found and put the element and occurrence in a new IMolecularFormula.

getMinPSCluster() - Method in class org.openscience.cdk.protein.ProteinPocketFinder

getMinPSPocket() - Method in class org.openscience.cdk.protein.ProteinPocketFinder

getMinx() - Method in class org.openscience.cdk.tools.GridGenerator

getMiny() - Method in class org.openscience.cdk.tools.GridGenerator

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.

getMolecularWeight(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator

Calculate the molecular weight of a molecule.

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.structgen.RandomGenerator

Returns the molecule which reflects the current state of this stochastic structure generator.

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.libio.md.Residue

getName() - Method in class org.openscience.cdk.protein.data.PDBAtom

get the Atom name of this atom.

getName() - Method in class org.openscience.cdk.silent.PDBAtom

get the Atom name of this atom.

getName(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable

Get the name of the element.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.ABINITFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.Aces2Format

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.ADFFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.AlchemyFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.BGFFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.BSFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.CACheFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format

getNameExtensions() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.CIFFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.CMLFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.CRK2DFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.CRK3DFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.CrystClustFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.CTXFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.DaltonFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.DMol3Format

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.DOCK5Format

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.FingerprintFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.GamessFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian03Format

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian90Format

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian92Format

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian94Format

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian95Format

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian98Format

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.GROMOS96Format

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.HINFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.INChIFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in interface org.openscience.cdk.io.formats.IResourceFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.JaguarFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.JMEFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.MacroModelFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.MDLFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.MDLRXNV2000Format

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.MDLV2000Format

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.MDLV3000Format

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.MMODFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.Mol2Format

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC7Format

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC93Format

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC97Format

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.MPQCFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.NWChemFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.PCModelFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.PDBFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.PDBMLFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.PMPFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.POVRayFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.PQSChemFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.QChemFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.RawCopyFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.SDFFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.ShelXFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.SMARTSFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.SMILESFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.SpartanFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.SVGFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.VASPFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.ViewmolFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.XEDFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.XYZFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.YasaraFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.ZindoFormat

Returns an array of common resource name extensions.

getNameExtensions() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat

Returns an array of common resource name extensions.

getNames() - Static method in class org.openscience.cdk.config.fragments.EStateFragments

Get the fragment names.

getNames() - Method in class org.openscience.cdk.qsar.DescriptorValue

Returns an array of names for each descriptor value calculated.

getNativeRingRadius(IRing, double) - Method in class org.openscience.cdk.layout.RingPlacer

Returns the ring radius of a perfect polygons of size ring.getAtomCount() The ring radius is the distance of each atom to the ringcenter.

getNaturalAbundance() - Method in class org.openscience.cdk.AtomRef

Gets the NaturalAbundance attribute of the Isotope object.

getNaturalAbundance() - Method in class org.openscience.cdk.debug.DebugAtom

Gets the NaturalAbundance attribute of the Isotope object.

getNaturalAbundance() - Method in class org.openscience.cdk.debug.DebugAtomType

Gets the NaturalAbundance attribute of the Isotope object.

getNaturalAbundance() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Gets the NaturalAbundance attribute of the Isotope object.

getNaturalAbundance() - Method in class org.openscience.cdk.debug.DebugIsotope

Gets the NaturalAbundance attribute of the Isotope object.

getNaturalAbundance() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Gets the NaturalAbundance attribute of the Isotope object.

getNaturalAbundance() - Method in interface org.openscience.cdk.interfaces.IIsotope

Gets the NaturalAbundance attribute of the Isotope object.

getNaturalAbundance() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Gets the NaturalAbundance attribute of the Isotope object.

getNaturalAbundance() - Method in class org.openscience.cdk.Isotope

Gets the NaturalAbundance attribute of the Isotope object.

getNaturalAbundance() - Method in class org.openscience.cdk.silent.Isotope

Gets the NaturalAbundance attribute of the Isotope object.

getNaturalExactMass(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator

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.

getNeighbors(int) - Method in class org.openscience.cdk.geometry.surface.NeighborList

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.

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.

getNextUnplacedHeavyAtomWithAliphaticPlacedNeighbour(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D

Gets the nextUnplacedHeavyAtomWithAliphaticPlacedNeighbour from an atom container or molecule.

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.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.

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.

getOptions() - Method in class org.openscience.cdk.io.setting.OptionIOSetting

Returns a Vector of Strings containing all possible options.

getOrbit(int) - Method in class org.openscience.cdk.group.Permutation

Get all the elements in the same orbit in the permutation (unsorted).

getOrder() - Method in class org.openscience.cdk.Bond

Returns the bond order of this bond.

getOrder() - Method in class org.openscience.cdk.BondRef

Returns the bond order of this bond.

getOrder() - Method in class org.openscience.cdk.debug.DebugBond

Returns the bond order of this bond.

getOrder() - Method in interface org.openscience.cdk.interfaces.IBond

Returns the bond order of this bond.

getOrder() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond

Returns the query bond order of this query bond.

getOrder() - Method in class org.openscience.cdk.silent.Bond

Returns the bond order of this bond.

getOther(IAtom) - Method in class org.openscience.cdk.Bond

Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correct IBond.getConnectedAtoms(IAtom) should be used.

getOther(IAtom) - Method in class org.openscience.cdk.BondRef

Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correct IBond.getConnectedAtoms(IAtom) should be used.

getOther(IAtom) - Method in class org.openscience.cdk.debug.DebugBond

Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correct IBond.getConnectedAtoms(IAtom) should be used.

getOther(IAtom) - Method in interface org.openscience.cdk.interfaces.IBond

Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correct IBond.getConnectedAtoms(IAtom) should be used.

getOther(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond

Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correct IBond.getConnectedAtoms(IAtom) should be used.

getOther(IAtom) - Method in class org.openscience.cdk.silent.Bond

Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correct IBond.getConnectedAtoms(IAtom) should be used.

getOtherBondAtom(IAtom, IBond) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

Returns the other atom of the bond.

getOverlaps(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester

Returns all the maximal common substructure between two atom containers.

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.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.molecular.AcidicGroupCountDescriptor

Returns the names of the parameters for this descriptor.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor

Gets the parameterNames attribute of the AromaticAtomsCountDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor

Gets the parameterNames attribute of the APolDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor

Gets the parameterNames attribute of the AromaticAtomsCountDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor

Gets the parameterNames attribute of the AromaticBondsCountDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor

Gets the parameterNames attribute of the AtomCountDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor

Returns the names of the parameters for this descriptor.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor

Gets the parameterNames attribute of the BCUTDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor

Gets the parameterNames attribute of the BondCountDescriptor object

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor

Gets the parameterNames attribute of the BPolDescriptor object

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor

Gets the parameterNames attribute of the GravitationalIndexDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor

Gets the parameterNames attribute of the CPSADescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor

Gets the parameterNames attribute of the EccentricConnectivityIndexDescriptor object

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor

Returns the names of the parameters for this descriptor.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalCSP3Descriptor

Returns the names of the parameters for this descriptor.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor

Returns the names of the parameters for this descriptor.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor

Gets the parameterNames attribute of the FragmentComplexityDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor

Gets the parameterNames attribute of the GravitationalIndexDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor

Gets the parameterNames attribute of the HBondAcceptorCountDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor

Gets the parameterNames of the HBondDonorCountDescriptor.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor

Gets the parameterNames attribute of the HybridizationRatioDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor

Gets the parameterNames attribute of the KappaShapeIndicesDescriptor object

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor

Gets the parameterNames attribute of the descriptor.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor

Gets the parameterNames attribute of the LargestPiSystemDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor

Gets the parameterNames attribute of the LargestPiSystemDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor

Gets the parameterNames attribute of the PetitjeanNumberDescriptor object

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor

Gets the parameterNames attribute of the LongestAliphaticChainDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor

Gets the parameterNames attribute for this descriptor.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

Gets the parameterNames attribute of the WeightDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor

Gets the parameterNames attribute of the MomentOfInertiaDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor

Gets the parameterNames attribute of the PetitjeanNumberDescriptor object

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor

Gets the parameterNames attribute of the PetitjeanShapeIndexDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor

Gets the parameterNames attribute of the RotatableBondsCountDescriptor object

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor

Gets the parameterNames attribute of the RuleOfFiveDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor

Get parameters: empty, there are none.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.SpiroAtomCountDescriptor

Returns the names of the parameters for this descriptor.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor

Gets the parameterNames attribute of the TPSADescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor

Returns the names of the parameters for this descriptor.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor

Gets the parameterNames attribute of the VAdjMaDescriptor object

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor

Gets the parameterNames attribute of the WeightDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor

Gets the parameterNames attribute of the WeightedPathDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor

Gets the parameterNames attribute of the WHIMDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor

Gets the parameterNames attribute of the WienerNumbersDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor

Gets the parameterNames attribute of the XLogPDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor

Gets the parameterNames attribute of the ZagrebIndexDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor

Gets the parameterNames attribute of the TaeAminOAcidDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.substance.OxygenAtomCountDescriptor

Returns the names of the parameters for this descriptor.

getParameterNames() - Method in class org.openscience.cdk.qsar.DescriptorValue

getParameterNames() - Method in interface org.openscience.cdk.qsar.IDescriptor

Returns the names of the parameters for this descriptor.

getParameters() - Method in class org.openscience.cdk.dict.EntryReact

Get the parameters of the reaction.

getParameters() - Method in class org.openscience.cdk.fingerprint.AbstractFingerprinter

Base classes should override this method to report the parameters they are configured with.

getParameters() - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter

getParameters() - Method in class org.openscience.cdk.fingerprint.Fingerprinter

getParameters() - Method in class org.openscience.cdk.fingerprint.LingoFingerprinter

getParameters() - Method in class org.openscience.cdk.fingerprint.SignatureFingerprinter

getParameters() - Method in class org.openscience.cdk.formula.rules.ChargeRule

Gets the parameters attribute of the ChargeRule object.

getParameters() - Method in class org.openscience.cdk.formula.rules.ElementRule

Gets the parameters attribute of the ElementRule object.

getParameters() - Method in interface org.openscience.cdk.formula.rules.IRule

Returns the current parameter values.

getParameters() - Method in class org.openscience.cdk.formula.rules.IsotopePatternRule

Gets the parameters attribute of the IsotopePatternRule object.

getParameters() - Method in class org.openscience.cdk.formula.rules.MMElementRule

Gets the parameters attribute of the MMElementRule object.

getParameters() - Method in class org.openscience.cdk.formula.rules.NitrogenRule

Gets the parameters attribute of the NitrogenRule object.

getParameters() - Method in class org.openscience.cdk.formula.rules.RDBERule

Gets the parameters attribute of the RDBRule object.

getParameters() - Method in class org.openscience.cdk.formula.rules.ToleranceRangeRule

Gets the parameters attribute of the ToleranceRangeRule object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor

Gets the parameters attribute of the AtomDegreeDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor

Gets the parameters attribute of the VdWRadiusDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor

Gets the parameters attribute of the AtomHybridizationVSEPRDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor

Gets the parameters attribute of the VdWRadiusDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor

Gets the parameters attribute of the BondsToAtomDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor

Gets the parameters attribute of the VdWRadiusDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor

Gets the parameters attribute of the DistanceToAtomDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor

Gets the parameters attribute of the EffectiveAtomPolarizabilityDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor

Gets the parameters attribute of the InductiveAtomicHardnessDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor

Gets the parameters attribute of the InductiveAtomicSoftnessDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor

Gets the parameters attribute of the IPAtomicHOSEDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.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.molecular.AcidicGroupCountDescriptor

Returns the current parameter values.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor

Gets the parameters attribute of the AminoAcidsCountDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor

Gets the parameters attribute of the APolDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor

Gets the parameters attribute of the AromaticAtomsCountDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor

Gets the parameters attribute of the AromaticBondsCountDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor

Gets the parameters attribute of the AtomCountDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor

Returns the current parameter values.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor

Gets the parameters attribute of the BCUTDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor

Gets the parameters attribute of the BondCountDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor

Gets the parameters attribute of the BPolDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor

Gets the parameters attribute of the GravitationalIndexDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor

Gets the parameters attribute of the CPSADescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor

Gets the parameters attribute of the EccentricConnectivityIndexDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor

Returns the current parameter values.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalCSP3Descriptor

Returns the current parameter values.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor

Returns the current parameter values.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor

Gets the parameters attribute of the FragmentComplexityDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor

Gets the parameters attribute of the GravitationalIndexDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor

Gets the parameters attribute of the HBondAcceptorCountDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor

Gets the parameters of the HBondDonorCountDescriptor instance.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor

Gets the parameters attribute of the HybridizationRatioDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor

Gets the parameters attribute of the KappaShapeIndicesDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor

Gets the parameters attribute of the descriptor.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor

Gets the parameters attribute of the LargestChainDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor

Gets the parameters attribute of the LargestPiSystemDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor

Gets the parameters attribute of the PetitjeanNumberDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor

Gets the parameters attribute of the LongestAliphaticChainDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor

Gets the parameters attribute of the MannholdLogPDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

Gets the parameters attribute of the WeightDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor

Gets the parameters attribute of the MomentOfInertiaDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor

Gets the parameters attribute of the PetitjeanNumberDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor

Gets the parameters attribute of the PetitjeanShapeIndexDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor

Gets the parameters attribute of the RotatableBondsCountDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor

Gets the parameters attribute of the RuleOfFiveDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor

Get parameters: returns empty array, there are none.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.SpiroAtomCountDescriptor

Returns the current parameter values.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor

Gets the parameters attribute of the TPSADescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor

Returns the current parameter values.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor

Gets the parameters attribute of the VAdjMaDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor

Gets the parameters attribute of the WeightDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor

Gets the parameters attribute of the WeightedPathDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor

Gets the parameters attribute of the WHIMDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor

Gets the parameters attribute of the WienerNumbersDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor

Gets the parameters attribute of the XLogPDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor

Gets the parameters attribute of the ZagrebIndexDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor

Gets the parameters attribute of the TaeAminoAcidDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.substance.OxygenAtomCountDescriptor

Returns the current parameter values.

getParameters() - Method in class org.openscience.cdk.qsar.DescriptorValue

getParameters() - Method in interface org.openscience.cdk.qsar.IDescriptor

Returns the current parameter values.

getParameters() - Method in class org.openscience.cdk.renderer.generators.AtomContainerBoundsGenerator

Returns the list of IGeneratorParameter for this particular generator.

getParameters() - Method in class org.openscience.cdk.renderer.generators.AtomNumberGenerator

Returns the list of IGeneratorParameter for this particular generator.

getParameters() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator

Returns the list of IGeneratorParameter for this particular generator.

getParameters() - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator

Returns the list of IGeneratorParameter for this particular generator.

getParameters() - Method in class org.openscience.cdk.renderer.generators.BasicGenerator

Returns the list of IGeneratorParameter for this particular generator.

getParameters() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator

Returns the list of IGeneratorParameter for this particular generator.

getParameters() - Method in class org.openscience.cdk.renderer.generators.BoundsGenerator

Returns the list of IGeneratorParameter for this particular generator.

getParameters() - Method in class org.openscience.cdk.renderer.generators.ExtendedAtomGenerator

Returns the list of IGeneratorParameter for this particular generator.

getParameters() - Method in class org.openscience.cdk.renderer.generators.HighlightGenerator

Returns the list of IGeneratorParameter for this particular generator.

getParameters() - Method in interface org.openscience.cdk.renderer.generators.IGenerator

Returns the list of IGeneratorParameter for this particular generator.

getParameters() - Method in class org.openscience.cdk.renderer.generators.LonePairGenerator

Returns the list of IGeneratorParameter for this particular generator.

getParameters() - Method in class org.openscience.cdk.renderer.generators.MappingGenerator

Returns the list of IGeneratorParameter for this particular generator.

getParameters() - Method in class org.openscience.cdk.renderer.generators.ProductsBoxGenerator

Returns the list of IGeneratorParameter for this particular generator.

getParameters() - Method in class org.openscience.cdk.renderer.generators.RadicalGenerator

Returns the list of IGeneratorParameter for this particular generator.

getParameters() - Method in class org.openscience.cdk.renderer.generators.ReactantsBoxGenerator

Returns the list of IGeneratorParameter for this particular generator.

getParameters() - Method in class org.openscience.cdk.renderer.generators.ReactionArrowGenerator

Returns the list of IGeneratorParameter for this particular generator.

getParameters() - Method in class org.openscience.cdk.renderer.generators.ReactionBoxGenerator

Returns the list of IGeneratorParameter for this particular generator.

getParameters() - Method in class org.openscience.cdk.renderer.generators.ReactionPlusGenerator

Returns the list of IGeneratorParameter for this particular generator.

getParameters() - Method in class org.openscience.cdk.renderer.generators.ReactionSceneGenerator

Returns the list of IGeneratorParameter for this particular generator.

getParameters() - Method in class org.openscience.cdk.renderer.generators.RingGenerator

Returns the list of IGeneratorParameter for this particular generator.

getParameters() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator

Returns the list of IGeneratorParameter for this particular generator.

getParameterSet() - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator

Gets the parameterSet attribute of the ForceFieldConfigurator object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor

Gets the parameterType attribute of the AtomDegreeDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor

Gets the parameterType attribute of the VdWRadiusDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor

Gets the parameterType attribute of the AtomHybridizationVSEPRDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor

Gets the parameterType attribute of the VdWRadiusDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor

Gets the parameterType attribute of the BondsToAtomDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor

Gets the parameterType attribute of the VdWRadiusDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor

Gets the parameterType attribute of the DistanceToAtomDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor

Gets the parameterType attribute of the EffectiveAtomPolarizabilityDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor

Gets the parameterType attribute of the InductiveAtomicHardnessDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor

Gets the parameterType attribute of the InductiveAtomicSoftnessDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor

Gets the parameterType attribute of the IPAtomicHOSEDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.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.molecular.AcidicGroupCountDescriptor

Returns a class matching that of the parameter with the given name.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor

Gets the parameterType attribute of the AromaticAtomsCountDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor

Gets the parameterType attribute of the APolDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor

Gets the parameterType attribute of the AromaticAtomsCountDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor

Gets the parameterType attribute of the AromaticBondsCountDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor

Gets the parameterType attribute of the AtomCountDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor

Returns a class matching that of the parameter with the given name.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor

Gets the parameterType attribute of the BCUTDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor

Gets the parameterType attribute of the BondCountDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor

Gets the parameterType attribute of the BPolDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor

Gets the parameterType attribute of the GravitationalIndexDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor

Gets the parameterType attribute of the CPSADescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor

Gets the parameterType attribute of the EccentricConnectivityIndexDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor

Returns a class matching that of the parameter with the given name.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalCSP3Descriptor

Returns a class matching that of the parameter with the given name.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor

Returns a class matching that of the parameter with the given name.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor

Gets the parameterType attribute of the FragmentComplexityDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor

Gets the parameterType attribute of the GravitationalIndexDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor

Gets the parameterType attribute of the HBondAcceptorCountDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor

Gets the parameterType of the HBondDonorCountDescriptor.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor

Gets the parameterType attribute of the HybridizationRatioDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor

Gets the parameterType attribute of the KappaShapeIndicesDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor

Gets the parameterType attribute of the descriptor.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor

Gets the parameterType attribute of the LargestChainDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor

Gets the parameterType attribute of the LargestPiSystemDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor

Gets the parameterType attribute of the PetitjeanNumberDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor

Gets the parameterType attribute of the LongestAliphaticChainDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor

Gets the parameterType attribute for a given parameter name.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

Gets the parameterType attribute of the WeightDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor

Gets the parameterType attribute of the MomentOfInertiaDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor

Gets the parameterType attribute of the PetitjeanNumberDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor

Gets the parameterType attribute of the PetitjeanShapeIndexDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor

Gets the parameterType attribute of the RotatableBondsCountDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor

Gets the parameterType attribute of the RuleOfFiveDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor

Parameter types: there aren't any.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.SpiroAtomCountDescriptor

Returns a class matching that of the parameter with the given name.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor

Gets the parameterType attribute of the TPSADescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor

Returns a class matching that of the parameter with the given name.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor

Gets the parameterType attribute of the VAdjMaDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor

Gets the parameterType attribute of the WeightDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor

Gets the parameterType attribute of the WeightedPathDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor

Gets the parameterType attribute of the WHIMDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor

Gets the parameterType attribute of the WienerNumbersDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor

Gets the parameterType attribute of the XLogPDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor

Gets the parameterType attribute of the ZagrebIndexDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor

Gets the parameterType attribute of the TaeAminoAcidDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.substance.OxygenAtomCountDescriptor

Returns a class matching that of the parameter with the given name.

getParameterType(String) - Method in interface org.openscience.cdk.qsar.IDescriptor

Returns a class matching that of the parameter with the given name.

getParameterValue() - Method in class org.openscience.cdk.dict.EntryReact

Get the parameter value of the reaction.

getParamterSet() - Method in class org.openscience.cdk.modeling.builder3d.MM2BasedParameterSetReader

getParamterSet() - Method in class org.openscience.cdk.modeling.builder3d.MMFF94BasedParameterSetReader

getParentMolecule() - Method in class org.openscience.cdk.libio.md.ChargeGroup

getParentMolecule() - Method in class org.openscience.cdk.libio.md.Residue

getParents() - Method in class org.openscience.cdk.sgroup.Sgroup

Access the parents of this Sgroup.

getPath(IAtomContainer, IAtom, IAtom) - Method in class org.openscience.cdk.graph.SpanningTree

Find a path connected a1 and a2 in the tree.

getPathsOfLength(IAtomContainer, IAtom, int) - Static method in class org.openscience.cdk.graph.PathTools

Get the paths starting from an atom of specified length.

getPathsOfLengthUpto(IAtomContainer, IAtom, int) - Static method in class org.openscience.cdk.graph.PathTools

Get all the paths starting from an atom of length 0 upto the specified length.

getPatterns() - Static method in class org.openscience.cdk.config.fragments.EStateFragments

getPaulingElectronegativities(IAtomContainer, boolean) - Method in class org.openscience.cdk.charges.InductivePartialCharges

Gets the paulingElectronegativities attribute of the InductivePartialCharges object.

getPaulingElectronegativity(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable

Get the Pauling electronegativity of an element.

getPeriod(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable

Get the period of the element.

getPharmacophoreQuery() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher

Get the query pharmacophore.

getPhase(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable

Get the phase of the element.

getPlacedAtoms(IAtomContainer) - Static method in class org.openscience.cdk.layout.AtomPlacer

Get all the placed atoms in an AtomContainer

getPlacedAtomsInAtomContainer(IAtom, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

Gets all placed neighbouring atoms of a atom.

getPlacedHeavyAtom(IAtomContainer, IAtom) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D

Returns a placed atom connected to a given atom.

getPlacedHeavyAtom(IAtomContainer, IAtom, IAtom) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D

Gets the first placed Heavy Atom around atomA which is not atomB.

getPlacedHeavyAtomInAtomContainer(IAtom, IAtom, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

Returns a placed neighbouring atom of a central atom atomA, which is not atomB.

getPlacedHeavyAtoms(IAtomContainer, IAtom) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D

Gets the placed Heavy Atoms connected to an atom.

getPockets() - Method in class org.openscience.cdk.protein.ProteinPocketFinder

getPocketSize() - Method in class org.openscience.cdk.protein.ProteinPocketFinder

getPoint2d() - Method in class org.openscience.cdk.Atom

Returns a point specifying the location of this atom in a 2D space.

getPoint2d() - Method in class org.openscience.cdk.AtomRef

Returns a point specifying the location of this atom in a 2D space.

getPoint2d() - Method in class org.openscience.cdk.debug.DebugAtom

Returns a point specifying the location of this atom in a 2D space.

getPoint2d() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Returns a point specifying the location of this atom in a 2D space.

getPoint2d() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Returns a point specifying the location of this atom in a 2D space.

getPoint2d() - Method in interface org.openscience.cdk.interfaces.IAtom

Returns a point specifying the location of this atom in a 2D space.

getPoint2d() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Returns a point specifying the location of this atom in a 2D space.

getPoint2d() - Method in class org.openscience.cdk.silent.Atom

Returns a point specifying the location of this atom in a 2D space.

getPoint3d() - Method in class org.openscience.cdk.Atom

Returns a point specifying the location of this atom in a 3D space.

getPoint3d() - Method in class org.openscience.cdk.AtomRef

Returns a point specifying the location of this atom in a 3D space.

getPoint3d() - Method in class org.openscience.cdk.debug.DebugAtom

Returns a point specifying the location of this atom in a 3D space.

getPoint3d() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Returns a point specifying the location of this atom in a 3D space.

getPoint3d() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Returns a point specifying the location of this atom in a 3D space.

getPoint3d() - Method in interface org.openscience.cdk.interfaces.IAtom

Returns a point specifying the location of this atom in a 3D space.

getPoint3d() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Returns a point specifying the location of this atom in a 3D space.

getPoint3d() - Method in class org.openscience.cdk.silent.Atom

Returns a point specifying the location of this atom in a 3D space.

getPolarizabilitiyFactorForAtom(IAtomContainer, IAtom) - Method in class org.openscience.cdk.charges.Polarizability

Gets the polarizabilitiyFactorForAtom.

getPolarizability(String) - Method in class org.openscience.cdk.tools.AtomicProperties

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ABINITFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Aces2Format

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ADFFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.AlchemyFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.BGFFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.BSFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CACheFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CIFFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CMLFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CRK2DFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CRK3DFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CrystClustFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CTXFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.DaltonFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.DMol3Format

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.DOCK5Format

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.FingerprintFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.GamessFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian03Format

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian90Format

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian92Format

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian94Format

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian95Format

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian98Format

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.GROMOS96Format

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.HINFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.INChIFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in interface org.openscience.cdk.io.formats.IResourceFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.JaguarFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.JMEFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MacroModelFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MDLFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MDLRXNV2000Format

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MDLV2000Format

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MDLV3000Format

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MMODFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Mol2Format

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC7Format

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC93Format

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC97Format

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MPQCFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.NWChemFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PCModelFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PDBFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PDBMLFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PMPFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.POVRayFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PQSChemFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.QChemFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.RawCopyFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SDFFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ShelXFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SMARTSFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SMILESFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SpartanFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SVGFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.VASPFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ViewmolFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.XEDFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.XYZFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.YasaraFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ZindoFormat

Returns the preferred resource name extension.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat

Returns the preferred resource name extension.

getPrime() - Method in class org.openscience.cdk.smiles.InvPair

Get the current prime number.

getPrimeAt(int) - Static method in class org.openscience.cdk.math.Primes

Deprecated.

Returns the i-th prime number in the sequence of all prime numbers below 19700.

getProductCoefficient(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugReaction

Returns the stoichiometry coefficient of the given product.

getProductCoefficient(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IReaction

Returns the stoichiometry coefficient of the given product.

getProductCoefficient(IAtomContainer) - Method in class org.openscience.cdk.Reaction

Returns the stoichiometry coefficient of the given product.

getProductCoefficient(IAtomContainer) - Method in class org.openscience.cdk.silent.Reaction

Returns the stoichiometry coefficient of the given product.

getProductCoefficients() - Method in class org.openscience.cdk.debug.DebugReaction

Returns an array of double with the stoichiometric coefficients of the products.

getProductCoefficients() - Method in interface org.openscience.cdk.interfaces.IReaction

Returns an array of double with the stoichiometric coefficients of the products.

getProductCoefficients() - Method in class org.openscience.cdk.Reaction

Returns an array of double with the stoichiometric coefficients of the products.

getProductCoefficients() - Method in class org.openscience.cdk.silent.Reaction

Returns an array of double with the stoichiometric coefficients of the products.

getProductCount() - Method in class org.openscience.cdk.debug.DebugReaction

Returns the number of products in this reaction.

getProductCount() - Method in interface org.openscience.cdk.interfaces.IReaction

Returns the number of products in this reaction.

getProductCount() - Method in class org.openscience.cdk.Reaction

Returns the number of products in this reaction.

getProductCount() - Method in class org.openscience.cdk.silent.Reaction

Returns the number of products in this reaction.

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

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.

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.

getRAtom() - Method in class org.openscience.cdk.protein.ProteinPocketFinder

getRawContent() - Method in class org.openscience.cdk.dict.Entry

getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.AtomPairs2DFingerprinter

getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter

Invalid: it is not appropriate to convert the integer hash codes into strings.

getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.EStateFingerprinter

Returns the raw representation of the fingerprint for the given IAtomContainer.

getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter

Returns the raw representation of the fingerprint for the given IAtomContainer.

getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.Fingerprinter

Returns the raw representation of the fingerprint for the given IAtomContainer.

getRawFingerprint(IAtomContainer) - Method in interface org.openscience.cdk.fingerprint.IFingerprinter

Returns the raw representation of the fingerprint for the given IAtomContainer.

getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.LingoFingerprinter

getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.MACCSFingerprinter

Returns the raw representation of the fingerprint for the given IAtomContainer.

getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.PubchemFingerprinter

Returns the raw representation of the fingerprint for the given IAtomContainer.

getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.ShortestPathFingerprinter

Returns the raw representation of the fingerprint for the given IAtomContainer.

getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.SignatureFingerprinter

getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.SubstructureFingerprinter

Returns the raw representation of the fingerprint for the given IAtomContainer.

getRDBEValue(IMolecularFormula) - Method in class org.openscience.cdk.formula.rules.RDBERule

Method to extract the Ring Double Bond Equivalents (RDB) value.

getReactantCoefficient(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugReaction

Returns the stoichiometry coefficient of the given reactant.

getReactantCoefficient(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IReaction

Returns the stoichiometry coefficient of the given reactant.

getReactantCoefficient(IAtomContainer) - Method in class org.openscience.cdk.Reaction

Returns the stoichiometry coefficient of the given reactant.

getReactantCoefficient(IAtomContainer) - Method in class org.openscience.cdk.silent.Reaction

Returns the stoichiometry coefficient of the given reactant.

getReactantCoefficients() - Method in class org.openscience.cdk.debug.DebugReaction

Returns an array of double with the stoichiometric coefficients of the reactants.

getReactantCoefficients() - Method in interface org.openscience.cdk.interfaces.IReaction

Returns an array of double with the stoichiometric coefficients of the reactants.

getReactantCoefficients() - Method in class org.openscience.cdk.Reaction

Returns an array of double with the stoichiometric coefficients of the reactants.

getReactantCoefficients() - Method in class org.openscience.cdk.silent.Reaction

Returns an array of double with the stoichiometric coefficients of the reactants.

getReactantCount() - Method in class org.openscience.cdk.debug.DebugReaction

Returns the number of reactants in this reaction.

getReactantCount() - Method in interface org.openscience.cdk.interfaces.IReaction

Returns the number of reactants in this reaction.

getReactantCount() - Method in class org.openscience.cdk.Reaction

Returns the number of reactants in this reaction.

getReactantCount() - Method in class org.openscience.cdk.silent.Reaction

Returns the number of reactants in this reaction.

getReactants() - Method in class org.openscience.cdk.debug.DebugReaction

Returns a MoleculeSet containing the reactants in this reaction.

getReactants() - Method in interface org.openscience.cdk.interfaces.IReaction

Returns a IAtomContaineSet containing the reactants in this reaction.

getReactants() - Method in class org.openscience.cdk.Reaction

Returns a MoleculeSet containing the reactants in this reaction.

getReactants() - Method in class org.openscience.cdk.silent.Reaction

Returns a MoleculeSet containing the reactants in this reaction.

getReaction(int) - Method in class org.openscience.cdk.debug.DebugReactionSet

Returns the Reaction at position number in the container.

getReaction(int) - Method in interface org.openscience.cdk.interfaces.IReactionSet

Returns the Reaction at position number in the container.

getReaction(int) - Method in class org.openscience.cdk.reaction.ReactionChain

Get the reaction of this chain reaction object at the position.

getReaction(int) - Method in class org.openscience.cdk.ReactionSet

Returns the Reaction at position number in the container.

getReaction(int) - Method in class org.openscience.cdk.silent.ReactionSet

Returns the Reaction at position number in the container.

getReactionByAtomContainerID(IReactionSet, String) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator

Gets a reaction from a ReactionSet by ID of any product or reactant.

getReactionByReactionID(IReactionSet, String) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator

Gets a reaction from a ReactionSet by ID.

getReactionCount() - Method in class org.openscience.cdk.debug.DebugReactionSet

Returns the number of Reactions in this Container.

getReactionCount() - Method in interface org.openscience.cdk.interfaces.IReactionSet

Returns the number of Reactions in this Container.

getReactionCount() - Method in class org.openscience.cdk.ReactionSet

Returns the number of Reactions in this Container.

getReactionCount() - Method in class org.openscience.cdk.silent.ReactionSet

Returns the number of Reactions in this Container.

getReactionMetadata() - Method in class org.openscience.cdk.dict.EntryReact

getReactions() - Method in class org.openscience.cdk.tools.StructureResonanceGenerator

Get the reactions that must be presents in the generation of the resonance.

getReactionSchemeCount() - Method in class org.openscience.cdk.debug.DebugReactionScheme

Returns the number of ReactionScheme in this Scheme.

getReactionSchemeCount() - Method in interface org.openscience.cdk.interfaces.IReactionScheme

Returns the number of ReactionScheme in this Scheme.

getReactionSchemeCount() - Method in class org.openscience.cdk.ReactionScheme

Returns the number of ReactionScheme in this Scheme.

getReactionSchemeCount() - Method in class org.openscience.cdk.silent.ReactionScheme

Returns the number of ReactionScheme in this Scheme.

getReactionSet() - Method in class org.openscience.cdk.ChemModel

Gets the ReactionSet contained in this ChemModel.

getReactionSet() - Method in class org.openscience.cdk.debug.DebugChemModel

Gets the ReactionSet contained in this ChemModel.

getReactionSet() - Method in interface org.openscience.cdk.interfaces.IChemModel

Gets the ReactionSet contained in this ChemModel.

getReactionSet() - Method in class org.openscience.cdk.silent.ChemModel

Gets the ReactionSet contained in this ChemModel.

getReactionStep(IReaction) - Method in class org.openscience.cdk.reaction.ReactionChain

Get the position of the reaction into this chain reaction object.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.ABINITFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.Aces2Format

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.ADFFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.AlchemyFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.BGFFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.BSFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.CACheFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format

getReaderClassName() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.CIFFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.CMLFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.CRK2DFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.CRK3DFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.CrystClustFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.CTXFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.DaltonFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.DMol3Format

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.DOCK5Format

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.FingerprintFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.GamessFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian03Format

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian90Format

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian92Format

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian94Format

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian95Format

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian98Format

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.GROMOS96Format

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.HINFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in interface org.openscience.cdk.io.formats.IChemFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.INChIFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.JaguarFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.JMEFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.MacroModelFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.MDLFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.MDLRXNV2000Format

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.MDLV2000Format

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.MDLV3000Format

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.MMODFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.Mol2Format

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC7Format

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC93Format

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC97Format

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.MPQCFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.NWChemFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.PCModelFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.PDBFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.PDBMLFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.PMPFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.PQSChemFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.QChemFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.RawCopyFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.SDFFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.ShelXFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.SMARTSFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.SMILESFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.SpartanFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.VASPFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.ViewmolFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.XEDFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.XYZFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.YasaraFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.ZindoFormat

Returns the class name of the CDK Reader for this format.

getReaderClassName() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat

Returns the class name of the CDK Reader for this format.

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.

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.

getRenderer2DModel() - Method in class org.openscience.cdk.renderer.AbstractRenderer

Get the RendererModel used by this renderer, which provides access to the various parameters used to generate and draw the diagram.

getRenderer2DModel() - Method in interface org.openscience.cdk.renderer.IRenderer

Returns the drawing model, giving access to drawing parameters.

getRendererModel() - Method in class org.openscience.cdk.renderer.visitor.AWTDrawVisitor

Returns the current RendererModel.

getRenderingParameters() - Method in class org.openscience.cdk.renderer.RendererModel

Returns all IGeneratorParameters for the current RendererModel.

getRepresentations() - Method in class org.openscience.cdk.dict.EntryReact

Get the Representation of the reaction.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.CDKSourceCodeWriter

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ABINITFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Aces2Format

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ADFFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.AlchemyFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.BGFFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.BSFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CACheFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CIFFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CMLFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CRK2DFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CRK3DFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CrystClustFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CTXFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.DaltonFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.DMol3Format

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.DOCK5Format

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.FingerprintFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.GamessFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian03Format

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian90Format

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian92Format

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian94Format

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian95Format

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian98Format

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.GROMOS96Format

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.HINFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in interface org.openscience.cdk.io.formats.IChemFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.INChIFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.JaguarFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.JMEFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MacroModelFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLRXNV2000Format

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLV2000Format

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLV3000Format

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MMODFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Mol2Format

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC7Format

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC93Format

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC97Format

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MPQCFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.NWChemFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PCModelFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PDBFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PDBMLFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PMPFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PQSChemFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.QChemFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.RawCopyFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SDFFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ShelXFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SMARTSFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SMILESFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SpartanFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.VASPFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ViewmolFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.XEDFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.XYZFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.YasaraFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ZindoFormat

Returns an integer indicating the data features that this format requires.

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat

Returns an integer indicating the data features that this format requires.

getRequiredRGroupNumber() - Method in 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

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

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.

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.

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.

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).

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.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.

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

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 the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getSingleElectronCount().

getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Get the single electron at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getSingleElectronCount().

getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer

Get the single electron at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getSingleElectronCount().

getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Get the single electron at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getSingleElectronCount().

getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugCrystal

Get the single electron at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getSingleElectronCount().

getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugMonomer

Get the single electron at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getSingleElectronCount().

getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugPolymer

Get the single electron at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getSingleElectronCount().

getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugRing

Get the single electron at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getSingleElectronCount().

getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugStrand

Get the single electron at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getSingleElectronCount().

getSingleElectron(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Get the single electron at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getSingleElectronCount().

getSingleElectron(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Get the single electron at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getSingleElectronCount().

getSingleElectron(int) - Method in class org.openscience.cdk.silent.AtomContainer

Get the single electron at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getSingleElectronCount().

getSingleElectronCount() - Method in class org.openscience.cdk.AtomContainer

Returns the number of the single electrons in this container.

getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugAminoAcid

Returns the number of the single electrons in this container.

getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugAtomContainer

Returns the number of the single electrons in this container.

getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer

Returns the number of the single electrons in this container.

getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugCrystal

Returns the number of the single electrons in this container.

getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugMonomer

Returns the number of the single electrons in this container.

getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugPolymer

Returns the number of the single electrons in this container.

getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugRing

Returns the number of the single electrons in this container.

getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugStrand

Returns the number of the single electrons in this container.

getSingleElectronCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the number of the single electrons in this container.

getSingleElectronCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Returns the number of the single electrons in this container,

getSingleElectronCount() - Method in class org.openscience.cdk.silent.AtomContainer

Returns the number of the single electrons in this container.

getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.AtomContainer

Returns the position of a given single electron in the single electron array.

getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Returns the position of a given single electron in the single electron array.

getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Returns the position of a given single electron in the single electron array.

getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugCrystal

Returns the position of a given single electron in the single electron array.

getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugMonomer

Returns the position of a given single electron in the single electron array.

getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugPolymer

Returns the position of a given single electron in the single electron array.

getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugRing

Returns the position of a given single electron in the single electron array.

getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugStrand

Returns the position of a given single electron in the single electron array.

getSingleElectronNumber(ISingleElectron) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Deprecated.

use IAtomContainer.indexOf(ISingleElectron)

getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Returns the position of a given single electron in the single electron array.

getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.silent.AtomContainer

Returns the position of a given single electron in the single electron array.

getSingleElectrons() - Method in enum org.openscience.cdk.io.MDLV2000Writer.SPIN_MULTIPLICITY

The number of single electrons that correspond to the spin multiplicity.

getSize() - Method in class org.openscience.cdk.config.AtomTypeFactory

Returns the number of atom types in this list.

getSize() - Method in class org.openscience.cdk.config.IsotopeFactory

Returns the number of isotopes defined by this class.

getSize() - Method in class org.openscience.cdk.fingerprint.AtomPairs2DFingerprinter

getSize() - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter

Returns the extent of the folded fingerprints.

getSize() - Method in class org.openscience.cdk.fingerprint.EStateFingerprinter

Returns the size (or length) of the fingerprint.

getSize() - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter

Returns the size (or length) of the fingerprint.

getSize() - Method in class org.openscience.cdk.fingerprint.Fingerprinter

getSize() - Method in interface org.openscience.cdk.fingerprint.IFingerprinter

Returns the size (or length) of the fingerprint.

getSize() - Method in class org.openscience.cdk.fingerprint.LingoFingerprinter

getSize() - Method in class org.openscience.cdk.fingerprint.MACCSFingerprinter

Returns the size (or length) of the fingerprint.

getSize() - Method in class org.openscience.cdk.fingerprint.PubchemFingerprinter

Get the size of the fingerprint.

getSize() - Method in class org.openscience.cdk.fingerprint.ShortestPathFingerprinter

getSize() - Method in class org.openscience.cdk.fingerprint.SignatureFingerprinter

getSize() - Method in class org.openscience.cdk.fingerprint.SubstructureFingerprinter

Returns the size (or length) of the fingerprint.

getSize() - Method in class org.openscience.cdk.group.PermutationGroup

Get the number of elements in each permutation in the group.

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.

getSolutions() - Method in class org.openscience.cdk.isomorphism.mcss.RGraph

Returns the list of solutions.

getSolvantValue() - Method in class org.openscience.cdk.protein.ProteinPocketFinder

getSource() - Method in interface org.openscience.cdk.interfaces.IChemObjectChangeEvent

IChemObject that fired the event.

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.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.molecular.AcidicGroupCountDescriptor

Returns a IImplementationSpecification which specifies which descriptor is implemented by this class.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor

Returns a Map which specifies which descriptor is implemented by this class.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor

Returns a Map which specifies which descriptor is implemented by this class.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor

Returns a Map which specifies which descriptor is implemented by this class.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor

Returns a Map which specifies which descriptor is implemented by this class.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor

Returns a Map which specifies which descriptor is implemented by this class.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor

Returns a IImplementationSpecification which specifies which descriptor is implemented by this class.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor

Gets the specification attribute of the BondCountDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor

Returns a Map which specifies which descriptor is implemented by this class.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalCSP3Descriptor

Returns a IImplementationSpecification which specifies which descriptor is implemented by this class.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor

Returns a IImplementationSpecification which specifies which descriptor is implemented by this class.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor

Returns a Map which specifies which descriptor is implemented by this class.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor

Gets the specification attribute of the HBondAcceptorCountDescriptor object.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor

Gets the specification attribute of the HBondDonorCountDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor

Returns a DescriptorSpecification which specifies which descriptor is implemented by this class.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor

Gets the specification attribute of the KappaShapeIndicesDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor

Returns a Map which specifies which descriptor is implemented by this class.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor

Returns a Map which specifies which descriptor is implemented by this class.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor

Returns a Map which specifies which descriptor is implemented by this class.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor

Gets the specification attribute of the PetitjeanNumberDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor

Returns a Map which specifies which descriptor is implemented by this class.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor

Gets the specification attribute of the MannholdLogPDescriptor object.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

Returns a Map which specifies which descriptor is implemented by this class.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor

Gets the specification attribute of the PetitjeanNumberDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor

Gets the specification attribute of the RotatableBondsCountDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor

Returns a Map which specifies which descriptor is implemented by this class.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor

Fetch descriptor specification.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.SpiroAtomCountDescriptor

Returns a IImplementationSpecification which specifies which descriptor is implemented by this class.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor

Gets the specification attribute of the TPSADescriptor object.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor

Returns a IImplementationSpecification which specifies which descriptor is implemented by this class.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor

Gets the specification attribute of the VAdjMaDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor

Returns a Map which specifies which descriptor is implemented by this class.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor

Returns a Map which specifies which descriptor is implemented by this class.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor

Gets the specification attribute of the XLogPDescriptor object.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor

Gets the specification attribute of the ZagrebIndexDescriptor object.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.substance.OxygenAtomCountDescriptor

Returns a IImplementationSpecification which specifies which descriptor is implemented by this class.

getSpecification() - Method in class org.openscience.cdk.qsar.DescriptorValue

getSpecification() - Method in interface org.openscience.cdk.qsar.IDescriptor

Returns a IImplementationSpecification which specifies which descriptor is implemented by this class.

getSpecification() - Method in interface org.openscience.cdk.reaction.IReactionProcess

Returns a Map which specifies which reaction is implemented by this class.

getSpecification() - Method in class org.openscience.cdk.reaction.type.AdductionProtonLPReaction

Gets the specification attribute of the AdductionProtonLPReaction object.

getSpecification() - Method in class org.openscience.cdk.reaction.type.AdductionProtonPBReaction

Gets the specification attribute of the AdductionProtonPBReaction object.

getSpecification() - Method in class org.openscience.cdk.reaction.type.AdductionSodiumLPReaction

Gets the specification attribute of the AdductionSodiumLPReaction object.

getSpecification() - Method in class org.openscience.cdk.reaction.type.CarbonylEliminationReaction

Gets the specification attribute of the CarbonylEliminationReaction object.

getSpecification() - Method in class org.openscience.cdk.reaction.type.ElectronImpactNBEReaction

Gets the specification attribute of the ElectronImpactNBEReaction object.

getSpecification() - Method in class org.openscience.cdk.reaction.type.ElectronImpactPDBReaction

Gets the specification attribute of the ElectronImpactPDBReaction object.

getSpecification() - Method in class org.openscience.cdk.reaction.type.ElectronImpactSDBReaction

Gets the specification attribute of the ElectronImpactSDBReaction object.

getSpecification() - Method in class org.openscience.cdk.reaction.type.HeterolyticCleavagePBReaction

Gets the specification attribute of the HeterolyticCleavagePBReaction object.

getSpecification() - Method in class org.openscience.cdk.reaction.type.HeterolyticCleavageSBReaction

Gets the specification attribute of the HeterolyticCleavageSBReaction object.

getSpecification() - Method in class org.openscience.cdk.reaction.type.HomolyticCleavageReaction

Gets the specification attribute of the HomolyticCleavageReaction object.

getSpecification() - Method in class org.openscience.cdk.reaction.type.HyperconjugationReaction

Gets the specification attribute of the HyperconjugationReaction object

getSpecification() - Method in class org.openscience.cdk.reaction.type.PiBondingMovementReaction

Gets the specification attribute of the PiBondingMovementReaction object

getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalChargeSiteInitiationHReaction

Gets the specification attribute of the RadicalChargeSiteInitiationHReaction object

getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalChargeSiteInitiationReaction

Gets the specification attribute of the RadicalChargeSiteInitiationReaction object

getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrAlphaReaction

Gets the specification attribute of the RadicalSiteHrAlphaReaction object

getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrBetaReaction

Gets the specification attribute of the RadicalSiteHrBetaReaction object

getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrDeltaReaction

Gets the specification attribute of the RadicalSiteHrDeltaReaction object

getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrGammaReaction

Gets the specification attribute of the RadicalSiteHrGammaReaction object

getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteInitiationHReaction

Gets the specification attribute of the RadicalSiteInitiationHReaction object

getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteInitiationReaction

Gets the specification attribute of the RadicalSiteInitiationReaction object

getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrAlphaReaction

Gets the specification attribute of the RadicalSiteRrAlphaReaction object

getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrBetaReaction

Gets the specification attribute of the RadicalSiteRrBetaReaction object

getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrDeltaReaction

Gets the specification attribute of the RadicalSiteRrDeltaReaction object

getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrGammaReaction

Gets the specification attribute of the RadicalSiteRrGammaReaction object

getSpecification() - Method in class org.openscience.cdk.reaction.type.RearrangementAnionReaction

Gets the specification attribute of the RearrangementAnionReaction object

getSpecification() - Method in class org.openscience.cdk.reaction.type.RearrangementCationReaction

Gets the specification attribute of the RearrangementCationReaction object

getSpecification() - Method in class org.openscience.cdk.reaction.type.RearrangementLonePairReaction

Gets the specification attribute of the RearrangementLonePairReaction object

getSpecification() - Method in class org.openscience.cdk.reaction.type.RearrangementRadicalReaction

Gets the specification attribute of the RearrangementRadicalReaction object

getSpecification() - Method in class org.openscience.cdk.reaction.type.SharingAnionReaction

Gets the specification attribute of the SharingAnionReaction object.

getSpecification() - Method in class org.openscience.cdk.reaction.type.SharingChargeDBReaction

Gets the specification attribute of the SharingChargeDBReaction object

getSpecification() - Method in class org.openscience.cdk.reaction.type.SharingChargeSBReaction

Gets the specification attribute of the SharingChargeSBReaction object

getSpecification() - Method in class org.openscience.cdk.reaction.type.SharingLonePairReaction

Gets the specification attribute of the SharingLonePairReaction object.

getSpecification() - Method in class org.openscience.cdk.reaction.type.TautomerizationReaction

Gets the specification attribute of the TautomerizationReaction object.

getSpecificationReference() - Method in interface org.openscience.cdk.IImplementationSpecification

Pointer to a dictionary or ontology describing a unique algorithm.

getSpecificationReference() - Method in class org.openscience.cdk.qsar.DescriptorSpecification

getSpecificationReference() - Method in class org.openscience.cdk.reaction.ReactionSpecification

getSpheres(IAtomContainer, IAtom, int, boolean) - Method in class org.openscience.cdk.tools.HOSECodeGenerator

This method is intended to be used to get the atoms around an atom in spheres.

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.

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.BondRef

Returns the stereo descriptor for this bond.

getStereo() - Method in class org.openscience.cdk.debug.DebugBond

Returns the stereo descriptor for this bond.

getStereo() - Method in interface org.openscience.cdk.interfaces.IBond

Returns the stereo descriptor for this bond.

getStereo() - Method in interface org.openscience.cdk.interfaces.IDoubleBondStereochemistry

Defines the stereochemistry around the double bond.

getStereo() - Method in interface org.openscience.cdk.interfaces.ITetrahedralChirality

Defines the stereochemistry around the chiral atom.

getStereo() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond

Returns the stereo descriptor for this query bond.

getStereo() - Method in class org.openscience.cdk.silent.Bond

Returns the stereo descriptor for this bond.

getStereo() - Method in class org.openscience.cdk.stereo.DoubleBondStereochemistry

Defines the stereochemistry around the double bond.

getStereo(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

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.

getStereoParity() - Method in class org.openscience.cdk.Atom

Returns the stereo parity of this atom.

getStereoParity() - Method in class org.openscience.cdk.AtomRef

Returns the stereo parity of this atom.

getStereoParity() - Method in class org.openscience.cdk.debug.DebugAtom

Returns the stereo parity of this atom.

getStereoParity() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Returns the stereo parity of this atom.

getStereoParity() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Returns the stereo parity of this atom.

getStereoParity() - Method in interface org.openscience.cdk.interfaces.IAtom

Deprecated.

use IStereoElements for storing stereochemistry

getStereoParity() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Returns the stereo parity of this atom.

getStereoParity() - Method in class org.openscience.cdk.silent.Atom

Returns the stereo parity of this atom.

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, String[], boolean, 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.

getString(IMolecularFormula, boolean, 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.

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.

getSubgraphMap(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester

Returns the first subgraph 'bond mapping' found for g2 in g1.

getSubgraphMaps(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester

Returns all the subgraph 'bond mappings' found for g2 in g1.

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.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.CDKSourceCodeWriter

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ABINITFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Aces2Format

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ADFFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.AlchemyFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.BGFFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.BSFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CACheFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CIFFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CMLFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CRK2DFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CRK3DFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CrystClustFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CTXFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.DaltonFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.DMol3Format

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.DOCK5Format

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.FingerprintFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.GamessFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian03Format

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian90Format

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian92Format

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian94Format

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian95Format

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian98Format

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.GROMOS96Format

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.HINFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in interface org.openscience.cdk.io.formats.IChemFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.INChIFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.JaguarFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.JMEFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MacroModelFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLRXNV2000Format

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLV2000Format

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLV3000Format

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MMODFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Mol2Format

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC7Format

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC93Format

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC97Format

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MPQCFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.NWChemFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PCModelFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PDBFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PDBMLFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PMPFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PQSChemFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.QChemFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.RawCopyFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SDFFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ShelXFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SMARTSFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SMILESFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SpartanFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.VASPFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ViewmolFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.XEDFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.XYZFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.YasaraFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ZindoFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat

Returns an integer indicating the data features that this format supports.

getSupportedDataFeatures(IAtomContainer) - Static method in class org.openscience.cdk.tools.DataFeaturesTool

Determines the features present in the given IAtomContainer.

getSurfaceArea(int) - Method in class org.openscience.cdk.geometry.surface.NumericalSurface

Get the surface area for the specified atom.

getSurfacePoints(int) - Method in class org.openscience.cdk.geometry.surface.NumericalSurface

Get an array of the points on the accessible surface of a specific atom.

getSwitchingAtom() - Method in class org.openscience.cdk.libio.md.ChargeGroup

getSymbol() - Method in class org.openscience.cdk.AtomRef

Returns the element symbol of this element.

getSymbol() - Method in class org.openscience.cdk.debug.DebugAtom

Returns the element symbol of this element.

getSymbol() - Method in class org.openscience.cdk.debug.DebugAtomType

Returns the element symbol of this element.

getSymbol() - Method in class org.openscience.cdk.debug.DebugElement

Returns the element symbol of this element.

getSymbol() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Returns the element symbol of this element.

getSymbol() - Method in class org.openscience.cdk.debug.DebugIsotope

Returns the element symbol of this element.

getSymbol() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Returns the element symbol of this element.

getSymbol() - Method in class org.openscience.cdk.Element

Returns the element symbol of this element.

getSymbol() - Method in interface org.openscience.cdk.interfaces.IElement

Returns the element symbol of this element.

getSymbol() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Returns the element symbol of this element.

getSymbol() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom

getSymbol() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryAtom

Returns the element symbol of this element.

getSymbol() - Method in class org.openscience.cdk.silent.Element

Returns the element symbol of this element.

getSymbol(int) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable

Get the symbol for the specified atomic number.

getTargetQueryBondMappings() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher

Return a list of HashMap's that allows one to get the query constraint for a given pharmacophore bond.

getTautomers(IAtomContainer) - Method in class org.openscience.cdk.tautomers.InChITautomerGenerator

Public method to get tautomers for an input molecule, based on the InChI which will be calculated by JNI-InChI.

getTautomers(IAtomContainer, String) - Method in class org.openscience.cdk.tautomers.InChITautomerGenerator

Deprecated.

use InChITautomerGenerator.getTautomers(IAtomContainer) directly

getTempFactor() - Method in class org.openscience.cdk.debug.DebugPDBAtom

get the Temperature factor of this atom.

getTempFactor() - Method in interface org.openscience.cdk.interfaces.IPDBAtom

get the Temperature factor of this atom.

getTempFactor() - Method in class org.openscience.cdk.protein.data.PDBAtom

get the Temperature factor of this atom.

getTempFactor() - Method in class org.openscience.cdk.silent.PDBAtom

get the Temperature factor of this atom.

getTemplateAt(int) - Method in class org.openscience.cdk.layout.TemplateHandler

Gets the templateAt attribute of the TemplateHandler object

getTemplateAt(int) - Method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D

Gets the templateAt attribute of the TemplateHandler object.

getTemplateCount() - Method in class org.openscience.cdk.layout.TemplateHandler

Gets the templateCount attribute of the TemplateHandler object

getTemplateCount() - Method in class org.openscience.cdk.modeling.builder3d.ModelBuilder3D

Returns the number of loaded templates.

getTemplateCount() - Method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D

Gets the templateCount attribute of the TemplateHandler object.

getTemplateHandler() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

Deprecated.

always null, substructure templates are not used anymore

getTessAsPoint3ds() - Method in class org.openscience.cdk.geometry.surface.Tessellate

getTessAsTriangles() - Method in class org.openscience.cdk.geometry.surface.Tessellate

getTextBasePoint(String, double, double, Graphics2D) - Method in class org.openscience.cdk.renderer.visitor.AbstractAWTDrawVisitor

Calculates the base point where text should be rendered, as text in Java is typically placed using the left-lower corner point in screen coordinates.

getTextBounds(String, double, double, Graphics2D) - Method in class org.openscience.cdk.renderer.visitor.AbstractAWTDrawVisitor

Calculates the boundaries of a text string in screen coordinates.

getTextBounds(String, Graphics2D) - Method in class org.openscience.cdk.renderer.visitor.AbstractAWTDrawVisitor

Obtain the exact bounding box of the text in the provided graphics environment.

getTimeout() - Method in class org.openscience.cdk.ringsearch.AllRingsFinder

Deprecated.

timeout not used

getTitle() - Method in class org.openscience.cdk.AtomContainer

Access the title of the record.

getTitle() - Method in class org.openscience.cdk.ConformerContainer

Get the title of the conformers.

getTitle() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Access the title of the record.

getTitle() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Access the title of the record.

getTitle() - Method in class org.openscience.cdk.silent.AtomContainer

Access the title of the record.

getTitlemap() - Method in class org.openscience.cdk.io.RssWriter

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.sgroup.Sgroup

Access the type of the Sgroup.

getUniqueMatchingPharmacophoreAtoms() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher

Get the uniue matching pharmacophore groups.

getUnplacedRingHeavyAtom(IAtomContainer, IAtom) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D

Gets the unplacedRingHeavyAtom attribute of the AtomPlacer3D object.

getUnsetAtomsInAtomContainer(IAtom, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

Gets the unsetAtomsInAtomContainer attribute of the AtomTetrahedralLigandPlacer3D object.

getUpper() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryAngleBond

getUpper() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryBond

getUseTemplates() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

Deprecated.

always false, substructure templates are not used anymore

getUSmilesNumbers(IAtomContainer) - Static method in class org.openscience.cdk.graph.invariant.InChINumbersTools

Obtain the InChI numbers for the input container to be used to order atoms in Universal SMILES (O'Boyle, Noel. Journal of Cheminformatics. 2012. 4).

getValence(IAtom) - Static method in class org.openscience.cdk.qsar.AtomValenceTool

getValency() - Method in class org.openscience.cdk.AtomRef

Gets the the exact electron valency of the AtomType object.

getValency() - Method in class org.openscience.cdk.AtomType

Gets the the exact electron valency of the AtomType object.

getValency() - Method in class org.openscience.cdk.debug.DebugAtom

Gets the the exact electron valency of the AtomType object.

getValency() - Method in class org.openscience.cdk.debug.DebugAtomType

Gets the the exact electron valency of the AtomType object.

getValency() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Gets the the exact electron valency of the AtomType object.

getValency() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Gets the the exact electron valency of the AtomType object.

getValency() - Method in interface org.openscience.cdk.interfaces.IAtomType

Gets the the exact electron valency of the AtomType object.

getValency() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Gets the the exact electron valency of the AtomType object.

getValency() - Method in class org.openscience.cdk.silent.AtomType

Gets the the exact electron valency of the AtomType object.

getValue() - Method in enum org.openscience.cdk.io.MDLV2000Writer.SPIN_MULTIPLICITY

Radical value for the spin multiplicity in the properties block.

getValue() - Method in class org.openscience.cdk.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.

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.

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

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.MDLRXNV2000Format

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.MDLV2000Format

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.MDLV3000Format

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.MMODFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.Mol2Format

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC7Format

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC93Format

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC97Format

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.MPQCFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.NWChemFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.PCModelFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.PDBFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.PDBMLFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.PMPFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.PQSChemFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.QChemFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.RawCopyFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.SDFFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.ShelXFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.SMARTSFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.SMILESFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.SpartanFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.VASPFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.ViewmolFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.XEDFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.XYZFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.YasaraFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.ZindoFormat

Returns the class name of the CDK Writer for this format.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat

Returns the class name of the CDK Writer for this format.

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

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

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.

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

HAFNIUM - Static variable in enum org.openscience.cdk.config.Elements

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.

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.GeometryUtil

Determines if all this IAtomContainer's atoms contain 2D coordinates.

has2DCoordinates(IReaction) - Static method in class org.openscience.cdk.geometry.GeometryUtil

Determine if all parts of a reaction have coodinates

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.GeometryUtil

Deprecated.

use GeometryUtil.get2DCoordinateCoverage(org.openscience.cdk.interfaces.IAtomContainer) for determining partial coordinates

has3DCoordinates(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil

Determines if all this IAtomContainer's atoms contain 3D coordinates.

has3DCoordinates(IChemModel) - Static method in class org.openscience.cdk.geometry.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.Atom

hashCode() - Method in class org.openscience.cdk.AtomRef

hashCode() - Method in class org.openscience.cdk.Bond

hashCode() - Method in class org.openscience.cdk.BondRef

hashCode() - Method in class org.openscience.cdk.DynamicFactory.ConstructorKey

hashCode() - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint

hashCode - 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.Expr

hashCode() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

hashCode() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond

hashCode() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList

hashCode() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom

hashCode() - Method in class org.openscience.cdk.silent.Atom

hashCode() - Method in class org.openscience.cdk.silent.Bond

HashGeneratorMaker - Class in org.openscience.cdk.hash

Fluent API for creating hash generators.

HashGeneratorMaker() - Constructor for class org.openscience.cdk.hash.HashGeneratorMaker

HashSpacing() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.HashSpacing

HASHYBRIDIZATION - Static variable in class org.openscience.cdk.libio.jena.CDK

HASLABEL - 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.

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.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

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

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

HBPY8 - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Hexagonal Bipyramidal (HBPY-8)

HBPY9 - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Heptagonal Bipyramidal (HBPY-9)

hCounts - Variable in class org.openscience.cdk.io.cml.CMLCoreModule

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

HeptagonalBipyramidal - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Heptagonal Bipyramidal (HBPY-9)

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.

HexagonalBipyramidal - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Hexagonal Bipyramidal (HBPY-8)

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.HighlightRadius - Class in org.openscience.cdk.renderer.generators

Magic number with unknown units that defines the radius around an atom, e.g.

HighlightGenerator.Palette - Interface in org.openscience.cdk.renderer.generators

Defines a color palette, the palette should provide a color the specified identifier (id).

Highlighting() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.Highlighting

HighlightPalette() - Constructor for class org.openscience.cdk.renderer.generators.HighlightGenerator.HighlightPalette

HighlightRadius() - Constructor for class org.openscience.cdk.renderer.generators.HighlightGenerator.HighlightRadius

highThresh - Variable in class org.openscience.cdk.fingerprint.model.Bayesian

HINFormat - Class in org.openscience.cdk.io.formats

See here.

HINFormat() - Constructor for class org.openscience.cdk.io.formats.HINFormat

HINReader - Class in org.openscience.cdk.io

Reads an object from HIN formated input.

HINReader(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

HOLMIUM - Static variable in enum org.openscience.cdk.config.Elements

HomolyticCleavageMechanism - Class in org.openscience.cdk.reaction.mechanism

This mechanism breaks the chemical bond between atoms.

HomolyticCleavageMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.HomolyticCleavageMechanism

HomolyticCleavageReaction - Class in org.openscience.cdk.reaction.type

IReactionProcess which breaks the bond homogeneously leading to radical ions.

HomolyticCleavageReaction() - Constructor for class org.openscience.cdk.reaction.type.HomolyticCleavageReaction

Constructor of the HomolyticCleavageReaction object.

HOSECode - Variable in class org.openscience.cdk.tools.HOSECodeGenerator

The HOSECode string that we assemble

HOSECodeAnalyser - Class in org.openscience.cdk.tools

Analyses a molecular formula given in String format and builds an AtomContainer with the Atoms in the molecular formula.

HOSECodeAnalyser() - Constructor for class org.openscience.cdk.tools.HOSECodeAnalyser

HOSECodeGenerator - Class in org.openscience.cdk.tools

Generates HOSE codes (Bremser, W.. Analytica Chimica Acta. 1978. 103).

HOSECodeGenerator() - Constructor for class org.openscience.cdk.tools.HOSECodeGenerator

Constructor for the HOSECodeGenerator.

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

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.

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.

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

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

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.

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.

ICDKChangeListener - Interface in org.openscience.cdk.event

A ChangeListener for the CDK, to be independent from the Swing package.

ICDKObject - Interface in org.openscience.cdk.interfaces

The base class for all data objects in this CDK.

ICDKSelectionChangeListener - Interface in org.openscience.cdk.event

A ChangeListener for the CDK, to be independent from the Swing package.

IChargeCalculator - Interface in org.openscience.cdk.charges

Interface for classes that calculate (partial) charges centered on atom nuclei.

IChemFile - Interface in org.openscience.cdk.interfaces

An IChemObject containing a number of ChemSequences.

IChemFormat - Interface in org.openscience.cdk.io.formats

This class is the interface that all ChemFormat's should implement.

IChemFormatMatcher - Interface in org.openscience.cdk.io.formats

This interface is used for classes that are able to match a certain chemical file format.

IChemFormatMatcher.MatchResult - Class in org.openscience.cdk.io.formats

Simple class holds whether a format matcher matched, when it matched and what the format was.

IChemModel - Interface in org.openscience.cdk.interfaces

An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.

IChemObject - Interface in org.openscience.cdk.interfaces

The base class for all chemical objects in this cdk.

IChemObjectBuilder - Interface in org.openscience.cdk.interfaces

A helper class to instantiate a ICDKObject instance for a specific implementation.

IChemObjectChangeEvent - Interface in org.openscience.cdk.interfaces

Event fired by CDK IChemObject classes to their registered listeners in case something changed within them.

IChemObjectIO - Interface in org.openscience.cdk.io

This class is the interface that all IO readers should implement.

IChemObjectIOListener - Interface in org.openscience.cdk.io.listener

Allows monitoring of progress of file reader activities.

IChemObjectListener - Interface in org.openscience.cdk.interfaces

Classes implementing this interface must implement this method such that they react appropriately to changes in the object they are interested in.

IChemObjectReader - Interface in org.openscience.cdk.io

This interface specifies the common functionality all IO readers should provide.

IChemObjectReader.Mode - Enum in org.openscience.cdk.io

IChemObjectReaderErrorHandler - Interface in org.openscience.cdk.io

Interface for classes aimed to handle IChemObjectReader errors.

IChemObjectSelection - Interface in org.openscience.cdk.renderer.selection

A selection of some atoms and bonds from an IAtomContainer or IChemModel.

IChemObjectWriter - Interface in org.openscience.cdk.io

This class is the interface that all IO writers should implement.

IChemSequence - Interface in org.openscience.cdk.interfaces

A sequence of ChemModels, which can, for example, be used to store the course of a reaction.

ICMLConvention - Interface in org.openscience.cdk.io.cml

This interface describes the procedures classes must implement to be plugable into the CMLHandler.

ICMLCustomizer - Interface in org.openscience.cdk.libio.cml

Interface for classes that allow the Convertor to be customized for certain features.

ICMLModule - Interface in org.openscience.cdk.io.cml

This interface describes the procedures classes must implement to be plugable into the CMLHandler.

ICountFingerprint - Interface in org.openscience.cdk.fingerprint

Interface for count fingerprint representations.

ICrystal - Interface in org.openscience.cdk.interfaces

Class representing a molecular crystal.

ID - Static variable in class org.openscience.cdk.templates.AminoAcids

ID_KEY - Static variable in class org.openscience.cdk.renderer.elements.MarkedElement

ID_MAP - Static variable in class org.openscience.cdk.renderer.generators.HighlightGenerator

Property key.

IDCreator - Class in org.openscience.cdk.tools

Class that provides methods to give unique IDs to ChemObjects.

IDCreator() - Constructor for class org.openscience.cdk.tools.IDCreator

IDeduceBondOrderTool - Interface in org.openscience.cdk.tools

A common interface for tools that deduce bond orders from connectivity and optionally additional information, like number of implicit or explicit hydrogens, or hybridization states.

IDENTIFIER - Static variable in class org.openscience.cdk.libio.jena.CDK

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.

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.

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.

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.

IMapping - Interface in org.openscience.cdk.interfaces

Represents a mapping of two atoms.

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.

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

INCHI - Static variable in class org.openscience.cdk.CDKConstants

The IUPAC International Chemical Identifier.

inchi - Variable in class org.openscience.cdk.io.cml.CMLCoreModule

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.

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

InductiveAtomicHardnessDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic

Inductive atomic hardness of an atom in a polyatomic system can be defined as the "resistance" to a change of the atomic charge.

InductiveAtomicHardnessDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor

Constructor for the InductiveAtomicHardnessDescriptor object

InductiveAtomicSoftnessDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic

Inductive atomic softness of an atom in a polyatomic system can be defined as charge delocalizing ability.

InductiveAtomicSoftnessDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor

Constructor for the InductiveAtomicSoftnessDescriptor object

InductivePartialCharges - Class in org.openscience.cdk.charges

The calculation of the inductive partial atomic charges and equalization of effective electronegativities is based on (Cherkasov, A.. J. Chem. Inf. Comput. Sci.. 2003. 43).

InductivePartialCharges() - Constructor for class org.openscience.cdk.charges.InductivePartialCharges

Constructor for the InductivePartialCharges object.

INFO - Static variable in interface org.openscience.cdk.tools.ILoggingTool

Info, Warn, Error, and Fatal messages will be emitted.

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

initialise(IChemObjectBuilder) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor

initialise(IChemObjectBuilder) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor

initialise(IChemObjectBuilder) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor

initialise(IChemObjectBuilder) - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor

initialise(IChemObjectBuilder) - Method in class org.openscience.cdk.qsar.descriptors.molecular.SpiroAtomCountDescriptor

initialise(IChemObjectBuilder) - Method in class org.openscience.cdk.qsar.descriptors.substance.OxygenAtomCountDescriptor

Initialise the descriptor with the specified chem object builder.

initialise(IChemObjectBuilder) - Method in interface org.openscience.cdk.qsar.IDescriptor

Initialise the descriptor with the specified chem object builder.

initialize(Map<String, List>) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94ParametersCall

Initialize the AtomOrder class.

initializeGrid(double) - Method in class org.openscience.cdk.tools.GridGenerator

Method initialise the given grid points with a value.

initializeGrid(double[][][], double) - Method in class org.openscience.cdk.tools.GridGenerator

Method initialise the given grid points with a value.

initializeSpecifications(List<IDescriptor>) - Method in class org.openscience.cdk.qsar.DescriptorEngine

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.

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

inputBuffer - Variable in class org.openscience.cdk.io.VASPReader

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 integers.

IntegerArrayResultType(int) - Constructor for class org.openscience.cdk.qsar.result.IntegerArrayResultType

IntegerDifference - Class in org.openscience.cdk.tools.diff.tree

IDifference between two Integer.

IntegerIOSetting - Class in org.openscience.cdk.io.setting

An class for a reader setting which must be of type String.

IntegerIOSetting(String, IOSetting.Importance, String, String) - Constructor for class org.openscience.cdk.io.setting.IntegerIOSetting

IntegerResult - Class in org.openscience.cdk.qsar.result

Object that provides access to the calculated descriptor value.

IntegerResult(int) - Constructor for class org.openscience.cdk.qsar.result.IntegerResult

IntegerResultType - Class in org.openscience.cdk.qsar.result

IDescriptorResult type for integer.

IntegerResultType() - Constructor for class org.openscience.cdk.qsar.result.IntegerResultType

interpretProjections(Projection...) - Method in class org.openscience.cdk.stereo.StereoElementFactory

Indicate that stereochemistry drawn as a certain projection should be interpreted.

intf() - Method in class org.openscience.cdk.DynamicFactory.ConstructorKey

Access the interface this key indexes.

Intractable - Exception in org.openscience.cdk.exception

Indicates a computation did not complete within some predefined bound.

Intractable(String) - Constructor for exception org.openscience.cdk.exception.Intractable

Create a new exception with the specified message.

intValue() - Method in class org.openscience.cdk.qsar.result.IntegerResult

inUpper() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager

Test to see if the upper virtual pointer is in use.

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.

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

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.

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.

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.

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.

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

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

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() - Method in class org.openscience.cdk.Atom

Access whether this atom has been marked as aromatic.

isAromatic() - Method in class org.openscience.cdk.AtomRef

Access whether this atom has been marked as aromatic.

isAromatic() - Method in class org.openscience.cdk.Bond

Access whether this bond has been marked as aromatic.

isAromatic() - Method in class org.openscience.cdk.BondRef

Access whether this bond has been marked as aromatic.

ISAROMATIC - 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.

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.

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.BondRef

Checks whether a bond is connected to another one.

isConnectedTo(IBond) - Method in class org.openscience.cdk.debug.DebugBond

Checks whether a bond is connected to another one.

isConnectedTo(IBond) - Method in interface org.openscience.cdk.interfaces.IBond

Checks whether a bond is connected to another one.

isConnectedTo(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond

Checks whether a query bond is connected to another one.

isConnectedTo(IBond) - Method in class org.openscience.cdk.silent.Bond

Checks whether a bond is connected to another one.

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. et. al.. Angew. Chem. Int. Ed.. 1966. 5).

ISetting - Interface in org.openscience.cdk.interfaces

A simple setting that can be managed by the SettingManager.

isExpanded() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Helper method to indicate that the method should be drawn fully, and not just the abbreviated form.

isExpanded() - Method in class org.openscience.cdk.FragmentAtom

isExpanded() - Method in interface org.openscience.cdk.interfaces.IFragmentAtom

Helper method to indicate that the method should be drawn fully, and not just the abbreviated form.

isExpanded() - Method in class org.openscience.cdk.silent.FragmentAtom

isFilled() - Method in interface org.openscience.cdk.renderer.selection.IChemObjectSelection

The opposite of a method like "isEmpty".

isFinished() - Method in interface org.openscience.cdk.group.PermutationGroup.Backtracker

Check to see if the backtracker is finished.

isHigherOrder(IBond.Order, IBond.Order) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator

Returns true if the first bond has a higher bond order than the second bond.

isHydrogen(IAtom) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator

Determines if the atom is a hydrogen.

isIdentity() - Method in class org.openscience.cdk.group.Permutation

Check to see if this permutation is the identity permutation.

ISimpleChemObjectReader - Interface in org.openscience.cdk.io

This class is the interface that all IO readers should implement.

isIndexCreated() - Method in class org.openscience.cdk.io.random.RandomAccessReader

ISingleElectron - Interface in org.openscience.cdk.interfaces

A Single Electron is an orbital which is occupied by only one electron.

isInRing() - Method in class org.openscience.cdk.Atom

Access whether this atom has been flagged as in a ring.

isInRing() - Method in class org.openscience.cdk.AtomRef

Access whether this atom has been flagged as in a ring.

isInRing() - Method in class org.openscience.cdk.Bond

Access whether this bond has been flagged as in a ring.

isInRing() - Method in class org.openscience.cdk.BondRef

Access whether this bond has been flagged as in a ring.

ISINRING - 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.

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.

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.

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.

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.

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.

IsotopeContainer(IsotopeContainer) - Constructor for class org.openscience.cdk.formula.IsotopeContainer

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 - 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.

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.

isSubgraph(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester

Deprecated.

Use the Pattern APIs from the cdk-isomorphism module

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.

IStereoElement<F extends IChemObject,C extends IChemObject> - Interface in org.openscience.cdk.interfaces

Representation of stereochemical configuration.

isTetrahedral(IAtomContainer, IAtom, boolean) - Static method in class org.openscience.cdk.geometry.BondTools

Says if an atom as a center of a tetrahedral chirality.

isTheSame(IIsotope, IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormula

Compare to IIsotope.

isTheSame(IIsotope, IIsotope) - Method in class org.openscience.cdk.silent.MolecularFormula

Compare to IIsotope.

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.

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.MDLRXNV2000Format

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.MDLV2000Format

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.MDLV3000Format

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.MMODFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.Mol2Format

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.MOPAC7Format

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.MOPAC93Format

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.MOPAC97Format

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.MPQCFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.NWChemFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.PCModelFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.PDBFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.PDBMLFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.PMPFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.POVRayFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.PQSChemFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.QChemFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.RawCopyFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.SDFFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.ShelXFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.SMARTSFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.SMILESFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.SpartanFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.SVGFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.VASPFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.ViewmolFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.XEDFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.XYZFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.YasaraFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.ZindoFormat

Indicates if the format is an XML-based language.

isXMLBased() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat

Indicates if the format is an XML-based language.

ITALIC_DISPLAY_PREFIX - Static variable in class org.openscience.cdk.renderer.generators.standard.StandardGenerator

A special markup for annotation labels that hints the generator to renderer the annotation label in italic.

IteratingMDLConformerReader - Class in org.openscience.cdk.io.iterator

Iterate over conformers of a collection of molecules stored in SDF format.

IteratingMDLConformerReader(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. Pure Appl. Chem. 2008. 80).

iupacRecommendationsWithoutTerminalCarbon() - Static method in class org.openscience.cdk.renderer.SymbolVisibility

Displays a symbol based on the acceptable representation from the IUPAC guidelines (GR-2.1.2) (Jonathan Brecher. Pure Appl. Chem. 2008. 80).

IValencyChecker - Interface in org.openscience.cdk.tools

A common interface for SaturationChecker and ValencyChecker.

IValidator - Interface in org.openscience.cdk.validate

Interface that Validators need to implement to be used in validation.

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.

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

KabschAlignment - Class in org.openscience.cdk.geometry.alignment

Aligns two structures to minimize the RMSD using the Kabsch algorithm.

KabschAlignment(IAtom[], IAtom[]) - Constructor for class org.openscience.cdk.geometry.alignment.KabschAlignment

Sets up variables for the alignment algorithm.

KabschAlignment(IAtom[], IAtom[], double[]) - Constructor for class org.openscience.cdk.geometry.alignment.KabschAlignment

Sets up variables for the alignment algorithm.

KabschAlignment(IAtomContainer, IAtomContainer) - Constructor for class org.openscience.cdk.geometry.alignment.KabschAlignment

Sets up variables for the alignment algorithm.

KabschAlignment(IAtomContainer, IAtomContainer, double[]) - Constructor for class org.openscience.cdk.geometry.alignment.KabschAlignment

Sets up variables for the alignment algorithm.

KappaShapeIndicesDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

Kier and Hall kappa molecular shape indices compare the molecular graph with minimal and maximal molecular graphs; a description is given at: http://www.chemcomp.com/Journal_of_CCG/Features/descr.htm#KH : "they are intended to capture different aspects of molecular shape.

KappaShapeIndicesDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor

Constructor for the KappaShapeIndicesDescriptor object

KekuleStructure() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.KekuleStructure

kekulise(boolean) - Method in class org.openscience.cdk.smiles.SmilesParser

Indicated whether structures should be automatically kekulised if they are provided as aromatic.

Kekulization - Class in org.openscience.cdk.aromaticity

Assign a Kekulé representation to the aromatic systems of a compound.

Kekulization() - Constructor for class org.openscience.cdk.aromaticity.Kekulization

kekulize(IAtomContainer) - Static method in class org.openscience.cdk.aromaticity.Kekulization

Assign a Kekulé representation to the aromatic systems of a compound.

KETO_ENOL - Static variable in class org.openscience.cdk.tautomers.InChITautomerGenerator

Generate InChI with -KET (keto-enol tautomers) option.

key(Class<?>, Class<?>...) - Static method in class org.openscience.cdk.DynamicFactory

Creates a constructor key for use in accessing constructors.

KierHallSmartsDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

A fragment count descriptor that uses e-state fragments.

KierHallSmartsDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor

KlekotaRothFingerprinter - Class in org.openscience.cdk.fingerprint

SMARTS based substructure fingerprint based on Chemical substructures that enrich for biological activity (Klekota, Justin and Roth, Frederick P.. Bioinformatics. 2008. 24).

KlekotaRothFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.KlekotaRothFingerprinter

KRYPTON - Static variable in enum org.openscience.cdk.config.Elements

L

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.

label(IAtomContainer, int[][], Comparator<IAtom>) - Static method in class org.openscience.cdk.graph.invariant.Canon

Compute the canonical labels for the provided structure.

LANTHANUM - Static variable in enum org.openscience.cdk.config.Elements

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

lastError - Static variable in class org.openscience.cdk.smarts.Smarts

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

LEAD - Static variable in enum org.openscience.cdk.config.Elements

LEFT - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

left() - Method in class org.openscience.cdk.isomorphism.matchers.Expr

Access the left sub-expression of this atom expression being tested.

length() - Method in class org.openscience.cdk.io.cml.CMLModuleStack

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

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.

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. et. al.. J. Chem. Inf. Model.. 2005. 45).

LingoFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.LingoFingerprinter

Initialize the fingerprinter with a default substring length of 4.

LingoFingerprinter(int) - Constructor for class org.openscience.cdk.fingerprint.LingoFingerprinter

Initialize the fingerprinter.

LingoSimilarity - Class in org.openscience.cdk.similarity

A class to evaluate the similarity between two LINGO's as described in (Vidal, D. et. al.. J. Chem. Inf. Model.. 2005. 45).

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

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

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

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

Counts the number of atoms in the longest aliphatic chain.

LongestAliphaticChainDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor

Constructor for the LongestAliphaticChainDescriptor object.

lowThresh - Variable in class org.openscience.cdk.fingerprint.model.Bayesian

LUTETIUM - Static variable in enum org.openscience.cdk.config.Elements

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

MAGNESIUM - Static variable in enum org.openscience.cdk.config.Elements

main(String[]) - Static method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor

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.

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.

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.

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.

makeEdge(int, int, String, String, String) - Method in class org.openscience.cdk.signature.MoleculeFromSignatureBuilder

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.

makeGraph() - Method in class org.openscience.cdk.signature.MoleculeFromSignatureBuilder

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.

makeLabel(int) - Static method in class org.openscience.cdk.isomorphism.matchers.RGroup

Makes a label/title to be used for a substituent.

makeReferencesExplicit(IChemObject) - Static method in class org.openscience.cdk.dict.CDKDictionaryReferences

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.

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

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<IChemObject, IChemObject>) - Method in interface org.openscience.cdk.interfaces.IStereoElement

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.TetrahedralChirality

map(Map<IChemObject, IChemObject>) - Method in class org.openscience.cdk.stereo.TetrahedralChirality

mapAtomsOfAlignedStructures(IAtomContainer, IAtomContainer, double, Map<Integer, Integer>) - Static method in class org.openscience.cdk.geometry.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.MappingLineWidth - Class in org.openscience.cdk.renderer.generators

The width on screen of an atom-atom mapping line.

MappingGenerator.ShowAtomAtomMapping - Class in org.openscience.cdk.renderer.generators

Boolean by which atom-atom mapping depiction can be temporarily disabled.

MappingLineWidth() - Constructor for class org.openscience.cdk.renderer.generators.MappingGenerator.MappingLineWidth

mappings() - Method in interface org.openscience.cdk.interfaces.IReaction

Returns the mappings between the reactant and the product side.

Mappings - 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

Deprecated.

Use TemplateHandler3D.mapTemplates(org.openscience.cdk.interfaces.IAtomContainer, int)

mapTemplates(IAtomContainer, int) - Method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D

Checks if one of the loaded templates is a substructure in the given Molecule.

Margin() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.Margin

markAromaticRings(IRing) - Static method in class org.openscience.cdk.tools.manipulator.RingManipulator

Marks the ring aromatic if all atoms and all bonds are aromatic.

markAromaticRings(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator

Iterates over the rings in the ring set, and marks the ring aromatic if all atoms and all bonds are aromatic.

MarkedElement - Class in org.openscience.cdk.renderer.elements

A marked element adds meta-data (id and tags) to a CDK rendering element (or group of elements).

MarkedOutput() - Constructor for class org.openscience.cdk.renderer.RendererModel.MarkedOutput

markNotPlaced(IAtomContainer) - Static method in class org.openscience.cdk.layout.AtomPlacer

Marks all the atoms in the given AtomContainer as not placed

markPlaced(IAtomContainer) - Static method in class org.openscience.cdk.layout.AtomPlacer

Marks all the atoms in the given AtomContainer as placed

markPlaced(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D

Mark all atoms in chain as placed.

markRingAtomsAndBonds(IAtomContainer) - Static method in class org.openscience.cdk.graph.Cycles

Find and mark all cyclic atoms and bonds in the provided molecule.

markRingAtomsAndBonds(IAtomContainer, int[][], GraphUtil.EdgeToBondMap) - Static method in class org.openscience.cdk.graph.Cycles

Find and mark all cyclic atoms and bonds in the provided molecule.

markup(IRenderingElement, String...) - Static method in class org.openscience.cdk.renderer.elements.MarkedElement

Markup a rendering element with the specified classes.

markupAtom(IRenderingElement, IAtom) - Static method in class org.openscience.cdk.renderer.elements.MarkedElement

Markup a atom with the class 'atom' and optionally the ids/classes from it's properties.

markupBond(IRenderingElement, IBond) - Static method in class org.openscience.cdk.renderer.elements.MarkedElement

Markup a bond with the class 'bond' and optionally the ids/classes from it's properties.

markupMol(IRenderingElement, IAtomContainer) - Static method in class org.openscience.cdk.renderer.elements.MarkedElement

Markup a molecule with the class 'mol' and optionally the ids/classes from it's properties.

markWithError(IChemObject) - Static method in class org.openscience.cdk.validate.ProblemMarker

markWithWarning(IChemObject) - Static method in class org.openscience.cdk.validate.ProblemMarker

MASS_ELECTRON - Static variable in class org.openscience.cdk.PhysicalConstants

Mass of an electron.

MASS_PROTON - Static variable in class org.openscience.cdk.PhysicalConstants

Mass of a proton.

match(int, int) - Method in class org.openscience.cdk.graph.Matching

Add the edge '{u,v}' to the matched edge set.

match(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.DfPattern

Find a matching of this pattern in the target.

match(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.Pattern

Find a matching of this pattern in the target.

match(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.Ullmann

match(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.VentoFoggia

Find a matching of this pattern in the target.

match(IAtomContainer) - Method in class org.openscience.cdk.smarts.SmartsPattern

Find a matching of this pattern in the target.

matchAll(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.DfPattern

Find all mappings of this pattern in the target.

matchAll(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.Pattern

Find all mappings of this pattern in the target.

matchAll(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.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.MDLRXNV2000Format

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.MDLRXNV3000Format

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.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(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.DfPattern

Determine if there is a mapping of this pattern in the target.

matches(IBond, int) - Method in class org.openscience.cdk.isomorphism.matchers.Expr

matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.Expr

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.Expr

Test whether this expression matches an atom instance.

matches(IAtom, int) - Method in class org.openscience.cdk.isomorphism.matchers.Expr

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(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Returns true of the given atom matches this IQueryAtom.

matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond

Returns true of the given bond matches this IQueryBond.

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolChargeIDQueryAtom

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.

matchesRoot(IAtom) - Method in class org.openscience.cdk.isomorphism.DfPattern

Test whether the pattern matches at the provided atom.

Matching - Class in org.openscience.cdk.graph

A matching is an independent edge set of a graph.

matchOccurence(int) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList

Matches the 'occurrence' condition with a provided maximum number of RGroup attachments.

MatchResult(boolean, IChemFormat, int) - Constructor for class org.openscience.cdk.io.formats.IChemFormatMatcher.MatchResult

MatrixNotInvertibleException - Exception in org.openscience.cdk.graph.invariant.exception

MatrixNotInvertibleException() - Constructor for exception org.openscience.cdk.graph.invariant.exception.MatrixNotInvertibleException

MAX_AXIS_ANGLE - Static variable in class org.openscience.cdk.stereo.StereoTool

The maximum angle in radians for two lines to be 'diaxial'.

MAX_FLAG_INDEX - Static variable in class org.openscience.cdk.CDKConstants

Maximum flags array index.

MAX_POINTER_INDEX - Static variable in class org.openscience.cdk.CDKConstants

Maximum pointers array index.

MaxDrawableAromaticRing() - Constructor for class org.openscience.cdk.renderer.generators.RingGenerator.MaxDrawableAromaticRing

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.

MDEC11 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

MDEC12 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

MDEC13 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

MDEC14 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

MDEC22 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

MDEC23 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

MDEC24 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

MDEC33 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

MDEC34 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

MDEC44 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

MDEDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

Calculates the Molecular Distance Edge descriptor described in (Liu, S. et. al.. Journal of Chemical Information and Computer Sciences. 1998. 38).

MDEDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

MDEN11 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

MDEN12 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

MDEN13 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

MDEN22 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

MDEN23 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

MDEN33 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

MDEO11 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

MDEO12 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

MDEO22 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

MDLFormat - Class in org.openscience.cdk.io.formats

See here.

MDLFormat() - Constructor for class org.openscience.cdk.io.formats.MDLFormat

MDLMolConvention - Class in org.openscience.cdk.io.cml

Implementation of the MDLMol Covention for CML.

MDLMolConvention(IChemFile) - Constructor for class org.openscience.cdk.io.cml.MDLMolConvention

MDLMolConvention(ICMLModule) - Constructor for class org.openscience.cdk.io.cml.MDLMolConvention

MDLReader - Class in org.openscience.cdk.io

Deprecated.

This reader is only for molfiles without a version tag, typically the most common molfile now encountered is V2000 and the MDLV2000Reader should be used instead. The V2000 reader can actually read files missing the version tag when in relaxed mode.

MDLReader() - Constructor for class org.openscience.cdk.io.MDLReader

Deprecated.

MDLReader(InputStream) - Constructor for class org.openscience.cdk.io.MDLReader

Deprecated.

Constructs a new MDLReader that can read Molecule from a given InputStream.

MDLReader(InputStream, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLReader

Deprecated.

MDLReader(Reader) - Constructor for class org.openscience.cdk.io.MDLReader

Deprecated.

Constructs a new MDLReader that can read Molecule from a given Reader.

MDLReader(Reader, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLReader

Deprecated.

MDLRXNFormat - Class in org.openscience.cdk.io.formats

See here.

MDLRXNFormat() - Constructor for class org.openscience.cdk.io.formats.MDLRXNFormat

MDLRXNReader - Class in org.openscience.cdk.io

Deprecated.

Use V2000 or V3000

MDLRXNReader(Reader) - Constructor for class org.openscience.cdk.io.MDLRXNReader

Deprecated.

Constructs a new MDLReader that can read Molecule from a given Reader.

MDLRXNReader(Reader, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLRXNReader

Deprecated.

MDLRXNReader(InputStream) - Constructor for class org.openscience.cdk.io.MDLRXNReader

Deprecated.

MDLRXNReader(InputStream, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLRXNReader

Deprecated.

MDLRXNReader() - Constructor for class org.openscience.cdk.io.MDLRXNReader

Deprecated.

MDLRXNV2000Format - Class in org.openscience.cdk.io.formats

See here.

MDLRXNV2000Format() - Constructor for class org.openscience.cdk.io.formats.MDLRXNV2000Format

MDLRXNV2000Reader - Class in org.openscience.cdk.io

Reads a molecule from an MDL RXN file (Dalby, A. et. al.. Journal of Chemical Information and Computer Sciences. 1992. 32).

MDLRXNV2000Reader(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. et. al.. Journal of Chemical Information and Computer Sciences. 1992. 32)).

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

MEITNERIUM - Static variable in enum org.openscience.cdk.config.Elements

MENDELEVIUM - Static variable in enum org.openscience.cdk.config.Elements

MERCURY - Static variable in enum org.openscience.cdk.config.Elements

merge(ICountFingerprint) - Method in interface org.openscience.cdk.fingerprint.ICountFingerprint

Merge all from fp into the current fingerprint.

merge(ICountFingerprint) - Method in class org.openscience.cdk.fingerprint.IntArrayCountFingerprint

method1(ICountFingerprint, ICountFingerprint) - Static method in class org.openscience.cdk.similarity.Tanimoto

Calculates Tanimoto distance for two count fingerprints using method 1.

method2(ICountFingerprint, ICountFingerprint) - Static method in class org.openscience.cdk.similarity.Tanimoto

Calculates Tanimoto distance for two count fingerprints using method 2 (J.A. Grant, J.A. Haigh, B.T. Pickup, A. Nicholls and R.A. Sayle. J. Chem. Inf. Model.. 2006. 46).

MIN_COLINEAR_NORMAL - Static variable in class org.openscience.cdk.stereo.StereoTool

The maximum tolerance for the normal calculated during colinearity.

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.

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

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

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.

moleculeCustomProperty - Variable in class org.openscience.cdk.io.cml.CMLCoreModule

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.

MoleculeHashGenerator - Interface in org.openscience.cdk.hash

A hash function which generates a single 64-bit hash code for a molecule.

MoleculeSetManipulator - Class in org.openscience.cdk.tools.manipulator

MoleculeSetManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator

MoleculeSetRenderer - Class in org.openscience.cdk.renderer

A general renderer for IChemModels, IReactions, and IAtomContainers.

MoleculeSetRenderer(List<IGenerator<IAtomContainer>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.MoleculeSetRenderer

A renderer that generates diagrams using the specified generators and manages fonts with the supplied font manager.

MoleculeSetRenderer(RendererModel, List<IGenerator<IAtomContainer>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.MoleculeSetRenderer

MoleculeSignature - Class in org.openscience.cdk.signature

A molecule signature is a way to produce AtomSignatures and to get the canonical (Faulon, J. L., Collins, M. J., and Carr, R. D.. Journal of Chemical Information and Computer Sciences. 2004. 44) signature string for a molecule.

MoleculeSignature(IAtomContainer) - Constructor for class org.openscience.cdk.signature.MoleculeSignature

Creates a signature that represents this molecule.

MoleculeSignature(IAtomContainer, int) - Constructor for class org.openscience.cdk.signature.MoleculeSignature

Creates a signature with a maximum height of height for molecule molecule.

MOLYBDENUM - Static variable in enum org.openscience.cdk.config.Elements

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.. J.Chem.Doc.. 1965. 5).

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

multipliers - Variable in class org.openscience.cdk.AtomContainerSet

Defines the number of instances of a certain molecule in the set.

multipliers - Variable in class org.openscience.cdk.silent.AtomContainerSet

Defines the number of instances of a certain molecule in the set.

multiply(double) - Method in class org.openscience.cdk.graph.invariant.GIMatrix

Returns the result of the scalar multiplication of the matrix, that is the multiplication of every of its elements by a given number.

multiply(GIMatrix) - Method in class org.openscience.cdk.graph.invariant.GIMatrix

Returns the result of the matrix multiplication of this matrix by another one.

multiply(Permutation) - Method in class org.openscience.cdk.group.Permutation

Multiply this permutation by another such that for all i, this[i] = this[other[i]].

multiplyLine(int, double) - Method in class org.openscience.cdk.graph.invariant.GIMatrix

Returns the resulting matrix of an elementary linear operation that consists of multiplying a single line of the matrix by a constant.

MurckoFragmenter - Class in org.openscience.cdk.fragment

An implementation of the Murcko fragmenation method (Bemis, G.W. and Murcko, M.A. . Journal of Medicinal Chemistry. 1996. 39).

MurckoFragmenter() - Constructor for class org.openscience.cdk.fragment.MurckoFragmenter

Instantiate Murcko fragmenter.

MurckoFragmenter(boolean, int) - Constructor for class org.openscience.cdk.fragment.MurckoFragmenter

Instantiate Murcko fragmenter.

MurckoFragmenter(boolean, int, MoleculeHashGenerator) - Constructor for class org.openscience.cdk.fragment.MurckoFragmenter

Instantiate Murcko fragmenter.

mutate(IAtomContainer) - Method in class org.openscience.cdk.structgen.RandomGenerator

Randomly chooses four atoms and alters the bonding pattern between them according to rules described in "Faulon, JCICS 1996, 36, 731".

N

n() - Method in class org.openscience.cdk.DynamicFactory.ConstructorKey

Access the number of parameters in the constructor.

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.

nComponents() - Method in class org.openscience.cdk.graph.ConnectedComponents

negate() - Method in class org.openscience.cdk.isomorphism.matchers.Expr

Negate the expression, the expression will not return true only if the condition is not met.

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

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

NEON - Static variable in enum org.openscience.cdk.config.Elements

NEPTUNIUM - Static variable in enum org.openscience.cdk.config.Elements

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

next() - Method in class org.openscience.cdk.graph.AtomContainerPermutor

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

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".

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.

NICKEL - Static variable in enum org.openscience.cdk.config.Elements

NIOBIUM - Static variable in enum org.openscience.cdk.config.Elements

NITROGEN - Static variable in enum org.openscience.cdk.config.Elements

NitrogenRule - Class in org.openscience.cdk.formula.rules

This class validate if the rule of nitrogen is kept.

NitrogenRule() - Constructor for class org.openscience.cdk.formula.rules.NitrogenRule

Constructor for the NitrogenRule object.

NMRSHIFT_CARBON - Static variable in class org.openscience.cdk.CDKConstants

Carbon NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.

NMRSHIFT_DEUTERIUM - Static variable in class org.openscience.cdk.CDKConstants

Deuterium NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.

NMRSHIFT_FLUORINE - Static variable in class org.openscience.cdk.CDKConstants

Fluorine NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.

NMRSHIFT_HYDROGEN - Static variable in class org.openscience.cdk.CDKConstants

Hydrogen NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.

NMRSHIFT_NITROGEN - Static variable in class org.openscience.cdk.CDKConstants

Nitrogen NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.

NMRSHIFT_PHOSPORUS - Static variable in class org.openscience.cdk.CDKConstants

Phosphorus NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.

NMRSHIFT_SULFUR - Static variable in class org.openscience.cdk.CDKConstants

Sulfur NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.

NMRSIGNAL_INTENSITY - Static variable in class org.openscience.cdk.CDKConstants

NMR signal intensity constant for use as a key in the IChemObject.physicalProperties hashtable.

NMRSIGNAL_MULTIPLICITY - Static variable in class org.openscience.cdk.CDKConstants

NMR signal multiplicity constant for use as a key in the IChemObject.physicalProperties hashtable.

NMRSPECTYPE_1D - Static variable in class org.openscience.cdk.CDKConstants

NMR spectrum type constant for use as key for an arbitrary 1-dimensional NMR experiment.

NMRSPECTYPE_1D_DEPT135 - Static variable in class org.openscience.cdk.CDKConstants

NMR spectrum type constant for use as key for a 1-dimensional DEPT135 NMR experiment.

NMRSPECTYPE_1D_DEPT90 - Static variable in class org.openscience.cdk.CDKConstants

NMR spectrum type constant for use as key for a 1-dimensional DEPT90 NMR experiment.

NMRSPECTYPE_2D_HHCOSY - Static variable in class org.openscience.cdk.CDKConstants

NMR spectrum type constant for use as key for a 2-dimensional H,H-COSY NMR experiment.

NMRSPECTYPE_2D_HMBC - Static variable in class org.openscience.cdk.CDKConstants

NMR spectrum type constant for use as key for a 2-dimensional HMBC NMR experiment.

NMRSPECTYPE_2D_HSQC - Static variable in class org.openscience.cdk.CDKConstants

NMR spectrum type constant for use as key for a 2-dimensional HSQC NMR experiment.

NMRSPECTYPE_2D_INADEQUATE - Static variable in class org.openscience.cdk.CDKConstants

NMR spectrum type constant for use as key for a 2-dimensional INADEQUATE NMR experiment.

NO_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

NONE - Static variable in class org.openscience.cdk.tools.DataFeatures

Indicated that no feature are defined.

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.GeometryUtil

Normalizes a point.

normalize() - Method in class org.openscience.cdk.stereo.Octahedral

Normalize the configuration to the lowest order (1).

normalize() - Method in class org.openscience.cdk.stereo.SquarePlanar

Normalize the configuration to the lowest configuration order (1) - U-shaped.

normalize() - Method in class org.openscience.cdk.stereo.TrigonalBipyramidal

Normalize the configuration to the lowest configuration order (1) - the axis goes from the first to last carrier, the three middle carriers are anti-clockwise looking from the first carrier.

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.

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.

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

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

OBJECT_UNIQUE_POLICY - Static variable in class org.openscience.cdk.tools.IDCreator

New ID generation policy - to generate IDs unique only in a molecule

OC - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Octahedral (OC-6)

occupancies - Variable in class org.openscience.cdk.io.cml.CMLCoreModule

Octahedral - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Octahedral (OC-6)

Octahedral - Class in org.openscience.cdk.stereo

Represents an octahedral configuration of an atom six neighbors.

Octahedral(IAtom, IAtom[], int) - Constructor for class org.openscience.cdk.stereo.Octahedral

Create a new octahedral configuration.

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.

Offset() - Constructor for class org.openscience.cdk.renderer.generators.AtomNumberGenerator.Offset

ofNumber(int) - Static method in enum org.openscience.cdk.config.Elements

Obtain the element with the specified atomic number.

ofString(String) - Static method in enum org.openscience.cdk.config.Elements

Obtain the element with the specified symbol or name.

ofValue(int) - Static method in enum org.openscience.cdk.io.MDLV2000Writer.SPIN_MULTIPLICITY

Create a SPIN_MULTIPLICITY instance for the specified value.

OmitMajorIsotopes() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.OmitMajorIsotopes

ONE_FIVE_SHIFT - Static variable in class org.openscience.cdk.tautomers.InChITautomerGenerator

Generate InChI with -15T (1,5-shift tautomers) option.

OPPOSITE - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

OptForceWriteAs2DCoordinates - Static variable in class org.openscience.cdk.io.MDLV2000Writer

OptionIOSetting - Class in org.openscience.cdk.io.setting

An class for a reader setting which must be found in the list of possible settings.

OptionIOSetting(String, IOSetting.Importance, String, List<String>, String) - Constructor for class org.openscience.cdk.io.setting.OptionIOSetting

OptionIOSetting is IOSetting for which the value must be in the list of possible options.

OptWriteAromaticBondTypes - Static variable in class org.openscience.cdk.io.MDLV2000Writer

OptWriteDefaultProperties - Static variable in class org.openscience.cdk.io.MDLV2000Writer

OptWriteMajorIsotopes - Static variable in class org.openscience.cdk.io.MDLV2000Writer

OptWriteQueryFormatValencies - Static variable in class org.openscience.cdk.io.MDLV2000Writer

or(IBitFingerprint) - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint

or(IBitFingerprint) - Method in interface org.openscience.cdk.fingerprint.IBitFingerprint

Performs a logical OR of the bits in this target bit set with the bits in the argument fingerprint.

or(IBitFingerprint) - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint

or(IntArrayFingerprint) - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint

or(CycleFinder, CycleFinder) - Static method in class org.openscience.cdk.graph.Cycles

Use an auxiliary cycle finder if the primary method was intractable.

or(Expr) - Method in class org.openscience.cdk.isomorphism.matchers.Expr

Utility, combine this expression with another, using disjunction.

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.

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.

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.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.mcss - package org.openscience.cdk.isomorphism.mcss

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.modeling.builder3d - package org.openscience.cdk.modeling.builder3d

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.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.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

OSMIUM - Static variable in enum org.openscience.cdk.config.Elements

other(int) - Method in class org.openscience.cdk.graph.Matching

Access the vertex matched with 'v'.

OuterGlowWidth() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.OuterGlowWidth

outline(double) - Method in class org.openscience.cdk.renderer.elements.GeneralPath

Outline the general path with the specified stroke size.

outlineOf(Shape, double, Color) - Static method in class org.openscience.cdk.renderer.elements.GeneralPath

Create an outline path of the specified Java 2D Shape and color.

output - Variable in class org.openscience.cdk.inchi.InChIGenerator

output - Variable in class org.openscience.cdk.inchi.InChIToStructure

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.

OverlapPair(IChemObject, IChemObject) - Constructor for class org.openscience.cdk.layout.OverlapResolver.OverlapPair

Deprecated.

Constructor for the OverlapPair object.

OverlapResolver - Class in org.openscience.cdk.layout

Deprecated.

does not resolve overlaps correctly

OverlapResolver() - Constructor for class org.openscience.cdk.layout.OverlapResolver

Deprecated.

OverlapResolver.OverlapPair - Class in org.openscience.cdk.layout

Deprecated.

A little helper class to store pairs of overlapping atoms.

OWLAtomTypeHandler - Class in org.openscience.cdk.config.atomtypes

SAX Handler for the OWLAtomTypeReader.

OWLAtomTypeHandler(IChemObjectBuilder) - Constructor for class org.openscience.cdk.config.atomtypes.OWLAtomTypeHandler

Constructs a new AtomTypeHandler and will create IAtomType implementations using the given IChemObjectBuilder.

OWLAtomTypeMappingHandler - Class in org.openscience.cdk.config.atomtypes

SAX Handler for the OWLAtomTypeMappingReader.

OWLAtomTypeMappingHandler() - Constructor for class org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingHandler

Constructs a new OWLAtomTypeMappingHandler.

OWLAtomTypeMappingReader - Class in org.openscience.cdk.config.atomtypes

XML Reader for the OWLBasedAtomTypeConfigurator.

OWLAtomTypeMappingReader(Reader) - Constructor for class org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingReader

Instantiates the XML based AtomTypeReader.

OWLAtomTypeReader - Class in org.openscience.cdk.config.atomtypes

XML Reader for the OWLBasedAtomTypeConfigurator.

OWLAtomTypeReader(Reader) - Constructor for class org.openscience.cdk.config.atomtypes.OWLAtomTypeReader

Instantiates the XML based AtomTypeReader.

OWLBasedAtomTypeConfigurator - Class in org.openscience.cdk.config

AtomType resource that reads the atom type configuration from an OWL file.

OWLBasedAtomTypeConfigurator() - Constructor for class org.openscience.cdk.config.OWLBasedAtomTypeConfigurator

OWLFile - Class in org.openscience.cdk.dict

Dictionary with entries build from an OWL file.

OWLFile() - Constructor for class org.openscience.cdk.dict.OWLFile

OWLReact - Class in org.openscience.cdk.dict

Dictionary with entries build from an OWL React.

OWLReact() - Constructor for class org.openscience.cdk.dict.OWLReact

Constructor of the OWLReact object.

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

P

Padding() - Constructor for class org.openscience.cdk.renderer.RendererModel.Padding

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

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(IAtomContainer, String, int) - Static method in class org.openscience.cdk.smarts.Smarts

Parse the provided SMARTS string appending query atom/bonds to the provided molecule.

parse(IAtomContainer, String) - Static method in class org.openscience.cdk.smarts.Smarts

Parse the provided SMARTS string appending query atom/bonds to the provided molecule.

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

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.BondRefinerBuilder - Class in org.openscience.cdk.group

partitionRings(IRingSet) - Static method in class org.openscience.cdk.ringsearch.RingPartitioner

Partitions a RingSet into RingSets of connected rings.

PartitionRingsFromComplexRing(String) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor

PathBuilder - Class in org.openscience.cdk.renderer.elements.path

Builder class for paths.

PathBuilder() - Constructor for class org.openscience.cdk.renderer.elements.path.PathBuilder

Make a new path builder with a default color of black.

PathBuilder(Color) - Constructor for class org.openscience.cdk.renderer.elements.path.PathBuilder

Make a path builder that will make a path with a particular color.

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.

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

PBPY - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Pentagonal Bipyramidal (PBPY-7)

PCCompoundASNReader - Class in org.openscience.cdk.io

Reads an object from ASN formated input for PubChem Compound entries.

PCCompoundASNReader(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

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.

PentagonalBipyramidal - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Pentagonal Bipyramidal (PBPY-7)

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.

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.

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.

perturbed() - Method in class org.openscience.cdk.hash.HashGeneratorMaker

Discriminate atoms experiencing uniform environments.

PetitjeanNumberDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

According to the Petitjean definition, the eccentricity of a vertex corresponds to the distance from that vertex to the most remote vertex in the graph.

PetitjeanNumberDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor

Constructor for the PetitjeanNumberDescriptor object

PetitjeanShapeIndexDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

Evaluates the Petitjean shape indices, These original Petitjean number was described by Petitjean (( Petitjean, M. . Journal of Chemical Information and Computer Science. 1992. 32)) and considered the molecular graph.

PetitjeanShapeIndexDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor

PharmacophoreAngleBond - Class in org.openscience.cdk.pharmacophore

Represents an angle relationship between three pharmacophore groups.

PharmacophoreAngleBond(PharmacophoreAtom, PharmacophoreAtom, PharmacophoreAtom) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreAngleBond

Create a pharmacophore distance constraint.

PharmacophoreAtom - Class in org.openscience.cdk.pharmacophore

A representation of a pharmacophore group.

PharmacophoreAtom(String, String, Point3d) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreAtom

Create a pharmacophore group.

PharmacophoreAtom(PharmacophoreAtom) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreAtom

Create a pharmacophore group.

PharmacophoreBond - Class in org.openscience.cdk.pharmacophore

Represents a distance relationship between two pharmacophore groups.

PharmacophoreBond(PharmacophoreAtom, PharmacophoreAtom) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreBond

Create a pharmacophore distance constraint.

PharmacophoreMatcher - Class in org.openscience.cdk.pharmacophore

Identifies atoms whose 3D arrangement matches a specified pharmacophore query.

PharmacophoreMatcher() - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreMatcher

An empty constructor.

PharmacophoreMatcher(PharmacophoreQuery) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreMatcher

Initialize the matcher with a query.

PharmacophoreQuery - Class in org.openscience.cdk.pharmacophore

Represents a colleciton of pharmacophore groups and constraints.

PharmacophoreQuery() - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreQuery

PharmacophoreQueryAngleBond - Class in org.openscience.cdk.pharmacophore

Represents a pharmacophore query angle constraint.

PharmacophoreQueryAngleBond() - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreQueryAngleBond

PharmacophoreQueryAngleBond(PharmacophoreQueryAtom, PharmacophoreQueryAtom, PharmacophoreQueryAtom, double, 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

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

PLUTOMNIUM - Static variable in enum org.openscience.cdk.config.Elements

Deprecated.

PLUTONIUM - Static variable in enum org.openscience.cdk.config.Elements

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.

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.. Theoretica Chimica Acta. 1982. 61) and (Gasteiger, J. and Hutchings, M.G.. J. Amer. Chem. Soc.. 1984. 106) Limitations in parameterization of atoms: H, Csp3, Csp2, Csp2arom, Csp3, Nsp3, Nsp2, Nsp3, P, Osp3 and Osp2.

Polarizability() - Constructor for class org.openscience.cdk.charges.Polarizability

Constructor for the Polarizability object.

POLONIUM - Static variable in enum org.openscience.cdk.config.Elements

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.

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.

POTASSIUM - Static variable in enum org.openscience.cdk.config.Elements

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

PRASEODYMIUM - Static variable in enum org.openscience.cdk.config.Elements

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

prepare(IAtomContainer) - Static method in class org.openscience.cdk.smarts.SmartsPattern

prepareNode(IAtomContainer) - Method in class org.openscience.cdk.graph.invariant.EquivalentClassPartitioner

Prepare the node identifier.

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.

PRIORITY - Static variable in class org.openscience.cdk.layout.AtomPlacer

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.

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

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.

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.

projectG2(BitSet) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph

Projects a RGraph 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.

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

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

ProteinBuilderTool - Class in org.openscience.cdk.tools

Class that facilitates building protein structures.

ProteinBuilderTool() - Constructor for class org.openscience.cdk.tools.ProteinBuilderTool

proteinGridToPmesh(String) - Method in class org.openscience.cdk.protein.ProteinPocketFinder

Method writes the protein grid points to pmesh format.

ProteinPocketFinder - Class in org.openscience.cdk.protein

The detection of pocket and cavities in a bioPolymer is done similar to the program LIGSITE (Hendlich, M. et. al.. Journal of Molecular Graphics and Modelling. 1997. 15).

ProteinPocketFinder(String, boolean) - Constructor for class org.openscience.cdk.protein.ProteinPocketFinder

ProteinPocketFinder(String, double, 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.

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.

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

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.

QueryAtom - Class in org.openscience.cdk.isomorphism.matchers

QueryAtom(String, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryAtom

QueryAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryAtom

QueryAtom(Expr) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryAtom

Create a new query atom with the given an expression.

QueryAtom(Expr.Type) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryAtom

Create a new query atom with the given an predicate expression type.

QueryAtom(Expr.Type, int) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryAtom

Create a new query atom with the given an value expression type.

QueryAtomContainer - Class in org.openscience.cdk.isomorphism.matchers

QueryAtomContainer(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

Utilities for creating queries from 'real' molecules.

QueryAtomContainerCreator() - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator

QueryBond - Class in org.openscience.cdk.isomorphism.matchers

Implements the concept of a "query bond" between two or more atoms.

QueryBond(IAtom, IAtom, Expr) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryBond

Constructs an query bond from an expression.

QueryBond(IAtom, IAtom, Expr.Type) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryBond

Constructs an query bond from an expression type.

QueryBond(IAtom, IAtom, Expr.Type, int) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryBond

Constructs an query bond from an expression type and value.

QueryBond(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryBond

Constructs an empty query bond.

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

question - Variable in class org.openscience.cdk.io.setting.IOSetting

R

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)_5-C6[R] => A([R])-(C_5)-[C6*].

RadicalSiteRrDeltaReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalSiteRrDeltaReaction

Constructor of the RadicalSiteRrDeltaReaction object

RadicalSiteRrGammaReaction - Class in org.openscience.cdk.reaction.type

This reaction could be represented as [A*]-(C)_4-C5[R] => A([R])-(C_4)-[C5*].

RadicalSiteRrGammaReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalSiteRrGammaReaction

Constructor of the RadicalSiteRrGammaReaction object

RADIUM - Static variable in enum org.openscience.cdk.config.Elements

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

RDBERule - Class in org.openscience.cdk.formula.rules

Ring Double Bond Equivalents (RDBE) or Double Bond Equivalents (DBE) are calculated from valence values of elements contained in a formula and should tell the number of bonds - or rings.

RDBERule() - Constructor for class org.openscience.cdk.formula.rules.RDBERule

Constructor for the RDBE object.

RDBERule.Combinations - Class in org.openscience.cdk.formula.rules

RDFCalculator - Class in org.openscience.cdk.geometry

Calculator of radial distribution functions.

RDFCalculator(double, double, double, double) - Constructor for class org.openscience.cdk.geometry.RDFCalculator

Constructs a RDF calculator that calculates a unweighted, digitized RDF function.

RDFCalculator(double, double, double, double, IRDFWeightFunction) - Constructor for class org.openscience.cdk.geometry.RDFCalculator

Constructs a RDF calculator that calculates a digitized RDF function.

rdFields - Variable in class org.openscience.cdk.io.MDLRXNWriter

RDFProtonDescriptor_G3R - Class in org.openscience.cdk.qsar.descriptors.atomic

This class calculates G3R proton descriptors used in neural networks for H1 NMR shift (Aires-de-Sousa, J. et. al.. J. Chem. Inf. Mod.. 2002. 74).

RDFProtonDescriptor_G3R() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R

Constructor for the RDFProtonDescriptor object

RDFProtonDescriptor_GDR - Class in org.openscience.cdk.qsar.descriptors.atomic

This class calculates GDR proton descriptors used in neural networks for H1 NMR shift (Aires-de-Sousa, J. et. al.. J. Chem. Inf. Mod.. 2002. 74).

RDFProtonDescriptor_GDR() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR

Constructor for the RDFProtonDescriptor object

RDFProtonDescriptor_GHR - Class in org.openscience.cdk.qsar.descriptors.atomic

This class calculates GHR proton descriptors used in neural networks for H1 NMR shift (Aires-de-Sousa, J. et. al.. J. Chem. Inf. Mod.. 2002. 74).

RDFProtonDescriptor_GHR() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR

Constructor for the RDFProtonDescriptor object

RDFProtonDescriptor_GHR_topol - Class in org.openscience.cdk.qsar.descriptors.atomic

This class calculates GHR topological proton descriptors used in neural networks for H1 NMR shift (Aires-de-Sousa, J. et. al.. J. Chem. Inf. Mod.. 2002. 74).

RDFProtonDescriptor_GHR_topol() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol

Constructor for the RDFProtonDescriptor object

RDFProtonDescriptor_GSR - Class in org.openscience.cdk.qsar.descriptors.atomic

This class calculates GDR proton descriptors used in neural networks for H1 NMR shift (Aires-de-Sousa, J. et. al.. J. Chem. Inf. Mod.. 2002. 74).

RDFProtonDescriptor_GSR() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR

Constructor for the RDFProtonDescriptor object

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.

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

reactions() - Method in class org.openscience.cdk.debug.DebugReactionSet

Get an iterator for this reaction set.

reactions() - Method in interface org.openscience.cdk.interfaces.IReactionSet

Returns the Iterable over Reactions of this container.

reactions() - Method in class org.openscience.cdk.ReactionSet

Get an iterator for this reaction set.

reactions() - Method in class org.openscience.cdk.silent.ReactionSet

Get an iterator for this reaction set.

ReactionSceneGenerator - Class in org.openscience.cdk.renderer.generators

Generator for general reaction scene components.

ReactionSceneGenerator() - Constructor for class org.openscience.cdk.renderer.generators.ReactionSceneGenerator

ReactionSceneGenerator.ArrowHeadWidth - Class in org.openscience.cdk.renderer.generators

Double which indicates how wide the arrow head is in screen pixels.

ReactionSceneGenerator.ShowReactionBoxes - Class in org.openscience.cdk.renderer.generators

Boolean that indicates if boxes are drawn around the reaction.

ReactionScheme - Class in org.openscience.cdk

Classes that extends the definition of reaction to a scheme.

ReactionScheme() - 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

Deprecated.

Takes an object which subclasses IChemObject, e.g.Molecule, and will read this (from file, database, internet etc).

read(T) - Method in class org.openscience.cdk.io.MDLRXNV2000Reader

Takes an object which subclasses IChemObject, e.g.Molecule, and will read this (from file, database, internet etc).

read(T) - Method in class org.openscience.cdk.io.MDLRXNV3000Reader

read(T) - Method in class org.openscience.cdk.io.MDLV2000Reader

Takes an object which subclasses IChemObject, e.g.

read(T) - Method in class org.openscience.cdk.io.MDLV3000Reader

read(T) - Method in class org.openscience.cdk.io.Mol2Reader

read(T) - Method in class org.openscience.cdk.io.Mopac7Reader

read(T) - Method in class org.openscience.cdk.io.MoSSOutputReader

Read a IAtomContainerSet from the input source.

read(T) - Method in class org.openscience.cdk.io.PCCompoundASNReader

read(T) - Method in class org.openscience.cdk.io.PCCompoundXMLReader

read(T) - Method in class org.openscience.cdk.io.PCSubstanceXMLReader

read(T) - Method in class org.openscience.cdk.io.PDBReader

Takes an object which subclasses IChemObject, e.g.

read(T) - Method in class org.openscience.cdk.io.PMPReader

reads the content from a PMP input.

read(T) - Method in class org.openscience.cdk.io.rdf.CDKOWLReader

Reads an IChemObject of type "object" from input.

read(T) - Method in class org.openscience.cdk.io.RGroupQueryReader

Check input IChemObject and proceed to parse.

read(T) - Method in class org.openscience.cdk.io.ShelXReader

Read a ChemFile from input.

read(T) - Method in class org.openscience.cdk.io.SMILESReader

Reads the content from a XYZ input.

read(T) - Method in class org.openscience.cdk.io.VASPReader

read(T) - Method in class org.openscience.cdk.io.XYZReader

reads the content from a XYZ input.

read(T) - Method in class org.openscience.cdk.io.ZMatrixReader

Returns a IChemObject of type object bye reading from the input.

readAtomBlock(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.

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.

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).

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

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 (C_R) of a graph.

RelevantCycles(int[][]) - Constructor for class org.openscience.cdk.graph.RelevantCycles

Generate the relevant cycle basis for a graph.

REMARK - Static variable in class org.openscience.cdk.CDKConstants

A remark for a IChemObject.

remove(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(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(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(IAtom) - Method in class org.openscience.cdk.AtomContainer

Safely remove an atom from the container.

removeAtom(int) - Method in class org.openscience.cdk.AtomContainer

Safely remove an atom from the container.

removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Safely remove an atom from the container.

removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer

Safely remove an atom from the container.

removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Safely remove an atom from the container.

removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal

Safely remove an atom from the container.

removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer

Safely remove an atom from the container.

removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer

Safely remove an atom from the container.

removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugRing

Safely remove an atom from the container.

removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand

Safely remove an atom from the container.

removeAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Safely remove an atom from the container.

removeAtom(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Safely remove an atom from the container.

removeAtom(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Removes the given atom and all connected electronContainers from the AtomContainer.

removeAtom(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Safely remove an atom from the container.

removeAtom(IAtom) - Method in class org.openscience.cdk.sgroup.Sgroup

Remove an atom from this Sgroup.

removeAtom(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer

Safely remove an atom from the container.

removeAtom(int) - Method in class org.openscience.cdk.silent.AtomContainer

Safely remove an atom from the container.

removeAtomAndConnectedElectronContainers(IAtom) - Method in class org.openscience.cdk.AtomContainer

Deprecated.

removeAtomAndConnectedElectronContainers(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Deprecated.

Method has be renamed IAtomContainer.removeAtom(IAtom).

removeAtomAndConnectedElectronContainers(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Deprecated.

removeAtomAndConnectedElectronContainers(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer

Deprecated.

removeAtomAndConnectedElectronContainers(IAtomContainerSet, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator

removeAtomAndConnectedElectronContainers(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.

removeAtomOnly(int) - Method in class org.openscience.cdk.AtomContainer

Unsafely remove atom at index.

removeAtomOnly(IAtom) - Method in class org.openscience.cdk.AtomContainer

Unsafely remove atom.

removeAtomOnly(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Unsafely remove atom at index.

removeAtomOnly(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Unsafely remove atom.

removeAtomOnly(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer

Unsafely remove atom at index.

removeAtomOnly(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer

Unsafely remove atom.

removeAtomOnly(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Unsafely remove atom at index.

removeAtomOnly(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Unsafely remove atom.

removeAtomOnly(int) - Method in class org.openscience.cdk.debug.DebugCrystal

Unsafely remove atom at index.

removeAtomOnly(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal

Unsafely remove atom.

removeAtomOnly(int) - Method in class org.openscience.cdk.debug.DebugMonomer

Unsafely remove atom at index.

removeAtomOnly(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer

Unsafely remove atom.

removeAtomOnly(int) - Method in class org.openscience.cdk.debug.DebugPolymer

Unsafely remove atom at index.

removeAtomOnly(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer

Unsafely remove atom.

removeAtomOnly(int) - Method in class org.openscience.cdk.debug.DebugRing

Unsafely remove atom at index.

removeAtomOnly(IAtom) - Method in class org.openscience.cdk.debug.DebugRing

Unsafely remove atom.

removeAtomOnly(int) - Method in class org.openscience.cdk.debug.DebugStrand

Unsafely remove atom at index.

removeAtomOnly(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand

Unsafely remove atom.

removeAtomOnly(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Unsafely remove atom at index.

removeAtomOnly(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Unsafely remove atom.

removeAtomOnly(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Removes the atom at the given position from the AtomContainer.

removeAtomOnly(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Removes the given atom from the AtomContainer.

removeAtomOnly(int) - Method in class org.openscience.cdk.silent.AtomContainer

Unsafely remove atom at index.

removeAtomOnly(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer

Unsafely remove atom.

removeAtomVectors() - Method in class org.openscience.cdk.Vibration

Removes all atom vectors from this vibration.

removeBond(int) - Method in class org.openscience.cdk.AtomContainer

Removes the bond at the given position from the AtomContainer.

removeBond(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(IBond) - Method in class org.openscience.cdk.sgroup.Sgroup

Remove a bond from this Sgroup.

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.

removeHydrogensPreserveMultiplyBonded(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator

Deprecated.

AtomContainerManipulator.suppressHydrogens(org.openscience.cdk.interfaces.IAtomContainer) will now not removed bridging hydrogens by default

removeIsotope(IIsotope) - Method in class org.openscience.cdk.debug.DebugMolecularFormula

Removes the given isotope from the MolecularFormula.

removeIsotope(IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormula

Removes the given isotope from the MolecularFormula.

removeIsotope(IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormulaRange

Removes the given isotope from the MolecularFormulaExpand.

removeIsotope(IIsotope) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula

Removes the given isotope from the MolecularFormula.

removeIsotope(IIsotope) - Method in class org.openscience.cdk.silent.MolecularFormula

Removes the given isotope from the MolecularFormula.

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.ChemObject

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAtom

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAtomContainer

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAtomType

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugBond

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugChemFile

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugChemModel

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugChemObject

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugChemSequence

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugCrystal

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugElectronContainer

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugElement

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugIsotope

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugLonePair

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugMapping

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugMonomer

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugPolymer

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugReaction

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugReactionScheme

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugReactionSet

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugRing

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugSingleElectron

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugStrand

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugSubstance

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeListener(IChemObjectListener) - Method in interface org.openscience.cdk.interfaces.IChemObject

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.silent.ChemObject

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeLonePair(int) - Method in class org.openscience.cdk.AtomContainer

Removes the lone pair at the given position from the AtomContainer.

removeLonePair(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.

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.

removeValidator(IValidator) - Method in class org.openscience.cdk.validate.ValidatorEngine

RemovingSEofBMechanism - Class in org.openscience.cdk.reaction.mechanism

This mechanism extracts a single electron from a bonding orbital which located in an bond.

RemovingSEofBMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.RemovingSEofBMechanism

RemovingSEofNBMechanism - Class in org.openscience.cdk.reaction.mechanism

This mechanism extracts a single electron from a non-bonding orbital which located in a ILonePair container.

RemovingSEofNBMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.RemovingSEofNBMechanism

rendererModel - Variable in class org.openscience.cdk.renderer.AbstractRenderer

The renderer model is final as it is not intended to be replaced.

RendererModel - Class in org.openscience.cdk.renderer

Model for IRenderer that contains settings for drawing objects.

RendererModel() - Constructor for class org.openscience.cdk.renderer.RendererModel

Construct a renderer model with no parameters.

RendererModel.ColorHash - Class in org.openscience.cdk.renderer

The color hash is used to color substructures.

RendererModel.ExternalHighlightColor - Class in org.openscience.cdk.renderer

The color used to highlight external selections.

RendererModel.MarkedOutput - Class in org.openscience.cdk.renderer

If format supports it (e.g.

RendererModel.Padding - Class in org.openscience.cdk.renderer

Padding between molecules in a grid or row.

RendererModel.SelectionColor - Class in org.openscience.cdk.renderer

Color of a selection.

RendererModel.TitleColor - Class in org.openscience.cdk.renderer

Color of title text.

RendererModel.TitleFontScale - Class in org.openscience.cdk.renderer

Size of title font relative compared to atom symbols

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(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).

resetFlags(IAtomContainer) - Static method in class org.openscience.cdk.graph.PathTools

resetFlags(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor

resetVirtualCounts() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager

Reset the virtual counts.

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.

RHENIUM - Static variable in enum org.openscience.cdk.config.Elements

RHODIUM - Static variable in enum org.openscience.cdk.config.Elements

RIGHT - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

right() - Method in class org.openscience.cdk.isomorphism.matchers.Expr

Access the right sub-expression of this atom expression being tested.

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.

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.

ringFragments() - Method in class org.openscience.cdk.ringsearch.RingSearch

Extract the cyclic atom and bond fragments of the container.

RingGenerator - Class in org.openscience.cdk.renderer.generators

Generates just the aromatic indicators for rings : circles, or light-gray inner bonds, depending on the value of CDKStyleAromaticity.

RingGenerator() - Constructor for class org.openscience.cdk.renderer.generators.RingGenerator

Make a generator for ring elements.

RingGenerator.CDKStyleAromaticity - Class in org.openscience.cdk.renderer.generators

Depicts aromaticity of rings in the original CDK style.

RingGenerator.MaxDrawableAromaticRing - Class in org.openscience.cdk.renderer.generators

The maximum ring size for which an aromatic ring should be drawn.

RingGenerator.RingProportion - Class in org.openscience.cdk.renderer.generators

The proportion of a ring bounds to use to draw the ring.

RingGenerator.ShowAromaticity - Class in org.openscience.cdk.renderer.generators

Determines whether rings should be drawn with a circle if they are aromatic.

RingManipulator - Class in org.openscience.cdk.tools.manipulator

RingManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.RingManipulator

RingPartitioner - Class in org.openscience.cdk.ringsearch

Partitions a RingSet into RingSets of connected rings.

RingPartitioner() - Constructor for class org.openscience.cdk.ringsearch.RingPartitioner

RingPlacer - Class in org.openscience.cdk.layout

Class providing methods for generating coordinates for ring atoms.

RingPlacer() - Constructor for class org.openscience.cdk.layout.RingPlacer

The empty constructor.

RingProportion() - Constructor for class org.openscience.cdk.renderer.generators.RingGenerator.RingProportion

RingSearch - Class in org.openscience.cdk.ringsearch

Efficiently search for atoms that are members of a ring.

RingSearch(IAtomContainer) - Constructor for class org.openscience.cdk.ringsearch.RingSearch

Create a new RingSearch for the specified container.

RingSearch(IAtomContainer, int[][]) - Constructor for class org.openscience.cdk.ringsearch.RingSearch

Create a new RingSearch for the specified container and graph.

RingSearch(IAtomContainer, CyclicVertexSearch) - Constructor for class org.openscience.cdk.ringsearch.RingSearch

Create a new RingSearch for the specified container using the provided search.

ringSet - Variable in class org.openscience.cdk.ChemModel

A RingSet.

ringSet - Variable in class org.openscience.cdk.renderer.generators.BasicBondGenerator

Necessary for calculating inner-ring bond elements.

RingSet - 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.

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

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 - 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.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.

RssWriter - Class in org.openscience.cdk.io

Generates an RSS feed.

RssWriter() - Constructor for class org.openscience.cdk.io.RssWriter

RUBIDIUM - Static variable in enum org.openscience.cdk.config.Elements

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

RUTHERFORDIUM - Static variable in enum org.openscience.cdk.config.Elements

S

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.

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

scaffold(IAtomContainer) - Static method in class org.openscience.cdk.fragment.MurckoFragmenter

Computes the Murcko Scaffold for the provided molecule in linear time.

Scale() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.Scale

scaleMolecule(IAtomContainer, double[], 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

SDFFormat - Class in org.openscience.cdk.io.formats

See here.

SDFFormat() - Constructor for class org.openscience.cdk.io.formats.SDFFormat

SDFWriter - Class in org.openscience.cdk.io

Writes MDL SD files ((Dalby, A. et. al.. Journal of Chemical Information and Computer Sciences. 1992. 32)).

SDFWriter(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

SEABORGIUM - Static variable in enum org.openscience.cdk.config.Elements

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.

secondPointX - Variable in class org.openscience.cdk.renderer.elements.LineElement

The x-coordinate of the second point.

secondPointY - Variable in class org.openscience.cdk.renderer.elements.LineElement

The y-coordinate of the second point.

select(IChemModel) - Method in class org.openscience.cdk.renderer.selection.AbstractSelection

Perform a selection by some method.

select(IChemModel) - Method in interface org.openscience.cdk.renderer.selection.IChemObjectSelection

Perform a selection by some method.

SelectionColor() - Constructor for class org.openscience.cdk.renderer.RendererModel.SelectionColor

SelectionVisibility - Class in org.openscience.cdk.renderer.generators.standard

Extended existing symbol visibility options to account for selection of atoms in the standard generator.

SELENIUM - Static variable in enum org.openscience.cdk.config.Elements

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(Expr) - Method in class org.openscience.cdk.isomorphism.matchers.Expr

Set this expression to another (shallow copy).

set(Class<T>, U) - Method in class org.openscience.cdk.renderer.RendererModel

Sets the IGeneratorParameter for the active IRenderer.

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.

setAllStructure(boolean) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph

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

setArrayValue(double[][]) - Method in class org.openscience.cdk.graph.invariant.GIMatrix

Resets the value of the matrix to the given array of double numbers.

setAsPermutation(int) - Method in class org.openscience.cdk.group.Partition

Fill the elements of a permutation from the first element of each cell, up to the point upTo.

setAtom(int, IAtom) - Method in class org.openscience.cdk.AtomContainer

Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().

setAtom(IAtom, int) - Method in class org.openscience.cdk.Bond

Sets an Atom in this bond.

setAtom(IAtom, int) - Method in class org.openscience.cdk.BondRef

Sets an Atom in this bond.

setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().

setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer

Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().

setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().

setAtom(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

Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().

setAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugLonePair

Sets the associated Atom.

setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer

Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().

setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer

Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().

setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugRing

Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().

setAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugSingleElectron

Sets the associated Atom.

setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugStrand

Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().

setAtom(int, IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().

setAtom(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

Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().

setAtom(IAtom, int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond

Sets an atom in this query bond.

setAtom(IAtom) - Method in class org.openscience.cdk.LonePair

Sets the associated Atom.

setAtom(int, IAtom) - Method in class org.openscience.cdk.silent.AtomContainer

Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().

setAtom(IAtom, 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.

setAtomCheckRadius(double) - Method in class org.openscience.cdk.protein.ProteinPocketFinder

setAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.structgen.SingleStructureRandomGenerator

Sets the AtomContainer attribute of the SingleStructureRandomGenerator object.

setAtomicNumber(Integer) - Method in class org.openscience.cdk.AtomRef

Sets the atomic number of this element.

setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugAtom

Sets the atomic number of this element.

setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugAtomType

Sets the atomic number of this element.

setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugElement

Sets the atomic number of this element.

setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Sets the atomic number of this element.

setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugIsotope

Sets the atomic number of this element.

setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Sets the atomic number of this element.

setAtomicNumber(Integer) - Method in class org.openscience.cdk.Element

Sets the atomic number of this element.

setAtomicNumber(Integer) - Method in interface org.openscience.cdk.interfaces.IElement

Sets the atomic number of this element.

setAtomicNumber(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Sets the atomic number of this element.

setAtomicNumber(Integer) - Method in class org.openscience.cdk.silent.Element

Sets the atomic number of this element.

setAtomPlacer(AtomPlacer) - Method in class org.openscience.cdk.layout.RingPlacer

setAtomProperties(IAtomContainer, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator

Sets a property on all Atoms in the given container.

setAtomProperties(IAtomContainerSet, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator

setAtomProperties(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.BondRef

Sets the array of atoms making up this bond.

setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Sets the array of atoms of this AtomContainer.

setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugAtomContainer

Sets the array of atoms of this AtomContainer.

setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Sets the array of atoms of this AtomContainer.

setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugBond

Sets the array of atoms making up this bond.

setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugCrystal

Sets the array of atoms of this AtomContainer.

setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugMonomer

Sets the array of atoms of this AtomContainer.

setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugPolymer

Sets the array of atoms of this AtomContainer.

setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugRing

Sets the array of atoms of this AtomContainer.

setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugStrand

Sets the array of atoms of this AtomContainer.

setAtoms(IAtom[]) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Sets the array of atoms of this AtomContainer.

setAtoms(IAtom[]) - Method in interface org.openscience.cdk.interfaces.IBond

Sets the array of atoms making up this bond.

setAtoms(IAtom[]) - Method in class org.openscience.cdk.isomorphism.matchers.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.silent.AtomContainer

Sets the array of atoms of this AtomContainer.

setAtoms(IAtom[]) - Method in class org.openscience.cdk.silent.Bond

Sets the array of atoms making up this bond.

setAtomTypeName(String) - Method in class org.openscience.cdk.AtomRef

Sets the if attribute of the AtomType object.

setAtomTypeName(String) - Method in class org.openscience.cdk.AtomType

Sets the if attribute of the AtomType object.

setAtomTypeName(String) - Method in class org.openscience.cdk.debug.DebugAtom

Sets the if attribute of the AtomType object.

setAtomTypeName(String) - Method in class org.openscience.cdk.debug.DebugAtomType

Sets the if attribute of the AtomType object.

setAtomTypeName(String) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Sets the if attribute of the AtomType object.

setAtomTypeName(String) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Sets the if attribute of the AtomType object.

setAtomTypeName(String) - Method in interface org.openscience.cdk.interfaces.IAtomType

Sets the if attribute of the AtomType object.

setAtomTypeName(String) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Sets the if attribute of the AtomType object.

setAtomTypeName(String) - Method in class org.openscience.cdk.silent.AtomType

Sets the if attribute of the AtomType object.

setAtomTypes(List<IAtomType>) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator

Sets the atomTypes attribute of the ForceFieldConfigurator object

setAttachPointNum(int) - Method in interface org.openscience.cdk.interfaces.IPseudoAtom

Set the attachment point number.

setAttachPointNum(int) - Method in class org.openscience.cdk.PseudoAtom

Set the attachment point number.

setAttachPointNum(int) - Method in class org.openscience.cdk.silent.PseudoAtom

Set the attachment point number.

setB(Vector3d) - Method in class org.openscience.cdk.Crystal

Sets the B unit cell axes in Cartesian coordinates.

setB(Vector3d) - Method in class org.openscience.cdk.debug.DebugCrystal

Sets the B unit cell axes in Cartesian coordinates.

setB(Vector3d) - Method in interface org.openscience.cdk.interfaces.ICrystal

Sets the B unit cell axes in carthesian coordinates.

setB(Vector3d) - Method in class org.openscience.cdk.silent.Crystal

Sets the B unit cell axes in Cartesian coordinates.

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

setBondLength(double) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

Deprecated.

use GeometryUtil.scaleMolecule(IAtomContainer, double)

setBondOrderSum(Double) - Method in class org.openscience.cdk.AtomRef

Sets the the exact bond order sum attribute of the AtomType object.

setBondOrderSum(Double) - Method in class org.openscience.cdk.AtomType

Sets the the exact bond order sum attribute of the AtomType object.

setBondOrderSum(Double) - Method in class org.openscience.cdk.debug.DebugAtom

Sets the the exact bond order sum attribute of the AtomType object.

setBondOrderSum(Double) - Method in class org.openscience.cdk.debug.DebugAtomType

Sets the the exact bond order sum attribute of the AtomType object.

setBondOrderSum(Double) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Sets the the exact bond order sum attribute of the AtomType object.

setBondOrderSum(Double) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Sets the the exact bond order sum attribute of the AtomType object.

setBondOrderSum(Double) - Method in interface org.openscience.cdk.interfaces.IAtomType

Sets the the exact bond order sum attribute of the AtomType object.

setBondOrderSum(Double) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Sets the the exact bond order sum attribute of the AtomType object.

setBondOrderSum(Double) - Method in class org.openscience.cdk.silent.AtomType

Sets the the exact bond order sum attribute of the AtomType object.

setBonds(IBond[]) - Method in class org.openscience.cdk.AtomContainer

Sets the array of bonds of this AtomContainer.

setBonds(IBond[]) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Sets the array of bonds of this AtomContainer.

setBonds(IBond[]) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Sets the array of bonds of this AtomContainer.

setBonds(IBond[]) - Method in class org.openscience.cdk.silent.AtomContainer

Sets the array of bonds of this AtomContainer.

setBuilder(IChemObjectBuilder) - Method in class org.openscience.cdk.stereo.DoubleBondStereochemistry

setBuilder(IChemObjectBuilder) - Method in class org.openscience.cdk.stereo.TetrahedralChirality

setC(Vector3d) - Method in class org.openscience.cdk.Crystal

Sets the C unit cell axes in Cartesian coordinates.

setC(Vector3d) - Method in class org.openscience.cdk.debug.DebugCrystal

Sets the C unit cell axes in Cartesian coordinates.

setC(Vector3d) - Method in interface org.openscience.cdk.interfaces.ICrystal

Sets the C unit cell axes in carthesian coordinates.

setC(Vector3d) - Method in class org.openscience.cdk.silent.Crystal

Sets the C unit cell axes in Cartesian coordinates.

setChainID(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom

set the Chain identifier of this atom.

setChainID(String) - Method in class org.openscience.cdk.debug.DebugPDBMonomer

Sets the Chain ID of this monomer.

setChainID(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom

set the Chain identifier of this atom.

setChainID(String) - Method in interface org.openscience.cdk.interfaces.IPDBMonomer

Sets the Chain ID of this monomer.

setChainID(String) - Method in class org.openscience.cdk.protein.data.PDBAtom

set the Chain identifier of this atom.

setChainID(String) - Method in class org.openscience.cdk.protein.data.PDBMonomer

setChainID(String) - Method in class org.openscience.cdk.silent.PDBAtom

set the Chain identifier of this atom.

setChainID(String) - Method in class org.openscience.cdk.silent.PDBMonomer

setCharge(Double) - Method in class org.openscience.cdk.Atom

Sets the partial charge of this atom.

setCharge(Double) - Method in class org.openscience.cdk.AtomRef

Sets the partial charge of this atom.

setCharge(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.

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.

setColumn(int, GIMatrix) - Method in class org.openscience.cdk.graph.invariant.GIMatrix

Sets the column of the matrix at the specified index to a new value.

setComputeRingFragments(boolean) - Method in class org.openscience.cdk.fragment.MurckoFragmenter

Sets whether to calculate ring fragments (true by default).

setConfigOrder(int) - Method in interface org.openscience.cdk.interfaces.IStereoElement

Set the configuration order of the stereochemistry.

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.

setCovalentRadius(Double) - Method in class org.openscience.cdk.AtomRef

Sets the covalent radius for this AtomType.

setCovalentRadius(Double) - Method in class org.openscience.cdk.AtomType

Sets the covalent radius for this AtomType.

setCovalentRadius(Double) - Method in class org.openscience.cdk.debug.DebugAtom

Sets the covalent radius for this AtomType.

setCovalentRadius(Double) - Method in class org.openscience.cdk.debug.DebugAtomType

Sets the covalent radius for this AtomType.

setCovalentRadius(Double) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Sets the covalent radius for this AtomType.

setCovalentRadius(Double) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Sets the covalent radius for this AtomType.

setCovalentRadius(Double) - Method in interface org.openscience.cdk.interfaces.IAtomType

Sets the covalent radius for this AtomType.

setCovalentRadius(Double) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Sets the covalent radius for this AtomType.

setCovalentRadius(Double) - Method in class org.openscience.cdk.silent.AtomType

Sets the covalent radius for this AtomType.

setCreator(String) - Method in class org.openscience.cdk.io.RssWriter

setCreatormap(Map) - Method in class org.openscience.cdk.io.RssWriter

setCrystal(ICrystal) - Method in class org.openscience.cdk.ChemModel

Sets the Crystal contained in this ChemModel.

setCrystal(ICrystal) - Method in class org.openscience.cdk.debug.DebugChemModel

Sets the Crystal contained in this ChemModel.

setCrystal(ICrystal) - Method in interface org.openscience.cdk.interfaces.IChemModel

Sets the Crystal contained in this ChemModel.

setCrystal(ICrystal) - Method in class org.openscience.cdk.silent.ChemModel

Sets the Crystal contained in this ChemModel.

setCurr(long) - Method in class org.openscience.cdk.smiles.InvPair

Set the value of the seed.

setDatemap(Map) - Method in class org.openscience.cdk.io.RssWriter

setDebugEnabled(boolean) - Method in class org.openscience.cdk.tools.SystemOutLoggingTool

Deprecated.

use SystemOutLoggingTool.setLevel(int)

setDefaultReactions() - Method in class org.openscience.cdk.tools.StructureResonanceGenerator

Set the default reactions that must be presents to generate the resonance.

setDefinition(String) - Method in class org.openscience.cdk.dict.Entry

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.

setDocumentProperty(String, String) - Method in class org.openscience.cdk.io.iterator.event.EventCMLHandler

Procedure required by the CDOInterface.

setDrawCenter(double, double) - Method in class org.openscience.cdk.renderer.AbstractRenderer

Set the point on the screen to draw the diagram.

setElectronCount(Integer) - Method in class org.openscience.cdk.BondRef

Sets the number of electrons in this electron container.

setElectronCount(Integer) - Method in class org.openscience.cdk.debug.DebugBond

Sets the number of electrons in this electron container.

setElectronCount(Integer) - Method in class org.openscience.cdk.debug.DebugElectronContainer

Sets the number of electrons in this electron container.

setElectronCount(Integer) - Method in class org.openscience.cdk.debug.DebugLonePair

Sets the number of electrons in this electron container.

setElectronCount(Integer) - Method in class org.openscience.cdk.debug.DebugSingleElectron

Sets the number of electrons in this electron container.

setElectronCount(Integer) - Method in class org.openscience.cdk.ElectronContainer

Sets the number of electrons in this electron container.

setElectronCount(Integer) - Method in interface org.openscience.cdk.interfaces.IElectronContainer

Sets the number of electrons in this electron container.

setElectronCount(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond

Sets the number of electrons in this bond

setElectronCount(Integer) - Method in class org.openscience.cdk.silent.ElectronContainer

Sets the number of electrons in this electron container.

setEnabled(String, boolean) - Method in class org.openscience.cdk.depict.Abbreviations

Set whether an abbreviation is enabled or disabled.

setEndChainID(Character) - Method in class org.openscience.cdk.debug.DebugPDBStructure

set the ending Chain identifier of this structure.

setEndChainID(Character) - Method in interface org.openscience.cdk.interfaces.IPDBStructure

set the ending Chain identifier of this structure.

setEndChainID(Character) - Method in class org.openscience.cdk.protein.data.PDBStructure

set the ending Chain identifier of this structure.

setEndChainID(Character) - Method in class org.openscience.cdk.silent.PDBStructure

set the ending Chain identifier of this structure.

setEndInsertionCode(Character) - Method in class org.openscience.cdk.debug.DebugPDBStructure

set the ending Code for insertion of residues of this structure.

setEndInsertionCode(Character) - Method in interface org.openscience.cdk.interfaces.IPDBStructure

set the ending Code for insertion of residues of this structure.

setEndInsertionCode(Character) - Method in class org.openscience.cdk.protein.data.PDBStructure

set the ending Code for insertion of residues of this structure.

setEndInsertionCode(Character) - Method in class org.openscience.cdk.silent.PDBStructure

set the ending Code for insertion of residues of this structure.

setEndSequenceNumber(Integer) - Method in class org.openscience.cdk.debug.DebugPDBStructure

set the ending sequence number of this structure.

setEndSequenceNumber(Integer) - Method in interface org.openscience.cdk.interfaces.IPDBStructure

set the ending sequence number of this structure.

setEndSequenceNumber(Integer) - Method in class org.openscience.cdk.protein.data.PDBStructure

set the ending sequence number of this structure.

setEndSequenceNumber(Integer) - Method in class org.openscience.cdk.silent.PDBStructure

set the ending sequence number of this structure.

setErrorHandler(IChemObjectReaderErrorHandler) - Method in class org.openscience.cdk.io.DefaultChemObjectReader

Sets an error handler that is sent events when file format issues occur.

setErrorHandler(IChemObjectReaderErrorHandler) - Method in interface org.openscience.cdk.io.IChemObjectReader

Sets an error handler that is sent events when file format issues occur.

setErrorHandler(IChemObjectReaderErrorHandler) - Method in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader

Sets an error handler that is sent events when file format issues occur.

setExactMass(Double) - Method in class org.openscience.cdk.AtomRef

Sets the ExactMass attribute of the Isotope object.

setExactMass(Double) - Method in class org.openscience.cdk.debug.DebugAtom

Sets the ExactMass attribute of the Isotope object.

setExactMass(Double) - Method in class org.openscience.cdk.debug.DebugAtomType

Sets the ExactMass attribute of the Isotope object.

setExactMass(Double) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Sets the ExactMass attribute of the Isotope object.

setExactMass(Double) - Method in class org.openscience.cdk.debug.DebugIsotope

Sets the ExactMass attribute of the Isotope object.

setExactMass(Double) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Sets the ExactMass attribute of the Isotope object.

setExactMass(Double) - Method in class org.openscience.cdk.FragmentAtom

setExactMass(Double) - Method in interface org.openscience.cdk.interfaces.IIsotope

Sets the ExactMass attribute of the Isotope object.

setExactMass(Double) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Sets the ExactMass attribute of the Isotope object.

setExactMass(Double) - Method in class org.openscience.cdk.Isotope

Sets the ExactMass attribute of the Isotope object.

setExactMass(Double) - Method in class org.openscience.cdk.silent.FragmentAtom

setExactMass(Double) - Method in class org.openscience.cdk.silent.Isotope

Sets the ExactMass attribute of the Isotope object.

setExpanded(boolean) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Sets whether this atom is to be fully drawn and not just in the abbreviated form.

setExpanded(boolean) - Method in class org.openscience.cdk.FragmentAtom

setExpanded(boolean) - Method in interface org.openscience.cdk.interfaces.IFragmentAtom

Sets whether this atom is to be fully drawn and not just in the abbreviated form.

setExpanded(boolean) - Method in class org.openscience.cdk.silent.FragmentAtom

setExpression(Expr) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Set the atom-expression predicate for this query atom.

setExpression(Expr) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond

Set the bond expression for this query bond.

setExtendGrid(double) - Method in class org.openscience.cdk.tools.GridGenerator

setExtension(BitSet) - Method in class org.openscience.cdk.isomorphism.mcss.RNode

Sets the extension attribute of the RNode object.

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.

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.

setForceFieldConfigurator(String, IChemObjectBuilder) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator

Constructor for the ForceFieldConfigurator object

setFormalCharge(Integer) - Method in class org.openscience.cdk.AtomRef

Sets the formal charge of this atom.

setFormalCharge(Integer) - Method in class org.openscience.cdk.AtomType

Sets the formal charge of this atom.

setFormalCharge(Integer) - Method in class org.openscience.cdk.debug.DebugAtom

Sets the formal charge of this atom.

setFormalCharge(Integer) - Method in class org.openscience.cdk.debug.DebugAtomType

Sets the formal charge of this atom.

setFormalCharge(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Sets the formal charge of this atom.

setFormalCharge(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Sets the formal charge of this atom.

setFormalCharge(Integer) - Method in interface org.openscience.cdk.interfaces.IAtomType

Sets the formal charge of this atom.

setFormalCharge(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Sets the formal charge of this atom.

setFormalCharge(Integer) - Method in class org.openscience.cdk.silent.AtomType

Sets the formal charge of this atom.

setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.AtomRef

Sets the formal neighbour count of this atom.

setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.AtomType

Sets the formal neighbour count of this atom.

setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.debug.DebugAtom

Sets the formal neighbour count of this atom.

setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.debug.DebugAtomType

Sets the formal neighbour count of this atom.

setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Sets the formal neighbour count of this atom.

setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Sets the formal neighbour count of this atom.

setFormalNeighbourCount(Integer) - Method in interface org.openscience.cdk.interfaces.IAtomType

Sets the formal neighbour count of this atom.

setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Sets the formal neighbour count of this atom.

setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.silent.AtomType

Sets the formal neighbour count of this atom.

setFormula(IMolecularFormula) - Method in class org.openscience.cdk.formula.IsotopeContainer

Set IMolecularFormula object of this container.

setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.Atom

Sets a point specifying the location of this atom in a Crystal unit cell.

setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.AtomRef

Sets a point specifying the location of this atom in a Crystal unit cell.

setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugAtom

Sets a point specifying the location of this atom in a Crystal unit cell.

setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Sets a point specifying the location of this atom in a Crystal unit cell.

setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Sets a point specifying the location of this atom in a Crystal unit cell.

setFractionalPoint3d(Point3d) - Method in interface org.openscience.cdk.interfaces.IAtom

Sets a point specifying the location of this atom in a Crystal unit cell.

setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Sets a point specifying the location of this atom in a Crystal unit cell.

setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.silent.Atom

Sets a point specifying the location of this atom in a Crystal unit cell.

setFragment(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Sets the fully expended form of the IFragmentAtom.

setFragment(IAtomContainer) - Method in class org.openscience.cdk.FragmentAtom

setFragment(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IFragmentAtom

Sets the fully expended form of the IFragmentAtom.

setFragment(IAtomContainer) - Method in class org.openscience.cdk.silent.FragmentAtom

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

setHetAtom(Boolean) - Method in class org.openscience.cdk.debug.DebugPDBAtom

Mark the atom as a heteroatom.

setHetAtom(Boolean) - Method in interface org.openscience.cdk.interfaces.IPDBAtom

Mark the atom as a heteroatom.

setHetAtom(Boolean) - Method in class org.openscience.cdk.protein.data.PDBAtom

setHetAtom(Boolean) - Method in class org.openscience.cdk.silent.PDBAtom

setHighlightedAtom(IAtom) - Method in class org.openscience.cdk.renderer.RendererModel

Sets the atom currently highlighted.

setHighlightedBond(IBond) - Method in class org.openscience.cdk.renderer.RendererModel

Sets the Bond currently highlighted.

setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.AtomRef

Sets the hybridization of this atom.

setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.AtomType

Sets the hybridization of this atom.

setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.debug.DebugAtom

Sets the hybridization of this atom.

setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.debug.DebugAtomType

Sets the hybridization of this atom.

setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Sets the hybridization of this atom.

setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Sets the hybridization of this atom.

setHybridization(IAtomType.Hybridization) - Method in interface org.openscience.cdk.interfaces.IAtomType

Sets the hybridization of this atom.

setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Sets the hybridization of this atom.

setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.silent.AtomType

Sets the hybridization of this atom.

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.

setId2(int) - Method in class org.openscience.cdk.isomorphism.mcss.RMap

Sets the id2 attribute of the RMap 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

setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.Atom

Sets the number of implicit hydrogen count of this atom.

setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.AtomRef

Sets the implicit hydrogen count of this atom.

setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.debug.DebugAtom

Sets the number of implicit hydrogen count of this atom.

setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Sets the number of implicit hydrogen count of this atom.

setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Sets the number of implicit hydrogen count of this atom.

setImplicitHydrogenCount(Integer) - Method in interface org.openscience.cdk.interfaces.IAtom

Sets the implicit hydrogen count of this atom.

setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Sets the number of implicit hydrogen count of this atom.

setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.silent.Atom

Sets the number of implicit hydrogen count of this atom.

setInchimap(Map) - Method in class org.openscience.cdk.io.RssWriter

setIndexCreated(boolean) - Method in class org.openscience.cdk.io.random.RandomAccessReader

setInputReader(Reader) - Method in class org.openscience.cdk.io.listener.TextGUIListener

Overwrites the default reader from which the input is taken.

setInputStream(InputStream) - Method in class org.openscience.cdk.config.CDKBasedAtomTypeConfigurator

Sets the file containing the configuration data.

setInputStream(InputStream) - Method in interface org.openscience.cdk.config.IAtomTypeConfigurator

Sets the file containing the configuration data.

setInputStream(InputStream) - Method in class org.openscience.cdk.config.OWLBasedAtomTypeConfigurator

Sets the file containing the configuration data.

setInputStream(InputStream) - Method in class org.openscience.cdk.config.TXTBasedAtomTypeConfigurator

Sets the file containing the configuration data.

setInputStream(InputStream) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator

Sets the inputStream attribute of the ForceFieldConfigurator object

setInputStream(InputStream) - Method in class org.openscience.cdk.modeling.builder3d.MM2BasedParameterSetReader

Sets the file containing the config data.

setInputStream(InputStream) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94BasedParameterSetReader

Sets the file containing the config data

setIntensity(double) - Method in class org.openscience.cdk.formula.IsotopeContainer

Set the intensity value of this container.

setIsAromatic(boolean) - Method in class org.openscience.cdk.Atom

Mark this atom as being aromatic.

setIsAromatic(boolean) - Method in class org.openscience.cdk.AtomRef

Mark this atom as being aromatic.

setIsAromatic(boolean) - Method in class org.openscience.cdk.Bond

Mark this bond as being aromatic.

setIsAromatic(boolean) - Method in class org.openscience.cdk.BondRef

Mark this bond as being aromatic.

setIsAromatic(boolean) - Method in interface org.openscience.cdk.interfaces.IAtom

Mark this atom as being aromatic.

setIsAromatic(boolean) - Method in interface org.openscience.cdk.interfaces.IBond

Mark this bond as being aromatic.

setIsAromatic(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Mark this atom as being aromatic.

setIsAromatic(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond

Mark this bond as being aromatic.

setIsAromatic(boolean) - Method in class org.openscience.cdk.silent.Atom

Mark this atom as being aromatic.

setIsAromatic(boolean) - Method in class org.openscience.cdk.silent.Bond

Mark this bond as being aromatic.

setIsInRing(boolean) - Method in class org.openscience.cdk.Atom

Mark this atom as being in a ring.

setIsInRing(boolean) - Method in class org.openscience.cdk.AtomRef

Mark this atom as being in a ring.

setIsInRing(boolean) - Method in class org.openscience.cdk.Bond

Mark this bond as being in a ring.

setIsInRing(boolean) - Method in class org.openscience.cdk.BondRef

Mark this bond as being in a ring.

setIsInRing(boolean) - Method in interface org.openscience.cdk.interfaces.IAtom

Mark this atom as being in a ring.

setIsInRing(boolean) - Method in interface org.openscience.cdk.interfaces.IBond

Mark this bond as being in a ring.

setIsInRing(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Mark this atom as being in a ring.

setIsInRing(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond

Mark this bond as being in a ring.

setIsInRing(boolean) - Method in class org.openscience.cdk.silent.Atom

Mark this atom as being in a ring.

setIsInRing(boolean) - Method in class org.openscience.cdk.silent.Bond

Mark this bond as being in a ring.

setLabel(String) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Sets the label of this PseudoAtom.

setLabel(String) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Sets the label of this PseudoAtom.

setLabel(String) - Method in class org.openscience.cdk.dict.Entry

setLabel(String) - Method in interface org.openscience.cdk.interfaces.IPseudoAtom

Sets the label of this PseudoAtom.

setLabel(String) - Method in class org.openscience.cdk.PseudoAtom

Sets the label of this PseudoAtom.

setLabel(String) - Method in class org.openscience.cdk.silent.PseudoAtom

Sets the label of this PseudoAtom.

setLast(long) - Method in class org.openscience.cdk.smiles.InvPair

setLatticeConstant(double) - Method in class org.openscience.cdk.protein.ProteinPocketFinder

setLatticeConstant(double) - Method in class org.openscience.cdk.tools.GridGenerator

setLevel(IOSetting.Importance) - Method in class org.openscience.cdk.io.listener.SwingGUIListener

setLevel(IOSetting.Importance) - Method in class org.openscience.cdk.io.listener.TextGUIListener

setLevel(int) - Method in interface org.openscience.cdk.tools.ILoggingTool

Set the level of this logger.

setLevel(int) - Method in class org.openscience.cdk.tools.LoggingTool

Set the level of this logger.

setLevel(int) - Method in class org.openscience.cdk.tools.SystemOutLoggingTool

Set the level of this logger.

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

setLoggingToolClass(Class<? extends ILoggingTool>) - Static method in class org.openscience.cdk.tools.LoggingToolFactory

Sets the ILoggingTool implementation to be used.

setLogical(Expr.Type, Expr, Expr) - Method in class org.openscience.cdk.isomorphism.matchers.Expr

Set the logical value of this atom expression.

setMass(double) - Method in class org.openscience.cdk.formula.IsotopeContainer

Set the mass value of this container.

setMassNumber(Integer) - Method in class org.openscience.cdk.AtomRef

Sets the atomic mass of this element.

setMassNumber(Integer) - Method in class org.openscience.cdk.debug.DebugAtom

Sets the atomic mass of this element.

setMassNumber(Integer) - Method in class org.openscience.cdk.debug.DebugAtomType

Sets the atomic mass of this element.

setMassNumber(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Sets the atomic mass of this element.

setMassNumber(Integer) - Method in class org.openscience.cdk.debug.DebugIsotope

Sets the atomic mass of this element.

setMassNumber(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Sets the atomic mass of this element.

setMassNumber(Integer) - Method in interface org.openscience.cdk.interfaces.IIsotope

Sets the atomic mass of this element.

setMassNumber(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Sets the atomic mass of this element.

setMassNumber(Integer) - Method in class org.openscience.cdk.Isotope

Sets the atomic mass of this element.

setMassNumber(Integer) - Method in class org.openscience.cdk.silent.Isotope

Sets the atomic mass of this element.

setMatchingAtoms(int[]) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom

Set the atoms of a target molecule that correspond to this group.

setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.AtomRef

Sets the MaxBondOrder attribute of the AtomType object.

setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.AtomType

Sets the MaxBondOrder attribute of the AtomType object.

setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.debug.DebugAtom

Sets the MaxBondOrder attribute of the AtomType object.

setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.debug.DebugAtomType

Sets the MaxBondOrder attribute of the AtomType object.

setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Sets the MaxBondOrder attribute of the AtomType object.

setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Sets the MaxBondOrder attribute of the AtomType object.

setMaxBondOrder(IBond.Order) - Method in interface org.openscience.cdk.interfaces.IAtomType

Sets the MaxBondOrder attribute of the AtomType object.

setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Sets the MaxBondOrder attribute of the AtomType object.

setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.silent.AtomType

Sets the MaxBondOrder attribute of the AtomType object.

setMaxGasteigerDamp(double) - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges

Sets the maxGasteigerDamp attribute of the GasteigerMarsiliPartialCharges object.

setMaxGasteigerIters(double) - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges

Sets the maxGasteigerIters attribute of the GasteigerMarsiliPartialCharges object.

setMaxGasteigerIters(int) - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges

Sets the maxGasteigerIters attribute of the GasteigerPEPEPartialCharges object.

setMaximalStructures(int) - Method in class org.openscience.cdk.tools.StructureResonanceGenerator

Set the number maximal of resonance structures to be found.

setMaxIteration(int) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph

Sets the maxIteration for the RGraph parsing.

setMaxIterations(int) - Method in class org.openscience.cdk.charges.Electronegativity

set the maximum number of Iterations.

setMaxIterations(int) - Method in class org.openscience.cdk.charges.PiElectronegativity

set the maximum number of Iterations.

setMaxResonStruc(int) - Method in class org.openscience.cdk.charges.Electronegativity

set the maximum number of resonance structures.

setMaxResonStruc(int) - Method in class org.openscience.cdk.charges.PiElectronegativity

set the maximum number of resonance structures.

setMaxResoStruc(int) - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges

Sets the maximum resonance structures to be searched.

setMechanism(String) - Method in class org.openscience.cdk.dict.EntryReact

Set the mechanism of this reaction.

setMinimumFragmentSize(int) - Method in class org.openscience.cdk.fragment.ExhaustiveFragmenter

Set the minimum fragment size.

setMinIntensity(double) - Method in class org.openscience.cdk.formula.IsotopePatternGenerator

Set the minimum (normalised) intensity to generate.

setMinPSCluster(int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder

setMinPSPocket(int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder

setMinResolution(double) - Method in class org.openscience.cdk.formula.IsotopePatternGenerator

Set the minimum resolution at which peaks within this mass difference should be considered equivalent.

setMM2Parameters(IChemObjectBuilder) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator

Sets the parameters attribute of the ForceFieldConfigurator object, default is mm2 force field

setMMFF94Parameters(IChemObjectBuilder) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator

setMode(int) - Method in class org.openscience.cdk.smarts.SmartsFragmentExtractor

Set the mode of SMARTS substructure selection

setModelCenter(double, double) - Method in class org.openscience.cdk.renderer.AbstractRenderer

Set the position of the center of the model.

setMolecule(IAtomContainer) - Method in class org.openscience.cdk.layout.AtomPlacer

Sets the molecule the AtomPlacer currently works with

setMolecule(IAtomContainer) - Method in class org.openscience.cdk.layout.RingPlacer

setMolecule(IAtomContainer, 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.libio.md.Residue

setName(String) - Method in class org.openscience.cdk.protein.data.PDBAtom

set the Atom name of this atom.

setName(String) - Method in class org.openscience.cdk.silent.PDBAtom

set the Atom name of this atom.

setNaturalAbundance(Double) - Method in class org.openscience.cdk.AtomRef

Sets the NaturalAbundance attribute of the Isotope object.

setNaturalAbundance(Double) - Method in class org.openscience.cdk.debug.DebugAtom

Sets the NaturalAbundance attribute of the Isotope object.

setNaturalAbundance(Double) - Method in class org.openscience.cdk.debug.DebugAtomType

Sets the NaturalAbundance attribute of the Isotope object.

setNaturalAbundance(Double) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Sets the NaturalAbundance attribute of the Isotope object.

setNaturalAbundance(Double) - Method in class org.openscience.cdk.debug.DebugIsotope

Sets the NaturalAbundance attribute of the Isotope object.

setNaturalAbundance(Double) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Sets the NaturalAbundance attribute of the Isotope object.

setNaturalAbundance(Double) - Method in interface org.openscience.cdk.interfaces.IIsotope

Sets the NaturalAbundance attribute of the Isotope object.

setNaturalAbundance(Double) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Sets the NaturalAbundance attribute of the Isotope object.

setNaturalAbundance(Double) - Method in class org.openscience.cdk.Isotope

Sets the NaturalAbundance attribute of the Isotope object.

setNaturalAbundance(Double) - Method in class org.openscience.cdk.silent.Isotope

Sets the NaturalAbundance attribute of the Isotope object.

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.

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.SymbolChargeIDQueryAtom

setOrder(IBond.Order) - Method in class org.openscience.cdk.Bond

Sets the bond order of this bond.

setOrder(IBond.Order) - Method in class org.openscience.cdk.BondRef

Sets the bond order of this bond.

setOrder(IBond.Order) - Method in class org.openscience.cdk.debug.DebugBond

Sets the bond order of this bond.

setOrder(IBond.Order) - Method in interface org.openscience.cdk.interfaces.IBond

Sets the bond order of this bond.

setOrder(IBond.Order) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond

Sets the bond order of this query bond.

setOrder(IBond.Order) - Method in class org.openscience.cdk.silent.Bond

Sets the bond order of this bond.

setOutputWriter(Writer) - Method in class org.openscience.cdk.io.listener.PropertiesListener

Overwrites the default writer to which the output is directed.

setOutputWriter(Writer) - Method in class org.openscience.cdk.io.listener.TextGUIListener

Overwrites the default writer to which the output is directed.

setOverrideBondWidth(double) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator

Set the width to use for all bonds, overriding any standard bond widths.

setOverrideColor(Color) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator

Set the color to use for all bonds, overriding the standard bond colors.

setOxt(Boolean) - Method in class org.openscience.cdk.debug.DebugPDBAtom

Change the state of this atom in being the PDB OXT atom.

setOxt(Boolean) - Method in interface org.openscience.cdk.interfaces.IPDBAtom

Change the state of this atom in being the PDB OXT atom.

setOxt(Boolean) - Method in class org.openscience.cdk.protein.data.PDBAtom

setOxt(Boolean) - Method in class org.openscience.cdk.silent.PDBAtom

setParameter(boolean) - Method in interface org.openscience.cdk.reaction.type.parameters.IParameterReact

Set the parameter to take account.

setParameter(boolean) - Method in class org.openscience.cdk.reaction.type.parameters.ParameterReact

Set the parameter to take account.

setParameterList(List<IParameterReact>) - Method in interface org.openscience.cdk.reaction.IReactionProcess

Sets the parameters for this reaction.

setParameterList(List<IParameterReact>) - Method in class org.openscience.cdk.reaction.ReactionEngine

Returns the current parameter Map for this reaction.

setParameters(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.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.molecular.AcidicGroupCountDescriptor

Sets the parameters for this descriptor.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor

Sets the parameters attribute of the AminoAcidsCountDescriptor object.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor

Sets the parameters attribute of the APolDescriptor object.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor

Sets the parameters attribute of the AromaticAtomsCountDescriptor object.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor

Sets the parameters attribute of the AromaticBondsCountDescriptor object.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor

Sets the parameters attribute of the AtomCountDescriptor object.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor

Sets the parameters for this descriptor.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor

Sets the parameters attribute of the BCUTDescriptor object.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor

Sets the parameters attribute of the BondCountDescriptor object

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor

Sets the parameters attribute of the BPolDescriptor object

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor

Sets the parameters attribute of the GravitationalIndexDescriptor object.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor

Sets the parameters attribute of the CPSADescriptor object.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor

Sets the parameters attribute of the EccentricConnectivityIndexDescriptor object

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor

Sets the parameters for this descriptor.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalCSP3Descriptor

Sets the parameters for this descriptor.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor

Sets the parameters for this descriptor.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor

Sets the parameters attribute of the FragmentComplexityDescriptor object.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor

Sets the parameters attribute of the GravitationalIndexDescriptor object.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor

Sets the parameters attribute of the HBondAcceptorCountDescriptor object.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor

Sets the parameter of this HBondDonorCountDescriptor instance.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor

Sets the parameters attribute of the HybridizationRatioDescriptor object.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor

Sets the parameters attribute of the KappaShapeIndicesDescriptor object

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor

Sets the parameters attribute of the descriptor.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor

Sets the parameters attribute of the LargestChain object.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor

Sets the parameters attribute of the LargestPiSystemDescriptor object.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor

Sets the parameters attribute of the PetitjeanNumberDescriptor object

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor

Sets the parameters attribute of the LongestAliphaticChainDescriptor object.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor

This IDescriptor does not have any parameters.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

Sets the parameters attribute of the WeightDescriptor object.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor

Sets the parameters attribute of the MomentOfInertiaDescriptor object.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor

Sets the parameters attribute of the PetitjeanNumberDescriptor object

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor

Sets the parameters attribute of the PetitjeanShapeIndexDescriptor object.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor

Sets the parameters attribute of the RotatableBondsCountDescriptor object

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor

Sets the parameters attribute of the RuleOfFiveDescriptor object.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor

Set parameters: ignored, there are none.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.SpiroAtomCountDescriptor

Sets the parameters for this descriptor.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor

Sets the parameters attribute of the TPSADescriptor object.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor

Sets the parameters for this descriptor.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor

Sets the parameters attribute of the VAdjMaDescriptor object

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor

Sets the parameters attribute of the WeightDescriptor object.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor

Sets the parameters attribute of the WeightedPathDescriptor object.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor

Sets the parameters attribute of the WHIMDescriptor object.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor

Sets the parameters attribute of the WienerNumbersDescriptor object.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor

Sets the parameters attribute of the XLogPDescriptor object.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor

Sets the parameters attribute of the ZagrebIndexDescriptor object.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor

Sets the parameters attribute of the TaeAminoAcidDescriptor object.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.substance.OxygenAtomCountDescriptor

Sets the parameters for this descriptor.

setParameters(Object[]) - Method in interface org.openscience.cdk.qsar.IDescriptor

Sets the parameters for this descriptor.

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

setPerceiveStereo(boolean) - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter

Sets whether stereochemistry should be re-perceived from 2D/3D coordinates.

setPerceiveStereo(boolean) - Method in class org.openscience.cdk.fingerprint.model.Bayesian

Sets whether stereochemistry should be re-perceived from 2D/3D coordinates.

setPermutation(int[]) - Method in class org.openscience.cdk.graph.Permutor

Set the currently used permutation.

setPharmacophoreQuery(PharmacophoreQuery) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher

Set a pharmacophore query.

setPocketSize(int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder

setPoint2d(Point2d) - Method in class org.openscience.cdk.Atom

Sets a point specifying the location of this atom in a 2D space.

setPoint2d(Point2d) - Method in class org.openscience.cdk.AtomRef

Sets a point specifying the location of this atom in a 2D space.

setPoint2d(Point2d) - Method in class org.openscience.cdk.debug.DebugAtom

Sets a point specifying the location of this atom in a 2D space.

setPoint2d(Point2d) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Sets a point specifying the location of this atom in a 2D space.

setPoint2d(Point2d) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Sets a point specifying the location of this atom in a 2D space.

setPoint2d(Point2d) - Method in interface org.openscience.cdk.interfaces.IAtom

Sets a point specifying the location of this atom in a 2D space.

setPoint2d(Point2d) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Sets a point specifying the location of this atom in a 2D space.

setPoint2d(Point2d) - Method in class org.openscience.cdk.silent.Atom

Sets a point specifying the location of this atom in a 2D space.

setPoint3d(Point3d) - Method in class org.openscience.cdk.Atom

Sets a point specifying the location of this atom in 3D space.

setPoint3d(Point3d) - Method in class org.openscience.cdk.AtomRef

Sets a point specifying the location of this atom in 3D space.

setPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugAtom

Sets a point specifying the location of this atom in 3D space.

setPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Sets a point specifying the location of this atom in 3D space.

setPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Sets a point specifying the location of this atom in 3D space.

setPoint3d(Point3d) - Method in interface org.openscience.cdk.interfaces.IAtom

Sets a point specifying the location of this atom in 3D space.

setPoint3d(Point3d) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Sets a point specifying the location of this atom in 3D space.

setPoint3d(Point3d) - Method in class org.openscience.cdk.silent.Atom

Sets a point specifying the location of this atom in 3D space.

setPrepare(boolean) - Method in class org.openscience.cdk.smarts.SmartsPattern

Sets whether the molecule should be "prepared" for a SMARTS match, including set ring flags and perceiving aromaticity.

setPreservingAromaticity(boolean) - Method in class org.openscience.cdk.smiles.SmilesParser

Deprecated.

setPrime() - Method in class org.openscience.cdk.smiles.InvPair

Sets the prime number based on the current seed.

setPrimitive(Expr.Type, int) - Method in class org.openscience.cdk.isomorphism.matchers.Expr

Set the primitive value of this atom expression.

setPrimitive(Expr.Type) - Method in class org.openscience.cdk.isomorphism.matchers.Expr

Set the primitive value of this atom expression.

setProductCoefficient(IAtomContainer, Double) - Method in class org.openscience.cdk.debug.DebugReaction

Sets the coefficient of a a product to a given value.

setProductCoefficient(IAtomContainer, Double) - Method in interface org.openscience.cdk.interfaces.IReaction

Sets the coefficient of a a product to a given value.

setProductCoefficient(IAtomContainer, Double) - Method in class org.openscience.cdk.Reaction

Sets the coefficient of a a product to a given value.

setProductCoefficient(IAtomContainer, Double) - Method in class org.openscience.cdk.silent.Reaction

Sets the coefficient of a a product to a given value.

setProductCoefficients(Double[]) - Method in class org.openscience.cdk.debug.DebugReaction

Sets the coefficient of the products.

setProductCoefficients(Double[]) - Method in interface org.openscience.cdk.interfaces.IReaction

Sets the coefficient of the products.

setProductCoefficients(Double[]) - Method in class org.openscience.cdk.Reaction

Sets the coefficient of the products.

setProductCoefficients(Double[]) - Method in class org.openscience.cdk.silent.Reaction

Sets the coefficient of the products.

setProducts(IAtomContainerSet) - Method in class org.openscience.cdk.debug.DebugReaction

Assigns a MoleculeSet to the products of this reaction.

setProducts(IAtomContainerSet) - Method in interface org.openscience.cdk.interfaces.IReaction

Assigns a IAtomContaineSet to the products of this reaction.

setProducts(IAtomContainerSet) - Method in class org.openscience.cdk.Reaction

Assigns a MoleculeSet to the products of this reaction.

setProducts(IAtomContainerSet) - Method in class org.openscience.cdk.silent.Reaction

Assigns a MoleculeSet to the products of this reaction.

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.ChemObject

Set the properties of this object to the provided map (shallow copy).

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugChemObject

Set the properties of this object to the provided map (shallow copy).

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugMolecularFormula

Sets the properties of this object.

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.formula.MolecularFormula

Sets the properties of this object.

setProperties(Map<Object, Object>) - Method in interface org.openscience.cdk.interfaces.IChemObject

Set the properties of this object to the provided map (shallow copy).

setProperties(Map<Object, Object>) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula

Sets the properties of this object.I should integrate into ChemObject.

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject

Set the properties of this object to the provided map (shallow copy).

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.silent.ChemObject

Set the properties of this object to the provided map (shallow copy).

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.silent.MolecularFormula

Sets the properties of this object.

setProperty(Object, Object) - Method in class org.openscience.cdk.ChemObject

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugAtom

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugAtomContainer

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugAtomType

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugBond

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugChemFile

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugChemModel

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugChemObject

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugChemSequence

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugCrystal

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugElectronContainer

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugElement

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugIsotope

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugLonePair

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugMapping

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugMolecularFormula

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugMonomer

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugPolymer

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugReaction

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugReactionScheme

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugReactionSet

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugRing

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugSingleElectron

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugStrand

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugSubstance

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.formula.MolecularFormula

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in interface org.openscience.cdk.interfaces.IChemObject

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.silent.ChemObject

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in class org.openscience.cdk.silent.MolecularFormula

Sets a property for a IChemObject.

setProtein(IBioPolymer) - Method in class org.openscience.cdk.protein.ProteinPocketFinder

setProteinInterior(int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder

setPublisher(String) - Method in class org.openscience.cdk.io.RssWriter

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.

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

Deprecated.

setReader(InputStream) - Method in class org.openscience.cdk.io.MDLRXNReader

Deprecated.

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

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

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

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.

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.

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.

setSolvantValue(int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder

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.BondRef

Sets the stereo descriptor for this bond.

setStereo(IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugBond

Sets the stereo descriptor for this bond.

setStereo(IBond.Stereo) - Method in interface org.openscience.cdk.interfaces.IBond

Sets the stereo descriptor for this bond.

setStereo(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

setStereoElements(List<IStereoElement>) - Method in class org.openscience.cdk.AtomContainer

Set the stereo elements - this will replace the existing instance with a new instance.

setStereoElements(List<IStereoElement>) - Method in class org.openscience.cdk.debug.DebugAtomContainer

Set the stereo elements - this will replace the existing instance with a new instance.

setStereoElements(List<IStereoElement>) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Set the stereo elements - this will replace the existing instance with a new instance.

setStereoElements(List<IStereoElement>) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

setStereoElements(List<IStereoElement>) - Method in class org.openscience.cdk.silent.AtomContainer

Set the stereo elements - this will replace the existing instance with a new instance.

setStereoParity(Integer) - Method in class org.openscience.cdk.Atom

Sets the stereo parity for this atom.

setStereoParity(Integer) - Method in class org.openscience.cdk.AtomRef

Sets the stereo parity for this atom.

setStereoParity(Integer) - Method in class org.openscience.cdk.debug.DebugAtom

Sets the stereo parity for this atom.

setStereoParity(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Dummy method: the stereo parity is undefined, final.

setStereoParity(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Dummy method: the stereo parity is undefined, final.

setStereoParity(Integer) - Method in interface org.openscience.cdk.interfaces.IAtom

Deprecated.

use IStereoElements for storing stereochemistry

setStereoParity(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Sets the stereo parity for this atom.

setStereoParity(Integer) - Method in class org.openscience.cdk.PseudoAtom

Dummy method: the stereo parity is undefined, final.

setStereoParity(Integer) - Method in class org.openscience.cdk.silent.Atom

Sets the stereo parity for this atom.

setStereoParity(Integer) - Method in class org.openscience.cdk.silent.PseudoAtom

Dummy method: the stereo parity is undefined, final.

setStoreFormulas(boolean) - Method in class org.openscience.cdk.formula.IsotopePatternGenerator

When generating the isotope containers store the MF for each IsotopeContainer.

setStrandName(String) - Method in class org.openscience.cdk.debug.DebugStrand

Sets the name of the Strand object.

setStrandName(String) - Method in interface org.openscience.cdk.interfaces.IStrand

Set the name of the Strand object.

setStrandName(String) - Method in class org.openscience.cdk.silent.Strand

Sets the name of the Strand object.

setStrandName(String) - Method in class org.openscience.cdk.Strand

Sets the name of the Strand object.

setStrandType(String) - Method in class org.openscience.cdk.debug.DebugStrand

Sets the type of the Strand object.

setStrandType(String) - Method in interface org.openscience.cdk.interfaces.IStrand

Set the type of the Strand object.

setStrandType(String) - Method in class org.openscience.cdk.silent.Strand

Sets the type of the Strand object.

setStrandType(String) - Method in class org.openscience.cdk.Strand

Sets the type of the Strand object.

setStructureType(String) - Method in class org.openscience.cdk.debug.DebugPDBStructure

set the Structure Type of this structure.

setStructureType(String) - Method in interface org.openscience.cdk.interfaces.IPDBStructure

set the Structure Type of this structure.

setStructureType(String) - Method in class org.openscience.cdk.protein.data.PDBStructure

set the Structure Type of this structure.

setStructureType(String) - Method in class org.openscience.cdk.silent.PDBStructure

set the Structure Type of this structure.

setSubgraph(List<Integer>) - Method in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph

setSubscript(String) - Method in class org.openscience.cdk.sgroup.Sgroup

Set the subscript value.

setSwitchingAtom(IAtom) - Method in class org.openscience.cdk.libio.md.ChargeGroup

setSymbol(String) - Method in class org.openscience.cdk.AtomRef

Sets the element symbol of this element.

setSymbol(String) - Method in class org.openscience.cdk.debug.DebugAtom

Sets the element symbol of this element.

setSymbol(String) - Method in class org.openscience.cdk.debug.DebugAtomType

Sets the element symbol of this element.

setSymbol(String) - Method in class org.openscience.cdk.debug.DebugElement

Sets the element symbol of this element.

setSymbol(String) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Sets the element symbol of this element.

setSymbol(String) - Method in class org.openscience.cdk.debug.DebugIsotope

Sets the element symbol of this element.

setSymbol(String) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Sets the element symbol of this element.

setSymbol(String) - Method in class org.openscience.cdk.Element

Sets the element symbol of this element.

setSymbol(String) - Method in interface org.openscience.cdk.interfaces.IElement

Sets the element symbol of this element.

setSymbol(String) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Sets the element symbol of this element.

setSymbol(String) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom

setSymbol(String) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryAtom

Sets the element symbol of this element.

setSymbol(String) - Method in class org.openscience.cdk.silent.Element

Sets the element symbol of this element.

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

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)

setTimezone(String) - Method in class org.openscience.cdk.io.RssWriter

setting - Variable in class org.openscience.cdk.io.setting.IOSetting

SettingManager<T extends ISetting> - Class in org.openscience.cdk.io.setting

Provides dynamic management of settings.

SettingManager() - Constructor for class org.openscience.cdk.io.setting.SettingManager

setTitle(String) - Method in class org.openscience.cdk.AtomContainer

Modify the title of the record.

setTitle(String) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Modify the title of the record.

setTitle(String) - Method in class org.openscience.cdk.io.RssWriter

setTitle(String) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

Modify the title of the record.

setTitle(String) - Method in class org.openscience.cdk.silent.AtomContainer

Modify the title of the record.

setTitlemap(Map) - Method in class org.openscience.cdk.io.RssWriter

setTo(Permutation) - Method in class org.openscience.cdk.group.Permutation

Alter a permutation by setting it to the values in the other permutation.

setToolTipTextMap(Map<IAtom, String>) - Method in class org.openscience.cdk.renderer.RendererModel

Sets the toolTipTextMap.

setTransform(AffineTransform) - Method in interface org.openscience.cdk.renderer.elements.IRenderingVisitor

Sets the affine transformations used.

setTransform(AffineTransform) - Method in class org.openscience.cdk.renderer.visitor.AbstractAWTDrawVisitor

Sets a new affine transformation to convert world coordinates into screen coordinates.

setType(SgroupType) - Method in class org.openscience.cdk.sgroup.Sgroup

Set the type of the Sgroup.

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.AtomRef

Sets the the exact electron valency of the AtomType object.

setValency(Integer) - Method in class org.openscience.cdk.AtomType

Sets the the exact electron valency of the AtomType object.

setValency(Integer) - Method in class org.openscience.cdk.debug.DebugAtom

Sets the the exact electron valency of the AtomType object.

setValency(Integer) - Method in class org.openscience.cdk.debug.DebugAtomType

Sets the the exact electron valency of the AtomType object.

setValency(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

Sets the the exact electron valency of the AtomType object.

setValency(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

Sets the the exact electron valency of the AtomType object.

setValency(Integer) - Method in interface org.openscience.cdk.interfaces.IAtomType

Sets the the exact electron valency of the AtomType object.

setValency(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom

Sets the the exact electron valency of the AtomType object.

setValency(Integer) - Method in class org.openscience.cdk.silent.AtomType

Sets the the exact electron valency of the AtomType object.

setValue(Object) - Method in interface org.openscience.cdk.reaction.type.parameters.IParameterReact

Set the value of the parameter.

setValue(Object) - Method in class org.openscience.cdk.reaction.type.parameters.ParameterReact

Set the value of the parameter.

setValue(T) - Method in interface org.openscience.cdk.renderer.generators.IGeneratorParameter

Sets the value for this parameter.

setValue(T) - Method in class org.openscience.cdk.renderer.generators.parameter.AbstractGeneratorParameter

Sets the value for this parameter.

setValueAt(int, int, double) - Method in class org.openscience.cdk.graph.invariant.GIMatrix

Sets the value of the element at the given index.

setVanDerWaalsFile(String) - Method in class org.openscience.cdk.protein.ProteinPocketFinder

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

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.

SgroupBracket(SgroupBracket) - Constructor for class org.openscience.cdk.sgroup.SgroupBracket

Copy constructor.

SgroupBracketDepth() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.SgroupBracketDepth

SgroupFontScale() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.SgroupFontScale

SgroupKey - Enum in org.openscience.cdk.sgroup

Keys for indexing common Sgroup attributes.

SgroupManipulator - Class in org.openscience.cdk.tools.manipulator

Utilities related to Ctab Sgroups.

SgroupType - Enum in org.openscience.cdk.sgroup

Enumeration of Ctab Sgroup types.

shallowCopy() - Method in class org.openscience.cdk.ChemObject

Clones this IChemObject, but preserves references to Objects.

shallowCopy() - Method in class org.openscience.cdk.silent.ChemObject

Clones this IChemObject, but preserves references to Objects.

shapeOf(Shape, Color) - Static method in class org.openscience.cdk.renderer.elements.GeneralPath

Create a filled path of the specified Java 2D Shape and color.

SharingAnionReaction - Class in org.openscience.cdk.reaction.type

IReactionProcess which participate in movement resonance.

SharingAnionReaction() - Constructor for class org.openscience.cdk.reaction.type.SharingAnionReaction

Constructor of the SharingAnionReaction object.

SharingChargeDBReaction - Class in org.openscience.cdk.reaction.type

IReactionProcess which participate in movement resonance.

SharingChargeDBReaction() - Constructor for class org.openscience.cdk.reaction.type.SharingChargeDBReaction

Constructor of the SharingChargeDBReaction object.

SharingChargeSBReaction - Class in org.openscience.cdk.reaction.type

IReactionProcess which participate in movement resonance.

SharingChargeSBReaction() - Constructor for class org.openscience.cdk.reaction.type.SharingChargeSBReaction

Constructor of the SharingChargeSBReaction object.

SharingElectronMechanism - Class in org.openscience.cdk.reaction.mechanism

This mechanism displaces the charge (lonePair) because of deficiency of charge.

SharingElectronMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.SharingElectronMechanism

SharingLonePairReaction - Class in org.openscience.cdk.reaction.type

IReactionProcess which participate in movement resonance.

SharingLonePairReaction() - Constructor for class org.openscience.cdk.reaction.type.SharingLonePairReaction

Constructor of the SharingLonePairReaction object.

SHEET - Static variable in class org.openscience.cdk.protein.data.PDBStructure

SHEET - Static variable in class org.openscience.cdk.silent.PDBStructure

ShelXFormat - Class in org.openscience.cdk.io.formats

See here.

ShelXFormat() - Constructor for class org.openscience.cdk.io.formats.ShelXFormat

ShelXReader - Class in org.openscience.cdk.io

A reader for ShelX output (RES) files.

ShelXReader(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, 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, 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.

ShowAromaticity() - Constructor for class org.openscience.cdk.renderer.generators.RingGenerator.ShowAromaticity

ShowAtomAtomMapping() - Constructor for class org.openscience.cdk.renderer.generators.MappingGenerator.ShowAtomAtomMapping

ShowAtomTypeNames() - Constructor for class org.openscience.cdk.renderer.generators.ExtendedAtomGenerator.ShowAtomTypeNames

showCarbon(IAtom, IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.AtomMassGenerator

Returns true if the mass number of this element is set and not equal the mass number of the most abundant isotope of this element.

showCarbon(IAtom, IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator

Checks a carbon atom to see if it should be shown.

ShowEndCarbons() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.ShowEndCarbons

ShowExplicitHydrogens() - Constructor for class org.openscience.cdk.renderer.generators.BasicAtomGenerator.ShowExplicitHydrogens

ShowImplicitHydrogens() - Constructor for class org.openscience.cdk.renderer.generators.ExtendedAtomGenerator.ShowImplicitHydrogens

ShowMoleculeTitle() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ShowMoleculeTitle

ShowReactionBoxes() - Constructor for class org.openscience.cdk.renderer.generators.ReactionSceneGenerator.ShowReactionBoxes

ShowReactionTitle() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ShowReactionTitle

ShowTooltip() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ShowTooltip

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.

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

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

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.

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() - 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.

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.

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

Smarts - Class in org.openscience.cdk.smarts

Parse and generate the SMARTS query language.

Smarts() - Constructor for class org.openscience.cdk.smarts.Smarts

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.

SmartsPattern - Class in org.openscience.cdk.smarts

A Pattern for matching a single SMARTS query against multiple target compounds.

SmiFlavor - Class in org.openscience.cdk.smiles

Flags for customising SMILES generation.

SMILES - Static variable in class org.openscience.cdk.CDKConstants

The Daylight SMILES.

SMILESFIXFormat - Class in org.openscience.cdk.io.formats

SMILESFIXFormat() - Constructor for class org.openscience.cdk.io.formats.SMILESFIXFormat

SMILESFormat - Class in org.openscience.cdk.io.formats

See here.

SMILESFormat() - Constructor for class org.openscience.cdk.io.formats.SMILESFormat

SmilesGenerator - Class in org.openscience.cdk.smiles

SMILES (Weininger, David. Journal of Chemical Information and Computer Sciences. 1988. 28, Weininger, David et. al.. Journal of Chemical Information and Computer Sciences. 1989. 29) provides a compact representation of chemical structures and reactions.

SmilesGenerator() - Constructor for class org.openscience.cdk.smiles.SmilesGenerator

Deprecated.

use SmilesGenerator.SmilesGenerator(int) configuring with SmiFlavor.

SmilesGenerator(int) - Constructor for class org.openscience.cdk.smiles.SmilesGenerator

Create a SMILES generator with the specified SmiFlavor.

SmilesParser - Class in org.openscience.cdk.smiles

Read molecules and reactions from a SMILES (?Authors?, SMILES Tutorial) string.

SmilesParser(IChemObjectBuilder) - Constructor for class org.openscience.cdk.smiles.SmilesParser

Create a new SMILES parser which will create IAtomContainers with the specified builder.

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

SODIUM - Static variable in enum org.openscience.cdk.config.Elements

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.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.

SP - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Square Planar (SP-4) (e.g.

SP4 - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Square Planar Configutation in 4 Shape

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

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

SpiroAtomCountDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

Returns the number of spiro atoms.

SpiroAtomCountDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.SpiroAtomCountDescriptor

Creates a new SpiroAtomCountDescriptor.

SPLIT_MODE_BREADTH_FIRST - Static variable in class org.openscience.cdk.structgen.stochastic.operator.CrossoverMachine

Indicates that crossover is using SPLIT_MODE_BREADTH_FIRST mode.

SPLIT_MODE_DEPTH_FIRST - Static variable in class org.openscience.cdk.structgen.stochastic.operator.CrossoverMachine

Indicates that crossover is using SPLIT_MODE_DEPTH_FIRST mode.

SPLIT_MODE_RADNDOM - Static variable in class org.openscience.cdk.structgen.stochastic.operator.CrossoverMachine

Indicates that crossover is using SPLIT_MODE_RADNDOM mode.

splitAfter(int, int) - Method in class org.openscience.cdk.group.Partition

Splits this partition by taking the cell at cellIndex and making two new cells - the first with the the rest of the elements from that cell and the second with the singleton splitElement.

splitBefore(int, int) - Method in class org.openscience.cdk.group.Partition

Splits this partition by taking the cell at cellIndex and making two new cells - the first with the singleton splitElement and the second with the rest of the elements from that cell.

splitMolecule(IAtomContainer, IBond) - Static method in class org.openscience.cdk.fragment.FragmentUtils

Non destructively split a molecule into two parts at the specified bond.

SPU - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Square Planar Configutation in U Shape

SPY - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Square Pyramidal (SPY-5)

SPZ - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Square Planar Configutation in Z Shape

SquarePlanar - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Square Planar (SP-4) (e.g.

SquarePlanar - Class in org.openscience.cdk.stereo

Describes square planar configuration.

SquarePlanar(IAtom, IAtom[], int) - Constructor for class org.openscience.cdk.stereo.SquarePlanar

Create a square-planar configuration around a provided focus atom.

SquarePyramidal - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Square Pyramidal (SPY-5)

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.

st - Variable in class org.openscience.cdk.io.VASPReader

StabilizationCharges - Class in org.openscience.cdk.charges

The stabilization of the positive and the negative charge obtained (e.g in the polar breaking of a bond) is calculated from the sigma- and lone pair-electronegativity values of the atoms that are in conjugation to the atoms obtaining the charges.

StabilizationCharges() - Constructor for class org.openscience.cdk.charges.StabilizationCharges

Constructor for the StabilizationCharges object.

StabilizationPlusChargeDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic

The stabilization of the positive charge (e.g.) obtained in the polar breaking of a bond is calculated from the sigma- and lone pair-electronegativity values of the atoms that are in conjugation to the atoms obtaining the charges.

StabilizationPlusChargeDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor

Constructor for the StabilizationPlusChargeDescriptor object

StandardGenerator - Class in org.openscience.cdk.renderer.generators.standard

The standard generator creates IRenderingElements for the atoms and bonds of a structure diagram.

StandardGenerator(Font) - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator

Create a new standard generator that utilises the specified font to display atom symbols.

StandardGenerator.AnnotationColor - Class in org.openscience.cdk.renderer.generators.standard

The color of the atom numbers.

StandardGenerator.AnnotationDistance - Class in org.openscience.cdk.renderer.generators.standard

The distance of atom numbers from their parent atom as a percentage of bond length, default value is 0.25 (25%)

StandardGenerator.AnnotationFontScale - Class in org.openscience.cdk.renderer.generators.standard

Annotation font size relative to element symbols, default = 0.4 (40%).

StandardGenerator.AtomColor - Class in org.openscience.cdk.renderer.generators.standard

Defines the color of unselected atoms (and bonds).

StandardGenerator.BondSeparation - Class in org.openscience.cdk.renderer.generators.standard

Defines the ratio of the separation between lines in double bonds as a percentage of length (BasicSceneGenerator.BondLength).

StandardGenerator.DashSection - Class in org.openscience.cdk.renderer.generators.standard

The number of sections to render in a dashed 'unknown' bond, default = 4;

StandardGenerator.FancyBoldWedges - Class in org.openscience.cdk.renderer.generators.standard

Modify bold wedges to be flush with adjacent bonds, default = true.

StandardGenerator.FancyHashedWedges - Class in org.openscience.cdk.renderer.generators.standard

Modify hashed wedges to be flush when there is a single adjacent bond, default = true.

StandardGenerator.ForceDelocalisedBondDisplay - Class in org.openscience.cdk.renderer.generators.standard

Indicate delocalised/aromatic bonds should always be rendered, even when there is a valid Kekule structure.

StandardGenerator.HashSpacing - Class in org.openscience.cdk.renderer.generators.standard

The preferred spacing between lines in hashed bonds.

StandardGenerator.Highlighting - Class in org.openscience.cdk.renderer.generators.standard

Parameter defines the style of highlight used to emphasis atoms and bonds.

StandardGenerator.HighlightStyle - Enum in org.openscience.cdk.renderer.generators.standard

Enumeration of highlight style.

StandardGenerator.OmitMajorIsotopes - Class in org.openscience.cdk.renderer.generators.standard

Whether Major Isotopes e.g.

StandardGenerator.OuterGlowWidth - Class in org.openscience.cdk.renderer.generators.standard

The width of outer glow as a percentage of stroke width.

StandardGenerator.SgroupBracketDepth - Class in org.openscience.cdk.renderer.generators.standard

How "deep" are brackets drawn.

StandardGenerator.SgroupFontScale - Class in org.openscience.cdk.renderer.generators.standard

Scale Sgroup annotations relative to the normal font size (atom symbol).

StandardGenerator.StrokeRatio - Class in org.openscience.cdk.renderer.generators.standard

Defines the ratio of the stroke to the width of the stroke of the font used to depict atom symbols.

StandardGenerator.SymbolMarginRatio - Class in org.openscience.cdk.renderer.generators.standard

Defines the margin between an atom symbol and a connected bond based on the stroke width.

StandardGenerator.Visibility - Class in org.openscience.cdk.renderer.generators.standard

Defines which atoms have their symbol displayed.

StandardGenerator.WaveSpacing - Class in org.openscience.cdk.renderer.generators.standard

The spacing of waves (semi circles) drawn in wavy bonds with.

StandardGenerator.WedgeRatio - Class in org.openscience.cdk.renderer.generators.standard

Ratio of the wide end of wedge compared to the narrow end (stroke width).

StandardSubstructureSets - Class in org.openscience.cdk.fingerprint

Default sets of atom containers aimed for use with the substructure.

StandardSubstructureSets() - Constructor for class org.openscience.cdk.fingerprint.StandardSubstructureSets

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.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

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 notify objects that implemented this interface and registered with them as ChemObjectListeners.

stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.AtomContainerSet

Called by objects to which this object has registered as a listener.

stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.ChemFile

Called by objects to which this object has registered as a listener.

stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.ChemModel

Called by objects to which this object has registered as a listener.

stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.ChemSequence

Called by objects to which this object has registered as a listener.

stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugAminoAcid

Called by objects to notify objects that implemented this interface and registered with them as ChemObjectListeners.

stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugBioPolymer

Called by objects to notify objects that implemented this interface and registered with them as ChemObjectListeners.

stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugCrystal

Called by objects to notify objects that implemented this interface and registered with them as ChemObjectListeners.

stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugMonomer

Called by objects to notify objects that implemented this interface and registered with them as ChemObjectListeners.

stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugPolymer

Called by objects to notify objects that implemented this interface and registered with them as ChemObjectListeners.

stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugRing

Called by objects to notify objects that implemented this interface and registered with them as ChemObjectListeners.

stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugStrand

Called by objects to notify objects that implemented this interface and registered with them as ChemObjectListeners.

stateChanged(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 notify objects that implemented this interface and registered with them as ChemObjectListeners.

stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.AtomContainerSet

Called by objects to which this object has registered as a listener.

stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.ChemFile

Called by objects to which this object has registered as a listener.

stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.ChemModel

Called by objects to which this object has registered as a listener.

stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.ChemSequence

Called by objects to which this object has registered as a listener.

stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.ReactionSet

stateChanged(List) - Method in interface org.openscience.cdk.structgen.IStructureGenerationListener

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.

Stereocenters - Class in org.openscience.cdk.stereo

Find atoms which can support stereo chemistry based on the connectivity.

Stereocenters.Stereocenter - Enum in org.openscience.cdk.stereo

Defines the type of a stereocenter.

Stereocenters.Type - Enum in org.openscience.cdk.stereo

stereocenterType(int) - Method in class org.openscience.cdk.stereo.Stereocenters

Determine the type of stereocenter is the atom at index v.

stereochemistry() - Method in class org.openscience.cdk.isomorphism.Mappings

Deprecated.

Results now automatically consider stereo if it's present, to match without stereochemistry remove the stereo features.

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.

StereoExCisTrans - Static variable in class org.openscience.cdk.smiles.SmiFlavor

StereoExTetrahedral - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Output extended tetrahedral stereochemistry on atoms as @ and @@.

stereoGiven - Variable in class org.openscience.cdk.io.cml.CMLCoreModule

stereoParity - Variable in class org.openscience.cdk.Atom

A stereo parity descriptor for the stereochemistry of this atom.

stereoParity - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom

A stereo parity descriptor for the stereochemistry of this atom.

stereoParity - Variable in class org.openscience.cdk.silent.Atom

A stereo parity descriptor for the stereochemistry of this atom.

stereosAreOpposite(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.BondTools

Says if of four atoms connected two one atom the up and down bonds are opposite or not, i.

StereoTetrahedral - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Output tetrahedral stereochemistry on atoms as @ and @@.

StereoTool - Class in org.openscience.cdk.stereo

Methods to determine or check the stereo class of a set of atoms.

StereoTool() - Constructor for class org.openscience.cdk.stereo.StereoTool

StereoTool.SquarePlanarShape - Enum in org.openscience.cdk.stereo

The shape that four atoms take in a plane.

StereoTool.StereoClass - Enum in org.openscience.cdk.stereo

Currently unused, but intended for the StereoTool to indicate what it 'means' by an assignment of some atoms to a class.

StereoTool.TetrahedralSign - Enum in org.openscience.cdk.stereo

The handedness of a tetrahedron, in terms of the point-plane distance of three of the corners, compared to the fourth.

storeAtomData() - Method in class org.openscience.cdk.io.cml.CMLCoreModule

storeAtomData() - Method in class org.openscience.cdk.io.cml.PDBConvention

storeBondData() - Method in class org.openscience.cdk.io.cml.CMLCoreModule

storeData() - Method in class org.openscience.cdk.io.cml.CMLCoreModule

storeData() - Method in class org.openscience.cdk.io.cml.PDBConvention

Strand - Class in org.openscience.cdk.silent

A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms.

Strand() - 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.

StrokeRatio() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.StrokeRatio

STRONTIUM - Static variable in enum org.openscience.cdk.config.Elements

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.

subgraph(int[][], int[]) - Static method in class org.openscience.cdk.graph.GraphUtil

Create a subgraph by specifying the vertices from the original graph to include in the subgraph.

subGraph - Variable in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph

subList(int, int) - Method in class org.openscience.cdk.ConformerContainer

subquery() - Method in class org.openscience.cdk.isomorphism.matchers.Expr

Access the sub-query, only applicable to recursive types.

subscript - Variable in class org.openscience.cdk.renderer.elements.TextGroupElement.Child

A subscript (if any) for the child.

Substance - Class in org.openscience.cdk.silent

An implementation of the ISubstance interface.

Substance() - 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(String[]) - Constructor for class org.openscience.cdk.fingerprint.SubstructureFingerprinter

Set up the fingerprinter to use a user-defined set of fragments.

SubstructureFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.SubstructureFingerprinter

Set up the fingerprinter to use the fragments from StandardSubstructureSets.

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

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.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

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

SymbolMarginRatio() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.SymbolMarginRatio

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.err 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

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

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.

TBPY - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Trigonal Bipyramidal (TBPY-5)

TECHNETIUM - Static variable in enum org.openscience.cdk.config.Elements

TELLURIUM - Static variable in enum org.openscience.cdk.config.Elements

TEMPLATE_PATH - Static variable in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D

TemplateExtractor - Class in org.openscience.cdk.modeling.builder3d

Helper class that help setup a template library of CDK's Builder3D.

TemplateExtractor() - Constructor for class org.openscience.cdk.modeling.builder3d.TemplateExtractor

TemplateHandler - Class in org.openscience.cdk.layout

Helper class for Structure Diagram Generation.

TemplateHandler(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.

TERBIUM - Static variable in enum org.openscience.cdk.config.Elements

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.

Tetrahedral - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Tetrahedral (T-4) (e.g.

TETRAHEDRAL_ANGLE - Static variable in class org.openscience.cdk.geometry.AtomTools

TETRAHEDRAL_ANGLE - Static variable in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

TetrahedralChirality - Class in org.openscience.cdk.stereo

Stereochemistry specification for tetravalent atoms.

TetrahedralChirality(IAtom, IAtom[], ITetrahedralChirality.Stereo) - Constructor for class org.openscience.cdk.stereo.TetrahedralChirality

TetrahedralChirality(IAtom, IAtom[], int) - Constructor for class org.openscience.cdk.stereo.TetrahedralChirality

TetrahedralElementEncoderFactory - Class in org.openscience.cdk.hash.stereo

Defines a stereo encoder factory for the hash code.

TetrahedralElementEncoderFactory() - Constructor for class org.openscience.cdk.hash.stereo.TetrahedralElementEncoderFactory

text - Variable in class org.openscience.cdk.renderer.elements.TextElement

The text to be displayed.

text - Variable in class org.openscience.cdk.renderer.elements.TextGroupElement.Child

The text of this child.

TextElement - Class in org.openscience.cdk.renderer.elements

Text element as used in the chemical drawing.

TextElement(double, double, String, Color) - Constructor for class org.openscience.cdk.renderer.elements.TextElement

Constructs a new TextElement with the content text to be drawn at position (x,y) in the color color.

TextGroupElement - Class in org.openscience.cdk.renderer.elements

A group of text elements, particularly the element symbol (eg: "C") surrounded by other annotations such as mass number, charge, etc.

TextGroupElement(double, double, String, Color) - Constructor for class org.openscience.cdk.renderer.elements.TextGroupElement

Make a text group at (x, y) with the text and color given.

TextGroupElement.Child - Class in org.openscience.cdk.renderer.elements

A string of text that should be shown around the parent.

TextGroupElement.Position - Enum in org.openscience.cdk.renderer.elements

Compass-point positions for text element annotation children.

TextGUIListener - Class in org.openscience.cdk.io.listener

Allows processing of IOSetting quesions which are passed to the user by using the System.out and System.in by default.

TextGUIListener(IOSetting.Importance) - Constructor for class org.openscience.cdk.io.listener.TextGUIListener

TH - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Tetrahedral (T-4) (e.g.

THALLIUM - Static variable in enum org.openscience.cdk.config.Elements

THIOPHENE_RING - Static variable in class org.openscience.cdk.tools.AtomTypeTools

THORIUM - Static variable in enum org.openscience.cdk.config.Elements

THULIUM - Static variable in enum org.openscience.cdk.config.Elements

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.

TIN - Static variable in enum org.openscience.cdk.config.Elements

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

TITLE - Static variable in class org.openscience.cdk.CDKConstants

The title for a IChemObject.

TitleColor() - Constructor for class org.openscience.cdk.renderer.RendererModel.TitleColor

TitleFontScale() - Constructor for class org.openscience.cdk.renderer.RendererModel.TitleFontScale

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.

toConfig(IDoubleBondStereochemistry.Conformation) - Static method in enum org.openscience.cdk.interfaces.IDoubleBondStereochemistry.Conformation

toConfig(ITetrahedralChirality.Stereo) - Static method in enum org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo

toConformation(int) - Static method in enum org.openscience.cdk.interfaces.IDoubleBondStereochemistry.Conformation

toCycleString() - Method in class org.openscience.cdk.group.Permutation

An easily-readable version of the permutation as a product of cycles.

toEpsStr() - Method in class org.openscience.cdk.depict.Depiction

Render the image to an EPS (Encapsulated PostScript) format string.

TOGETHER - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

toIElement() - Method in enum org.openscience.cdk.config.Elements

Access an IElement instance of the chemical element.

toImg() - Method in class org.openscience.cdk.depict.Depiction

Render the depiction to a Java AWT BufferedImage.

ToleranceRangeRule - Class in org.openscience.cdk.formula.rules

This class validate if the mass from an IMolecularFormula is between the tolerance range give a experimental mass.

ToleranceRangeRule() - Constructor for class org.openscience.cdk.formula.rules.ToleranceRangeRule

Constructor for the ToleranceRangeRule object.

toMiddle() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager

Set the font size pointer to the middle of the range.

toModelCoordinates(double, double) - Method in class org.openscience.cdk.renderer.AbstractRenderer

Convert a point in screen space into a point in model space.

toModelCoordinates(double, double) - Method in interface org.openscience.cdk.renderer.IRenderer

Converts screen coordinates into model (or world) coordinates.

toMolecule(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator

Converts a reaction to an 'inlined' reaction stored as a molecule.

toPdfStr() - Method in class org.openscience.cdk.depict.Depiction

Render the image to an PDF format string.

toPermutation() - Method in class org.openscience.cdk.group.Partition

Converts the whole partition into a permutation.

TopologicalMatrix - Class in org.openscience.cdk.graph.matrix

Calculator for a topological matrix representation of this AtomContainer.

TopologicalMatrix() - Constructor for class org.openscience.cdk.graph.matrix.TopologicalMatrix

toPsStr() - Method in class org.openscience.cdk.depict.Depiction

Render the image to an PS (PostScript) format string.

toReaction(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator

Converts an 'inlined' reaction stored in a molecule back to a reaction.

toRingSet() - Method in class org.openscience.cdk.graph.Cycles

Convert the cycles to a IRingSet containing the IAtoms and IBonds of the input molecule.

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.

toStereo(int) - Static method in enum org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo

toString() - Method in class org.openscience.cdk.AminoAcid

toString() - Method in class org.openscience.cdk.Association

Returns a one line string representation of this Container.

toString() - Method in class org.openscience.cdk.Atom

Returns a one line string representation of this Atom.

toString() - Method in class org.openscience.cdk.AtomContainer

Returns a one line description of this IChemObject.

toString() - Method in class org.openscience.cdk.AtomContainerSet

Returns the String representation of this AtomContainerSet.

toString() - Method in class org.openscience.cdk.AtomRef

toString() - Method in class org.openscience.cdk.AtomType

toString() - Method in class org.openscience.cdk.BioPolymer

toString() - Method in class org.openscience.cdk.Bond

Returns a one line string representation of this Container.

toString() - Method in class org.openscience.cdk.BondRef

toString() - Method in class org.openscience.cdk.ChemFile

Returns a String representation of this class.

toString() - Method in class org.openscience.cdk.ChemModel

Returns a String representation of the contents of this IChemObject.

toString() - Method in class org.openscience.cdk.ChemSequence

toString() - Method in class org.openscience.cdk.Crystal

Returns a String representation of this crystal.

toString() - Method in class org.openscience.cdk.dict.DictRef

toString() - Method in class org.openscience.cdk.dict.Entry

toString() - Method in class org.openscience.cdk.DynamicFactory.ConstructorKey

toString() - Method in class org.openscience.cdk.ElectronContainer

toString() - Method in class org.openscience.cdk.Element

toString() - Method in class org.openscience.cdk.fingerprint.ShortestPathWalker

toString() - Method in class org.openscience.cdk.formula.IsotopeContainer

toString() - Method in class org.openscience.cdk.FragmentAtom

toString() - Method in class org.openscience.cdk.graph.Matching

toString() - Method in class org.openscience.cdk.graph.rebond.Bspt

toString() - Method in class org.openscience.cdk.graph.rebond.Point

toString() - Method in class org.openscience.cdk.group.DisjointSetForest

toString() - Method in class org.openscience.cdk.group.Partition

toString() - Method in class org.openscience.cdk.group.Permutation

toString() - Method in class org.openscience.cdk.group.PermutationGroup

toString() - Method in interface org.openscience.cdk.interfaces.IChemObject

Returns a one line description of this IChemObject.

toString() - Method in class org.openscience.cdk.io.cml.CMLModuleStack

Returns a String representation of the stack.

toString() - Method in class org.openscience.cdk.io.random.RandomAccessReader

toString() - Method in class org.openscience.cdk.isomorphism.matchers.Expr

toString() - Method in class org.openscience.cdk.isomorphism.matchers.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.SymbolChargeIDQueryAtom

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.LonePair

Returns a one line string representation of this LonePair.

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.RingSet

Returns the String representation of this RingSet.

toString() - Method in class org.openscience.cdk.sgroup.SgroupBracket

toString() - Method in class org.openscience.cdk.signature.Orbit

toString() - Method in class org.openscience.cdk.silent.AminoAcid

toString() - Method in class org.openscience.cdk.silent.Atom

Returns a one line string representation of this Atom.

toString() - Method in class org.openscience.cdk.silent.AtomContainer

Returns a one line description of this IChemObject.

toString() - Method in class org.openscience.cdk.silent.AtomContainerSet

Returns the String representation of this AtomContainerSet.

toString() - Method in class org.openscience.cdk.silent.AtomType

toString() - Method in class org.openscience.cdk.silent.BioPolymer

toString() - Method in class org.openscience.cdk.silent.Bond

Returns a one line string representation of this Container.

toString() - Method in class org.openscience.cdk.silent.ChemFile

Returns a String representation of this class.

toString() - Method in class org.openscience.cdk.silent.ChemModel

Returns a String representation of the contents of this IChemObject.

toString() - Method in class org.openscience.cdk.silent.ChemSequence

toString() - Method in class org.openscience.cdk.silent.Crystal

Returns a String representation of this crystal.

toString() - Method in class org.openscience.cdk.silent.ElectronContainer

toString() - Method in class org.openscience.cdk.silent.Element

toString() - Method in class org.openscience.cdk.silent.FragmentAtom

toString() - Method in class org.openscience.cdk.silent.Isotope

A string representation of this isotope.

toString() - Method in class org.openscience.cdk.silent.LonePair

Returns a one line string representation of this LonePair.

toString() - Method in class org.openscience.cdk.silent.Monomer

toString() - Method in class org.openscience.cdk.silent.PDBAtom

Returns a one line string representation of this Atom.

toString() - Method in class org.openscience.cdk.silent.PDBMonomer

Returns a one line string representation of this Atom.

toString() - Method in class org.openscience.cdk.silent.PDBPolymer

toString() - Method in class org.openscience.cdk.silent.Polymer

toString() - Method in class org.openscience.cdk.silent.PseudoAtom

Returns a one line string representation of this Atom.

toString() - Method in class org.openscience.cdk.silent.Reaction

Returns a one line string representation of this Atom.

toString() - Method in class org.openscience.cdk.silent.ReactionSet

toString() - Method in class org.openscience.cdk.silent.Ring

toString() - Method in class org.openscience.cdk.silent.RingSet

Returns the String representation of this RingSet.

toString() - Method in class org.openscience.cdk.silent.SingleElectron

Returns a one line string representation of this SingleElectron.

toString() - Method in class org.openscience.cdk.silent.Strand

toString() - Method in class org.openscience.cdk.SingleElectron

Returns a one line string representation of this SingleElectron.

toString() - Method in class org.openscience.cdk.smiles.InvPair

String representation.

toString() - Method in class org.openscience.cdk.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.

toSvgStr(String) - Method in class org.openscience.cdk.depict.Depiction

Render the image to an SVG image.

TOTAL_CONNECTIONS - Static variable in class org.openscience.cdk.CDKConstants

TOTAL_H_COUNT - Static variable in class org.openscience.cdk.CDKConstants

TowardsRingCenterProportion() - Constructor for class org.openscience.cdk.renderer.generators.BasicBondGenerator.TowardsRingCenterProportion

TPSADescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

Calculation of topological polar surface area based on fragment contributions (TPSA) (Ertl, P. et. al.. J. Med. Chem.. 2000. 43).

TPSADescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor

Constructor for the TPSADescriptor object.

trace() - Method in class org.openscience.cdk.graph.invariant.GIMatrix

Returns the trace of this matrix, that is the sum of the elements of its diagonal.

TRACE - Static variable in interface org.openscience.cdk.tools.ILoggingTool

Trace, Debug, Info, Warn, Error, and Fatal messages will be emitted.

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.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.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.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.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.

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

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

TrigonalBipyramidal - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Trigonal Bipyramidal (TBPY-5)

TrigonalBipyramidal - Class in org.openscience.cdk.stereo

Describes a trigonal-bipyramidal configuration.

TrigonalBipyramidal(IAtom, IAtom[], int) - Constructor for class org.openscience.cdk.stereo.TrigonalBipyramidal

Create a new trigonal bipyramidal configuration.

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

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

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() - Method in class org.openscience.cdk.isomorphism.matchers.Expr

Access the type of the atom expression.

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).

U

Ullmann - Class in org.openscience.cdk.isomorphism

A structure pattern which utilises the Ullmann algorithm (Ullmann J R. Journal of the Association for Computing Machinery. 1976. 23).

unchorded(CycleFinder) - Static method in class org.openscience.cdk.graph.Cycles

Derive a new cycle finder that only provides cycles without a chord.

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

UNITS_MM - Static variable in class org.openscience.cdk.depict.Depiction

Units in MM (specific to SVG).

UNITS_PX - Static variable in class org.openscience.cdk.depict.Depiction

Units in PX (specific to SVG).

UniversalIsomorphismTester - Class in org.openscience.cdk.isomorphism

This class implements a multipurpose structure comparison tool.

UniversalIsomorphismTester() - Constructor for class org.openscience.cdk.isomorphism.UniversalIsomorphismTester

UniversalSmiles - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Output canonical SMILES with stereochemistry and atomic masses, This output uses the InChI labelling algorithm to generate a 'Universal SMILES' (O'Boyle, Noel. Journal of Cheminformatics. 2012. 4).

UNKNOWN_STEREO - Static variable in class org.openscience.cdk.isomorphism.matchers.Expr

Sentinel value for indicating the stereochemistry configuration is not yet known.

unmark(IChemObject) - Static method in class org.openscience.cdk.validate.ProblemMarker

unmarkWithError(IChemObject) - Static method in class org.openscience.cdk.validate.ProblemMarker

unmarkWithWarning(IChemObject) - Static method in class org.openscience.cdk.validate.ProblemMarker

unmarshal(Reader) - Static method in class org.openscience.cdk.dict.Dictionary

unmarshal(Reader) - Static method in class org.openscience.cdk.dict.OWLFile

unmarshal(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

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

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

URI - Static variable in class org.openscience.cdk.libio.jena.CDK

UseAntiAliasing() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.UseAntiAliasing

UseAromaticSymbols - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Writes aromatic atoms as lower case letters.

UsedFontStyle() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.UsedFontStyle

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

VABCDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

Volume descriptor using the method implemented in the VABCVolume class.

VABCDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor

VABCVolume - Class in org.openscience.cdk.geometry.volume

Calculates the Van der Waals volume using the method proposed in (Zhao, Yuan H. et. al.. The Journal of Organic Chemistry. 2003. 68).

VABCVolume() - Constructor for class org.openscience.cdk.geometry.volume.VABCVolume

VAdjMaDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

Vertex adjacency information (magnitude): 1 + log2 m where m is the number of heavy-heavy bonds.

VAdjMaDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor

Constructor for the VAdjMaDescriptor object

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

value() - Method in class org.openscience.cdk.isomorphism.matchers.Expr

Access the value of this atom expression being tested.

valueOf(String) - Static method in enum 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.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.Expr.Type

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.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.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.Expr.Type

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.openscience.cdk.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.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

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, r_w, of an atom is the radius of an imaginary hard sphere which can be used to model the atom.

VdWRadiusDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic

This class return the VdW radius of a given atom.

VdWRadiusDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor

Constructor for the VdWRadiusDescriptor object.

VentoFoggia - Class in org.openscience.cdk.isomorphism

A structure pattern which utilises the Vento-Foggia (VF) algorithm (Cordella Luigi P et. al.. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE. 2004. 26).

vertexColor() - Method in interface org.openscience.cdk.ringsearch.CyclicVertexSearch

Build an indexed lookup of vertex color.

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.

Vibration - Class in org.openscience.cdk

A molecular vibration composed of a set of atom vectors.

Vibration(String) - Constructor for class org.openscience.cdk.Vibration

Create a vibration identified by the label.

VicinitySampler - Class in org.openscience.cdk.structgen

The VicinitySampler is a generator of constitutional isomers.

VicinitySampler() - Constructor for class org.openscience.cdk.structgen.VicinitySampler

ViewmolFormat - Class in org.openscience.cdk.io.formats

See here.

ViewmolFormat() - Constructor for class org.openscience.cdk.io.formats.ViewmolFormat

Visibility() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.Visibility

visible(IAtom, List<IBond>, RendererModel) - Method in class org.openscience.cdk.renderer.generators.standard.SelectionVisibility

Determine if an atom with the specified bonds is visible.

visible(IAtom, List<IBond>, RendererModel) - Method in class org.openscience.cdk.renderer.SymbolVisibility

Determine if an atom with the specified bonds is visible.

visit(IRenderingElement) - Method in interface org.openscience.cdk.renderer.elements.IRenderingVisitor

Translates a IRenderingElement into a widget toolkit specific rendering element.

visit(IRenderingElement) - Method in class org.openscience.cdk.renderer.visitor.AWTDrawVisitor

Translates a IRenderingElement into a widget toolkit specific rendering element.

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

WARN - Static variable in interface org.openscience.cdk.tools.ILoggingTool

Warn, Error, and Fatal messages will be emitted.

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

WaveSpacing() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.WaveSpacing

WedgeLineElement - Class in org.openscience.cdk.renderer.elements

A 'wedge' is a triangle aligned along a bond that indicates stereochemistry.

WedgeLineElement(double, double, double, double, double, WedgeLineElement.TYPE, WedgeLineElement.Direction, Color) - Constructor for class org.openscience.cdk.renderer.elements.WedgeLineElement

Make a wedge between the points (x1, y1) and (x2, y2) with a certain width, direction, dash, and color.

WedgeLineElement(LineElement, WedgeLineElement.TYPE, WedgeLineElement.Direction, Color) - Constructor for class org.openscience.cdk.renderer.elements.WedgeLineElement

Make a wedge along the given line element.

WedgeLineElement.Direction - Enum in org.openscience.cdk.renderer.elements

'toFirst' means that the wedge gets thicker in the direction of the first point in the line.

WedgeLineElement.TYPE - Enum in org.openscience.cdk.renderer.elements

If the bond is dashed ,wedged, or "up_or_down", i.e., not defined.

WedgeRatio() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.WedgeRatio

WedgeWidth() - Constructor for class org.openscience.cdk.renderer.generators.BasicBondGenerator.WedgeWidth

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

WHIMDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

Holistic descriptors described by Todeschini et al (Todeschini, R. and Gramatica, P.. Persepectives in Drug Discovery and Design. 1998. null).

WHIMDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor

width() - 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.

WillDrawAtomNumbers() - Constructor for class org.openscience.cdk.renderer.generators.AtomNumberGenerator.WillDrawAtomNumbers

WIND_EVEN_ODD - Static variable in class org.openscience.cdk.renderer.elements.GeneralPath

WIND_NON_ZERO - Static variable in class org.openscience.cdk.renderer.elements.GeneralPath

winding - Variable in class org.openscience.cdk.renderer.elements.GeneralPath

Winding rule for determining path interior.

winding() - Method in class org.openscience.cdk.stereo.ExtendedTetrahedral

The winding of the peripherals, when viewed from the first atom.

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 values on the molecule or reaction.

withBackgroundColor(Color) - Method in class org.openscience.cdk.depict.DepictionGenerator

Change the background color.

withCapacity(int) - Static method in class org.openscience.cdk.graph.Matching

Create an empty matching with the specified capacity.

withCarbonSymbols() - Method in class org.openscience.cdk.depict.DepictionGenerator

Display atom symbols for all atoms in the molecule.

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.

X

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.

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

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

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

YTTERBIUM - Static variable in enum org.openscience.cdk.config.Elements

YTTRIUM - Static variable in enum org.openscience.cdk.config.Elements

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

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

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

ZoomFactor() - Constructor for class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ZoomFactor

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