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

A

A - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

a - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

A - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

aaBondInfo() - Static method in class org.openscience.cdk.templates.AminoAcids

Creates matrix with info about the bonds in the amino acids.

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

abortOnErrors - Variable in class org.openscience.cdk.io.cml.CMLErrorHandler

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

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.

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

Diff between two IChemObjects.

AbstractValidator - Class in org.openscience.cdk.validate

Abstract validator that does nothing but provide all the methods that the ValidatorInterface requires.

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

AC - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

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

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

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

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

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

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

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

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

accepts(Class) - Method in class org.openscience.cdk.io.Gaussian03Reader

accepts(Class) - Method in class org.openscience.cdk.io.Gaussian98Reader

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

accepts(Class) - Method in class org.openscience.cdk.io.MDLV3000Reader

accepts(IChemObject) - Method in class org.openscience.cdk.io.MDLV3000Reader

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

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

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

accepts(Class) - Method in class org.openscience.cdk.io.Mol2Writer

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

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

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

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

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

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

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

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

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

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

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

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

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

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

accepts(Class) - 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.

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

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

ACTINIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

actionPerformed(ActionEvent) - Method in class org.openscience.cdk.renderer.JCPAction2D

Dummy method.

actionSuffix - Static variable in class org.openscience.cdk.renderer.JCPAction2D

Description of the Field

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(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

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

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

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

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

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

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

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

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

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

add(IMoleculeSet) - Method in class org.openscience.cdk.debug.DebugMoleculeSet

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

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

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

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

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

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

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(IMoleculeSet) - Method in interface org.openscience.cdk.interfaces.IMoleculeSet

Adds all molecules in the MoleculeSet to this container.

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

add(Complex) - Method in class org.openscience.cdk.math.Complex

Add a complex value

add(IMatrix) - Method in class org.openscience.cdk.math.IMatrix

Addition from two matrices

add(IMatrix, IMatrix) - Method in class org.openscience.cdk.math.IMatrix

Addition from two matrices

add(IVector) - Method in class org.openscience.cdk.math.IVector

Addition from two vectors

add(IVector, IVector) - Method in class org.openscience.cdk.math.IVector

Addition from two vectors

add(Matrix) - Method in class org.openscience.cdk.math.Matrix

Adds two matrices.

add(Quaternion) - Method in class org.openscience.cdk.math.Quaternion

add(Vector) - Method in class org.openscience.cdk.math.Vector

Addition from two vectors

add(IMoleculeSet) - Method in class org.openscience.cdk.MoleculeSet

Adds all molecules in the MoleculeSet 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(IRingSet) - Method in class org.openscience.cdk.RingSet

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

add3DCoordinates1(AtomContainer) - 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(IMolecule) - Method in class org.openscience.cdk.debug.DebugReaction

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

Adds an agent to this reaction.

addAgent(IMolecule) - Method in class org.openscience.cdk.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(BioPolymer, AminoAcid, Strand, AminoAcid) - 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(BioPolymer, AminoAcid, Strand, AminoAcid) - 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.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.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

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

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

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

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.MoleculeSet

Adds an atomContainer to this container.

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

Adds an atomContainer to this container with the given multiplier.

addAtomParity(IAtomParity) - Method in class org.openscience.cdk.AtomContainer

Adds an AtomParity to this container.

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

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

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

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

addAtomParity(IAtomParity) - Method in class org.openscience.cdk.debug.DebugMolecule

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

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

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

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

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

Adds an AtomParity to this container.

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, int) - 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Adds a Bond to this AtomContainer.

addBond(int, int, IBond.Order, int) - 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

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

Adds a CDK problem.

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

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

Adds an chemModel to this container.

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

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

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.iterator.DefaultIteratingChemObjectReader

addChemObjectIOListener(IChemObjectIOListener) - Method in class org.openscience.cdk.io.iterator.event.DefaultEventChemObjectReader

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

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

Adds an IChemSequence to this container.

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

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

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

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

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

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

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

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

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

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

addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugMolecule

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

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

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

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

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

Adds a ElectronContainer to this AtomContainer.

addEntry(Entry) - Method in class org.openscience.cdk.dict.Dictionary

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.

addFunction(IFunction) - Method in class org.openscience.cdk.renderer.GraphRendererModel

Add a function to the set of functions

addFunction(IFunction, Color) - Method in class org.openscience.cdk.renderer.GraphRendererModel

Add a function to the set of functions

addImplicitHydrogens(IAtomContainer) - Method in class org.openscience.cdk.tools.CDKHydrogenAdder

Sets implicit hydrogen counts for all atoms in the given IAtomContainer.

addImplicitHydrogens(IAtomContainer, IAtom) - Method in class org.openscience.cdk.tools.CDKHydrogenAdder

Sets the implicit hydrogen count for the indicated IAtom in the given IAtomContainer.

addIsotope(IIsotope) - Method in class org.openscience.cdk.debug.DebugMolecularFormula

addIsotope(IIsotope, int) - Method in class org.openscience.cdk.debug.DebugMolecularFormula

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.

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

addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAtom

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

addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet

addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAtomType

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

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

addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugChemFile

addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugChemModel

addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugChemObject

addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugChemSequence

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

addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugElectronContainer

addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugElement

addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugIsotope

addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugLonePair

addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugMapping

addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugMolecule

addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugMoleculeSet

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

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

addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugReaction

addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugReactionScheme

addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugReactionSet

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

addListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugSingleElectron

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

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.nonotify.NNAminoAcid

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNAtom

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNAtomContainer

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNAtomContainerSet

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNAtomType

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNBioPolymer

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNBond

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNChemFile

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNChemModel

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNChemObject

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNChemSequence

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNCrystal

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNElectronContainer

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNElement

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNFragmentAtom

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNIsotope

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNLonePair

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNMapping

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNMolecule

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNMoleculeSet

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNMonomer

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNPDBAtom

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNPDBMonomer

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNPDBPolymer

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNPDBStructure

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNPolymer

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNPseudoAtom

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNReaction

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNReactionScheme

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNReactionSet

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNRing

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNRingSet

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNSingleElectron

addListener(IChemObjectListener) - Method in class org.openscience.cdk.nonotify.NNStrand

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

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

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

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

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

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

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

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

addLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugMolecule

addLonePair(int) - Method in class org.openscience.cdk.debug.DebugMolecule

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

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

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

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

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

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

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

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

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.

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.

addMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugAdductFormula

addMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet

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.

addMolecule(IMolecule) - Method in class org.openscience.cdk.debug.DebugMoleculeSet

addMolecule(IMolecule) - Method in interface org.openscience.cdk.interfaces.IMoleculeSet

Adds an IMolecule to this container.

addMolecule(IAtomContainer) - Method in class org.openscience.cdk.layout.TemplateHandler

Adds a Molecule to the list of templates use by this TemplateHandler.

addMolecule(IMolecule) - Method in class org.openscience.cdk.MoleculeSet

Adds an molecule to this container.

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

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

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.

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

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

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

Adds a product to this reaction.

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

Adds a product to this reaction.

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

Adds a product to this reaction.

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

Adds a product to this reaction.

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

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

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

Adds a reactant to this reaction.

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

Adds a reactant to this reaction with a stoichiometry coefficient.

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

Adds a reactant to this reaction.

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

Adds a reactant to this reaction with a stoichiometry coefficient.

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

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.

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

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

Adds a single electron to this AtomContainer.

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

Adds a LonePair to this Atom.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.

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

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

addSymbol(String) - Method in class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom

Add a symbol to this QueryAtom

addSymbol(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom

Add a symbol to this QueryAtom

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).

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

AdjacencyMatrix - Class in org.openscience.cdk.graph.matrix

Calculator for a adjacency matrix representation of this AtomContainer.

AdjacencyMatrix() - Constructor for class org.openscience.cdk.graph.matrix.AdjacencyMatrix

adjustBeginLineColumn(int, int) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream

Method to adjust line and column numbers for the start of a token.

adjustBeginLineColumn(int, int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream

Method to adjust line and column numbers for the start of a token.

AG - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

AL - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

AL - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

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

align() - Method in class org.openscience.cdk.geometry.alignment.KabschAlignment

Perform an alignment.

Aliphatic() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

AliphaticAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts

This matcher any non-aromatic atom.

AliphaticAtom() - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AliphaticAtom

Creates a new instance

AliphaticSymbolAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts

This smarts atom matches aliphatic atom with element symbol specified

AliphaticSymbolAtom(String) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AliphaticSymbolAtom

Creates a new instance

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

A set of all rings computed for this molecule.

allBaseNumbers() - Method in class org.openscience.cdk.iupac.parser.NomParser

The usual numbers .

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

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

allPlaced(IAtomContainer) - 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

Finds the Set of all Rings.

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

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

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

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

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

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

This class calculates ALOGP (Ghose-Crippen LogKow) and the Ghose-Crippen molar refractivity [Ghose, A.K. and Crippen, G.M. , Atomic physicochemical parameters for three-dimensional structure-directed quantitative structure-activity relationships. I. Partition coefficients as a measure of hydrophobicity, Journal of Computational Chemistry, 1986, 7:565-577, Ghose, A.K. and Crippen, G.M. , Atomic physicochemical parameters for three-dimensional-structure-directed quantitative structure-activity relationships. 2. Modeling dispersive and hydrophobic interactions, Journal of Chemical Information and Computer Science, 1987, 27:21-35].

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

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

alphaOptimum - Variable in class org.openscience.cdk.modeling.forcefield.LineSearchForTheWolfeConditions

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

ALUMINIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

ALUMINO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

AM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

AMERCIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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

AMIDE - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

AMINE - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

AMINO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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.

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

Class that returns the number of each amino acid in an atom container.

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

Constructor for the AromaticAtomsCountDescriptor object.

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

Class with convenience methods that provide methods to manipulate AminoAcid's.

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

AminoAcids - Class in org.openscience.cdk.templates

Tool that provides templates for the (natural) amino acids.

AminoAcids() - Constructor for class org.openscience.cdk.templates.AminoAcids

AN - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

AngleBending - Class in org.openscience.cdk.modeling.forcefield

Angle bending calculator for the potential energy function.

AngleBending() - Constructor for class org.openscience.cdk.modeling.forcefield.AngleBending

Constructor for the AngleBending object

angleBetweenTwoBonds(IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.modeling.forcefield.ForceFieldTools

calculates the angle between two bonds, i-j and j-k, given the atoms i,j and k.

angleBetweenTwoBondsFrom3xNCoordinates(GVector, int, int, int) - Static method in class org.openscience.cdk.modeling.forcefield.ForceFieldTools

calculates the angle between two bonds, i-j and j-k, given the 3xN atoms coordinates and the atom i,j and k positions.

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

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

AngularMomentum - Class in org.openscience.cdk.math.qm

This class is used to calculate angular momentum states.

AngularMomentum(double) - Constructor for class org.openscience.cdk.math.qm.AngularMomentum

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

A List of annotation remarks.

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

ANTIMONY - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

ANY_BOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

AnyAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts

This matcher any Atom.

AnyAtom() - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AnyAtom

Creates a new instance

AnyAtom() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

AnyOrderQueryBond - Class in org.openscience.cdk.isomorphism.matchers.smarts

This matches a bond of any order

AnyOrderQueryBond() - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AnyOrderQueryBond

AnyOrderQueryBond(IQueryAtom, IQueryAtom, IBond.Order) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AnyOrderQueryBond

Creates a new instance

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

Sum of the atomic polarizabilities (including implicit hydrogens).

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

Constructor for the APolDescriptor object.

AR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

AR_BOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

areIntersected(IBond, IBond) - Method in class org.openscience.cdk.layout.OverlapResolver

Checks if two bonds cross each other.

ARGON - Static variable in class org.openscience.cdk.config.Elements

Aromatic() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

AromaticAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts

This matcher any aromatic atom.

AromaticAtom() - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AromaticAtom

Creates a new instance

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

Class that returns the number of aromatic atoms in an atom container.

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

Constructor for the AromaticAtomsCountDescriptor object.

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

This Class contains a method that returns the number of aromatic atoms in an AtomContainer.

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

Constructor for the AromaticBondsCountDescriptor object.

AromaticityCalculator - Class in org.openscience.cdk.aromaticity

AromaticityCalculator() - Constructor for class org.openscience.cdk.aromaticity.AromaticityCalculator

AromaticOrSingleQueryBond - Class in org.openscience.cdk.isomorphism.matchers.smarts

This matches an aromatic or a single bond, used when no bond is specified between an atom

AromaticOrSingleQueryBond() - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AromaticOrSingleQueryBond

Creates a new instance

AromaticOrSingleQueryBond(IQueryAtom, IQueryAtom, IBond.Order) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AromaticOrSingleQueryBond

Creates a new instance

AromaticQueryBond - Class in org.openscience.cdk.isomorphism.matchers.smarts

This matches an aromatic bond

AromaticQueryBond() - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AromaticQueryBond

Creates a new instance

AromaticQueryBond(IQueryAtom, IQueryAtom, IBond.Order) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AromaticQueryBond

Creates a new instance

AromaticSymbolAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts

This class matches aromatic atom with element symbol specified.

AromaticSymbolAtom(String) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AromaticSymbolAtom

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

ARSENIC - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

as - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

AS - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

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

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

Method assigns certain properties to an atom.

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

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

assignCoordinatesToMolecule(GVector, IAtomContainer) - Static method in class org.openscience.cdk.modeling.forcefield.ForceFieldTools

Assign the 3D coordinates saved in a GVector back to the molecule

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.

ASTAliphatic - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTAliphatic(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTAliphatic

Creates a new instance

ASTAliphatic(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTAliphatic

Creates a new instance

ASTAnyAtom - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTAnyAtom(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTAnyAtom

Creates a new instance

ASTAnyAtom(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTAnyAtom

Creates a new instance

ASTAromatic - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTAromatic(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTAromatic

Creates a new instance

ASTAromatic(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTAromatic

Creates a new instance

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

ASTAtom - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTAtom(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTAtom

Creates a new instance

ASTAtom(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTAtom

Creates a new instance

ASTAtomicMass - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTAtomicMass(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTAtomicMass

ASTAtomicMass(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTAtomicMass

ASTAtomicNumber - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTAtomicNumber(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTAtomicNumber

Creates a new instance.

ASTAtomicNumber(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTAtomicNumber

Creates a new instance.

ASTCharge - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTCharge(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTCharge

Creates a new instance.

ASTCharge(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTCharge

Creates a new instance.

ASTChirality - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTChirality(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTChirality

Creates a new instance

ASTChirality(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTChirality

Creates a new instance

ASTElement - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTElement(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTElement

Creates a new instance.

ASTElement(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTElement

Creates a new instance.

ASTExplicitAtom - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTExplicitAtom(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTExplicitAtom

Creates a new instance.

ASTExplicitAtom(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTExplicitAtom

Creates a new instance.

ASTExplicitConnectivity - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTExplicitConnectivity(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTExplicitConnectivity

Creates a new instance.

ASTExplicitConnectivity(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTExplicitConnectivity

Creates a new instance.

ASTExplicitHighAndBond - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTExplicitHighAndBond(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTExplicitHighAndBond

Creates a new instance.

ASTExplicitHighAndBond(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTExplicitHighAndBond

Creates a new instance.

ASTExplicitHighAndExpression - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTExplicitHighAndExpression(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTExplicitHighAndExpression

Creates a new instance.

ASTExplicitHighAndExpression(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTExplicitHighAndExpression

Creates a new instance.

ASTGroup - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTGroup(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTGroup

Creates a new instance

ASTGroup(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTGroup

Creates a new instance

ASTHybrdizationNumber - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTHybrdizationNumber(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTHybrdizationNumber

ASTHybrdizationNumber(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTHybrdizationNumber

ASTImplicitHCount - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTImplicitHCount(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTImplicitHCount

Creates a new instance.

ASTImplicitHCount(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTImplicitHCount

Creates a new instance.

ASTImplicitHighAndBond - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTImplicitHighAndBond(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTImplicitHighAndBond

Creates a new instance.

ASTImplicitHighAndBond(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTImplicitHighAndBond

Creates a new instance.

ASTImplicitHighAndExpression - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTImplicitHighAndExpression(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTImplicitHighAndExpression

Creates a new instance.

ASTImplicitHighAndExpression(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTImplicitHighAndExpression

Creates a new instance.

ASTLowAndBond - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTLowAndBond(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTLowAndBond

Creates a new instance.

ASTLowAndBond(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTLowAndBond

Creates a new instance.

ASTLowAndExpression - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTLowAndExpression(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTLowAndExpression

Creates a new instance.

ASTLowAndExpression(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTLowAndExpression

Creates a new instance.

ASTNonCHHeavyAtom - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTNonCHHeavyAtom(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTNonCHHeavyAtom

ASTNonCHHeavyAtom(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTNonCHHeavyAtom

ASTNotBond - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTNotBond(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTNotBond

Creates a new instance.

ASTNotBond(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTNotBond

Creates a new instance.

ASTNotExpression - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTNotExpression(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTNotExpression

Creates a new instance.

ASTNotExpression(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTNotExpression

Creates a new instance.

ASTOrBond - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTOrBond(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTOrBond

Creates a new instance.

ASTOrBond(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTOrBond

Creates a new instance.

ASTOrExpression - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTOrExpression(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTOrExpression

Creates a new instance.

ASTOrExpression(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTOrExpression

Creates a new instance.

ASTPeriodicGroupNumber - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTPeriodicGroupNumber(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTPeriodicGroupNumber

ASTPeriodicGroupNumber(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTPeriodicGroupNumber

ASTPrimitiveAtomExpression - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTPrimitiveAtomExpression(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTPrimitiveAtomExpression

Creates a new instance.

ASTPrimitiveAtomExpression(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTPrimitiveAtomExpression

Creates a new instance.

ASTReaction - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTReaction(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTReaction

Creates a new instance.

ASTReaction(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTReaction

Creates a new instance.

ASTRecursiveSmartsExpression - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTRecursiveSmartsExpression(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTRecursiveSmartsExpression

Creates a new instance.

ASTRecursiveSmartsExpression(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTRecursiveSmartsExpression

Creates a new instance.

ASTRingConnectivity - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTRingConnectivity(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTRingConnectivity

Creates a new instance/

ASTRingConnectivity(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTRingConnectivity

Creates a new instance.

ASTRingIdentifier - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTRingIdentifier(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTRingIdentifier

Creates a new instance.

ASTRingIdentifier(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTRingIdentifier

Creates a new instance.

ASTRingMembership - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTRingMembership(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTRingMembership

Creates a new instance.

ASTRingMembership(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTRingMembership

Creates a new instance.

ASTSimpleBond - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTSimpleBond(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTSimpleBond

Creates a new instance.

ASTSimpleBond(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTSimpleBond

Creates a new instance.

ASTSmallestRingSize - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTSmallestRingSize(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTSmallestRingSize

Creates a new instance.

ASTSmallestRingSize(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTSmallestRingSize

Creates a new instance.

ASTSmarts - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTSmarts(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTSmarts

Creates a new instance.

ASTSmarts(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTSmarts

Creates a new instance.

ASTStart - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTStart(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTStart

Creates a new instance

ASTStart(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTStart

Creates a new instance

ASTTotalConnectivity - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTTotalConnectivity(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTTotalConnectivity

Creates a new instance.

ASTTotalConnectivity(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTTotalConnectivity

Creates a new instance.

ASTTotalHCount - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTTotalHCount(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTTotalHCount

Creates a new instance.

ASTTotalHCount(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTTotalHCount

Creates a new instance.

ASTValence - Class in org.openscience.cdk.smiles.smarts.parser

An AST node.

ASTValence(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTValence

Creates a new instance.

ASTValence(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.ASTValence

Creates a new instance.

AT - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

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

Constructs an Atom from a String containing an element symbol.

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.

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.

AtomContainerAtomPermutor - Class in org.openscience.cdk.graph

This class allows to iterate trough the set of all possible permutations of the atom order in a given atom container.

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

AtomContainerBondPermutor - Class in org.openscience.cdk.graph

This class allows to iterate trough the set of all possible permutations of the bond order in a given atom container.

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

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

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

Compares two IAtomContainer classes.

AtomContainerDiff() - Constructor for class org.openscience.cdk.tools.diff.AtomContainerDiff

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 permutation code here is based on a pseudo code example on a tutorial site created and maintained by Phillip P.

AtomContainerPermutor() - Constructor for class org.openscience.cdk.graph.AtomContainerPermutor

atomContainers() - Method in class org.openscience.cdk.AtomContainerSet

Get an iterator for this AtomContainerSet.

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

atomContainers() - Method in class org.openscience.cdk.debug.DebugMoleculeSet

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

Get an Iterable 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.

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

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

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.

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

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

Compares two IAtom classes.

AtomDiff() - Constructor for class org.openscience.cdk.tools.diff.AtomDiff

AtomExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

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 - Static variable in class org.openscience.cdk.qsar.DescriptorEngine

AtomicMass() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

AtomicNumber() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

AtomicNumberAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts

This matches an atom using the atomic number.

AtomicNumberAtom(int) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.AtomicNumberAtom

Creates a new instance.

AtomicNumberDifferenceDescriptor - Class in org.openscience.cdk.qsar.descriptors.bond

Describes the imbalance in atomic number of the IBond.

AtomicNumberDifferenceDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptor

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

AtomParity - Class in org.openscience.cdk

Represents the concept of an atom parity identifying the stereochemistry around an atom, given four neighbouring atoms.

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

Constructs an completely unset AtomParity.

AtomPlacer - Class in org.openscience.cdk.layout

Methods for generating coordinates for atoms in various situations.

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

Constructor for the AtomPlacer object

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

Place aliphatic chains with Z matrix method.

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

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

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

Returns the Iterator to atoms making up this bond.

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

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

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

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

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

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

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

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

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

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

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.

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_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.

AtomTypeCharges - Class in org.openscience.cdk.charges

Assigns charges to atom types.

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

Compares two IAtomType classes.

AtomTypeDiff() - Constructor for class org.openscience.cdk.tools.diff.AtomTypeDiff

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 AtomType class.

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

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

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

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

XML Reader for the CDKBasedAtomTypeConfigurator.

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

Instantiates the XML based AtomTypeReader.

AtomTypeTools - Class in org.openscience.cdk.tools

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

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

Constructor for the MMFF94AtomTypeMatcher object.

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

This class returns the valence of an atom.

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

Constructor for the AtomValenceDescriptor object

AtomValenceTool - Class in org.openscience.cdk.qsar

This class returns the valence of an atom.

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

AttachedGroup - Class in org.openscience.cdk.iupac.parser

Holds data on a specific functional group or substituent.

AttachedGroup() - Constructor for class org.openscience.cdk.iupac.parser.AttachedGroup

Creates a new instance of FunctionalGroup

AttachedGroup(Vector, String) - Constructor for class org.openscience.cdk.iupac.parser.AttachedGroup

Creates a new instance of AttachedGroup with a Sting denoting the functional group

AttachedGroup(Vector, int) - Constructor for class org.openscience.cdk.iupac.parser.AttachedGroup

Creates a new instance of AttachedGroup with an int denoting the length of the substituent chain

attachLocationSpecified() - Method in class org.openscience.cdk.iupac.parser.NomParser

An attach position has been specified using a comma seperated list followed by a dash

AU - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

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

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

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

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

This class calculates ATS autocorrelation descriptor, where the weight equal to the scaled atomic mass [Moreau G. and Broto P., The autocorrelation of a topological structure: A new molecular descriptor, Nouveau Journal de Chimie, 1980, ?:359-360].

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

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

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

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

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

The IUPAC compatible name generated with AutoNom.

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

Method performs a scan; works only for cubic grids!

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

Method performs a scan; works only for cubic grids!

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

Method performs a scan; works only for cubic grids!

B

B - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

BA - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

backup(int) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream

backup(int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream

BadMatrixFormatException - Exception in org.openscience.cdk.graph.invariant.exception

BadMatrixFormatException() - Constructor for exception org.openscience.cdk.graph.invariant.exception.BadMatrixFormatException

BARIUM - Static variable in class org.openscience.cdk.config.Elements

BARIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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

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

Eigenvalue based descriptor noted for its utility in chemical diversity.

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

BE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

beginColumn - Variable in class org.openscience.cdk.iupac.parser.Token

beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.

beginColumn - Variable in class org.openscience.cdk.smiles.smarts.parser.Token

beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.

beginLine - Variable in class org.openscience.cdk.iupac.parser.Token

beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.

beginLine - Variable in class org.openscience.cdk.smiles.smarts.parser.Token

beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.

BeginToken() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream

BeginToken() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream

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

The Beilstein Registry Number.

BELOWAREA - Static variable in class org.openscience.cdk.renderer.GraphRendererModel

Paints the area below the function

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

BERKELIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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

BERYLLIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

BFSShortestPath - Class in org.openscience.cdk.graph

Utility class that finds the shortest bond path between two atoms using a breadth first search.

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

BI - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

biconnectedSets() - Method in class org.openscience.cdk.graph.BiconnectivityInspector

Returns a list of Sets, where each set contains all edge that are in the same biconnected component.

BiconnectivityInspector - Class in org.openscience.cdk.graph

Finds the biconnected components of a graph.

BiconnectivityInspector(UndirectedGraph) - Constructor for class org.openscience.cdk.graph.BiconnectivityInspector

Creates a biconnectivity inspector for the specified undirected graph.

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.

BISMUTH - Static variable in class org.openscience.cdk.config.Elements

BISMUTH - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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).

BK - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

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

Double constant that contains the convertion 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 class org.openscience.cdk.config.Elements

BOHRIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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, int) - 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.qsar.DescriptorEngine

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

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

Compares two IBond classes.

BondDiff() - Constructor for class org.openscience.cdk.tools.diff.BondDiff

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

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

A bond of degree 2.0.

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

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

A bond of degree 1.0.

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

A bond of degree 3.0.

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

IDifference between two IBond.Orders.

BondPartialPiChargeDescriptor - Class in org.openscience.cdk.qsar.descriptors.bond

The calculation of bond-pi Partial charge is calculated determining the difference the Partial Pi Charge on atoms A and B of a bond.

BondPartialPiChargeDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor

Constructor for the BondPartialPiChargeDescriptor object

BondPartialSigmaChargeDescriptor - Class in org.openscience.cdk.qsar.descriptors.bond

The calculation of bond-sigma Partial charge is calculated determining the difference the Partial Sigma Charge on atoms A and B of a bond.

BondPartialSigmaChargeDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor

Constructor for the BondPartialSigmaChargeDescriptor object

BondPartialTChargeDescriptor - Class in org.openscience.cdk.qsar.descriptors.bond

The calculation of bond total Partial charge is calculated determining the difference the Partial Total Charge on atoms A and B of a bond.

BondPartialTChargeDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor

Constructor for the BondPartialTChargeDescriptor object

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

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

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

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

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

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

bonds() - Method in class org.openscience.cdk.debug.DebugMolecule

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

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

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

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

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

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

BondSigmaElectronegativityDescriptor - Class in org.openscience.cdk.qsar.descriptors.bond

The calculation of bond-Polarizability is calculated determining the difference the Sigma electronegativity on atoms A and B of a bond.

BondSigmaElectronegativityDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor

Constructor for the BondSigmaElectronegativityDescriptor object

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

BondStretching - Class in org.openscience.cdk.modeling.forcefield

Bond Stretching calculator for the potential energy function.

BondStretching() - Constructor for class org.openscience.cdk.modeling.forcefield.BondStretching

Constructor for the BondStretching object

BondTools - Class in org.openscience.cdk.geometry

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

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

bondType() - Method in class org.openscience.cdk.iupac.parser.NomParser

Tokens which affect the bond order of the first bond.

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

Difference between two boolean[]'s.

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

IDifference between two Booleans.

BooleanIOSetting - Class in org.openscience.cdk.io.setting

An class for a reader setting which must be of type String.

BooleanIOSetting(String, int, String, String) - Constructor for class org.openscience.cdk.io.setting.BooleanIOSetting

BooleanResult - Class in org.openscience.cdk.qsar.result

Object that provides access to the calculated descriptor value.

BooleanResult(boolean) - Constructor for class org.openscience.cdk.qsar.result.BooleanResult

BooleanResultType - Class in org.openscience.cdk.qsar.result

IDescriptorResult type for booleans.

BooleanResultType() - Constructor for class org.openscience.cdk.qsar.result.BooleanResultType

booleanValue() - Method in class org.openscience.cdk.qsar.result.BooleanResult

BORON - Static variable in class org.openscience.cdk.config.Elements

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

Sum of the absolute value of the difference between atomic polarizabilities of all bonded atoms in the molecule (including implicit hydrogens) with polarizabilities taken from http://www.sunysccc.edu/academic/mst/ptable/p-table2.htm This descriptor assumes 2-centered bonds.

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

Constructor for the APolDescriptor object

BR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

bracketingTheMinimum() - Method in class org.openscience.cdk.modeling.forcefield.LineSearch

Bracketing the minimum: The bracketing phase determines the range of points on the line to be searched.

breadthFirstSearch(IAtomContainer, List<IAtom>, IMolecule) - 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>, IMolecule, 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, Vector, IAtomContainer[]) - 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

brentsMethod() - Method in class org.openscience.cdk.modeling.forcefield.LineSearch

Given a function f, and given a bracketing triplet of abscissas lambdaa, lambdab, lambdac (such that lambdab is between lambdaa and lambdac, and f(lambdab) is less than both f(lambdaa) and f(lambdac)), this routine isolates the minimum to a fractional precision of about t01=0.00001 using Brent`s method.

BROMINE - Static variable in class org.openscience.cdk.config.Elements

BROMO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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

See here.

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

bufpos - Variable in class org.openscience.cdk.iupac.parser.SimpleCharStream

bufpos - Variable in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream

build() - Method in interface org.openscience.cdk.qsar.model.IModel

Builds (trains) the model.

build() - Method in class org.openscience.cdk.qsar.model.R.CNNClassificationModel

Deprecated. Fits a CNN classification model.

build() - Method in class org.openscience.cdk.qsar.model.R.CNNRegressionModel

Deprecated. Fits a CNN regression model.

build() - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModel

Deprecated. Fits a linear regression model.

build() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModel

Deprecated. Fits a PLS model.

build() - Method in class org.openscience.cdk.qsar.model.R.RModel

Deprecated.

build() - Method in class org.openscience.cdk.qsar.model.R2.CNNRegressionModel

Fits a CNN regression model.

build() - Method in class org.openscience.cdk.qsar.model.R2.LinearRegressionModel

Fits a linear regression model.

build() - Method in class org.openscience.cdk.qsar.model.R2.RModel

buildBondMatrix() - Method in class org.openscience.cdk.graph.invariant.EquivalentClassPartitioner

Build bond matrix

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

BUT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

byAtomicNumber - Static variable in class org.openscience.cdk.config.Symbols

C

c - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

C - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

CA - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

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

See here.

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

See here.

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

CADMIUM - Static variable in class org.openscience.cdk.config.Elements

CADMIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

CAESIUM - Static variable in class org.openscience.cdk.config.Elements

calcD(double, double, double, double, Vector, Vector) - Method in class org.openscience.cdk.math.qm.GaussiansBasis

calcG(int, double, double, double, double, double, double) - Method in class org.openscience.cdk.math.qm.GaussiansBasis

Transfer equation for the calculation of core potentials

calcG(int, int, double, double, double, double, double, double, double, double, double) - Method in class org.openscience.cdk.math.qm.GaussiansBasis

Transfer equation for a four center integral.

calcI(int, int, int, int) - Method in class org.openscience.cdk.math.qm.FourierGridBasis

calcI(int, int, int, int, double, double, double, double, double, double, double, double, double) - Method in class org.openscience.cdk.math.qm.GaussiansBasis

Transfer equation for a four center integral.

calcI(int, int, int, int) - Method in class org.openscience.cdk.math.qm.GaussiansBasis

calcI(int, int, int, int) - Method in interface org.openscience.cdk.math.qm.IBasis

Calculates a two eletron fout center integral I = <chi_i chi_j | 1/r12 | chi_k chi_l >.

calcInvertedAxes(Vector3d, Vector3d, Vector3d) - Static method in class org.openscience.cdk.geometry.CrystalGeometryTools

Inverts three cell axes.

CALCIUM - Static variable in class org.openscience.cdk.config.Elements

CALCIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

calcJ(int, int) - Method in class org.openscience.cdk.math.qm.FourierGridBasis

calcJ(int, int, double, double, double, double) - Method in class org.openscience.cdk.math.qm.GaussiansBasis

Transfer equation the the calculation of the impulse

calcJ(int, int) - Method in class org.openscience.cdk.math.qm.GaussiansBasis

calcJ(int, int) - Method in interface org.openscience.cdk.math.qm.IBasis

Calculates the impulse J = -<d/dr chi_i | d/dr chi_j>.

calcS(int, int) - Method in class org.openscience.cdk.math.qm.FourierGridBasis

calcS(int, int) - Method in class org.openscience.cdk.math.qm.GaussiansBasis

calcS(int, int) - Method in interface org.openscience.cdk.math.qm.IBasis

Calculate the overlap integral S = <phi_i|phi_j>.

calculate(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() - Method in class org.openscience.cdk.math.qm.ClosedShellJob

calculate() - Method in class org.openscience.cdk.math.qm.OneElectronJob

calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor

This method calculates the number of not-H substituents of an atom.

calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor

This method calculates the hybridization of an atom.

calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor

This method calculates the hybridization of an atom.

calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor

This method calculates the valence of an atom.

calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor

This method calculate the number of bonds on the shortest path between two atoms.

calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor

This method calculate the Covalent radius of an atom.

calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor

This method calculate the 3D distance between two atoms.

calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor

The method calculates the Effective Atom Polarizability of a given atom It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.

calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor

It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder, and 3D coordinates.

calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor

It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder, and 3D coordinates.

calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor

This method calculates the ionization potential of an atom.

calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor

This method calculates the ionization potential of an atom.

calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor

The method is a proton descriptor that evaluate if a proton is bonded to an aromatic system or if there is distance of 2 bonds.

calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInConjugatedPiSystemDescriptor

The method is a proton descriptor that evaluates if a proton is joined to a conjugated system.

calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor

The method returns apha partial charges assigned to an heavy atom through Gasteiger Marsili It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.

calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor

The method returns apha partial charges assigned to an heavy atom through Gasteiger Marsili It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.

calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor

The method returns partial charges assigned to an heavy atom through MMFF94 method.

calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor

The method returns partial total charges assigned to an heavy atom through PEOE method.

calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor

This method calculates the period of an atom.

calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor

The method calculates the pi electronegativity of a given atom It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.

calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor

This method calculates the protonation affinity of an atom.

calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor

The method returns partial charges assigned to an heavy atom and its protons through Gasteiger Marsili It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.

calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R

calculate(IAtom, IAtomContainer, IRingSet) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R

calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR

calculate(IAtom, IAtomContainer, IRingSet) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR

calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR

calculate(IAtom, IAtomContainer, IRingSet) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR

calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol

calculate(IAtom, IAtomContainer, IRingSet) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol

calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR

calculate(IAtom, IAtomContainer, IRingSet) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR

calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor

The method calculates the sigma electronegativity of a given atom It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.

calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor

The method calculates the stabilization of charge of a given atom It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.

calculate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor

This method calculate the Van der Waals radius of an atom.

calculate(IAtom, IAtom, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor

The method returns if two atoms have pi-contact.

calculate(IBond, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptor

calculate(IBond, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor

The method calculates the bond-pi Partial charge of a given bond It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.

calculate(IBond, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor

The method calculates the bond-sigma Partial charge of a given bond It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.

calculate(IBond, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor

The method calculates the bond total Partial charge of a given bond It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.

calculate(IBond, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor

The method calculates the sigma electronegativity of a given bond It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.

calculate(IBond, IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor

This method calculates the ionization potential of a bond.

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.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.FragmentComplexityDescriptor

Calculate the complexity in the supplied AtomContainer.

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.IPMolecularLearningDescriptor

It calculates the first ionization energy of a molecule.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor

calculates the kier shape indices for an atom container

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor

This method calculates occurrences of the Kier & Hall E-state fragments.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor

Calculate the count of atoms of the largest chain in the supplied IAtomContainer.

calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor

Calculate the count of atoms of the largest pi system in the supplied AtomContainer.

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 AtomContainer.

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.TPSADescriptor

Calculates the TPSA for an atom container.

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(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(BitSet, BitSet) - Static method in class org.openscience.cdk.similarity.Tanimoto

Evaluates Tanimoto coefficient for two bit sets.

calculate(double[], double[]) - Static method in class org.openscience.cdk.similarity.Tanimoto

Evaluates the continuous Tanimoto coefficient for two real valued vectors.

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(AtomContainer, 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.

calculateBondPolarizability(IAtomContainer, IBond) - Method in class org.openscience.cdk.charges.Polarizability

calculate bond polarizability

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

calculateDeltar(GVector) - Method in class org.openscience.cdk.modeling.forcefield.BondStretching

Calculate the actual bond distance rij and the difference with the reference bond distances.

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

calculateNumberOfImplicitHydrogens(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker

Calculate the number of missing hydrogens by substracting 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, boolean) - Method in class org.openscience.cdk.tools.SaturationChecker

Calculate the number of missing hydrogens by substracting 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

calculatePerpendicularUnitVector(Point2d, Point2d) - Static method in class org.openscience.cdk.geometry.GeometryTools

Determines the normalized vector orthogonal on the vector p1->p2.

calculatePiElectronegativity(IAtomContainer, IAtom) - Method in class org.openscience.cdk.charges.PiElectronegativity

calculate the electronegativity of orbitals pi.

calculatePiElectronegativity(IAtomContainer, IAtom, int, int) - Method in class org.openscience.cdk.charges.PiElectronegativity

calculate the electronegativity of orbitals pi.

calculatePlus(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor

It calculates the 1,2,..

calculatePositive(IAtomContainer, IAtom) - Method in class org.openscience.cdk.charges.StabilizationCharges

calculate the stabilization of orbitals when they contain deficiency of charge.

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.

calcV(int, int) - Method in class org.openscience.cdk.math.qm.FourierGridBasis

calcV(int, int, Vector, double) - Method in class org.openscience.cdk.math.qm.GaussiansBasis

Calculates the core potential.

calcV(int, int) - Method in class org.openscience.cdk.math.qm.GaussiansBasis

Calculates the core potential.

calcV(int, int) - Method in interface org.openscience.cdk.math.qm.IBasis

Calculates the potential V = <chi_i | 1/r | chi_j>.

CALIFORNIUM - Static variable in class org.openscience.cdk.config.Elements

CALIFORNIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

CANONICAL_LABEL - Static variable in class org.openscience.cdk.smiles.InvPair

CanonicalLabeler - Class in org.openscience.cdk.graph.invariant

Canonically labels an atom container implementing the algorithm published in David Weininger et.al.

CanonicalLabeler() - Constructor for class org.openscience.cdk.graph.invariant.CanonicalLabeler

canonLabel(IAtomContainer) - Method in class org.openscience.cdk.graph.invariant.CanonicalLabeler

Canonically label the fragment.

CARBON - Static variable in class 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.

CARET - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

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.

CD - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

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

CDKAtomColors - Class in org.openscience.cdk.renderer.color

Gives a short table of atom colors for 3D display.

CDKAtomColors() - Constructor for class org.openscience.cdk.renderer.color.CDKAtomColors

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 occured.

CDKException(String) - Constructor for exception org.openscience.cdk.exception.CDKException

Constructs a new CDKException with the given message.

CDKException(String, Throwable) - Constructor for exception org.openscience.cdk.exception.CDKException

Constructs a new CDKException with the given message and the Exception as cause.

CDKHueckelAromaticityDetector - Class in org.openscience.cdk.aromaticity

This aromaticity detector detects the aromaticity based on the Hückel 4n+2 pi-electrons rule applied to isolated ring systems.

CDKHueckelAromaticityDetector() - Constructor for class org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector

CDKHydrogenAdder - Class in org.openscience.cdk.tools

Adds implicit hydrogens based on atom type definitions.

cdkMoleculeSetToCMLList(IMoleculeSet) - Method in class org.openscience.cdk.libio.cml.Convertor

cdkMoleculeToCMLMolecule(IMolecule) - Method in class org.openscience.cdk.libio.cml.Convertor

cdkMonomerToCMLMolecule(IMonomer) - Method in class org.openscience.cdk.libio.cml.Convertor

cdkPDBPolymerToCMLMolecule(IPDBPolymer) - Method in class org.openscience.cdk.libio.cml.Convertor

CDKPopupMenu - Class in org.openscience.cdk.controller

Basically, identical to the JPopupMenu class, except that this menu can also contain the source for which it was popped up.

CDKPopupMenu() - Constructor for class org.openscience.cdk.controller.CDKPopupMenu

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

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

CDKUtilities - Class in org.openscience.cdk.tools

Utility class written by Todd Martin, for help in his QSAR descriptors and SMILES parser.

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

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 datastructures, and tries to detect inconsistencies in it.

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

CE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

center(IAtomContainer, Dimension) - Static method in class org.openscience.cdk.geometry.GeometryTools

Centers the molecule in the given area See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets

CERIUM - Static variable in class org.openscience.cdk.config.Elements

CERIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

CESIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

CF - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

chainPrefix() - Method in class org.openscience.cdk.iupac.parser.NomParser

A list of known tokens denoting a chain's length.

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.elements.ElementPTHandler

characters(char[], int, int) - Method in class org.openscience.cdk.config.isotopes.IsotopeHandler

characters(char[], int, int) - Method in class org.openscience.cdk.dict.DictionaryHandler

characters(char[], int, int) - Method in class org.openscience.cdk.io.cml.CMLHandler

Implementation of the characters() procedure overwriting the DefaultHandler interface.

characters(char[], int, int) - Method in class org.openscience.cdk.io.inchi.INChIHandler

Implementation of the characters() procedure overwriting the DefaultHandler interface.

Charge() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

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.

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.

checkConvergence(double) - Method in class org.openscience.cdk.modeling.forcefield.GeometricMinimizer

To check convergence

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

checkSingleAtomCases(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester

Checks for single atom cases before doing subgraph/isomorphism search.

checkTimeout() - Method in class org.openscience.cdk.ringsearch.AllRingsFinder

Checks if the timeout has been reached and throws an exception if so.

Chem3D_Cartesian_1Format - Class in org.openscience.cdk.io.formats

Chem3D_Cartesian_2Format - Class in org.openscience.cdk.io.formats

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

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.

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.

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

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

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

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.

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.

ChemObjectDiff() - Constructor for class org.openscience.cdk.tools.diff.ChemObjectDiff

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

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.

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

Returns the Iterable to ChemSequences of this container.

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

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

Returns the Iterable to ChemSequences of this container.

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

See here.

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

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

Utility methods for chi index calculations.

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

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

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

childrenAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleNode

Accept the visitor.

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

Chirality() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

ChiralityAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts

This matches an atom with chirality property.

ChiralityAtom() - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom

Creates a new instance

CHLORINE - Static variable in class org.openscience.cdk.config.Elements

CHLORO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

CHROMIUM - Static variable in class org.openscience.cdk.config.Elements

CHROMIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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

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

CL - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

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.

clone() - Method in class org.openscience.cdk.AminoAcid

Clones this AminoAcid object.

clone() - Method in class org.openscience.cdk.Atom

Clones this atom object and its content.

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

Clones this AtomContainer object and its content.

clone() - Method in class org.openscience.cdk.AtomContainerSet

Clones this AtomContainerSet and its content.

clone() - Method in class org.openscience.cdk.AtomParity

Clones this AtomParity object.

clone() - Method in class org.openscience.cdk.AtomType

clone() - Method in class org.openscience.cdk.BioPolymer

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

Clones this bond object, including clones of the atoms between which the bond is defined.

clone() - Method in class org.openscience.cdk.ChemFile

Allows for getting an clone of this object.

clone() - Method in class org.openscience.cdk.ChemModel

Clones this ChemModel and its content.

clone() - Method in class org.openscience.cdk.ChemObject

Clones this IChemObject.

clone() - Method in class org.openscience.cdk.ChemSequence

clone() - Method in class org.openscience.cdk.Crystal

Makes a clone of this crystal.

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

clone() - Method in class org.openscience.cdk.debug.DebugAtom

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

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

clone() - Method in class org.openscience.cdk.debug.DebugAtomType

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

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

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

clone() - Method in class org.openscience.cdk.debug.DebugChemModel

clone() - Method in class org.openscience.cdk.debug.DebugChemObject

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

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

clone() - Method in class org.openscience.cdk.debug.DebugElectronContainer

clone() - Method in class org.openscience.cdk.debug.DebugElement

clone() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

clone() - Method in class org.openscience.cdk.debug.DebugIsotope

clone() - Method in class org.openscience.cdk.debug.DebugLonePair

clone() - Method in class org.openscience.cdk.debug.DebugMapping

clone() - Method in class org.openscience.cdk.debug.DebugMolecule

clone() - Method in class org.openscience.cdk.debug.DebugMoleculeSet

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

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

clone() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

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

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

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

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

clone() - Method in class org.openscience.cdk.debug.DebugSingleElectron

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

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 interface org.openscience.cdk.interfaces.IAdductFormula

Clones this IAdductFormula object and its content.

clone() - Method in interface org.openscience.cdk.interfaces.IChemObject

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.IReactionScheme

Clones this IReactionScheme object and its content.

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.Molecule

clone() - Method in class org.openscience.cdk.MoleculeSet

Clones this MoleculeSet and its content.

clone() - Method in class org.openscience.cdk.PeriodicTableElement

Clones this element object.

clone() - Method in class org.openscience.cdk.Polymer

clone() - Method in class org.openscience.cdk.PseudoAtom

clone() - Method in class org.openscience.cdk.Reaction

Clones this Reaction and its content.

clone() - Method in class org.openscience.cdk.ReactionScheme

Clones this ReactionScheme object and its content.

clone() - Method in class org.openscience.cdk.ReactionSet

Clones this ReactionSet and the contained Reactions too.

clone() - Method in class org.openscience.cdk.RingSet

Clones this RingSet including the Rings.

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.smiles.smarts.parser.SimpleNode

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.IteratingMDLReader

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.IteratingSMILESReader

Close the reader.

close() - Method in class org.openscience.cdk.io.MDLReader

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

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

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

close() - Method in class org.openscience.cdk.io.MDLRXNWriter

Flushes the output and closes this object.

close() - Method in class org.openscience.cdk.io.MDLV2000Reader

close() - Method in class org.openscience.cdk.io.MDLV3000Reader

close() - Method in class org.openscience.cdk.io.MDLWriter

Flushes the output and closes this object.

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.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.random.RandomAccessReader

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

ClosedShellJob - Class in org.openscience.cdk.math.qm

Calculates the orbitals and orbital energies of electron systems with closed shells

ClosedShellJob(Orbitals) - Constructor for class org.openscience.cdk.math.qm.ClosedShellJob

closeEnoughToBond(IAtom, IAtom, double) - Static method in class org.openscience.cdk.geometry.BondTools

Returns true if the two atoms are within the distance fudge factor of each other.

clusterPSPPocket(Point3d, List<Point3d>, int[]) - Method in class org.openscience.cdk.protein.ProteinPocketFinder

Method performs the clustering, is called by findPockets().

CM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

CMLCoreModule - Class in org.openscience.cdk.io.cml

Core CML 1.x and 2.x elements are parsed by this class.

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.

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.

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

CMLStack - Class in org.openscience.cdk.io.cml

Low weigth alternative to Sun's Stack class.

CMLStack() - Constructor for class org.openscience.cdk.io.cml.CMLStack

CMLWriter - Class in org.openscience.cdk.io

Serializes a IMoleculeSet or a IMolecule 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

CNNClassificationModel - Class in org.openscience.cdk.qsar.model.R

Deprecated.

CNNClassificationModel() - Constructor for class org.openscience.cdk.qsar.model.R.CNNClassificationModel

Deprecated. Constructs a CNNClassificationModel object.

CNNClassificationModel(double[][], String[], int) - Constructor for class org.openscience.cdk.qsar.model.R.CNNClassificationModel

Deprecated. Constructs a CNNClassificationModel object.

CNNClassificationModel(double[][], String[][], int) - Constructor for class org.openscience.cdk.qsar.model.R.CNNClassificationModel

Deprecated. Constructs a CNNClassificationModel object.

CNNClassificationModelFit - Class in org.openscience.cdk.qsar.model.R

Deprecated.

CNNClassificationModelFit(int, int, double[], double[], double[], double, double[]) - Constructor for class org.openscience.cdk.qsar.model.R.CNNClassificationModelFit

Deprecated. Constructs an object to contain a CNN classification fit.

CNNClassificationModelFit(int, int, double[], double[], double[], double) - Constructor for class org.openscience.cdk.qsar.model.R.CNNClassificationModelFit

Deprecated. Constructs an object to contain a CNN classification fit.

CNNClassificationModelPredict - Class in org.openscience.cdk.qsar.model.R

Deprecated.

CNNClassificationModelPredict(int, double[]) - Constructor for class org.openscience.cdk.qsar.model.R.CNNClassificationModelPredict

Deprecated. Create an object to hold predictions from a previously built CNN model.

CNNClassificationModelPredict(int, double) - Constructor for class org.openscience.cdk.qsar.model.R.CNNClassificationModelPredict

Deprecated. Create an object to hold predictions from a previously built CNN model.

CNNClassificationModelPredict(String[]) - Constructor for class org.openscience.cdk.qsar.model.R.CNNClassificationModelPredict

Deprecated. Create an object to hold predictions from a previously built CNN model.

CNNClassificationModelPredict(String) - Constructor for class org.openscience.cdk.qsar.model.R.CNNClassificationModelPredict

Deprecated. Create an object to hold predictions from a previously built CNN model.

CNNRegressionModel - Class in org.openscience.cdk.qsar.model.R

Deprecated.

CNNRegressionModel() - Constructor for class org.openscience.cdk.qsar.model.R.CNNRegressionModel

Deprecated. Constructs a CNNRegressionModel object.

CNNRegressionModel(double[][], double[], int) - Constructor for class org.openscience.cdk.qsar.model.R.CNNRegressionModel

Deprecated. Constructs a CNNRegressionModel object.

CNNRegressionModel(double[][], double[][], int) - Constructor for class org.openscience.cdk.qsar.model.R.CNNRegressionModel

Deprecated. Constructs a CNNRegressionModel object.

CNNRegressionModel - Class in org.openscience.cdk.qsar.model.R2

A modeling class that provides a computational neural network regression model.

CNNRegressionModel() - Constructor for class org.openscience.cdk.qsar.model.R2.CNNRegressionModel

Constructs a CNNRegressionModel object.

CNNRegressionModel(double[][], double[], int) - Constructor for class org.openscience.cdk.qsar.model.R2.CNNRegressionModel

Constructs a CNNRegressionModel object.

CNNRegressionModel(double[][], double[][], int) - Constructor for class org.openscience.cdk.qsar.model.R2.CNNRegressionModel

Constructs a CNNRegressionModel object.

CNNRegressionModelFit - Class in org.openscience.cdk.qsar.model.R

Deprecated.

CNNRegressionModelFit(int, int, double[], double[], double[], double, double[]) - Constructor for class org.openscience.cdk.qsar.model.R.CNNRegressionModelFit

Deprecated. Constructs an object to contain a CNN regression fit.

CNNRegressionModelFit(int, int, double[], double[], double[], double) - Constructor for class org.openscience.cdk.qsar.model.R.CNNRegressionModelFit

Deprecated. Constructs an object to contain a CNN regression fit.

CNNRegressionModelPredict - Class in org.openscience.cdk.qsar.model.R

Deprecated.

CNNRegressionModelPredict(int, double[]) - Constructor for class org.openscience.cdk.qsar.model.R.CNNRegressionModelPredict

Deprecated. Create an object to hold predictions from a previously built CNN model.

CNNRegressionModelPredict(int, double) - Constructor for class org.openscience.cdk.qsar.model.R.CNNRegressionModelPredict

Deprecated. Create an object to hold predictions from a previously built CNN model.

CNNRegressionModelSummary - Class in org.openscience.cdk.qsar.model.R

Deprecated.

CNNRegressionModelSummary(int[], boolean, boolean, boolean, double, double[]) - Constructor for class org.openscience.cdk.qsar.model.R.CNNRegressionModelSummary

Deprecated. Constructor for an object that wraps the return value from summary.lm.

CNNRegressionModelSummary(double[], boolean, boolean, boolean, double, double[]) - Constructor for class org.openscience.cdk.qsar.model.R.CNNRegressionModelSummary

Deprecated. Constructor for an object that wraps the return value from summary.lm.

CO - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

COBALT - Static variable in class org.openscience.cdk.config.Elements

COBALT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

columns - Variable in class org.openscience.cdk.math.IMatrix

the count of columns of the matrix

columns - Variable in class org.openscience.cdk.math.Matrix

the number of columns of this matrix

COMMA - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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

A String comment.

commit() - Method in class org.openscience.cdk.smiles.InvPair

compare(Object) - Method in class org.openscience.cdk.Atom

Compares a atom with this atom.

compare(Object) - Method in class org.openscience.cdk.AtomType

Compares a atom type with this atom type.

compare(Object) - Method in class org.openscience.cdk.Bond

Compares a bond with this bond.

compare(Object) - Method in class org.openscience.cdk.ChemObject

Compares a IChemObject with this IChemObject.

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

compare(Object) - Method in class org.openscience.cdk.Element

Compares an Element with this Element.

compare(IsotopePattern, IsotopePattern) - Method in class org.openscience.cdk.formula.IsotopePatternSimilarity

Compare the IMolecularFormula with a isotope abundance pattern.

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

Compares a bond with this bond.

compare(Object) - Method in class org.openscience.cdk.Isotope

Compares a atom type with this atom type.

compare(Object, Object) - 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(Object, Object) - Method in class org.openscience.cdk.tools.manipulator.AtomContainerComparator

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

completeChemicalName() - Method in class org.openscience.cdk.iupac.parser.NomParser

The general form all chemical names must follow.

Complex - Class in org.openscience.cdk.math

This class handles complex values.

Complex(double, double) - Constructor for class org.openscience.cdk.math.Complex

Creates a complex number

Complex(Complex) - Constructor for class org.openscience.cdk.math.Complex

Creates a copy of a complex object

computeFloydAPSP(int[][]) - Static method in class org.openscience.cdk.graph.PathTools

All-Pairs-Shortest-Path computation based on Floyds algorithm.

computeFloydAPSP(double[][]) - Static method in class org.openscience.cdk.graph.PathTools

All-Pairs-Shortest-Path computation based on Floyds algorithm Takes an nxn matrix C of edge costs and produces an nxn matrix A of lengths of shortest paths.

configure(IAtom) - Method in class org.openscience.cdk.config.AtomTypeFactory

Configures an atom.

configure(PeriodicTableElement) - Method in class org.openscience.cdk.config.ElementPTFactory

Configures a PeriodicTableElement.

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.

configureE(PeriodicTableElement) - Method in class org.openscience.cdk.config.ElementPTFactory

Configures a IElement given a PeridicTableElement.

configureLog4j() - Static method in class org.openscience.cdk.tools.LoggingTool

Forces the LoggingTool to configurate 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

ConjugateGradientMethod - Class in org.openscience.cdk.modeling.forcefield

Find a decrease direction of the energy fuction from a point of the 3xN coordinates space using the conjugate gradient approach.

ConjugateGradientMethod() - Constructor for class org.openscience.cdk.modeling.forcefield.ConjugateGradientMethod

Constructor for the ConjugateGradientMethod object

conjugateGradientMinimization(GVector, IPotentialFunction) - Method in class org.openscience.cdk.modeling.forcefield.GeometricMinimizer

Minimize the potential energy function using conjugate gradient method

connectingFunctionalGroupsConstruct() - Method in class org.openscience.cdk.iupac.parser.NomParser

The layout of a functional group(s) which can connect anywhere.

connectingFunctionalGroupSuffix() - Method in class org.openscience.cdk.iupac.parser.NomParser

Functional groups suffixs for groups which can be connected anywhere along the main chain.

ConnectionCountAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts

This matcher checks the total valency of the Atom.

ConnectionCountAtom(int) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.ConnectionCountAtom

Creates a new instance

ConnectionMatrix - Class in org.openscience.cdk.graph.matrix

Calculator for a connection matrix representation of this AtomContainer.

ConnectionMatrix() - Constructor for class org.openscience.cdk.graph.matrix.ConnectionMatrix

ConnectivityChecker - Class in org.openscience.cdk.graph

Tool class for checking whether the (sub)structure in an AtomContainer is connected.

ConnectivityChecker() - Constructor for class org.openscience.cdk.graph.ConnectivityChecker

CONSTANT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

construct(String, IAtomType.Hybridization, IAtomType.Hybridization) - Static method in class org.openscience.cdk.tools.diff.tree.AtomTypeHybridizationDifference

construct(String, IBond.Order, IBond.Order) - Static method in class org.openscience.cdk.tools.diff.tree.BondOrderDifference

construct(String, boolean[], boolean[]) - Static method in class org.openscience.cdk.tools.diff.tree.BooleanArrayDifference

construct(String, Boolean, Boolean) - Static method in class org.openscience.cdk.tools.diff.tree.BooleanDifference

construct(String, Double, Double) - Static method in class org.openscience.cdk.tools.diff.tree.DoubleDifference

construct(String, Integer, Integer) - Static method in class org.openscience.cdk.tools.diff.tree.IntegerDifference

construct(String, Point2d, Point2d) - Static method in class org.openscience.cdk.tools.diff.tree.Point2dDifference

construct(String, Point3d, Point3d) - Static method in class org.openscience.cdk.tools.diff.tree.Point3dDifference

construct(String, String, String) - Static method in class org.openscience.cdk.tools.diff.tree.StringDifference

CONT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

contains(IAtom) - Method in class org.openscience.cdk.Association

Returns true if the given atom participates in this Association.

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

True, if the AtomContainer contains the given atom object.

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

True, if the AtomContainer contains the given bond object.

contains(ILonePair) - Method in class org.openscience.cdk.AtomContainer

True, if the AtomContainer contains the given LonePair object.

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

True, if the AtomContainer contains the given SingleElectron object.

contains(IElectronContainer) - Method in class org.openscience.cdk.AtomContainer

True, if the AtomContainer contains the given ElectronContainer object.

contains(IAtom) - Method in class org.openscience.cdk.Bond

Returns true if the given atom participates in this bond.

contains(Object) - Method in class org.openscience.cdk.ConformerContainer

Checks to see whether the specified conformer is currently stored.

contains(IIsotope) - Method in class org.openscience.cdk.debug.DebugAdductFormula

contains(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugAdductFormula

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

contains(IAtom) - Method in class org.openscience.cdk.debug.DebugLonePair

contains(IIsotope) - Method in class org.openscience.cdk.debug.DebugMolecularFormula

contains(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet

contains(IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule

contains(IBond) - Method in class org.openscience.cdk.debug.DebugMolecule

contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugMolecule

contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugMolecule

contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugMolecule

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

contains(IAtom) - Method in class org.openscience.cdk.debug.DebugRingSet

contains(IAtom) - Method in class org.openscience.cdk.debug.DebugSingleElectron

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

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

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

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

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

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 class org.openscience.cdk.LonePair

Returns true if the given atom participates in this lone pair.

contains(IAtom) - Method in class org.openscience.cdk.RingSet

True, if at least one of the rings in the ringset contains the given atom.

contains(IAtomContainer) - Method in class org.openscience.cdk.RingSet

Checks for presence of a ring in this RingSet.

contains(IAtom) - Method in class org.openscience.cdk.SingleElectron

Returns true if the given atom participates in this SingleElectron.

contains(IMolecularFormulaSet, IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaSetManipulator

True, if the IMolecularFormulaSet contains the given IMolecularFormula but not as object.

containsAll(Collection<?>) - Method in class org.openscience.cdk.ConformerContainer

containsByID(IAtomContainerSet, String) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator

Tells if an AtomContainerSet contains at least one AtomContainer with the same ID as atomContainer.

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

True, if the MolecularFormula contains the given element as IIsotope object.

contraction() - Method in class org.openscience.cdk.math.IMatrix

Calculates the contraction from a matrix

contraction() - Method in class org.openscience.cdk.math.Matrix

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.

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.

COPPER - Static variable in class org.openscience.cdk.config.Elements

COPPER - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

COS - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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.

countExplicitHydrogens(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator

countHydrogens(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator

countMatches() - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool

Returns the number of times the pattern was found in the target molecule.

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

This class return 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

Colors atoms using CPK color scheme [Bernstein, H.J., Manual RasMol 2.7.2.1 - CPK Colours].

CPKAtomColors() - Constructor for class org.openscience.cdk.renderer.color.CPKAtomColors

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

Calculates 29 Charged Partial Surface Area (CPSA) descriptors.

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

CR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

createAAs() - Static method in class org.openscience.cdk.templates.AminoAcids

Creates amino acid AminoAcid objects.

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

Generates a cloned atomcontainer with all atoms being carbon, all bonds being single non-aromatic

createAnyAtomAnyBondContainer(IAtomContainer, boolean) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator

Creates a QueryAtomContainer with wildcard atoms and wildcard bonds.

createAnyAtomAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor

createAnyAtomContainer(IAtomContainer, boolean) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator

Creates a QueryAtomContainer with AnyAtoms / Aromatic Atoms and OrderQueryBonds / AromaticQueryBonds.

createAnyAtomForPseudoAtomQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator

Creates a QueryAtomContainer with SymbolQueryAtom's and OrderQueryBond's.

createBasicQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator

Creates a QueryAtomContainer with SymbolQueryAtom's, AromaticQueryBond's and OrderQueryBond's.

createBondOrder(double) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator

Convenience method to convert a double into an IBond.Order.

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

createChemObjectReader() - Method in class org.openscience.cdk.io.random.RandomAccessSDFReader

createChiralSMILES(IMolecule, boolean[]) - Method in class org.openscience.cdk.smiles.SmilesGenerator

Generate canonical and chiral SMILES from the molecule.

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

Method creates a cubic grid with the grid generator class.

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.

createNewMolecule(IChemModel) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator

Adds a new Molecule to the MoleculeSet inside a given ChemModel.

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 there one letter codes.

createReactionScheme(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator

Create a IReactionScheme give a IReactionSet object.

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.

createSMILES(IMolecule) - Method in class org.openscience.cdk.smiles.SmilesGenerator

Generate canonical SMILES from the molecule.

createSMILES(IReaction) - Method in class org.openscience.cdk.smiles.SmilesGenerator

Generate a SMILES for the given Reaction.

createSMILES(IMolecule, boolean, boolean[]) - Method in class org.openscience.cdk.smiles.SmilesGenerator

Generate canonical SMILES from the molecule.

createSymbolAndBondOrderQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator

Creates a QueryAtomContainer with SymbolQueryAtom's and OrderQueryBond's.

createSymbolAndChargeQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator

Creates a QueryAtomContainer with SymbolAncChargeQueryAtom's and OrderQueryBond's.

createSymbolChargeIDQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator

createWriter(IChemFormat) - Method in class org.openscience.cdk.io.WriterFactory

Creates a new IChemObjectWriter based on the given IChemFormat.

CRK2DFormat - Class in org.openscience.cdk.io.formats

See here.

CRK3DFormat - Class in org.openscience.cdk.io.formats

See here.

cross(Vector) - Method in class org.openscience.cdk.math.Vector

Cross product, only well definited in R^3

CrossoverMachine - Class in org.openscience.cdk.structgen.stochastic.operator

Modified molecular structures by applying crossover operator on a pair of parent structures and generate a pair of offspring structures.

CrossoverMachine() - Constructor for class org.openscience.cdk.structgen.stochastic.operator.CrossoverMachine

Constructs a new CrossoverMachine operator.

Crystal - 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.

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

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

CrystClustReader - Class in org.openscience.cdk.io

CrystClustReader() - Constructor for class org.openscience.cdk.io.CrystClustReader

CrystClustReader(Reader) - Constructor for class org.openscience.cdk.io.CrystClustReader

CrystClustReader(InputStream) - Constructor for class org.openscience.cdk.io.CrystClustReader

CrystClustWriter - Class in org.openscience.cdk.io

Rather stupid file format used for storing crystal information.

CrystClustWriter(Writer) - Constructor for class org.openscience.cdk.io.CrystClustWriter

Constructs a new CrystClustWriter class.

CrystClustWriter(OutputStream) - Constructor for class org.openscience.cdk.io.CrystClustWriter

CrystClustWriter() - Constructor for class org.openscience.cdk.io.CrystClustWriter

CS - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

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

CTXReader - Class in org.openscience.cdk.io

Reader that extracts information from the IDENT, NAME, ATOMS and BONDS blocks in CTX files.

CTXReader() - Constructor for class org.openscience.cdk.io.CTXReader

CTXReader(Reader) - Constructor for class org.openscience.cdk.io.CTXReader

CTXReader(InputStream) - Constructor for class org.openscience.cdk.io.CTXReader

CU - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

cubicInterpolation(double, double, double, double, double, double, double, double) - Method in class org.openscience.cdk.modeling.forcefield.LineSearchForTheWolfeConditions

CURIUM - Static variable in class org.openscience.cdk.config.Elements

CURIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

current() - Method in class org.openscience.cdk.io.cml.CMLStack

Returns the last added entry.

currentElement - Variable in class org.openscience.cdk.config.elements.ElementPTHandler

currentToken - Variable in exception org.openscience.cdk.iupac.parser.ParseException

This is the last token that has been consumed successfully.

currentToken - Variable in exception org.openscience.cdk.smiles.smarts.parser.ParseException

This is the last token that has been consumed successfully.

customize(IAtom, Object) - Method in interface org.openscience.cdk.libio.cml.ICMLCustomizer

Customized the nodeToAdd for the given Atom.

customize(IBond, Object) - Method in interface org.openscience.cdk.libio.cml.ICMLCustomizer

Customized the nodeToAdd for the given IBond.

customize(IAtomContainer, Object) - Method in interface org.openscience.cdk.libio.cml.ICMLCustomizer

Customized the nodeToAdd for the given Molecule.

customize(IBond, Object) - Method in class org.openscience.cdk.libio.cml.MDMoleculeCustomizer

No customization for bonds

customize(IAtom, Object) - Method in class org.openscience.cdk.libio.cml.MDMoleculeCustomizer

Customize Atom

customize(IAtomContainer, Object) - Method in class org.openscience.cdk.libio.cml.MDMoleculeCustomizer

Customize Molecule

customize(IAtom, Object) - Method in class org.openscience.cdk.libio.cml.PDBAtomCustomizer

customize(IAtomContainer, Object) - Method in class org.openscience.cdk.libio.cml.PDBAtomCustomizer

customize(IBond, Object) - Method in class org.openscience.cdk.libio.cml.PDBAtomCustomizer

customize(IBond, Object) - Method in class org.openscience.cdk.libio.cml.QSARCustomizer

customize(IAtom, Object) - Method in class org.openscience.cdk.libio.cml.QSARCustomizer

customize(IAtomContainer, Object) - Method in class org.openscience.cdk.libio.cml.QSARCustomizer

customizeJob() - Method in class org.openscience.cdk.io.iterator.IteratingMDLReader

customizeJob() - Method in class org.openscience.cdk.io.MDLReader

customizeJob() - Method in class org.openscience.cdk.io.MDLV2000Reader

customizeJob() - Method in class org.openscience.cdk.io.MDLWriter

customizeJob() - Method in class org.openscience.cdk.io.PDBReader

customizeJob() - Method in class org.openscience.cdk.io.SDFWriter

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).

cycle() - Method in class org.openscience.cdk.iupac.parser.NomParser

Deals with cyclic main chains.

CycleBasis - Class in org.openscience.cdk.ringsearch.cyclebasis

A minimum basis of all cycles in a graph.

CycleBasis(UndirectedGraph) - Constructor for class org.openscience.cdk.ringsearch.cyclebasis.CycleBasis

Constructs a minimum cycle basis of a graph.

cycles() - Method in class org.openscience.cdk.ringsearch.cyclebasis.CycleBasis

Returns the cycles that form the cycle basis.

cycles() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis

CYCLO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

D

D - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

D_BOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

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

DARMSTADTIUM - Static variable in class org.openscience.cdk.config.Elements

DASH - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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

dBlockMetals() - Method in class org.openscience.cdk.iupac.parser.NomParser

dbrentsMethod() - Method in class org.openscience.cdk.modeling.forcefield.LineSearch

Given a function f and its derivative function df, and given a bracketing triplet of abscissas lambdaa, lambdab, lambdac (such that lambdab is between lambdaa and lambdac, and f(lambdab) is less than both f(lambdaa) and f(lambdac)), this routine isolates the minimum to a fractional precision of about t01=0.00001 using a modification of Brent`s method that uses derivatives.

DeAromatizationTool - Class in org.openscience.cdk.tools

Methods that takes a ring of which all bonds are aromatic, and assigns single and double bonds.

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

deAromatize(IRing) - Static method in class org.openscience.cdk.tools.DeAromatizationTool

Methods that takes a ring of which all bonds are aromatic, and assigns single and double bonds.

DEBUG - Static variable in class org.openscience.cdk.graph.PathTools

debug - Static variable in class org.openscience.cdk.layout.AtomPlacer

debug - Static variable in class org.openscience.cdk.layout.HydrogenPlacer

debug - Variable in class org.openscience.cdk.ringsearch.AllRingsFinder

debug - Static variable in class org.openscience.cdk.ringsearch.RingPartitioner

Debugging on/off

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, int) - Method in class org.openscience.cdk.tools.LoggingTool

Shows DEBUG output for the given Object's.

debug(Object, double) - Method in class org.openscience.cdk.tools.LoggingTool

Shows DEBUG output for the given Object's.

debug(Object, boolean) - Method in class org.openscience.cdk.tools.LoggingTool

Shows DEBUG output for the given Object's.

debug(Object, Object, Object) - Method in class org.openscience.cdk.tools.LoggingTool

Shows DEBUG output for the given Object's.

debug(Object, Object, Object, Object) - Method in class org.openscience.cdk.tools.LoggingTool

Shows DEBUG output for the given Object's.

debug(Object, Object, Object, Object, Object) - Method in class org.openscience.cdk.tools.LoggingTool

Shows DEBUG output for the given Object's.

debug - Static variable in class org.openscience.cdk.tools.SwissArmyKnife

debug1 - Static variable in class org.openscience.cdk.layout.HydrogenPlacer

DebugAdductFormula - Class in org.openscience.cdk.debug

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

DebugAtomParity - Class in org.openscience.cdk.debug

Debugging data class.

DebugAtomParity(IAtom, IAtom, IAtom, IAtom, IAtom, int) - Constructor for class org.openscience.cdk.debug.DebugAtomParity

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, int) - 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 debug 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

DebugMolecularFormula() - Constructor for class org.openscience.cdk.debug.DebugMolecularFormula

DebugMolecularFormulaSet - Class in org.openscience.cdk.debug

DebugMolecularFormulaSet() - Constructor for class org.openscience.cdk.debug.DebugMolecularFormulaSet

DebugMolecularFormulaSet(IMolecularFormula) - Constructor for class org.openscience.cdk.debug.DebugMolecularFormulaSet

DebugMolecule - Class in org.openscience.cdk.debug

Debugging data class.

DebugMolecule() - Constructor for class org.openscience.cdk.debug.DebugMolecule

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

DebugMolecule(IAtomContainer) - Constructor for class org.openscience.cdk.debug.DebugMolecule

DebugMoleculeSet - Class in org.openscience.cdk.debug

Debugging data class.

DebugMoleculeSet() - Constructor for class org.openscience.cdk.debug.DebugMoleculeSet

DebugMonomer - Class in org.openscience.cdk.debug

Debugging data class.

DebugMonomer() - Constructor for class org.openscience.cdk.debug.DebugMonomer

DebugPDBAtom - Class in org.openscience.cdk.debug

Debugging data class.

DebugPDBAtom(IElement) - Constructor for class org.openscience.cdk.debug.DebugPDBAtom

DebugPDBAtom(String) - Constructor for class org.openscience.cdk.debug.DebugPDBAtom

DebugPDBAtom(String, Point3d) - Constructor for class org.openscience.cdk.debug.DebugPDBAtom

DebugPDBMonomer - Class in org.openscience.cdk.debug

Debugging data class.

DebugPDBMonomer() - Constructor for class org.openscience.cdk.debug.DebugPDBMonomer

DebugPDBPolymer - Class in org.openscience.cdk.debug

Debugging data class.

DebugPDBPolymer() - Constructor for class org.openscience.cdk.debug.DebugPDBPolymer

DebugPDBStructure - Class in org.openscience.cdk.debug

Debugging data class.

DebugPDBStructure() - Constructor for class org.openscience.cdk.debug.DebugPDBStructure

DebugPolymer - Class in org.openscience.cdk.debug

Debugging data class.

DebugPolymer() - Constructor for class org.openscience.cdk.debug.DebugPolymer

DebugPseudoAtom - Class in org.openscience.cdk.debug

Debugging data class.

DebugPseudoAtom() - Constructor for class org.openscience.cdk.debug.DebugPseudoAtom

DebugPseudoAtom(IElement) - Constructor for class org.openscience.cdk.debug.DebugPseudoAtom

DebugPseudoAtom(String) - Constructor for class org.openscience.cdk.debug.DebugPseudoAtom

DebugPseudoAtom(String, Point2d) - Constructor for class org.openscience.cdk.debug.DebugPseudoAtom

DebugPseudoAtom(String, Point3d) - Constructor for class org.openscience.cdk.debug.DebugPseudoAtom

DebugReaction - Class in org.openscience.cdk.debug

Debugging data class.

DebugReaction() - Constructor for class org.openscience.cdk.debug.DebugReaction

DebugReactionScheme - Class in org.openscience.cdk.debug

Debugging data class.

DebugReactionScheme() - Constructor for class org.openscience.cdk.debug.DebugReactionScheme

DebugReactionSet - Class in org.openscience.cdk.debug

Debugging data class.

DebugReactionSet() - Constructor for class org.openscience.cdk.debug.DebugReactionSet

DebugRing - Class in org.openscience.cdk.debug

Debugging data class.

DebugRing() - Constructor for class org.openscience.cdk.debug.DebugRing

DebugRing(int, String) - Constructor for class org.openscience.cdk.debug.DebugRing

DebugRing(int) - Constructor for class org.openscience.cdk.debug.DebugRing

DebugRing(IAtomContainer) - Constructor for class org.openscience.cdk.debug.DebugRing

DebugRingSet - Class in org.openscience.cdk.debug

Debugging data class.

DebugRingSet() - Constructor for class org.openscience.cdk.debug.DebugRingSet

DebugSingleElectron - Class in org.openscience.cdk.debug

Debugging data class.

DebugSingleElectron() - Constructor for class org.openscience.cdk.debug.DebugSingleElectron

DebugSingleElectron(IAtom) - Constructor for class org.openscience.cdk.debug.DebugSingleElectron

DebugStrand - Class in org.openscience.cdk.debug

Debugging data class.

DebugStrand() - Constructor for class org.openscience.cdk.debug.DebugStrand

debugStream - Variable in class org.openscience.cdk.iupac.parser.NomParserTokenManager

debugStream - Variable in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager

DEC - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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.

DeduceBondSystemTool - Class in org.openscience.cdk.smiles

Tool that tries to deduce bond orders based on connectivity and hybridization for a number of common ring systems.

DeduceBondSystemTool() - Constructor for class org.openscience.cdk.smiles.DeduceBondSystemTool

Constructor for the DeduceBondSystemTool object.

DEFAULT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

DEFAULT - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

DEFAULT_BOND_LENGTH_H - Static variable in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

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_STACK_LENGTH - Variable in class org.openscience.cdk.tools.LoggingTool

Default number of StackTraceElements to be printed by debug(Exception).

DefaultChemObjectBuilder - Class in org.openscience.cdk

A helper class to instantiate a IChemObject for a specific implementation.

DefaultChemObjectReader - Class in org.openscience.cdk.io

Abstract class that ChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners.

DefaultChemObjectReader() - Constructor for class org.openscience.cdk.io.DefaultChemObjectReader

DefaultChemObjectWriter - Class in org.openscience.cdk.io

Abstract class that ChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners.

DefaultChemObjectWriter() - Constructor for class org.openscience.cdk.io.DefaultChemObjectWriter

DefaultEventChemObjectReader - Class in org.openscience.cdk.io.iterator.event

Abstract class that IteratingChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners.

DefaultEventChemObjectReader() - Constructor for class org.openscience.cdk.io.iterator.event.DefaultEventChemObjectReader

DefaultIteratingChemObjectReader - 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

DegreeAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts

This matcher checks the number of connections of the checked Atom with other Atom's.

DegreeAtom(int) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.DegreeAtom

depthFirstTargetSearch(IAtomContainer, IAtom, IAtom, IAtomContainer) - Static method in class org.openscience.cdk.graph.PathTools

Recursivly perfoms 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.

derivativeSmallEnough - Variable in class org.openscience.cdk.modeling.forcefield.LineSearchForTheWolfeConditions

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>) - Constructor for class org.openscience.cdk.qsar.DescriptorEngine

Instantiates the DescriptorEngine.

DescriptorEngine(int) - Constructor for class org.openscience.cdk.qsar.DescriptorEngine

Constructor that generates a list of descriptors to calculate.

DescriptorEngine(int, String[]) - Constructor for class org.openscience.cdk.qsar.DescriptorEngine

Constructor that generates a list of descriptors to calculate.

DescriptorException - Exception in org.openscience.cdk.qsar

Exception that is thrown by descriptor routines when a problem has occured.

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.

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

Constrct 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

Constrct a descriptor value object, representing the numeric values as well as parameters and provenance.

destroyBondOrder(IBond.Order) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator

Convert a IBond.Order to a numeric value.

detect(IAtomContainer) - Static method in class org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector

Detect all conjugated pi systems in an AtomContainer.

detectAromaticity(IAtomContainer) - Static method in class org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector

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

Returns the determinant of this matrix.

determinat(GVector, GMatrix) - Method in class org.openscience.cdk.modeling.forcefield.NewtonRaphsonMethod

dfOptimum - Variable in class org.openscience.cdk.modeling.forcefield.LineSearchForTheWolfeConditions

DI - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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

Returns a matrix containing all of the diagonal elements of this matrix and zero (0) everywhere else.

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

Method performs a scan; works only for cubic grids!

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

Method performs a scan; works only for cubic grids!

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

Method performs a scan; works only for cubic grids!

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

Method performs a scan; works only for cubic grids!

diagonalize(int) - Method in class org.openscience.cdk.math.Matrix

Diagonalize this matrix with the Jacobi algorithm.

Dictionary - Class in org.openscience.cdk.dict

Dictionary with entries.

Dictionary() - Constructor for class org.openscience.cdk.dict.Dictionary

DictionaryDatabase - Class in org.openscience.cdk.dict

Database of dictionaries listing entries with compounds, fragments and entities.

DictionaryDatabase() - Constructor for class org.openscience.cdk.dict.DictionaryDatabase

DictionaryHandler - Class in org.openscience.cdk.dict

Class for unmarshalling a dictionary schema file.

DictionaryHandler() - Constructor for class org.openscience.cdk.dict.DictionaryHandler

DictionaryValidator - Class in org.openscience.cdk.validate

Validates the existence of references to dictionaries.

DictionaryValidator(DictionaryDatabase) - Constructor for class org.openscience.cdk.validate.DictionaryValidator

dictRef - Variable in class org.openscience.cdk.config.elements.ElementPTHandler

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

DICTREFPROPERTYNAME - Static variable in class org.openscience.cdk.dict.DictionaryDatabase

diff(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.AtomContainerDiff

diff(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.AtomDiff

diff(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.AtomTypeDiff

diff(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.BondDiff

diff(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.ChemObjectDiff

diff(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.ElectronContainerDiff

diff(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.ElementDiff

diff(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.IsotopeDiff

diff(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.LonePairDiff

diff(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.SingleElectronDiff

difference(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.AtomContainerDiff

difference(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.AtomDiff

difference(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.AtomTypeDiff

difference(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.BondDiff

difference(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.ChemObjectDiff

difference(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.ElectronContainerDiff

difference(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.ElementDiff

difference(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.IsotopeDiff

difference(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.LonePairDiff

difference(IChemObject, IChemObject) - Static method in class org.openscience.cdk.tools.diff.SingleElectronDiff

DIGIT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

DIGIT - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

disable_tracing() - Method in class org.openscience.cdk.iupac.parser.NomParser

disable_tracing() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

displace(IAtomContainer, Vector, Vector) - Method in class org.openscience.cdk.layout.OverlapResolver

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

distanceBetweenTwoAtomFromTwo3xNCoordinates(GVector, GVector, int, int) - Static method in class org.openscience.cdk.modeling.forcefield.ForceFieldTools

Calculate 3d distance between two atoms from two different 3xN coordinate vectors.

distanceBetweenTwoAtoms(IAtom, IAtom) - Static method in class org.openscience.cdk.modeling.forcefield.ForceFieldTools

Calculate 3d distance between two atoms coordinates

distanceBetweenTwoAtomsFrom3xNCoordinates(GVector, int, int) - Static method in class org.openscience.cdk.modeling.forcefield.ForceFieldTools

Calculate 3d distance between two atoms in one molecule from its 3xN coordinate vector.

distanceBetweenTwoAtomsFromNCoordinates3d(Vector, int, int) - Static method in class org.openscience.cdk.modeling.forcefield.ForceFieldTools

Calculate 3d distance between two atoms in one molecule from its N coordinates 3d

distanceCalculator(int[], double) - Static method in class org.openscience.cdk.geometry.GeometryTools

Gets the coordinates of two points (that represent a bond) and calculates for each the coordinates of two new points that have the given distance vertical to the bond.

distanceCalculator(double[], double) - Static method in class org.openscience.cdk.geometry.GeometryTools

DistanceMoment - Class in org.openscience.cdk.similarity

Fast similarity measure for 3D structures.

DistanceMoment() - Constructor for class org.openscience.cdk.similarity.DistanceMoment

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

This class returns the 3D distance between two atoms.

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

Constructor for the DistanceToAtomDescriptor object

distributePartners(IAtom, IAtomContainer, Point2d, IAtomContainer, double) - Method in class org.openscience.cdk.layout.AtomPlacer

Distribute the bonded atoms (neighbours) of an atom such that they fill the remaining space around an atom in a geometrically nice way.

div(Complex) - Method in class org.openscience.cdk.math.Complex

Div this value by a complex value

div(Quaternion) - Method in class org.openscience.cdk.math.Quaternion

DMol3Format - Class in org.openscience.cdk.io.formats

DN_OR_UNSPECIFIED_S_BOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

DN_S_BOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

DO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

DOCK5Format - Class in org.openscience.cdk.io.formats

See here.

doCrossover(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.structgen.stochastic.operator.CrossoverMachine

Performs the n point crossover of two MolChromosome supplied by the CrossInfo.parents class and stores the resulting chromosomes in CrossInfo.children.

doctypeDecl(String, String, String) - Method in class org.openscience.cdk.dict.DictionaryHandler

doctypeDecl(String, String, String) - Method in class org.openscience.cdk.io.cml.CMLHandler

doctypeDecl(String, String, String) - Method in class org.openscience.cdk.io.inchi.INChIHandler

DOLLAR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

Done() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream

Done() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream

dot(IVector) - Method in class org.openscience.cdk.math.IVector

Multiplication from two vectors

dot(Vector) - Method in class org.openscience.cdk.math.Vector

Multiplikation from two vectors

doTessellate() - Method in class org.openscience.cdk.geometry.surface.Tessellate

DoubleArrayResult - Class in org.openscience.cdk.qsar.result

DoubleArrayResult() - Constructor for class org.openscience.cdk.qsar.result.DoubleArrayResult

DoubleArrayResult(int) - Constructor for class org.openscience.cdk.qsar.result.DoubleArrayResult

DoubleArrayResultType - Class in org.openscience.cdk.qsar.result

IDescriptorResult type for booleans.

DoubleArrayResultType(int) - Constructor for class org.openscience.cdk.qsar.result.DoubleArrayResultType

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

IDifference between two Double.

DoubleResult - Class in org.openscience.cdk.qsar.result

DoubleResult(double) - Constructor for class org.openscience.cdk.qsar.result.DoubleResult

DoubleResultType - Class in org.openscience.cdk.qsar.result

IDescriptorResult type for booleans.

DoubleResultType() - Constructor for class org.openscience.cdk.qsar.result.DoubleResultType

doubleValue() - Method in class org.openscience.cdk.qsar.result.DoubleResult

DUBNIUM - Static variable in class org.openscience.cdk.config.Elements

DUBNIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

DUMMY - Static variable in class org.openscience.cdk.config.Elements

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

Flag used for JUnit testing the pointer functionality.

dump(String) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleNode

dumpClasspath() - Method in class org.openscience.cdk.tools.LoggingTool

Outputs the system property for java.class.path.

dumpSystemProperties() - Method in class org.openscience.cdk.tools.LoggingTool

Outputs system properties for the operating system and the java version.

duplicate() - Method in class org.openscience.cdk.math.IMatrix

Copy a matrix

duplicate(IMatrix) - Method in class org.openscience.cdk.math.IMatrix

Copy a matrix

duplicate() - Method in class org.openscience.cdk.math.IVector

Copy a vector

duplicate(IVector) - Method in class org.openscience.cdk.math.IVector

Copy a vector

duplicate() - Method in class org.openscience.cdk.math.Matrix

Copies a matrix.

duplicate() - Method in class org.openscience.cdk.math.Vector

Copy a vector

DY - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

DYSPROSIUM - Static variable in class org.openscience.cdk.config.Elements

DYSPROSIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

E

E - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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

A topological descriptor combining distance and adjacency information.

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

edgeAdded(GraphEdgeChangeEvent) - Method in class org.openscience.cdk.graph.BiconnectivityInspector

edgeRemoved(GraphEdgeChangeEvent) - Method in class org.openscience.cdk.graph.BiconnectivityInspector

edges() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis

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

Effective polarizability of an heavy atom

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

Constructor for the EffectiveAtomPolarizabilityDescriptor object

EICOS - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

EINSTEINIUM - Static variable in class org.openscience.cdk.config.Elements

EINSTEINIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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_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.

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

Compares two IChemObject classes.

ElectronContainerDiff() - Constructor for class org.openscience.cdk.tools.diff.ElectronContainerDiff

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

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

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

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

electronContainers() - Method in class org.openscience.cdk.debug.DebugMolecule

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

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

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

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

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

Returns an Iterable for looping over all electron containers in this container.

Electronegativity - Class in org.openscience.cdk.charges

Calculation of the electronegativity of orbitals of a molecule by the method Gasteiger based on electronegativity is given by X = a + bq + c(q*q).

Electronegativity() - Constructor for class org.openscience.cdk.charges.Electronegativity

Constructor for the PiElectronegativity object.

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

Constructor for the Electronegativity object.

ElectronImpactNBEReaction - Class in org.openscience.cdk.reaction.type

IReactionProcess which make an electron impact for for Non-Bonding Electron Lost.

ElectronImpactNBEReaction() - Constructor for class org.openscience.cdk.reaction.type.ElectronImpactNBEReaction

Constructor of the ElectronImpactNBEReaction object.

ElectronImpactPDBReaction - Class in org.openscience.cdk.reaction.type

IReactionProcess which make an electron impact for pi-Bond Dissociation.

ElectronImpactPDBReaction() - Constructor for class org.openscience.cdk.reaction.type.ElectronImpactPDBReaction

Constructor of the ElectronImpactPDBReaction object.

ElectronImpactSDBReaction - Class in org.openscience.cdk.reaction.type

IReactionProcess which make an electron impact for Sigma Bond Dissociation.

ElectronImpactSDBReaction() - Constructor for class org.openscience.cdk.reaction.type.ElectronImpactSDBReaction

Constructor of the ElectronImpactSDBReaction object.

ElectrostaticInteractions - Class in org.openscience.cdk.modeling.forcefield

MMFF94 Electrostatic Interactions energy.

ElectrostaticInteractions() - Constructor for class org.openscience.cdk.modeling.forcefield.ElectrostaticInteractions

Constructor for the ElectrostaticInteractions object

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, int) - Constructor for class org.openscience.cdk.Element

Constructs an Element with a given element symbol, atomic number and atomic mass.

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.

ElementDiff() - Constructor for class org.openscience.cdk.tools.diff.ElementDiff

ElementPTFactory - Class in org.openscience.cdk.config

Used to store and return data of a particular chemicalElement.

ElementPTHandler - Class in org.openscience.cdk.config.elements

Reads an element list in CML2 format.

ElementPTHandler() - Constructor for class org.openscience.cdk.config.elements.ElementPTHandler

ElementPTReader - Class in org.openscience.cdk.config.elements

Reader that instantiates an XML parser and customized handler to process the isotope information in the CML2 isotope data file.

ElementPTReader(Reader) - Constructor for class org.openscience.cdk.config.elements.ElementPTReader

Instantiates a new reader that parses the XML from the given input.

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 - Class in org.openscience.cdk.config

List of elements.

Elements() - Constructor for class org.openscience.cdk.config.Elements

elements(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator

Get a list of all Elements which are contained molecular.

elementType - Variable in class org.openscience.cdk.config.elements.ElementPTHandler

elimination(Matrix, Vector) - Static method in class org.openscience.cdk.math.Matrix

Solves a linear equation system with Gauss elimination.

EN - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

enable_tracing() - Method in class org.openscience.cdk.iupac.parser.NomParser

enable_tracing() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

endColumn - Variable in class org.openscience.cdk.iupac.parser.Token

beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.

endColumn - Variable in class org.openscience.cdk.smiles.smarts.parser.Token

beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.

endDocument() - Method in class org.openscience.cdk.io.cml.CMLCoreModule

endDocument() - Method in class org.openscience.cdk.io.cml.CMLHandler

Calling this procedure signals the end of the XML document.

endDocument() - Method in interface org.openscience.cdk.io.cml.ICMLModule

endDocument() - Method in class org.openscience.cdk.io.cml.PDBConvention

endDocument() - Method in class org.openscience.cdk.io.inchi.INChIHandler

endDocument() - Method in class org.openscience.cdk.io.iterator.event.EventCMLHandler

Procedure required by the CDOInterface.

endElement(String, String, String) - Method in class org.openscience.cdk.config.atomtypes.AtomTypeHandler

endElement(String, String, String) - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeHandler

endElement(String, String, String) - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingHandler

endElement(String, String, String) - Method in class org.openscience.cdk.config.elements.ElementPTHandler

endElement(String, String, String) - Method in class org.openscience.cdk.config.isotopes.IsotopeHandler

endElement(String, String, String) - Method in class org.openscience.cdk.dict.DictionaryHandler

endElement(CMLStack, String, String, String) - Method in class org.openscience.cdk.io.cml.CMLCoreModule

endElement(String, String, String) - Method in class org.openscience.cdk.io.cml.CMLHandler

endElement(CMLStack, String, String, String) - Method in class org.openscience.cdk.io.cml.CMLReactionModule

endElement(CMLStack, String, String, String) - Method in interface org.openscience.cdk.io.cml.ICMLModule

endElement(CMLStack, String, String, String) - Method in class org.openscience.cdk.io.cml.JMOLANIMATIONConvention

endElement(CMLStack, String, String, String) - Method in class org.openscience.cdk.io.cml.MDMoleculeConvention

Finish up parsing of elements in mdmolecule

endElement(CMLStack, String, String, String) - Method in class org.openscience.cdk.io.cml.PDBConvention

endElement(CMLStack, String, String, String) - Method in class org.openscience.cdk.io.cml.QSARConvention

endElement(String, String, String) - Method in class org.openscience.cdk.io.inchi.INChIHandler

endFunctionalGroups() - Method in class org.openscience.cdk.iupac.parser.NomParser

Functional groups which occur at the end of the main chain and need a connecting "an".

endLine - Variable in class org.openscience.cdk.iupac.parser.Token

beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.

endLine - Variable in class org.openscience.cdk.smiles.smarts.parser.Token

beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.

endObject(String) - Method in class org.openscience.cdk.io.iterator.event.EventCMLHandler

Procedure required by the CDOInterface.

endsWith(String) - Method in class org.openscience.cdk.io.cml.CMLStack

Convenience method to check the last added elements.

endsWith(String, String) - Method in class org.openscience.cdk.io.cml.CMLStack

Convenience method to check the last two added elements.

endsWith(String, String, String) - Method in class org.openscience.cdk.io.cml.CMLStack

Convenience method to check the last three added elements.

energy - Static variable in interface org.openscience.cdk.modeling.forcefield.IPotentialFunction

energyFunction(GVector) - Method in interface org.openscience.cdk.modeling.forcefield.IPotentialFunction

Evaluate the potential energy function given the cartesian coordinates.

energyFunction(GVector) - Method in class org.openscience.cdk.modeling.forcefield.MMFF94EnergyFunction

Evaluate the MMFF94 energy function for a given 3xN point

energyFunctionOfAMolecule(IAtomContainer) - Method in class org.openscience.cdk.modeling.forcefield.MMFF94EnergyFunction

Evaluate the MMFF94 energy function for a given molecule

energyFunctionShape - Static variable in interface org.openscience.cdk.modeling.forcefield.IPotentialFunction

energyGradient - Static variable in interface org.openscience.cdk.modeling.forcefield.IPotentialFunction

energyHessian - Static variable in interface org.openscience.cdk.modeling.forcefield.IPotentialFunction

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.

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(Atom) - Constructor for class org.openscience.cdk.EnzymeResidueLocator

Constructs an EnzymeResidueLocator from an existing Atom.

EOF - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

EOF - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

EOL - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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.isomorphism.mcss.RMap

The equals method.

equals(Object) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom

equals(Object) - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycle

equals(Object) - Method in class org.openscience.cdk.smiles.InvPair

Check whether this instance equals another instance.

equivalenceClasses() - Method in class org.openscience.cdk.ringsearch.cyclebasis.CycleBasis

Returns the connected components of this cycle basis, in regard to matroid theory.

equivalenceClasses() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis

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(AtomContainer) - Constructor for class org.openscience.cdk.graph.invariant.EquivalentClassPartitioner

Constructor for the TopologicalEquivalentClass object

ER - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

ERBIUM - Static variable in class org.openscience.cdk.config.Elements

ERBIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

error(SAXParseException) - Method in class org.openscience.cdk.io.cml.CMLErrorHandler

Outputs a SAXParseException error to the logger.

error(Object) - Method in class org.openscience.cdk.tools.LoggingTool

Shows ERROR output for the Object.

error(Object, int) - Method in class org.openscience.cdk.tools.LoggingTool

Shows ERROR output for the given Object's.

error(Object, double) - Method in class org.openscience.cdk.tools.LoggingTool

Shows ERROR output for the given Object's.

error(Object, boolean) - Method in class org.openscience.cdk.tools.LoggingTool

Shows ERROR output for the given Object's.

error(Object, Object) - Method in class org.openscience.cdk.tools.LoggingTool

Shows ERROR output for the given Object's.

error(Object, Object, Object) - Method in class org.openscience.cdk.tools.LoggingTool

Shows ERROR output for the given Object's.

error(Object, Object, Object, Object) - Method in class org.openscience.cdk.tools.LoggingTool

Shows ERROR output for the given Object's.

error(Object, Object, Object, Object, Object) - Method in class org.openscience.cdk.tools.LoggingTool

Shows ERROR output for the given Object's.

ERROR_MARKER - Static variable in class org.openscience.cdk.validate.ProblemMarker

ES - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

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

The essential rings computed for this molecule.

essentialCycles() - Method in class org.openscience.cdk.ringsearch.cyclebasis.CycleBasis

Returns the essential cycles of this cycle basis.

essentialCycles() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis

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

ETH - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

EU - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

EUROPIUM - Static variable in class org.openscience.cdk.config.Elements

EUROPIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

evalSimpleIndex(IAtomContainer, List<List<Integer>>) - Static method in class org.openscience.cdk.qsar.descriptors.molecular.ChiIndexUtils

Evaluates the simple chi index for a set of fragments.

evalValenceIndex(IAtomContainer, List) - Static method in class org.openscience.cdk.qsar.descriptors.molecular.ChiIndexUtils

Evaluates the valence corrected chi index for a set of fragments.

EventCMLHandler - Class in org.openscience.cdk.io.iterator.event

CDO object needed as interface with the JCFL library for reading CML in a event based manner.

EventCMLHandler(DefaultEventChemObjectReader, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.event.EventCMLHandler

Constructs an iterating-abled CDO.

EventCMLReader - Class in org.openscience.cdk.io.iterator.event

Reads a molecule in CML 1.x and 2.0 format.

EventCMLReader(Reader, IReaderListener, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.event.EventCMLReader

Define this CMLReader to take the input from a java.io.Reader class.

EX - Static variable in class org.openscience.cdk.math.Vector

Unary vector in 3 dimensional space

exactMass - Variable in class org.openscience.cdk.Isotope

Exact mass of this isotope.

exhaustStringTokenizer(StringTokenizer) - Method in class org.openscience.cdk.io.MDLV3000Reader

expectedTokenSequences - Variable in exception org.openscience.cdk.iupac.parser.ParseException

Each entry in this array is an array of integers.

expectedTokenSequences - Variable in exception org.openscience.cdk.smiles.smarts.parser.ParseException

Each entry in this array is an array of integers.

ExplicitAtomExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

ExplicitConnectionAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts

This smarts atom matches any atom with a certain number of explicit connections.

ExplicitConnectionAtom() - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.ExplicitConnectionAtom

Creates a new instance.

ExplicitConnectionAtom(int) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.ExplicitConnectionAtom

Creates a new instance.

ExplicitConnectivity() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

ExplicitHighAndBond() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

ExplicitHighAndExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

exponentialDouble(double) - Static method in class org.openscience.cdk.math.RandomNumbersTool

Generates a random double from an Exponential distribution with the specified mean value.

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.

extractTopReactions(IReactionScheme) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator

Extract a set of Reactions which are in top of a IReactionScheme.

extractUniqueRingSystemsFromFile(String) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor

EY - Static variable in class org.openscience.cdk.math.Vector

Unary vector in 3 dimensional space

EZ - Static variable in class org.openscience.cdk.math.Vector

Unary vector in 3 dimensional space

F

f(double) - Method in class org.openscience.cdk.modeling.forcefield.LineSearch

F - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

faculty(int) - Static method in class org.openscience.cdk.tools.SwissArmyKnife

Calculates the faculty for a given integer

fatal(Object) - Method in class org.openscience.cdk.tools.LoggingTool

Shows FATAL output for the Object.

fatalError(SAXParseException) - Method in class org.openscience.cdk.io.cml.CMLErrorHandler

Outputs as fatal SAXParseException error to the logger.

fBlockMetals() - Method in class org.openscience.cdk.iupac.parser.NomParser

FE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

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

FERMIUM - Static variable in class org.openscience.cdk.config.Elements

FERMIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

FiguerasSSSRFinder - Class in org.openscience.cdk.ringsearch

Deprecated. Use SSSRFinder instead (exact algorithm).

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

Deprecated.

findAllRings(IAtomContainer) - Method in class org.openscience.cdk.ringsearch.AllRingsFinder

Returns a ringset containing all rings in the given AtomContainer Calls AllRingsFinder.findAllRings(IAtomContainer, Integer) with max ring size argument set to null (=unlimited ring sizes)

findAllRings(IAtomContainer, Integer) - Method in class org.openscience.cdk.ringsearch.AllRingsFinder

Returns a ringset containing all rings up to a provided maximum size in a given AtomContainer

findAllRingsInIsolatedRingSystem(IAtomContainer) - Method in class org.openscience.cdk.ringsearch.AllRingsFinder

Fings the set of all rings in a molecule Calls AllRingsFinder.findAllRingsInIsolatedRingSystem(IAtomContainer,Integer) with max ring size argument set to null (=unlimited ring sizes)

findAllRingsInIsolatedRingSystem(IAtomContainer, Integer) - Method in class org.openscience.cdk.ringsearch.AllRingsFinder

Finds the set of all rings in a molecule

findChemFormats(int) - Method in class org.openscience.cdk.io.WriterFactory

Finds IChemFormats that provide a container for serialization for the given features.

findClosestByBond(IAtomContainer, IAtom, int) - Static method in class org.openscience.cdk.graph.PathTools

Returns the atoms which are closest to an atom in an AtomContainer by bonds.

findClosestInSpace(IAtomContainer, IAtom, int) - Static method in class org.openscience.cdk.geometry.GeometryTools

Returns the atoms which are closes to an atom in an AtomContainer by distance in 3d.

findEquivalenceClasses() - Method in class org.openscience.cdk.ringsearch.SSSRFinder

Finds the "interchangeability" equivalence classes.

findEssentialRings() - Method in class org.openscience.cdk.ringsearch.SSSRFinder

Finds the Set of Essential Rings.

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

Method determines the minimum and maximum values of a coordinate space up to 3D space.

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

Count and find first heavy atom(s) (non Hydrogens) in a chain

findMatchingAtomType(IAtomContainer) - Method in class org.openscience.cdk.atomtype.CDKAtomTypeMatcher

findMatchingAtomType(IAtomContainer, IAtom) - Method in class org.openscience.cdk.atomtype.CDKAtomTypeMatcher

findMatchingAtomType(IAtomContainer) - Method in class org.openscience.cdk.atomtype.EStateAtomTypeMatcher

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) - Method in interface org.openscience.cdk.atomtype.IAtomTypeMatcher

Method that assigns atom types to atoms in the given atom container.

findMatchingAtomType(IAtomContainer) - Method in class org.openscience.cdk.atomtype.MM2AtomTypeMatcher

findMatchingAtomType(IAtomContainer, IAtom) - Method in class org.openscience.cdk.atomtype.MM2AtomTypeMatcher

Assign the mm2 atom type to a given atom.

findMatchingAtomType(IAtomContainer) - Method in class org.openscience.cdk.atomtype.MMFF94AtomTypeMatcher

findMatchingAtomType(IAtomContainer, IAtom) - Method in class org.openscience.cdk.atomtype.MMFF94AtomTypeMatcher

Assign the mmff94 atom type to a given atom.

findMatchingAtomType(IAtomContainer) - Method in class org.openscience.cdk.atomtype.StructGenMatcher

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) - Method in class org.openscience.cdk.atomtype.SybylAtomTypeMatcher

findMatchingAtomType(IAtomContainer, IAtom) - Method in class org.openscience.cdk.atomtype.SybylAtomTypeMatcher

Sybyl atom type perception for a single atom.

findPathBetween(Graph, Object, Object) - Static method in class org.openscience.cdk.graph.BFSShortestPath

findRelevantRings() - Method in class org.openscience.cdk.ringsearch.SSSRFinder

Finds the Set of Relevant Rings.

findSSSR(Molecule) - Method in class org.openscience.cdk.ringsearch.FiguerasSSSRFinder

Deprecated. Finds the Smallest Set of Smallest Rings.

findSSSR() - Method in class org.openscience.cdk.ringsearch.SSSRFinder

Finds a Smallest Set of Smallest Rings.

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

first() - Method in interface org.openscience.cdk.io.random.IRandomAccessChemObjectReader

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

fixAromaticBondOrders(IMolecule) - Method in class org.openscience.cdk.smiles.DeduceBondSystemTool

fixAromaticityForXLogP(IMolecule) - Static method in class org.openscience.cdk.tools.CDKUtilities

FixedSizeStack - Class in org.openscience.cdk.tools

A LIFO queue for result structures.

FixedSizeStack(int) - Constructor for class org.openscience.cdk.tools.FixedSizeStack

Creates a fixed size stack

fixNitroGroups2(IMolecule) - Static method in class org.openscience.cdk.tools.CDKUtilities

fixSmiles(String) - Static method in class org.openscience.cdk.tools.CDKUtilities

fixSulphurH(IMolecule) - Static method in class org.openscience.cdk.tools.CDKUtilities

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 class org.openscience.cdk.config.Elements

FLUORO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

FM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

ForceField - Class in org.openscience.cdk.modeling.forcefield

To work with the coordinates of the molecule, like get the 3d coordinates of the atoms or calculate the distance between two atoms.

ForceField() - Constructor for class org.openscience.cdk.modeling.forcefield.ForceField

Constructor for the ForceField object

ForceField(Molecule) - Constructor for class org.openscience.cdk.modeling.forcefield.ForceField

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

ForceFieldTools - Class in org.openscience.cdk.modeling.forcefield

To work with the coordinates of the molecule, like get the 3d coordinates of the atoms or calculate the distance between two atoms.

ForceFieldTools() - Constructor for class org.openscience.cdk.modeling.forcefield.ForceFieldTools

forHessian - Static variable in interface org.openscience.cdk.modeling.forcefield.IPotentialFunction

FormalChargeAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts

This matcher checks the formal charge of the Atom.

FormalChargeAtom(int) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.FormalChargeAtom

Creates a new instance

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.

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.

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

FourierGridBasis - Class in org.openscience.cdk.math.qm

At this time this class does not work correcly.

FourierGridBasis(int, double, double, IFunction) - Constructor for class org.openscience.cdk.math.qm.FourierGridBasis

FR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

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

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.

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 class org.openscience.cdk.config.Elements

FRANCIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

fromRotationMatrix(Matrix) - Static method in class org.openscience.cdk.math.Quaternion

functionalGroupPrefix() - Method in class org.openscience.cdk.iupac.parser.NomParser

The functional group part of the prefix

functionCCGSumEvdWAv(GVector, double[]) - Method in class org.openscience.cdk.modeling.forcefield.VanDerWaalsInteractions

Evaluate the CCG Van Der Waals interaction term.

functionCCGSumEvdWSK(GVector, double[]) - Method in class org.openscience.cdk.modeling.forcefield.VanDerWaalsInteractions

Evaluate the CCG Van Der Waals interaction term.

functionEvaluationNumber - Static variable in interface org.openscience.cdk.modeling.forcefield.IPotentialFunction

functionMMFF94SumEA(GVector) - Method in class org.openscience.cdk.modeling.forcefield.AngleBending

Evaluate the MMFF94 angle bending term for the given atoms coordinates

functionMMFF94SumEB(GVector) - Method in class org.openscience.cdk.modeling.forcefield.BondStretching

Evaluate the MMFF94 bond stretching term for the given atoms cartesian coordinates.

functionMMFF94SumEQ(GVector) - Method in class org.openscience.cdk.modeling.forcefield.ElectrostaticInteractions

Evaluate the MMFF94 Electrostatic interaction energy.

functionMMFF94SumET(GVector) - Method in class org.openscience.cdk.modeling.forcefield.Torsions

Evaluate the MMFF94 torsions term.

G

G - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

GA - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

GADOLINIUM - Static variable in class org.openscience.cdk.config.Elements

GADOLINIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

GALLIUM - Static variable in class org.openscience.cdk.config.Elements

GALLIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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

See here.

GamessReader - Class in org.openscience.cdk.io

A reader for GAMESS log file.

GamessReader(Reader) - Constructor for class org.openscience.cdk.io.GamessReader

Constructs a new "GamessReader" object given a "Reader" object as input.

GamessReader(InputStream) - Constructor for class org.openscience.cdk.io.GamessReader

GamessReader() - Constructor for class org.openscience.cdk.io.GamessReader

GasteigerMarsiliPartialCharges - Class in org.openscience.cdk.charges

The calculation of the Gasteiger Marsili (PEOE) partial charges is based on [Gasteiger, J. and Marsili, M., Iterative partial equalization of orbital elektronegativity - a rapid access to atomic charges, Tetrahedron, 1980, 36:3219-3288].

GasteigerMarsiliPartialCharges() - Constructor for class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges

Constructor for the GasteigerMarsiliPartialCharges object

GasteigerPEPEPartialCharges - Class in org.openscience.cdk.charges

The calculation of the Gasteiger (PEPE) partial charges is based on [Unknown BibTeXML type: Saller85].

GasteigerPEPEPartialCharges() - Constructor for class org.openscience.cdk.charges.GasteigerPEPEPartialCharges

Constructor for the GasteigerPEPEPartialCharges object

Gaussian03Format - Class in org.openscience.cdk.io.formats

See here.

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

Gaussian92Format - Class in org.openscience.cdk.io.formats

Gaussian94Format - Class in org.openscience.cdk.io.formats

Gaussian95Format - Class in org.openscience.cdk.io.formats

Gaussian98Format - Class in org.openscience.cdk.io.formats

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.

GaussianInputWriter - Class in org.openscience.cdk.io.program

File writer thats generates input files for Gaussian calculation jobs.

GaussianInputWriter(Writer) - Constructor for class org.openscience.cdk.io.program.GaussianInputWriter

Constructs a new writer that produces input files to run a Gaussian QM job.

GaussianInputWriter(OutputStream) - Constructor for class org.openscience.cdk.io.program.GaussianInputWriter

GaussianInputWriter() - Constructor for class org.openscience.cdk.io.program.GaussianInputWriter

GaussiansBasis - Class in org.openscience.cdk.math.qm

This class contains the information to use gauss function as a base for calculation of quantum mechanics.

GaussiansBasis() - Constructor for class org.openscience.cdk.math.qm.GaussiansBasis

GaussiansBasis(int[], int[], int[], double[], Vector[], IAtom[]) - Constructor for class org.openscience.cdk.math.qm.GaussiansBasis

Set up basis with gauss funktions f(x,y,z) = (x-rx)^nx * (y-ry)^ny * (z-rz)^nz * exp(-alpha*(r-ri)^2).

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

Gauss-Jordan algorithm.

GD - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

GE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

generate(double) - Method in class org.openscience.cdk.formula.MassToFormulaTool

Method that actually does the work of extracting the molecular formula.

generate(String) - Static method in class org.openscience.cdk.iupac.parser.NomParser

Parses the chemical name and returns the built molecule.

generate() - Method in class org.openscience.cdk.structgen.SingleStructureRandomGenerator

Generates a random structure based on the atoms in the given IAtomContainer.

generate() - Method in class org.openscience.cdk.structgen.stochastic.PartialFilledStructureMerger

generate3DCoordinates(IMolecule, boolean) - Method in class org.openscience.cdk.modeling.builder3d.ModelBuilder3D

Generate 3D coordinates with force field information.

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.

generateExperimentalCoordinates() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

This method uses generateCoordinates, but it removes the hydrogens first, lays out the structuren and then adds them again.

generateExperimentalCoordinates(Vector2d) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

Generates 2D coordinates on the non-hydrogen skeleton, after which coordinates for the hydrogens are calculated.

GenerateFragments - Class in org.openscience.cdk.tools

Generate ring and Murcko-like fragments.

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

generateGrid() - Method in class org.openscience.cdk.tools.GridGenerator

Main method creates a grid between given boundaries (dimensions).

generateMoments(IAtomContainer) - Static method in class org.openscience.cdk.similarity.DistanceMoment

Evaluate the 12 descriptors used to characterize the 3D shape of a molecule.

generateMurckoFragments(IMolecule, boolean, boolean, int) - Method in class org.openscience.cdk.tools.GenerateFragments

generates Murcko fragments takes two parameters

generateOrderEle() - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator

Generate the order of the Elements according probability occurrence., beginning the C, H, O, N, Si, P, S, F, Cl, Br, I, Sn, B, Pb, Tl, Ba, In, Pd, Pt, Os, Ag, Zr, Se, Zn, Cu, Ni, Co, Fe, Cr, Ti, Ca, K, Al, Mg, Na, Ce, Hg, Au, Ir, Re, W, Ta, Hf, Lu, Yb, Tm, Er, Ho, Dy, Tb, Gd, Eu, Sm, Pm, Nd, Pr, La, Cs, Xe, Te, Sb, Cd, Rh, Ru, Tc, Mo, Nb, Y, Sr, Rb, Kr, As, Ge, Ga, Mn, V, Sc, Ar, Ne, Be, Li, Tl, Pb, Bi, Po, At, Rn, Fr, Ra, Ac, Th, Pa, U, Np, Pu.

generateParseException() - Method in class org.openscience.cdk.iupac.parser.NomParser

generateParseException() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

generateRingFragments(IMolecule) - Method in class org.openscience.cdk.tools.GenerateFragments

generates ring fragments from SSSR and RingPartitioner method

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

Calculates the geometric center of all placed atoms in the atomcontainer

GeometricMinimizer - Class in org.openscience.cdk.modeling.forcefield

Call the minimization methods.

GeometricMinimizer() - Constructor for class org.openscience.cdk.modeling.forcefield.GeometricMinimizer

Constructor for the GeometricMinimizer object

Geometry3DValidator - Class in org.openscience.cdk.validate

Validates the 3D geometry of the model.

Geometry3DValidator() - Constructor for class org.openscience.cdk.validate.Geometry3DValidator

GeometryTools - Class in org.openscience.cdk.geometry

A set of static utility classes for geometric calculations and operations.

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

GERMAINIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

GERMANIUM - Static variable in class 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.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;

get2DCenter() - Method in class org.openscience.cdk.Bond

Returns the geometric 2D center of the bond.

get2DCenter() - Method in class org.openscience.cdk.debug.DebugBond

get2DCenter(Iterable<IAtom>) - Static method in class org.openscience.cdk.geometry.GeometryTools

Calculates the center of the given atoms and returns it as a Point2d See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets

get2DCenter(Iterator<IAtom>) - Static method in class org.openscience.cdk.geometry.GeometryTools

Calculates the center of the given atoms and returns it as a Point2d See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets

get2DCenter(IRingSet) - Static method in class org.openscience.cdk.geometry.GeometryTools

Returns the geometric center of all the rings in this ringset.

get2DCenter(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools

Returns the geometric center of all the atoms in the atomContainer.

get2DCenter() - Method in interface org.openscience.cdk.interfaces.IBond

Returns the geometric 2D center of the bond.

get2DCentreOfMass(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools

Calculates the center of mass for the Atoms in the AtomContainer for the 2D coordinates.

get2DDimension(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools

Returns the java.awt.Dimension of a molecule See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets

get2ndOrderErrorApproximateGradientMMFF94SumEA() - Method in class org.openscience.cdk.modeling.forcefield.AngleBending

Get the 2nd order error approximate gradient of the angle bending term.

get2ndOrderErrorApproximateGradientMMFF94SumEBA() - Method in class org.openscience.cdk.modeling.forcefield.StretchBendInteractions

Get the 2nd order error approximate gradient for the stretch-bend term.

get2ndOrderErrorApproximateGradientMMFF94SumET() - Method in class org.openscience.cdk.modeling.forcefield.Torsions

Get the 2nd order error approximate gradient of the torsion term.

get2ndOrderErrorApproximateGradientMMFF94SumEvdW() - Method in class org.openscience.cdk.modeling.forcefield.VanDerWaalsInteractions

Get the 2nd order error approximate gradient for the Van Der Waals interaction term.

get2ndOrderErrorApproximateHessianMMFF94SumEA() - Method in class org.openscience.cdk.modeling.forcefield.AngleBending

Get the 2nd order error approximate Hessian for the angle bending energy term.

get2ndOrderErrorApproximateHessianMMFF94SumEB() - Method in class org.openscience.cdk.modeling.forcefield.BondStretching

Get the 2nd order error approximate Hessian for the bond stretching term.

get2ndOrderErrorApproximateHessianMMFF94SumET() - Method in class org.openscience.cdk.modeling.forcefield.Torsions

Get the 2nd order error approximate Hessian for the torsion term.

get3DCenter() - Method in class org.openscience.cdk.Bond

Returns the geometric 3D center of the bond.

get3DCenter() - Method in class org.openscience.cdk.debug.DebugBond

get3DCenter(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools

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.

get3DCentreOfMass(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools

Calculates the center of mass for the Atoms in the AtomContainer for the 2D coordinates.

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

get5OrderApproximateGradientMMFF94SumEvdW() - Method in class org.openscience.cdk.modeling.forcefield.VanDerWaalsInteractions

Get the 5th order error approximate gradient for the Van Der Waals interaction term.

get5thOrderErrorApproximateGradientMMFF94SumEA() - Method in class org.openscience.cdk.modeling.forcefield.AngleBending

Get the 5 order approximate gradient of the angle bending term.

get5thOrderErrorApproximateGradientMMFF94SumEBA() - Method in class org.openscience.cdk.modeling.forcefield.StretchBendInteractions

Get the 5 order approximate gradient of the stretch-bend interaction term.

get5thOrderErrorApproximateGradientMMFF94SumET() - Method in class org.openscience.cdk.modeling.forcefield.Torsions

Get the 5th order error approximate gradient of the torsion term.

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

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

Gets the A unit cell axes in carthesian coordinates as a three element double array.

getAction(JFrame, String, boolean) - Method in class org.openscience.cdk.renderer.JCPAction2D

Gets the action attribute of the JCPAction class

getAction(JFrame, String) - Method in class org.openscience.cdk.renderer.JCPAction2D

Gets the action attribute of the JCPAction class

getAdjRSQ() - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModelSummary

Deprecated. Return the adjusted R^2 value.

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

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

Returns a IMoleculeSet containing the agents in this reaction.

getAgents() - Method in class org.openscience.cdk.Reaction

Returns a MoleculeSet containing the agents in this reaction.

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(IMoleculeSet) - 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(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.GeometryTools

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(IMoleculeSet) - 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

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(IMoleculeSet) - 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.

getAllMolecules(IReactionScheme, IMoleculeSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator

Get all Molecules object from a set of Reactions given a IMoleculeSet to add.

getAllMolecules(IReactionScheme) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator

get all Molecules object from a set of Reactions.

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.

getAllRings() - Method in class org.openscience.cdk.graph.SpanningTree

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

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.

getAngle(double, double) - Static method in class org.openscience.cdk.geometry.GeometryTools

Gets the angle attribute of the GeometryTools class

getAngleBending2ndOrderErrorApproximateGradient() - Method in class org.openscience.cdk.modeling.forcefield.AngleBending

Get the angle bending 2nd order error approximate gradient.

getAngleBending2ndOrderErrorApproximateHessian() - Method in class org.openscience.cdk.modeling.forcefield.AngleBending

Get the 2nd order error approximate Hessian for the angle bending.

getAngleBendingFirstDerivative() - Method in class org.openscience.cdk.modeling.forcefield.AngleBending

Get the bond lengths first derivative respect to the cartesian coordinates of the atoms.

getAngleBendingSecondDerivative() - Method in class org.openscience.cdk.modeling.forcefield.AngleBending

Get the angle bending second derivative respect to the cartesian coordinates of the atoms.

getAngleData(String, String, String, String) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94ParametersCall

Gets the angle parameter set.

getAngleRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>) - Static method in class org.openscience.cdk.geometry.GeometryTools

Return the variation of each angle value between the 2 aligned molecules.

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.

getAssign() - Method in class org.openscience.cdk.qsar.model.R2.LinearRegressionModel

Gets the assign field of an 'lm' object.

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

Get the atom at position number in [0,..].

getAtom() - Method in class org.openscience.cdk.AtomParity

Returns the atom for which this parity is defined.

getAtom(int) - Method in class org.openscience.cdk.Bond

Returns an Atom from this bond.

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

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

getAtom() - Method in class org.openscience.cdk.debug.DebugAtomParity

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

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

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

getAtom() - Method in class org.openscience.cdk.debug.DebugLonePair

getAtom(int) - Method in class org.openscience.cdk.debug.DebugMolecule

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

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

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

getAtom() - Method in class org.openscience.cdk.debug.DebugSingleElectron

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

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

Get the atom at position number in [0,..].

getAtom() - Method in interface org.openscience.cdk.interfaces.IAtomParity

Returns the atom for which this parity is defined.

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() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RingIdentifierAtom

getAtom() - Method in class org.openscience.cdk.LonePair

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

Returna an atom in an atomcontainer identified by id

getAtomColor(IAtom) - Method in class org.openscience.cdk.renderer.color.CDK2DAtomColors

getAtomColor(IAtom, Color) - Method in class org.openscience.cdk.renderer.color.CDK2DAtomColors

getAtomColor(IAtom) - Method in class org.openscience.cdk.renderer.color.CDKAtomColors

getAtomColor(IAtom, Color) - Method in class org.openscience.cdk.renderer.color.CDKAtomColors

getAtomColor(IAtom) - Method in class org.openscience.cdk.renderer.color.CPKAtomColors

Returns the font color for atom given atom.

getAtomColor(IAtom, Color) - Method in class org.openscience.cdk.renderer.color.CPKAtomColors

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.PartialAtomicChargeColors

getAtomColor(IAtom, Color) - Method in class org.openscience.cdk.renderer.color.PartialAtomicChargeColors

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

getAtomContainer(int) - Method in class org.openscience.cdk.debug.DebugMoleculeSet

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.isomorphism.matchers.smarts.HydrogenAtom

Returns local copy of IAtomContainer.

getAtomContainer() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RecursiveSmartsAtom

getAtomContainer() - Method in class org.openscience.cdk.structgen.stochastic.PartialFilledStructureMerger

getAtomContainer(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator

Method that actually does the work of convert the IMolecularFormula to IAtomContainer.

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

Method that actually does the work of convert the IMolecularFormula to IAtomContainer given a IAtomContainer.

getAtomContainerCount() - Method in class org.openscience.cdk.AtomContainerSet

Returns the number of AtomContainers in this Container.

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

getAtomContainerCount() - Method in class org.openscience.cdk.debug.DebugMoleculeSet

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

Returns the number of AtomContainers in this Container.

getAtomCount() - Method in class org.openscience.cdk.Association

Returns the number of Atoms in this Association.

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

Returns the number of Atoms in this Container.

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

Returns the number of Atoms in this Bond.

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

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

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

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

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

getAtomCount() - Method in class org.openscience.cdk.debug.DebugMolecule

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

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

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

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

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(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.

getAtomDistance() - Method in class org.openscience.cdk.modeling.forcefield.VanDerWaalsInteractions

Get the atom distances values (Rij).

getAtomicNumber(PeriodicTableElement) - Method in class org.openscience.cdk.config.ElementPTFactory

Gets the atomic number of this element in the periodic table.

getAtomicNumber(String) - Static method in class org.openscience.cdk.config.Symbols

Returns the atomic number of the element identified by the given symbol.

getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugAtom

getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugAtomType

getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugElement

getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugIsotope

getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

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(String) - Static method in class org.openscience.cdk.tools.PeriodicTable

getAtomicSoftnessCore(IAtomContainer, int) - Method in class org.openscience.cdk.charges.InductivePartialCharges

Gets the atomicSoftnessCore attribute of the InductivePartialCharges object

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

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

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

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

getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule

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

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

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

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

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

Returns the position of a given atom in the atoms array.

getAtomOverlapScore(IAtomContainer, Vector) - Method in class org.openscience.cdk.layout.OverlapResolver

Calculates a score based on the overlap of atoms.

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

Returns the atom parity for the given Atom.

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

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

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

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

getAtomParity(IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule

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

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

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

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

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

Returns the atom parity for the given Atom.

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.

getAtomsDistancesFirstDerivative() - Method in class org.openscience.cdk.modeling.forcefield.VanDerWaalsInteractions

Get the atoms distances first order derivative respect to the cartesian coordinates of the atoms.

getAtomType(String) - Method in class org.openscience.cdk.config.AtomTypeFactory

Get an AtomType with the given ID.

getAtomTypeMappings() - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingHandler

Returns a Map with atom type mappings.

getAtomTypeName() - Method in class org.openscience.cdk.AtomType

Gets the id attribute of the AtomType object.

getAtomTypeName() - Method in class org.openscience.cdk.debug.DebugAtom

getAtomTypeName() - Method in class org.openscience.cdk.debug.DebugAtomType

getAtomTypeName() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

getAtomTypeName() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

getAtomTypeName() - Method in interface org.openscience.cdk.interfaces.IAtomType

Gets the id attribute of the AtomType object.

getAtomTypePatterns() - Method in class org.openscience.cdk.modeling.builder3d.MM2BasedAtomTypePattern

Gets the atomTypePatterns attribute of the MM2BasedAtomTypePattern object

getAtomTypePatterns() - Method in class org.openscience.cdk.modeling.builder3d.MMFF94BasedAtomTypePattern

Gets the atomTypePatterns attribute of the MM2BasedAtomTypePattern object

getAtomTypes(String) - Method in class org.openscience.cdk.config.AtomTypeFactory

Get an array of all atomTypes known to the AtomTypeFactory for the given element symbol and atomtype class.

getAtomTypes() - Method in class org.openscience.cdk.config.atomtypes.AtomTypeHandler

Returns a List with read IAtomType's.

getAtomTypes() - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeHandler

Returns a List with read IAtomType's.

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

Gets the atomTypes attribute of the ForceFieldConfigurator object

getAtomTypes() - Method in class org.openscience.cdk.modeling.builder3d.MM2BasedParameterSetReader

getAtomTypes() - Method in class org.openscience.cdk.modeling.builder3d.MMFF94BasedParameterSetReader

getAtomVector(int) - Method in class org.openscience.cdk.Vibration

Gets a atom vector at index given.

getAtomVectorCount() - Method in class org.openscience.cdk.Vibration

Gets the number of atom vectors in the vibration.

getAtomVectors() - Method in class org.openscience.cdk.Vibration

Returns an Enumeration of the atom vectors of this vibration.

getAtomWeights(AtomContainer) - Static method in class org.openscience.cdk.graph.invariant.HuLuIndexTool

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

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.qsar.model.R.PLSRegressionModelFit

getBasicRings() - Method in class org.openscience.cdk.graph.SpanningTree

getBasis() - Method in class org.openscience.cdk.math.qm.Orbitals

Returns the basis set of this orbitals

getBeginColumn() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream

getBeginColumn() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream

getBeginLine() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream

getBeginLine() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream

getBestAlignmentForLabel(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryTools

Determines the best alignment for the label of an atom in 2D space.

getBestAlignmentForLabelXY(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryTools

Determines the best alignment for the label of an atom in 2D space.

getBibData() - Method in class org.openscience.cdk.tools.BremserOneSphereHOSECodePredictor

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

Get the bond at position number in [0,..].

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

Returns the bond that connects the two given atoms.

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

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

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

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

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

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

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

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

getBond(int) - Method in class org.openscience.cdk.debug.DebugMolecule

getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule

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

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

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

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

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

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

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

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

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

Get the bond at position number in [0,..].

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

Returns the bond that connectes the two given atoms.

getBondAngleInteractionData(String, String, String, String) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94ParametersCall

Gets the bond-angle interaction parameter set.

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

Constructs an array of Bond objects from an AtomContainer.

getBondArray(List<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator

Constructs an array of Atom objects from a List of Atom objects.

getBondCoordinates(IBond) - Static method in class org.openscience.cdk.geometry.GeometryTools

Writes the coordinates of the atoms participating the given bond into an array.

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

Returns the number of Bonds in this Container.

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

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

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

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

getBondCount() - Method in class org.openscience.cdk.debug.DebugMolecule

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

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

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

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

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

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.pharmacophore.PharmacophoreAngleBond

Get the angle between the three pharmacophore groups that make up the constraint.

getBondLength() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreBond

Get the distance between the two pharmacophore groups that make up the constraint.

getBondLengthAverage(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools

An average of all 2D bond length values is produced.

getBondLengthAverage3D(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools

An average of all 3D bond length values is produced, using point3ds in atoms.

getBondLengthRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>, boolean) - Static method in class org.openscience.cdk.geometry.GeometryTools

Return the RMSD of bonds length between the 2 aligned molecules.

getBondLengthsFirstDerivative() - Method in class org.openscience.cdk.modeling.forcefield.BondStretching

Get the bond lengths first derivative respect to the cartesian coordinates of the atoms.

getBondLengthsSecondDerivative() - Method in class org.openscience.cdk.modeling.forcefield.BondStretching

Get the bond lengths second derivative respect to the cartesian coordinates of the atoms.

getBondLengthsSecondDerivative() - Method in class org.openscience.cdk.modeling.forcefield.VanDerWaalsInteractions

Get the bond lengths second derivative respect to the cartesian coordinates of the atoms.

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

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

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

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

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

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

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

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

getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule

getBondNumber(IBond) - Method in class org.openscience.cdk.debug.DebugMolecule

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

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

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

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

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

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

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

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

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

Returns the position of the bond between two given atoms in the electronContainers array.

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

Returns the position of a given bond in the electronContainers array.

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

Deprecated. Replaced by AtomContainerManipulator#getBondOrderSum(IAtomContainer, IAtom)

getBondOrderSum() - Method in class org.openscience.cdk.AtomType

Gets the bondOrderSum attribute of the AtomType object.

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

getBondOrderSum() - Method in class org.openscience.cdk.debug.DebugAtom

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

getBondOrderSum() - Method in class org.openscience.cdk.debug.DebugAtomType

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

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

getBondOrderSum() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule

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

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

getBondOrderSum() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

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

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

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

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.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

Calculates a score based on the intersection of bonds.

getBondsAcyclicCount() - Method in class org.openscience.cdk.graph.SpanningTree

getBondsCyclicCount() - Method in class org.openscience.cdk.graph.SpanningTree

getBondType() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTSimpleBond

Returns type of bond.

getBuilder() - Method in class org.openscience.cdk.ChemObject

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

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

getBuilder() - Method in class org.openscience.cdk.debug.DebugAtom

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

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

getBuilder() - Method in class org.openscience.cdk.debug.DebugAtomType

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

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

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

getBuilder() - Method in class org.openscience.cdk.debug.DebugChemModel

getBuilder() - Method in class org.openscience.cdk.debug.DebugChemObject

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

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

getBuilder() - Method in class org.openscience.cdk.debug.DebugElectronContainer

getBuilder() - Method in class org.openscience.cdk.debug.DebugElement

getBuilder() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

getBuilder() - Method in class org.openscience.cdk.debug.DebugIsotope

getBuilder() - Method in class org.openscience.cdk.debug.DebugLonePair

getBuilder() - Method in class org.openscience.cdk.debug.DebugMapping

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

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

getBuilder() - Method in class org.openscience.cdk.debug.DebugMolecule

getBuilder() - Method in class org.openscience.cdk.debug.DebugMoleculeSet

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

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

getBuilder() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

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

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

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

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

getBuilder() - Method in class org.openscience.cdk.debug.DebugSingleElectron

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

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.IAdductFormula

Returns a ChemObjectBuilder for the data classes that extend this class.

getBuilder() - Method in interface org.openscience.cdk.interfaces.IChemObject

Returns a ChemObjectBuilder for the data classes that extend this class.

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

Returns a ChemObjectBuilder for the data classes that extend this class.

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

Returns a ChemObjectBuilder for the data classes that extend this class.

getBuilder() - Method in class org.openscience.cdk.nonotify.NNAdductFormula

getBuilder() - Method in class org.openscience.cdk.nonotify.NNAminoAcid

getBuilder() - Method in class org.openscience.cdk.nonotify.NNAtom

getBuilder() - Method in class org.openscience.cdk.nonotify.NNAtomContainer

getBuilder() - Method in class org.openscience.cdk.nonotify.NNAtomContainerSet

getBuilder() - Method in class org.openscience.cdk.nonotify.NNAtomType

getBuilder() - Method in class org.openscience.cdk.nonotify.NNBioPolymer

getBuilder() - Method in class org.openscience.cdk.nonotify.NNBond

getBuilder() - Method in class org.openscience.cdk.nonotify.NNChemFile

getBuilder() - Method in class org.openscience.cdk.nonotify.NNChemModel

getBuilder() - Method in class org.openscience.cdk.nonotify.NNChemObject

getBuilder() - Method in class org.openscience.cdk.nonotify.NNChemSequence

getBuilder() - Method in class org.openscience.cdk.nonotify.NNCrystal

getBuilder() - Method in class org.openscience.cdk.nonotify.NNElectronContainer

getBuilder() - Method in class org.openscience.cdk.nonotify.NNElement

getBuilder() - Method in class org.openscience.cdk.nonotify.NNFragmentAtom

getBuilder() - Method in class org.openscience.cdk.nonotify.NNIsotope

getBuilder() - Method in class org.openscience.cdk.nonotify.NNLonePair

getBuilder() - Method in class org.openscience.cdk.nonotify.NNMapping

getBuilder() - Method in class org.openscience.cdk.nonotify.NNMolecularFormula

getBuilder() - Method in class org.openscience.cdk.nonotify.NNMolecularFormulaSet

getBuilder() - Method in class org.openscience.cdk.nonotify.NNMolecule

getBuilder() - Method in class org.openscience.cdk.nonotify.NNMoleculeSet

getBuilder() - Method in class org.openscience.cdk.nonotify.NNMonomer

getBuilder() - Method in class org.openscience.cdk.nonotify.NNPDBAtom

getBuilder() - Method in class org.openscience.cdk.nonotify.NNPDBMonomer

getBuilder() - Method in class org.openscience.cdk.nonotify.NNPDBPolymer

getBuilder() - Method in class org.openscience.cdk.nonotify.NNPDBStructure

getBuilder() - Method in class org.openscience.cdk.nonotify.NNPolymer

getBuilder() - Method in class org.openscience.cdk.nonotify.NNPseudoAtom

getBuilder() - Method in class org.openscience.cdk.nonotify.NNReaction

getBuilder() - Method in class org.openscience.cdk.nonotify.NNReactionScheme

getBuilder() - Method in class org.openscience.cdk.nonotify.NNReactionSet

getBuilder() - Method in class org.openscience.cdk.nonotify.NNRing

getBuilder() - Method in class org.openscience.cdk.nonotify.NNRingSet

getBuilder() - Method in class org.openscience.cdk.nonotify.NNSingleElectron

getBuilder() - Method in class org.openscience.cdk.nonotify.NNStrand

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

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

Gets the C unit cell axes in carthesian 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.

getCASid(PeriodicTableElement) - Method in class org.openscience.cdk.config.ElementPTFactory

Gets the CAS id of this element in the periodic table.

getCASid() - Method in class org.openscience.cdk.PeriodicTableElement

Returns the CAS (Chemical Abstracts Service), which this element has.

getCASId(String) - Static method in class org.openscience.cdk.tools.PeriodicTable

getCC(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ConnectionCountAtom

Returns the connection count of an atom.

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.

getCensored() - Method in class org.openscience.cdk.qsar.model.R.CNNRegressionModelSummary

Deprecated. Return whether censored was used.

getCensored() - Method in class org.openscience.cdk.qsar.model.R2.CNNRegressionModel

Gets the censored field of an 'nnet' object.

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.

getChainID() - Method in class org.openscience.cdk.debug.DebugPDBAtom

getChainID() - Method in class org.openscience.cdk.debug.DebugPDBMonomer

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

getCharge() - Method in class org.openscience.cdk.Atom

Returns the partial charge of this atom.

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

getCharge() - Method in class org.openscience.cdk.debug.DebugAtom

getCharge() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

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

getCharge() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

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

Returns the partial 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

Returns the partial charge of this IMolecularFormula.

getCharge() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTCharge

Returns the charge value.

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

getChemFile() - Method in class org.openscience.cdk.io.inchi.INChIHandler

getChemicalSerie(PeriodicTableElement) - Method in class org.openscience.cdk.config.ElementPTFactory

Gets the chemical serie of this element in the periodic table.

getChemicalSerie() - Method in class org.openscience.cdk.PeriodicTableElement

Returns the chemical series of this element.

getChemicalSeries(String) - Static method in class org.openscience.cdk.tools.PeriodicTable

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

getChemModel(int) - Method in interface org.openscience.cdk.interfaces.IChemSequence

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

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

Returns the number of ChemModels in this Container.

getChemObject(int) - Method in class org.openscience.cdk.debug.DebugMapping

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() - 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

getChemSequence(int) - Method in interface org.openscience.cdk.interfaces.IChemFile

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

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

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

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

getCID(XmlPullParser) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper

getClassName() - Method in class org.openscience.cdk.dict.Entry

getClosestAtom(int, int, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools

Returns the atom of the given molecule that is closest to the given coordinates.

getClosestAtom(double, double, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools

Returns the atom of the given molecule that is closest to the given coordinates.

getClosestBond(int, int, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools

Returns the bond of the given molecule that is closest to the given coordinates.

getClosestBond(double, double, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools

Returns the bond of the given molecule that is closest to the given coordinates.

getCoeff() - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModelSummary

Deprecated. Returns the coefficients and associated statistics.

getCoefficients() - Method in class org.openscience.cdk.math.qm.Orbitals

Get the coefficient matrix

getCoefficients() - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModelFit

Deprecated. Get the fitted coefficients.

getCoefficients() - Method in class org.openscience.cdk.qsar.model.R2.LinearRegressionModel

Gets the coefficients field of an 'lm' object.

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

Returns the column-matrix at the given line index

getColumn() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream

Deprecated.

getColumn() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream

Deprecated.

getColumns() - Method in class org.openscience.cdk.math.IMatrix

Returns the count of columns

getColumns() - Method in class org.openscience.cdk.math.Matrix

Returns the number of columns.

getConfidenceLimit(String) - Method in class org.openscience.cdk.tools.BremserOneSphereHOSECodePredictor

getConjugateGradientMinimum() - Method in class org.openscience.cdk.modeling.forcefield.GeometricMinimizer

Gets the conjugatedGradientMinimum attribute of the GeometricMinimizer object

getConn() - Method in class org.openscience.cdk.qsar.model.R2.CNNRegressionModel

Gets the conn field of an 'nnet' object.

getConnectedAtom(IAtom) - Method in class org.openscience.cdk.Bond

Returns the atom connected to the given atom.

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

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

Returns the atom connected to the given atom.

getConnectedAtoms(IAtom) - Method in class org.openscience.cdk.Bond

Returns all the atoms in the bond connected to the specified atom.

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

Returns all the atoms in the bond connected to the given atom.

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

Returns the number of atoms connected to the given atom.

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

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

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

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

getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule

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

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

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

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

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

Returns the number of atoms connected to the given atom.

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

Returns an ArrayList of all atoms connected to the given atom.

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

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

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

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

getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule

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

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

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

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

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

Returns an ArrayList of all atoms connected to the given atom.

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

Returns the number of Bonds for a given Atom.

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

Returns the number of connected atoms (degree) to the given atom.

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

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

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

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

getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule

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

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

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

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

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

Returns the number of Bonds for a given Atom.

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

Returns the number of connected atoms (degree) to the given atom.

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

Returns an ArrayList of all Bonds connected to the given atom.

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

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

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

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

getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule

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

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

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

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

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

Returns an ArrayList of all Bonds connected to the given atom.

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

Returns an ArrayList of all electronContainers connected to the given atom.

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

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

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

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

getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule

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

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

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

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

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

Returns an ArrayList of all electronContainers connected to the given atom.

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

Returns the number of LonePairs for a given Atom.

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

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

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

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

getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule

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

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

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

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

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

Returns the number of LonePairs for a given Atom.

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

Returns the array of lone pairs connected to an atom.

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

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

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

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

getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule

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

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

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

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

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

Returns the array of lone pairs connected to an atom.

getConnectedRings(IRing) - Method in class org.openscience.cdk.debug.DebugRingSet

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.

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

Returns the sum of the SingleElectron for a given Atom.

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

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

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

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

getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule

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

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

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

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

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

Returns the sum of the SingleElectron for a given Atom.

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

Returns an array of all SingleElectron connected to the given atom.

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

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

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

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

getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule

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

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

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

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

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

Returns an array of all SingleElectron connected to the given atom.

getContainer(IMolecule, IAtom) - Method in class org.openscience.cdk.tools.StructureResonanceGenerator

Get the container which the atom is found on resonance from a IMolecule.

getContainer(IMolecule, IBond) - Method in class org.openscience.cdk.tools.StructureResonanceGenerator

Get the container which the bond is found on resonance from a IMolecule.

getContainers(IMolecule) - Method in class org.openscience.cdk.tools.StructureResonanceGenerator

Get the container which is found resonance from a IMolecule.

getConvergenceParametersForCGM() - Method in class org.openscience.cdk.modeling.forcefield.GeometricMinimizer

getConvergenceParametersForNRM() - Method in class org.openscience.cdk.modeling.forcefield.GeometricMinimizer

getConvergenceParametersForSDM() - Method in class org.openscience.cdk.modeling.forcefield.GeometricMinimizer

getCoordinates3xNVector(IAtomContainer) - Static method in class org.openscience.cdk.modeling.forcefield.ForceFieldTools

Get the coordinates 3xN vector of a molecule of N atoms from its atom container

getCoordinatesFromGridPoint(Point3d) - Method in class org.openscience.cdk.tools.GridGenerator

Method calculates coordiantes from a given grid point.

getCoordinatesFromGridPoint(int) - Method in class org.openscience.cdk.tools.GridGenerator

Method calculates coordiantes from a given grid array position.

getCount() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTImplicitHCount

Returns implicit H count.

getCount() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTTotalHCount

Returns total H count.

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

Returns the number of CDK errors.

getCountBasis() - Method in class org.openscience.cdk.math.qm.Orbitals

Set the count of bases

getCountElectrons() - Method in class org.openscience.cdk.math.qm.Orbitals

Gets the count of electrons, which occupies the orbitals

getCountOrbitals() - Method in class org.openscience.cdk.math.qm.Orbitals

Returns the count of orbitals

getCovalentRadius() - Method in class org.openscience.cdk.AtomType

Returns the covalent radius for this AtomType.

getCovalentRadius(PeriodicTableElement) - Method in class org.openscience.cdk.config.ElementPTFactory

Gets the covalent radios of this element in the periodic table.

getCovalentRadius() - Method in class org.openscience.cdk.debug.DebugAtom

getCovalentRadius() - Method in class org.openscience.cdk.debug.DebugAtomType

getCovalentRadius() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

getCovalentRadius() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

getCovalentRadius() - Method in interface org.openscience.cdk.interfaces.IAtomType

Returns the covalent radius for this AtomType.

getCovalentRadius() - Method in class org.openscience.cdk.PeriodicTableElement

Get the covalent radius.

getCovalentRadius(String) - Static method in class org.openscience.cdk.tools.PeriodicTable

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

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

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

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

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.

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.

getDecay() - Method in class org.openscience.cdk.qsar.model.R2.CNNRegressionModel

Gets the decay field of an 'nnet' object.

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

getDegree() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom

getDegree() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTChirality

getDeltav() - Method in class org.openscience.cdk.modeling.forcefield.AngleBending

Get the current difference between the bond angles vijk and the reference angles.

getDescription() - Method in class org.openscience.cdk.dict.Entry

getDescriptorClassNameByInterface(String, String[]) - Static method in class org.openscience.cdk.qsar.DescriptorEngine

Returns a list containing the classes that implement a specific interface.

getDescriptorClassNameByPackage(String, String[]) - Static method in class org.openscience.cdk.qsar.DescriptorEngine

Returns a list containing the classes found in the specified descriptor package.

getDescriptorClassNames() - Method in class org.openscience.cdk.qsar.DescriptorEngine

Returns a list containing the names of the classes implementing the descriptors.

getDescriptorInstances() - Method in class org.openscience.cdk.qsar.DescriptorEngine

Returns a List containing the instantiated descriptor classes.

getDescriptorMetadata() - Method in class org.openscience.cdk.dict.Entry

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInConjugatedPiSystemDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor

getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor

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.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.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.IPMolecularLearningDescriptor

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.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.TPSADescriptor

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 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.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.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.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.IPMolecularLearningDescriptor

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.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.TPSADescriptor

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.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

getDF() - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModelPredict

Deprecated. Get the degrees of freedom.

getdfResidual() - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModelFit

Deprecated. Get the DOF of the residuals.

getDfResidual() - Method in class org.openscience.cdk.qsar.model.R2.LinearRegressionModel

Gets the df.residual field of an 'lm' object.

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(DescriptorSpecification) - 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(DescriptorSpecification) - 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

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.

getDisplayMode() - Method in class org.openscience.cdk.renderer.GraphRendererModel

Get the display mode

getDuration(long, long) - Static method in class org.openscience.cdk.tools.SwissArmyKnife

Returns a string reporting the time passed between startTime and endTime, both given in milliseconds, in hours, minutes, seconds and milliseconds

getDuration(long) - Static method in class org.openscience.cdk.tools.SwissArmyKnife

Returns a String reporting the time passed during a given number of milliseconds.

getEAIDNumber(AtomContainer) - Static method in class org.openscience.cdk.graph.invariant.HuLuIndexTool

Calculates the extended adjacency matrix index.

getEffects() - Method in class org.openscience.cdk.qsar.model.R2.LinearRegressionModel

Gets the effects field of an 'lm' object.

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

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

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

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

getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugMolecule

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

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

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

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

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

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

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

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

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

getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugMolecule

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

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

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

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

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

Returns the number of ElectronContainers in this Container.

getElectronCount() - Method in class org.openscience.cdk.Association

Returns the number of electrons in a Association.

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

getElectronCount() - Method in class org.openscience.cdk.debug.DebugElectronContainer

getElectronCount() - Method in class org.openscience.cdk.debug.DebugLonePair

getElectronCount() - Method in class org.openscience.cdk.debug.DebugSingleElectron

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.LonePair

Returns the number of electrons in a LonePair.

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.ElementPTFactory

Returns an Element with a given element symbol.

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.

getElements() - Method in class org.openscience.cdk.config.ElementPTFactory

Get all the elements loaded by the factory.

getElements() - Method in class org.openscience.cdk.config.elements.ElementPTHandler

Returns the element read from the XML file.

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.

getEndChainID() - Method in class org.openscience.cdk.debug.DebugPDBStructure

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.

getEndColumn() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream

getEndColumn() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream

getEndInsertionCode() - Method in class org.openscience.cdk.debug.DebugPDBStructure

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.

getEndLine() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream

getEndLine() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream

getEndSequenceNumber() - Method in class org.openscience.cdk.debug.DebugPDBStructure

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.

getEnergies() - Method in class org.openscience.cdk.math.qm.ClosedShellJob

getEnergies() - Method in class org.openscience.cdk.math.qm.OneElectronJob

Returns the energies of the orbitals

getEnergyGradient() - Method in interface org.openscience.cdk.modeling.forcefield.IPotentialFunction

Get the gradient of the potential energy function in a given point.

getEnergyGradient() - Method in class org.openscience.cdk.modeling.forcefield.MMFF94EnergyFunction

Get the gradient for the MMFF94 energy function in a given 3xN point

getEnergyHessian() - Method in interface org.openscience.cdk.modeling.forcefield.IPotentialFunction

Get the hessian of the potential energy function in a given point.

getEnergyHessian() - Method in class org.openscience.cdk.modeling.forcefield.MMFF94EnergyFunction

Get the hessian for the MMFF94 energy function.

getEntries() - Method in class org.openscience.cdk.dict.Dictionary

getEntropy() - Method in class org.openscience.cdk.qsar.model.R.CNNRegressionModelSummary

Deprecated. Return whether entropy was used.

getEntropy() - Method in class org.openscience.cdk.qsar.model.R2.CNNRegressionModel

Gets the entropy field of an 'nnet' object.

getEntry(String) - Method in class org.openscience.cdk.dict.Dictionary

getEquivalenceClassesSizeVector() - Method in class org.openscience.cdk.ringsearch.SSSRFinder

Returns a vector containing the size of the "interchangeability" equivalence classes.

getEquivalentClass(double[]) - Method in class org.openscience.cdk.graph.invariant.EquivalentClassPartitioner

Get the final equivalent class

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

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

Returns the number of failed tests.

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

Returns an array of ValidationTest errors.

getExactMass() - Method in class org.openscience.cdk.debug.DebugAtom

getExactMass() - Method in class org.openscience.cdk.debug.DebugAtomType

getExactMass() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

getExactMass() - Method in class org.openscience.cdk.debug.DebugIsotope

getExactMass() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

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.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

getExtendedAdjacenyMatrix(AtomContainer) - Static method in class org.openscience.cdk.graph.invariant.HuLuIndexTool

getExtendGrid() - Method in class org.openscience.cdk.tools.GridGenerator

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

Gets the extension attribute of the RNode object

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.EStateFingerprinter

Calculates the substructure fingerprint for the given AtomContainer.

getFingerprint(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 It contains the informations from getFingerprint() and bits which tell if the structure has 0 rings, 1 or less rings, 2 or less rings ...

getFingerprint(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 It contains the informations from getFingerprint() and bits which tell if the structure has 0 rings, 1 or less rings, 2 or less rings ...

getFingerprint(IAtomContainer, AllRingsFinder) - Method in class org.openscience.cdk.fingerprint.Fingerprinter

Generates a fingerprint of the default size for the given AtomContainer.

getFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.Fingerprinter

Generates a fingerprint of the default size for the given AtomContainer.

getFingerprint(IAtomContainer, int) - Method in class org.openscience.cdk.fingerprint.GraphOnlyFingerprinter

getFingerprint(IAtomContainer) - Method in interface org.openscience.cdk.fingerprint.IFingerprinter

Returns the fingerprint for the given IAtomContainer.

getFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.MACCSFingerprinter

Calculates the substructure fingerprint for the given AtomContainer.

getFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.SubstructureFingerprinter

Calculates the substructure fingerprint for the given AtomContainer.

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

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

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

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

getFirstAtom() - Method in class org.openscience.cdk.debug.DebugMolecule

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

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

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

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

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

Returns the atom at position 0 in the container.

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

Returns the size of the first of the two compared graphs.

getFitB() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModel

Deprecated. Gets the coefficents.

getFitCoefficients() - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModel

Deprecated. Returns the estimated coefficients.

getFitDFResidual() - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModel

Deprecated. Returns the residual degrees of freedom.

getFitFitted() - Method in class org.openscience.cdk.qsar.model.R.CNNClassificationModel

Deprecated. Gets fitted values from the final model.

getFitFitted() - Method in class org.openscience.cdk.qsar.model.R.CNNRegressionModel

Deprecated. Gets fitted values from the final model.

getFitFitted() - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModel

Deprecated. Returns the fitted mean values.

getFitHessian() - Method in class org.openscience.cdk.qsar.model.R.CNNClassificationModel

Deprecated. Gets the Hessian of the measure of fit.

getFitHessian() - Method in class org.openscience.cdk.qsar.model.R.CNNRegressionModel

Deprecated. Gets the Hessian of the measure of fit.

getFitMethod() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModel

Deprecated. The method used to build the PLS model.

getFitNComp() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModel

Deprecated. Returns the fit NComp value.

getFitRank() - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModel

Deprecated. Gets the rank of the fitted linear model.

getFitResiduals() - Method in class org.openscience.cdk.qsar.model.R.CNNClassificationModel

Deprecated. Gets residuals for the fitted values from the final model.

getFitResiduals() - Method in class org.openscience.cdk.qsar.model.R.CNNRegressionModel

Deprecated. Gets residuals for the fitted values from the final model.

getFitResiduals() - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModel

Deprecated. Returns the residuals.

getFitRMS() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModel

Deprecated. Get the Root Mean Square (RMS) error for the fit.

getFitted() - Method in class org.openscience.cdk.qsar.model.R.CNNClassificationModelFit

Deprecated. Get the fitted values.

getFitted() - Method in class org.openscience.cdk.qsar.model.R.CNNRegressionModelFit

Deprecated. Get the fitted values.

getFitted() - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModelFit

Deprecated. Get the fitted values.

getFittedValues() - Method in class org.openscience.cdk.qsar.model.R2.CNNRegressionModel

Gets the fitted.values field of an 'nnet' object.

getFittedValues() - Method in class org.openscience.cdk.qsar.model.R2.LinearRegressionModel

Gets the fitted.values field of an 'lm' object.

getFitValue() - Method in class org.openscience.cdk.qsar.model.R.CNNClassificationModel

Deprecated. Gets final value of the fitting criteria.

getFitValue() - Method in class org.openscience.cdk.qsar.model.R.CNNRegressionModel

Deprecated. Gets final value of the fitting criteria.

getFitWasValidated() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModel

Deprecated. Indicates whether CV was used to build the model.

getFitWeights() - Method in class org.openscience.cdk.qsar.model.R.CNNClassificationModel

Deprecated. Gets optimized weights for the model.

getFitWeights() - Method in class org.openscience.cdk.qsar.model.R.CNNRegressionModel

Deprecated. Gets optimized weights for the model.

getFitXLoading() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModel

Deprecated. Get the X loadings.

getFitXScores() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModel

Deprecated. Get the X scores.

getFitYLoading() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModel

Deprecated. Get the Y loadings.

getFitYPred() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModel

Deprecated. Get the predicted Y's.

getFitYScores() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModel

Deprecated. Get the Y scores.

getFlag(int) - Method in class org.openscience.cdk.ChemObject

Returns the value of some flag.

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

getFlag(int) - Method in class org.openscience.cdk.debug.DebugAtom

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

getFlag(int) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet

getFlag(int) - Method in class org.openscience.cdk.debug.DebugAtomType

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

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

getFlag(int) - Method in class org.openscience.cdk.debug.DebugChemFile

getFlag(int) - Method in class org.openscience.cdk.debug.DebugChemModel

getFlag(int) - Method in class org.openscience.cdk.debug.DebugChemObject

getFlag(int) - Method in class org.openscience.cdk.debug.DebugChemSequence

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

getFlag(int) - Method in class org.openscience.cdk.debug.DebugElectronContainer

getFlag(int) - Method in class org.openscience.cdk.debug.DebugElement

getFlag(int) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

getFlag(int) - Method in class org.openscience.cdk.debug.DebugIsotope

getFlag(int) - Method in class org.openscience.cdk.debug.DebugLonePair

getFlag(int) - Method in class org.openscience.cdk.debug.DebugMapping

getFlag(int) - Method in class org.openscience.cdk.debug.DebugMolecule

getFlag(int) - Method in class org.openscience.cdk.debug.DebugMoleculeSet

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

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

getFlag(int) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

getFlag(int) - Method in class org.openscience.cdk.debug.DebugReaction

getFlag(int) - Method in class org.openscience.cdk.debug.DebugReactionScheme

getFlag(int) - Method in class org.openscience.cdk.debug.DebugReactionSet

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

getFlag(int) - Method in class org.openscience.cdk.debug.DebugSingleElectron

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

getFlag(int) - Method in interface org.openscience.cdk.interfaces.IChemObject

Returns the value of some flag.

getFlag(int) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom

getFlags() - Method in class org.openscience.cdk.ChemObject

Returns the whole set of flags.

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

getFlags() - Method in class org.openscience.cdk.debug.DebugAtom

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

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

getFlags() - Method in class org.openscience.cdk.debug.DebugAtomType

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

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

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

getFlags() - Method in class org.openscience.cdk.debug.DebugChemModel

getFlags() - Method in class org.openscience.cdk.debug.DebugChemObject

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

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

getFlags() - Method in class org.openscience.cdk.debug.DebugElectronContainer

getFlags() - Method in class org.openscience.cdk.debug.DebugElement

getFlags() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

getFlags() - Method in class org.openscience.cdk.debug.DebugIsotope

getFlags() - Method in class org.openscience.cdk.debug.DebugLonePair

getFlags() - Method in class org.openscience.cdk.debug.DebugMapping

getFlags() - Method in class org.openscience.cdk.debug.DebugMolecule

getFlags() - Method in class org.openscience.cdk.debug.DebugMoleculeSet

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

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

getFlags() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

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

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

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

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

getFlags() - Method in class org.openscience.cdk.debug.DebugSingleElectron

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

getFlags() - Method in interface org.openscience.cdk.interfaces.IChemObject

Returns the whole set of flags.

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

Gets the forbidden attribute of the RNode object

getForEnergyHessian() - Method in interface org.openscience.cdk.modeling.forcefield.IPotentialFunction

Get the hessian of the potential energy function in a given point.

getForEnergyHessian() - Method in class org.openscience.cdk.modeling.forcefield.MMFF94EnergyFunction

Get the hessian for the MMFF94 energy function.

getForHessianMMFF94SumEB() - Method in class org.openscience.cdk.modeling.forcefield.BondStretching

Get the hessian for the bond stretching.

getForHessianMMFF94SumEQ() - Method in class org.openscience.cdk.modeling.forcefield.ElectrostaticInteractions

Get the hessian for the Electrostatic interaction energy.

getForHessianMMFF94SumEvdW() - Method in class org.openscience.cdk.modeling.forcefield.VanDerWaalsInteractions

Get the hessian for the van der Waals interactions.

getFormalCharge() - Method in class org.openscience.cdk.AtomType

Returns the formal charge of this atom.

getFormalCharge() - Method in class org.openscience.cdk.debug.DebugAtom

getFormalCharge() - Method in class org.openscience.cdk.debug.DebugAtomType

getFormalCharge() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

getFormalCharge() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

getFormalCharge() - Method in interface org.openscience.cdk.interfaces.IAtomType

Returns the formal charge of this atom.

getFormalNeighbourCount() - Method in class org.openscience.cdk.AtomType

Returns the formal neighbour count of this atom.

getFormalNeighbourCount() - Method in class org.openscience.cdk.debug.DebugAtom

getFormalNeighbourCount() - Method in class org.openscience.cdk.debug.DebugAtomType

getFormalNeighbourCount() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

getFormalNeighbourCount() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

getFormalNeighbourCount() - Method in interface org.openscience.cdk.interfaces.IAtomType

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.IteratingMDLReader

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.IteratingSMILESReader

Get the format for this reader.

getFormat() - Method in class org.openscience.cdk.io.MDLReader

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

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

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

getFormat() - Method in class org.openscience.cdk.io.MDLRXNWriter

getFormat() - Method in class org.openscience.cdk.io.MDLV2000Reader

getFormat() - Method in class org.openscience.cdk.io.MDLV3000Reader

getFormat() - Method in class org.openscience.cdk.io.MDLWriter

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.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.random.RandomAccessSDFReader

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

getFormatName() - Method in class org.openscience.cdk.io.formats.Aces2Format

getFormatName() - Method in class org.openscience.cdk.io.formats.ADFFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.AlchemyFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.BGFFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.BSFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.CACheFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format

getFormatName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format

getFormatName() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.CIFFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.CMLFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.CRK2DFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.CRK3DFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.CrystClustFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.CTXFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.DaltonFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.DMol3Format

getFormatName() - Method in class org.openscience.cdk.io.formats.DOCK5Format

getFormatName() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.FingerprintFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.GamessFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian03Format

getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian90Format

getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian92Format

getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian94Format

getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian95Format

getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian98Format

getFormatName() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.GROMOS96Format

getFormatName() - Method in class org.openscience.cdk.io.formats.HINFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.INChIFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat

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

getFormatName() - Method in class org.openscience.cdk.io.formats.JMEFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.MacroModelFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.MDLFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format

getFormatName() - Method in class org.openscience.cdk.io.formats.MDLV2000Format

getFormatName() - Method in class org.openscience.cdk.io.formats.MDLV3000Format

getFormatName() - Method in class org.openscience.cdk.io.formats.MMODFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.Mol2Format

getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format

getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC7Format

getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC93Format

getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC97Format

getFormatName() - Method in class org.openscience.cdk.io.formats.MPQCFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.NWChemFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.PCModelFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.PDBFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.PDBMLFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.PMPFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.POVRayFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.PQSChemFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.QChemFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.RawCopyFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.SDFFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.ShelXFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.SMARTSFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.SMILESFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.SpartanFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.SVGFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format

getFormatName() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.VASPFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.ViewmolFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.XEDFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.XYZFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.YasaraFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.ZindoFormat

getFormatName() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat

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.

getFractionalPoint3d() - Method in class org.openscience.cdk.Atom

Returns a point specifying the location of this atom in a Crystal unit cell.

getFractionalPoint3d() - Method in class org.openscience.cdk.debug.DebugAtom

getFractionalPoint3d() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

getFractionalPoint3d() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

getFractionalPoint3d() - Method in interface org.openscience.cdk.interfaces.IAtom

Returns a point specifying the location of this atom in a Crystal unit cell.

getFragment() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

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.

getFragments(IAtomContainer, QueryAtomContainer[]) - Static method in class org.openscience.cdk.qsar.descriptors.molecular.ChiIndexUtils

Gets the fragments from a target AtomContainer matching a set of query fragments.

getFStatistic() - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModelSummary

Deprecated. Returns the value of the F-statistic.

getFStatisticDF() - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModelSummary

Deprecated. Returns the degrees of freedom (DoF) for which the F-statistic was calculated.

getFunction(int) - Method in class org.openscience.cdk.renderer.GraphRendererModel

Get a function from this set

getFunctionalGroupSMARTS() - Static method in class org.openscience.cdk.fingerprint.StandardSubstructureSets

getFunctionColor(int) - Method in class org.openscience.cdk.renderer.GraphRendererModel

Get a color from a function in this set

getFunctionMMFF94SumEBA() - Method in class org.openscience.cdk.modeling.forcefield.StretchBendInteractions

Get the MMFF94 stretch-bend interaction term.

getFunctionMMFF94SumEvdW() - Method in class org.openscience.cdk.modeling.forcefield.VanDerWaalsInteractions

Get the MMFF94 Van Der Waals interaction energy for the current atoms coordinates.

getFunctionsSize() - Method in class org.openscience.cdk.renderer.GraphRendererModel

Get the count of functions in this set

getGradientMMFF94SumEA() - Method in class org.openscience.cdk.modeling.forcefield.AngleBending

Get the gradient of the angle bending term.

getGradientMMFF94SumEB() - Method in class org.openscience.cdk.modeling.forcefield.BondStretching

Get the gradient for the bond stretching in a given atoms coordinates

getGradientMMFF94SumEBA() - Method in class org.openscience.cdk.modeling.forcefield.StretchBendInteractions

Get the gradient of the stretch-bend interaction term.

getGradientMMFF94SumEQ() - Method in class org.openscience.cdk.modeling.forcefield.ElectrostaticInteractions

Get the gradient of the MMFF94 Electrostatic interaction term.

getGradientMMFF94SumET() - Method in class org.openscience.cdk.modeling.forcefield.Torsions

Get the gradient of the torsions term.

getGradientMMFF94SumEvdW() - Method in class org.openscience.cdk.modeling.forcefield.VanDerWaalsInteractions

Get the gradient of the MMFF94 Van Der Waals interaction term.

getGradientPerInverseHessian() - Method in class org.openscience.cdk.modeling.forcefield.NewtonRaphsonMethod

Gets the gradientPerInverseHessian attribute of the NewtonRaphsonMethod object

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

Returns the graph object of this RGraph.

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(PeriodicTableElement) - Method in class org.openscience.cdk.config.ElementPTFactory

Gets the group of this element in the periodic table.

getGroup() - Method in class org.openscience.cdk.PeriodicTableElement

Returns the Group which this element belongs.

getGroup(String) - Static method in class org.openscience.cdk.tools.PeriodicTable

getGroupNumber() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTPeriodicGroupNumber

Get the periodic table group number for this element.

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.

getHC(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.TotalHCountAtom

getHeaviestRing(IRingSet, IBond) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator

We define the heaviest ring as the one with the highest number of double bonds.

getHeavyAtomRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>, boolean, boolean) - Static method in class org.openscience.cdk.geometry.GeometryTools

Return the RMSD of the heavy atoms between the 2 aligned molecules.

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

getHessian() - Method in class org.openscience.cdk.qsar.model.R.CNNClassificationModelFit

Deprecated. Get the Hessian for the final network.

getHessian() - Method in class org.openscience.cdk.qsar.model.R.CNNRegressionModelFit

Deprecated. Get the Hessian for the final network.

getHessianMMFF94SumEA() - Method in class org.openscience.cdk.modeling.forcefield.AngleBending

Get the hessian for the angle bending.

getHessianMMFF94SumEB() - Method in class org.openscience.cdk.modeling.forcefield.BondStretching

Get the hessian for the bond stretching.

getHessianMMFF94SumEBA() - Method in class org.openscience.cdk.modeling.forcefield.StretchBendInteractions

Get the hessian of the stretch-bend interaction.

getHessianMMFF94SumEQ() - Method in class org.openscience.cdk.modeling.forcefield.ElectrostaticInteractions

Get the hessian for the Electrostatic interaction energy.

getHessianMMFF94SumET() - Method in class org.openscience.cdk.modeling.forcefield.Torsions

Get the hessian of the torsions.

getHessianMMFF94SumEvdW() - Method in class org.openscience.cdk.modeling.forcefield.VanDerWaalsInteractions

Get the hessian for the van der Waals interactions.

getHetAtom() - Method in class org.openscience.cdk.debug.DebugPDBAtom

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

getHetAtom() - Method in class org.openscience.cdk.protein.data.PDBAtom

getHillString(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator

getHOSECode(IAtomContainer, IAtom, int) - Method in class org.openscience.cdk.tools.HOSECodeGenerator

Produces a HOSE code for Atom root in the IAtomContainer ac.

getHOSECode(IAtomContainer, IAtom, int, boolean) - Method in class org.openscience.cdk.tools.HOSECodeGenerator

Produces a HOSE code for Atom root in the IAtomContainer ac.

getHTML(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator

Returns the string representation of the molecule formula 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 with numbers wrapped in  tags and the isotope of each Element in  tags and the total charge of IMolecularFormula in  tags.

getHybridization() - Method in class org.openscience.cdk.AtomType

Returns the hybridization of this atom.

getHybridization() - Method in class org.openscience.cdk.debug.DebugAtom

getHybridization() - Method in class org.openscience.cdk.debug.DebugAtomType

getHybridization() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

getHybridization() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

getHybridization() - Method in interface org.openscience.cdk.interfaces.IAtomType

Returns the hybridization of this atom.

getHybridizationNumber() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTHybrdizationNumber

getHydrogenCount() - Method in class org.openscience.cdk.Atom

Returns the hydrogen count of this atom.

getHydrogenCount() - Method in class org.openscience.cdk.debug.DebugAtom

getHydrogenCount() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

getHydrogenCount() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

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

Returns the implicit hydrogen count of this atom.

getICode() - Method in class org.openscience.cdk.debug.DebugPDBAtom

getICode() - Method in class org.openscience.cdk.debug.DebugPDBMonomer

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

getID() - Method in class org.openscience.cdk.ChemObject

Returns the identifier (ID) of this object.

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

getID() - Method in class org.openscience.cdk.debug.DebugAtom

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

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

getID() - Method in class org.openscience.cdk.debug.DebugAtomType

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

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

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

getID() - Method in class org.openscience.cdk.debug.DebugChemModel

getID() - Method in class org.openscience.cdk.debug.DebugChemObject

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

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

getID() - Method in class org.openscience.cdk.debug.DebugElectronContainer

getID() - Method in class org.openscience.cdk.debug.DebugElement

getID() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

getID() - Method in class org.openscience.cdk.debug.DebugIsotope

getID() - Method in class org.openscience.cdk.debug.DebugLonePair

getID() - Method in class org.openscience.cdk.debug.DebugMapping

getID() - Method in class org.openscience.cdk.debug.DebugMolecule

getID() - Method in class org.openscience.cdk.debug.DebugMoleculeSet

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

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

getID() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

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

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

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

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

getID() - Method in class org.openscience.cdk.debug.DebugSingleElectron

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

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.smiles.smarts.parser.SimpleNode

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

GetImage() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream

GetImage() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream

getImaginaryPart() - Method in class org.openscience.cdk.math.Complex

Gets the imaginary part of this value

getIminus() - Method in class org.openscience.cdk.math.qm.AngularMomentum

Calculates the I- operator

getImplementationIdentifier() - Method in interface org.openscience.cdk.IImplementationSpecification

Identifier for this implementation which must include version information.

getImplementationIdentifier() - Method in class org.openscience.cdk.qsar.DescriptorSpecification

getImplementationIdentifier() - Method in class org.openscience.cdk.reaction.ReactionSpecification

getImplementationTitle() - Method in interface org.openscience.cdk.IImplementationSpecification

Human-readable name for the implementation for the algorithm specified by the reference.

getImplementationTitle() - Method in class org.openscience.cdk.qsar.DescriptorSpecification

getImplementationTitle() - Method in class org.openscience.cdk.reaction.ReactionSpecification

getImplementationVendor() - Method in interface org.openscience.cdk.IImplementationSpecification

Human-readable name for the vendor that holds copyright for this implementation.

getImplementationVendor() - Method in class org.openscience.cdk.qsar.DescriptorSpecification

getImplementationVendor() - Method in class org.openscience.cdk.reaction.ReactionSpecification

getInchi() - Method in class org.openscience.cdk.inchi.InChIGenerator

Gets generated InChI string.

getInChIGenerator(IAtomContainer) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory

Gets InChI generator for CDK IAtomContainer.

getInChIGenerator(IAtomContainer, String) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory

Gets InChI generator for CDK IAtomContainer.

getInChIGenerator(IAtomContainer, List) - 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) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory

Gets structure generator for an InChI string.

getIndexFile(String) - Static method in class org.openscience.cdk.io.random.RandomAccessReader

Opens the file index _cdk.index in a temporary folder, as specified by "java.io.tmpdir" property.

getInitialLongestChain(IMolecule) - Method in class org.openscience.cdk.layout.AtomPlacer

Search an aliphatic molecule for the longest chain.

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

getInstance(IChemObjectBuilder) - Static method in class org.openscience.cdk.atomtype.SybylAtomTypeMatcher

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.ElementPTFactory

Returns an ElementPTFactory instance.

getInstance(IChemObjectBuilder) - Static method in class org.openscience.cdk.config.IsotopeFactory

Returns an IsotopeFactory instance.

getInstance() - Static method in class org.openscience.cdk.debug.DebugChemObjectBuilder

getInstance() - Static method in class org.openscience.cdk.DefaultChemObjectBuilder

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.CDKSourceCodeFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format

getInstance() - Static method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format

getInstance() - Static method in class org.openscience.cdk.io.formats.ChemDrawFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.ChemtoolFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.CIFFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.CMLFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.CMLRSSFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.CRK2DFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.CRK3DFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.CrystClustFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.CTXFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.DaltonFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.DMol3Format

getInstance() - Static method in class org.openscience.cdk.io.formats.DOCK5Format

getInstance() - Static method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.FingerprintFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.GamessFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.Gaussian03Format

getInstance() - Static method in class org.openscience.cdk.io.formats.Gaussian90Format

getInstance() - Static method in class org.openscience.cdk.io.formats.Gaussian92Format

getInstance() - Static method in class org.openscience.cdk.io.formats.Gaussian94Format

getInstance() - Static method in class org.openscience.cdk.io.formats.Gaussian95Format

getInstance() - Static method in class org.openscience.cdk.io.formats.Gaussian98Format

getInstance() - Static method in class org.openscience.cdk.io.formats.GaussianInputFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.GhemicalMMFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.GhemicalSPMFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.GROMOS96Format

getInstance() - Static method in class org.openscience.cdk.io.formats.HINFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.INChIFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.INChIPlainTextFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.JaguarFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.JMEFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.MacroModelFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.MDLFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.MDLRXNFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.MDLRXNV3000Format

getInstance() - Static method in class org.openscience.cdk.io.formats.MDLV2000Format

getInstance() - Static method in class org.openscience.cdk.io.formats.MDLV3000Format

getInstance() - Static method in class org.openscience.cdk.io.formats.MMODFormat

getInstance() - Static method in class org.openscience.cdk.io.formats.Mol2Format

getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC2002Format

getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC7Format

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.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.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) - Static method in class org.openscience.cdk.modeling.builder3d.ModelBuilder3D

getInstance() - 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.nonotify.NoNotificationChemObjectBuilder

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.

getInternuclearSeparation() - Method in class org.openscience.cdk.modeling.forcefield.ElectrostaticInteractions

Get the internuclear separation values (Rij).

getInternuclearSeparationFirstDerivative() - Method in class org.openscience.cdk.modeling.forcefield.ElectrostaticInteractions

Get the internuclear separation first order derivative respect to the cartesian coordinates of the atoms.

getInternuclearSeparationSecondDerivative() - Method in class org.openscience.cdk.modeling.forcefield.ElectrostaticInteractions

Get the internuclear separation second derivative respect to the cartesian coordinates of the atoms.

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.

getIntersectionSize(Path) - Method in class org.openscience.cdk.ringsearch.Path

getIOSettings() - Method in class org.openscience.cdk.io.CDKSourceCodeWriter

getIOSettings() - Method in class org.openscience.cdk.io.CMLWriter

getIOSettings() - Method in class org.openscience.cdk.io.DefaultChemObjectReader

getIOSettings() - Method in class org.openscience.cdk.io.DefaultChemObjectWriter

getIOSettings() - Method in class org.openscience.cdk.io.Gaussian98Reader

Gets the iOSettings attribute of the Gaussian98Reader object

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.iterator.DefaultIteratingChemObjectReader

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

getIOSettings() - Method in class org.openscience.cdk.io.iterator.IteratingMDLReader

getIOSettings() - Method in class org.openscience.cdk.io.MDLReader

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

getIOSettings() - Method in class org.openscience.cdk.io.MDLV2000Reader

getIOSettings() - Method in class org.openscience.cdk.io.MDLV3000Reader

getIOSettings() - Method in class org.openscience.cdk.io.MDLWriter

getIOSettings() - Method in class org.openscience.cdk.io.PDBReader

getIOSettings() - Method in class org.openscience.cdk.io.program.GaussianInputWriter

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

getIOSettings() - Method in class org.openscience.cdk.io.SDFWriter

getIplus() - Method in class org.openscience.cdk.math.qm.AngularMomentum

Calculates the I+ operator

getIsobutane() - Static method in class org.openscience.cdk.templates.saturatedhydrocarbons.IsoAlkanes

getIsohexane() - Static method in class org.openscience.cdk.templates.saturatedhydrocarbons.IsoAlkanes

getIsomorphAtomsMap(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester

Returns the first isomorph 'atom mapping' found for g2 in g1.

getIsomorphMap(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester

Returns the first isomorph mapping found or null.

getIsomorphMaps(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester

Returns all the isomorph 'mappings' found between two atom containers.

getIsopentane() - Static method in class org.openscience.cdk.templates.saturatedhydrocarbons.IsoAlkanes

getIsotope(int) - Method in class org.openscience.cdk.formula.IsotopePattern

Returns the a isotopes given a specific position.

getIsotopeCount(IIsotope) - Method in class org.openscience.cdk.debug.DebugAdductFormula

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

getIsotopeCount(IIsotope) - Method in class org.openscience.cdk.debug.DebugMolecularFormula

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

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.

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.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.

getIx() - Method in class org.openscience.cdk.math.qm.AngularMomentum

Calculates the Ix operator

getIy() - Method in class org.openscience.cdk.math.qm.AngularMomentum

Calculates the Iy operator

getIz() - Method in class org.openscience.cdk.math.qm.AngularMomentum

Calculates the Iz operator

getLabel() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

getLabel() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

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.Vibration

Gets the label identifying this vibration.

getLargestRingSet(List) - 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

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

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

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

getLastAtom() - Method in class org.openscience.cdk.debug.DebugMolecule

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

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

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

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

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

Returns the atom at the last position in the container.

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

getLatticeConstant() - Method in class org.openscience.cdk.tools.GridGenerator

getLeft() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom

getLeft() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond

getLength() - Method in class org.openscience.cdk.iupac.parser.AttachedGroup

Getter for property length.

getLength2D(IBond) - Static method in class org.openscience.cdk.geometry.GeometryTools

Returns the geometric length of this bond in 2D space.

getLevel() - Method in class org.openscience.cdk.io.setting.IOSetting

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

Returns the line-matrix at the given line index

getLine() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream

Deprecated.

getLine() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream

Deprecated.

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

getLinkerFragments() - Method in class org.openscience.cdk.tools.GenerateFragments

getLinkerFragmentsAsSmileArray() - Method in class org.openscience.cdk.tools.GenerateFragments

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

getListenerCount() - Method in class org.openscience.cdk.debug.DebugAtom

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

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

getListenerCount() - Method in class org.openscience.cdk.debug.DebugAtomType

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

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

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

getListenerCount() - Method in class org.openscience.cdk.debug.DebugChemModel

getListenerCount() - Method in class org.openscience.cdk.debug.DebugChemObject

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

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

getListenerCount() - Method in class org.openscience.cdk.debug.DebugElectronContainer

getListenerCount() - Method in class org.openscience.cdk.debug.DebugElement

getListenerCount() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

getListenerCount() - Method in class org.openscience.cdk.debug.DebugIsotope

getListenerCount() - Method in class org.openscience.cdk.debug.DebugLonePair

getListenerCount() - Method in class org.openscience.cdk.debug.DebugMapping

getListenerCount() - Method in class org.openscience.cdk.debug.DebugMolecule

getListenerCount() - Method in class org.openscience.cdk.debug.DebugMoleculeSet

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

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

getListenerCount() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

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

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

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

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

getListenerCount() - Method in class org.openscience.cdk.debug.DebugSingleElectron

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

getListenerCount() - Method in interface org.openscience.cdk.interfaces.IChemObject

Returns the number of ChemObjectListeners registered with this object.

getLocations() - Method in class org.openscience.cdk.iupac.parser.AttachedGroup

Getter for property locations.

getLog() - Method in class org.openscience.cdk.inchi.InChIGenerator

Gets generated log.

getLog() - Method in class org.openscience.cdk.inchi.InChIToStructure

Gets generated log.

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

Get the lone pair at position number in [0,..].

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

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

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

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

getLonePair(int) - Method in class org.openscience.cdk.debug.DebugMolecule

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

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

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

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

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

Get the lone pair at position number in [0,..].

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

Returns the number of LonePairs in this Container.

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

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

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

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

getLonePairCount() - Method in class org.openscience.cdk.debug.DebugMolecule

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

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

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

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

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

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

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

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

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

getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugMolecule

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

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

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

getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugStrand

getLonePairNumber(ILonePair) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the position of a given lone pair in the lone pair array.

getLongestUnplacedChain(IMolecule, IAtom) - 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

getLower() - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModelPredict

Deprecated. Get the lower confidence bounds.

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

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.

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.

getMass() - Method in class org.openscience.cdk.formula.IsotopeContainer

Get the mass value of this container.

getMass() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTAtomicMass

Returns the mass value.

getMass(String) - Method in class org.openscience.cdk.tools.AtomicProperties

getMassNumber() - Method in class org.openscience.cdk.debug.DebugAtom

getMassNumber() - Method in class org.openscience.cdk.debug.DebugAtomType

getMassNumber() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

getMassNumber() - Method in class org.openscience.cdk.debug.DebugIsotope

getMassNumber() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

getMassNumber() - Method in interface org.openscience.cdk.interfaces.IIsotope

Returns the atomic mass of this element.

getMassNumber() - Method in class org.openscience.cdk.Isotope

Returns the atomic mass of this element.

getMatchingAtoms() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom

Get the atoms of a target molecule that correspond to this group.

getMatchingAtoms() - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool

Get the atoms in the target molecule that match the query pattern.

getMatchingPharmacophoreAtoms() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher

Get the matching pharmacophore groups.

getMatchingPharmacophoreBonds() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher

Get the matching pharmacophore constraints.

getMatrix(IAtomContainer) - Static method in class org.openscience.cdk.graph.matrix.AdjacencyMatrix

Returns the adjacency matrix for the given AtomContainer.

getMatrix(IAtomContainer) - Static method in class org.openscience.cdk.graph.matrix.ConnectionMatrix

Returns the connection matrix representation of this AtomContainer.

getMatrix(IAtomContainer) - Static method in class org.openscience.cdk.graph.matrix.TopologicalMatrix

Returns the topological matrix for the given AtomContainer.

getMaxBondOrder() - Method in class org.openscience.cdk.AtomType

Gets the MaxBondOrder attribute of the AtomType object.

getMaxBondOrder() - Method in class org.openscience.cdk.debug.DebugAtom

getMaxBondOrder() - Method in class org.openscience.cdk.debug.DebugAtomType

getMaxBondOrder() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

getMaxBondOrder() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

getMaxBondOrder() - Method in interface org.openscience.cdk.interfaces.IAtomType

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

getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer

getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer

getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal

getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule

getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer

getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer

getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugRing

getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand

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(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.

getMaxIterations() - Method in class org.openscience.cdk.charges.Electronegativity

get the maximal number of Iterations.

getMaxIterations() - Method in class org.openscience.cdk.charges.PiElectronegativity

get the maximal number of Iterations.

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 maximal number of resonance structures.

getMaxResonStruc() - Method in class org.openscience.cdk.charges.PiElectronegativity

get the maximal number of resonance structures.

getMaxResoStruc() - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges

Gets the maximum resonance structures to be searched

getMaxX() - Method in class org.openscience.cdk.math.qm.FourierGridBasis

getMaxX() - Method in class org.openscience.cdk.math.qm.GaussiansBasis

Gets the dimension of the volume, which describes the base.

getMaxX() - Method in interface org.openscience.cdk.math.qm.IBasis

Gets the dimension of the volume, which describes the base.

getMaxx() - Method in class org.openscience.cdk.tools.GridGenerator

getMaxY() - Method in class org.openscience.cdk.math.qm.FourierGridBasis

getMaxY() - Method in class org.openscience.cdk.math.qm.GaussiansBasis

Gets the dimension of the volume, which describes the base.

getMaxY() - Method in interface org.openscience.cdk.math.qm.IBasis

Gets the dimension of the volume, which describes the base.

getMaxy() - Method in class org.openscience.cdk.tools.GridGenerator

getMaxZ() - Method in class org.openscience.cdk.math.qm.FourierGridBasis

getMaxZ() - Method in class org.openscience.cdk.math.qm.GaussiansBasis

Gets the dimension of the volume, which describes the base.

getMaxZ() - Method in interface org.openscience.cdk.math.qm.IBasis

Gets the dimension of the volume, which describes the base.

getMaxz() - Method in class org.openscience.cdk.tools.GridGenerator

getMechanism() - Method in class org.openscience.cdk.dict.EntryReact

Get the mechanism of this reaction.

getMessage() - Method in class org.openscience.cdk.inchi.InChIGenerator

Gets generated (error/warning) messages.

getMessage() - Method in class org.openscience.cdk.inchi.InChIToStructure

Gets generated (error/warning) messages.

getMessage() - Method in exception org.openscience.cdk.iupac.parser.ParseException

This method has the standard behavior when this object has been created using the standard constructors.

getMessage() - Method in error org.openscience.cdk.iupac.parser.TokenMgrError

You can also modify the body of this method to customize your error messages.

getMessage() - Method in exception org.openscience.cdk.smiles.smarts.parser.ParseException

This method has the standard behavior when this object has been created using the standard constructors.

getMessage() - Method in error org.openscience.cdk.smiles.smarts.parser.TokenMgrError

You can also modify the body of this method to customize your error messages.

getMethod() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModelFit

getMIMEType() - Method in class org.openscience.cdk.io.formats.ABINITFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.Aces2Format

getMIMEType() - Method in class org.openscience.cdk.io.formats.ADFFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.AlchemyFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.BGFFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.BSFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.CACheFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format

getMIMEType() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format

getMIMEType() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.CIFFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.CMLFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.CRK2DFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.CRK3DFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.CrystClustFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.CTXFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.DaltonFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.DMol3Format

getMIMEType() - Method in class org.openscience.cdk.io.formats.DOCK5Format

getMIMEType() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.FingerprintFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.GamessFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian03Format

getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian90Format

getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian92Format

getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian94Format

getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian95Format

getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian98Format

getMIMEType() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.GROMOS96Format

getMIMEType() - Method in class org.openscience.cdk.io.formats.HINFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.INChIFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat

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

getMIMEType() - Method in class org.openscience.cdk.io.formats.JMEFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.MacroModelFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.MDLFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format

getMIMEType() - Method in class org.openscience.cdk.io.formats.MDLV2000Format

getMIMEType() - Method in class org.openscience.cdk.io.formats.MDLV3000Format

getMIMEType() - Method in class org.openscience.cdk.io.formats.MMODFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.Mol2Format

getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format

getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC7Format

getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC93Format

getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC97Format

getMIMEType() - Method in class org.openscience.cdk.io.formats.MPQCFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.NWChemFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.PCModelFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.PDBFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.PDBMLFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.PMPFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.POVRayFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.PQSChemFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.QChemFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.RawCopyFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.SDFFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.ShelXFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.SMARTSFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.SMILESFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.SpartanFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.SVGFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format

getMIMEType() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.VASPFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.ViewmolFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.XEDFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.XYZFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.YasaraFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.ZindoFormat

getMIMEType() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat

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

getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer

getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer

getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal

getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule

getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer

getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer

getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugRing

getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand

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(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.

getMinimumFunctionValueCGM() - Method in class org.openscience.cdk.modeling.forcefield.GeometricMinimizer

Gets the conjugatedGradientMinimum attribute of the GeometricMinimizer object

getMinMax(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools

Returns the minimum and maximum X and Y coordinates of the atoms in the AtomContainer.

getMinOccurrenceElements(IMolecularFormulaSet) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaSetManipulator

Extract from a set of MolecularFormula the minimal occurrence of each element found and put the element and occurrence in a new IMolecularFormula.

getMinPSCluster() - Method in class org.openscience.cdk.protein.ProteinPocketFinder

getMinPSPocket() - Method in class org.openscience.cdk.protein.ProteinPocketFinder

getMinX() - Method in class org.openscience.cdk.math.qm.FourierGridBasis

getMinX() - Method in class org.openscience.cdk.math.qm.GaussiansBasis

Gets the dimension of the volume, which describes the base.

getMinX() - Method in interface org.openscience.cdk.math.qm.IBasis

Gets the dimension of the volume, which describes the base.

getMinx() - Method in class org.openscience.cdk.tools.GridGenerator

getMinY() - Method in class org.openscience.cdk.math.qm.FourierGridBasis

getMinY() - Method in class org.openscience.cdk.math.qm.GaussiansBasis

Gets the dimension of the volume, which describes the base.

getMinY() - Method in interface org.openscience.cdk.math.qm.IBasis

Gets the dimension of the volume, which describes the base.

getMiny() - Method in class org.openscience.cdk.tools.GridGenerator

getMinZ() - Method in class org.openscience.cdk.math.qm.FourierGridBasis

getMinZ() - Method in class org.openscience.cdk.math.qm.GaussiansBasis

Gets the dimension of the volume, which describes the base.

getMinZ() - Method in interface org.openscience.cdk.math.qm.IBasis

Gets the dimension of the volume, which describes the base.

getMinz() - Method in class org.openscience.cdk.tools.GridGenerator

getModel() - Method in class org.openscience.cdk.qsar.model.R2.LinearRegressionModel

Gets the model field of an 'lm' object.

getModelName() - Method in class org.openscience.cdk.qsar.model.R.RModel

Deprecated. Get the name of the model.

getModelName() - Method in class org.openscience.cdk.qsar.model.R2.RModel

Get the name of the model.

getModelObject() - Method in class org.openscience.cdk.qsar.model.R2.RModel

Get the actual model object.

getModelPredict() - Method in class org.openscience.cdk.qsar.model.R2.LinearRegressionModel

Get the R object obtained from predict.lm().

getMolecularFormula(int) - Method in class org.openscience.cdk.debug.DebugAdductFormula

getMolecularFormula(int) - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet

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(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator

Construct an instance of IMolecularFormula, initialized with a molecular formula string.

getMolecularFormula(String, IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator

add in a instance of IMolecularFormula the elements extracts form molecular formula string.

getMolecularFormula(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator

Method that actually does the work of convert the atomContainer to IMolecularFormula.

getMolecularFormula(IAtomContainer, IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator

Method that actually does the work of convert the atomContainer to IMolecularFormula given a IMolecularFormula.

getMolecularGraphDiameter(IAtomContainer) - Static method in class org.openscience.cdk.graph.PathTools

Returns the diameter of the molecular graph.

getMolecularGraphRadius(IAtomContainer) - Static method in class org.openscience.cdk.graph.PathTools

Returns the radius of the molecular graph.

getMolecule(int) - Method in class org.openscience.cdk.debug.DebugMoleculeSet

getMolecule(int) - Method in interface org.openscience.cdk.interfaces.IMoleculeSet

Returns the Molecule at position number in the container.

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.modeling.forcefield.GeometricMinimizer

getMolecule(int) - Method in class org.openscience.cdk.MoleculeSet

Returns the Molecule at position number in the container.

getMolecule() - Method in class org.openscience.cdk.structgen.RandomGenerator

Returns the molecule which reflects the current state of this stochastic structure generator.

getMoleculeCount() - Method in class org.openscience.cdk.debug.DebugMoleculeSet

getMoleculeCount() - Method in interface org.openscience.cdk.interfaces.IMoleculeSet

Returns the number of Molecules in this Container.

getMoleculeCount() - Method in class org.openscience.cdk.MoleculeSet

Returns the number of Molecules in this Container.

getMoleculeGraph(IAtomContainer) - Static method in class org.openscience.cdk.graph.MoleculeGraphs

Creates a molecule graph for use with jgrapht.

getMoleculeSet() - Method in class org.openscience.cdk.ChemModel

Returns the MoleculeSet of this ChemModel.

getMoleculeSet() - Method in class org.openscience.cdk.debug.DebugChemModel

getMoleculeSet() - Method in interface org.openscience.cdk.interfaces.IChemModel

Returns the MoleculeSet of this ChemModel.

getMoleculeSet(IMolecule, IMolecule, IReactionScheme) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator

Extract the list of molecules taking part in the IReactionScheme to originate a product given a reactant.

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

getMonomer(String, String) - Method in class org.openscience.cdk.debug.DebugBioPolymer

getMonomer(String) - Method in class org.openscience.cdk.debug.DebugPolymer

getMonomer(String) - Method in class org.openscience.cdk.debug.DebugStrand

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) - 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

getMonomerCount() - Method in class org.openscience.cdk.debug.DebugPolymer

getMonomerCount() - Method in class org.openscience.cdk.debug.DebugStrand

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.Strand

Returns the number of monomers present in the Strand.

getMonomerName() - Method in class org.openscience.cdk.debug.DebugAminoAcid

getMonomerName() - Method in class org.openscience.cdk.debug.DebugMonomer

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.

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

getMonomerNames() - Method in class org.openscience.cdk.debug.DebugPolymer

getMonomerNames() - Method in class org.openscience.cdk.debug.DebugStrand

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.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.

getMonomers() - Method in class org.openscience.cdk.debug.DebugStrand

getMonomers() - Method in interface org.openscience.cdk.interfaces.IStrand

Returns the monomers in this 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

getMonomerType() - Method in class org.openscience.cdk.debug.DebugMonomer

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.

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

getMultiplier(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet

getMultiplier(int) - Method in class org.openscience.cdk.debug.DebugMoleculeSet

getMultiplier(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugMoleculeSet

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.

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

getMultipliers() - Method in class org.openscience.cdk.debug.DebugMoleculeSet

getMultipliers() - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet

Returns an array of double with the stoichiometric coefficients of the products.

getMurckoFrameworks() - Method in class org.openscience.cdk.tools.GenerateFragments

getMurckoFrameworksAsSmileArray() - Method in class org.openscience.cdk.tools.GenerateFragments

getN() - Method in class org.openscience.cdk.qsar.model.R2.CNNRegressionModel

Gets the n field of an 'nnet' object.

getName(PeriodicTableElement) - Method in class org.openscience.cdk.config.ElementPTFactory

Gets the name of this element in the periodic table.

getName() - Method in class org.openscience.cdk.debug.DebugPDBAtom

getName() - Method in interface org.openscience.cdk.interfaces.IPDBAtom

get the Atom name of this atom.

getName() - Method in class org.openscience.cdk.io.setting.IOSetting

getName() - Method in class org.openscience.cdk.iupac.parser.AttachedGroup

Getter for property name.

getName() - Method in class org.openscience.cdk.libio.md.Residue

getName() - Method in class org.openscience.cdk.PeriodicTableElement

Returns the name of this element.

getName() - Method in class org.openscience.cdk.protein.data.PDBAtom

get the Atom name of this atom.

getName(String) - Static method in class org.openscience.cdk.tools.PeriodicTable

getNameExtensions() - Method in class org.openscience.cdk.io.formats.ABINITFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.Aces2Format

getNameExtensions() - Method in class org.openscience.cdk.io.formats.ADFFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.AlchemyFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.BGFFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.BSFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.CACheFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format

getNameExtensions() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format

getNameExtensions() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.CIFFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.CMLFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.CRK2DFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.CRK3DFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.CrystClustFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.CTXFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.DaltonFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.DMol3Format

getNameExtensions() - Method in class org.openscience.cdk.io.formats.DOCK5Format

getNameExtensions() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.FingerprintFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.GamessFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian03Format

getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian90Format

getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian92Format

getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian94Format

getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian95Format

getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian98Format

getNameExtensions() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.GROMOS96Format

getNameExtensions() - Method in class org.openscience.cdk.io.formats.HINFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.INChIFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat

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

getNameExtensions() - Method in class org.openscience.cdk.io.formats.JMEFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.MacroModelFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.MDLFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format

getNameExtensions() - Method in class org.openscience.cdk.io.formats.MDLV2000Format

getNameExtensions() - Method in class org.openscience.cdk.io.formats.MDLV3000Format

getNameExtensions() - Method in class org.openscience.cdk.io.formats.MMODFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.Mol2Format

getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format

getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC7Format

getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC93Format

getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC97Format

getNameExtensions() - Method in class org.openscience.cdk.io.formats.MPQCFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.NWChemFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.PCModelFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.PDBFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.PDBMLFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.PMPFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.POVRayFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.PQSChemFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.QChemFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.RawCopyFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.SDFFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.ShelXFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.SMARTSFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.SMILESFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.SpartanFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.SVGFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format

getNameExtensions() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.VASPFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.ViewmolFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.XEDFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.XYZFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.YasaraFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.ZindoFormat

getNameExtensions() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat

getNames() - Static method in class org.openscience.cdk.config.fragments.EStateFragments

Get the fragment names.

getNames() - Method in class org.openscience.cdk.qsar.DescriptorValue

Returns an array of names for each descriptor value calculated.

getNativeRingRadius(IRing, double) - Method in class org.openscience.cdk.layout.RingPlacer

Returns the ring radius of a perfect polygons of size ring.getAtomCount() The ring radius is the distance of each atom to the ringcenter.

getNaturalAbundance() - Method in class org.openscience.cdk.debug.DebugAtom

getNaturalAbundance() - Method in class org.openscience.cdk.debug.DebugAtomType

getNaturalAbundance() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

getNaturalAbundance() - Method in class org.openscience.cdk.debug.DebugIsotope

getNaturalAbundance() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

getNaturalAbundance() - Method in interface org.openscience.cdk.interfaces.IIsotope

Gets the NaturalAbundance attribute of the Isotope object.

getNaturalAbundance() - Method in class org.openscience.cdk.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.

getNComp() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModelFit

getNconn() - Method in class org.openscience.cdk.qsar.model.R2.CNNRegressionModel

Gets the nconn field of an 'nnet' object.

getNeighbors(int) - Method in class org.openscience.cdk.geometry.surface.NeighborList

getNewtonRaphsonMinimum() - Method in class org.openscience.cdk.modeling.forcefield.GeometricMinimizer

Gets the newtonRaphsonMinimum attribute of the GeometricMinimizer object

getNextBond(IBond, IAtom) - Method in class org.openscience.cdk.debug.DebugRing

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.

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.

getNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D

Gets the nextPlacedHeavyAtomWithAliphaticPlacedNeigbor from an atom container or molecule

getNextPlacedHeavyAtomWithUnplacedRingNeighbour(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D

Gets the nextPlacedHeavyAtomWithUnplacedRingNeighbour attribute of the AtomPlacer3D object

getNextToken() - Method in class org.openscience.cdk.iupac.parser.NomParser

getNextToken() - Method in class org.openscience.cdk.iupac.parser.NomParserTokenManager

getNextToken() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

getNextToken() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager

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

getNormalizationFactor(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools

Calculates the normalization factor in order to get an average bond length of 1.5.

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

getNotification() - Method in class org.openscience.cdk.ChemObject

getNotification() - Method in class org.openscience.cdk.debug.DebugChemObject

getNotification() - Method in interface org.openscience.cdk.interfaces.IChemObject

Returns the flag that indicates whether notification messages are sent around.

getNS() - Method in class org.openscience.cdk.dict.Dictionary

getNsunits() - Method in class org.openscience.cdk.qsar.model.R2.CNNRegressionModel

Gets the nsunits field of an 'nnet' object.

getNTerminus() - Method in class org.openscience.cdk.AminoAcid

Retrieves the N-terminus atom.

getNTerminus() - Method in class org.openscience.cdk.debug.DebugAminoAcid

getNTerminus() - Method in interface org.openscience.cdk.interfaces.IAminoAcid

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

getNumber() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTAtomicNumber

Returns the atomic number.

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

getNumNeurons() - Method in class org.openscience.cdk.qsar.model.R.CNNRegressionModelSummary

Deprecated. Return the number of neurons in the CNN layers.

getNumOfConnection() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ExplicitConnectionAtom

Returns number of explicit connections.

getNumOfConnection() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTExplicitConnectivity

Returns the number of explicit connections.

getNumOfConnection() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTRingConnectivity

Returns the number of ring connections.

getNumOfConnection() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTTotalConnectivity

Returns the number of total connections.

getNumOfMembership() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTRingMembership

Returns the number of SSSR rings this atom is in.

getNunits() - Method in class org.openscience.cdk.qsar.model.R2.CNNRegressionModel

Gets the nunits field of an 'nnet' object.

getOccupancy() - Method in class org.openscience.cdk.debug.DebugPDBAtom

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.

getOKCount() - Method in class org.openscience.cdk.validate.ValidationReport

Returns the number of tests without errors.

getOKs() - Method in class org.openscience.cdk.validate.ValidationReport

Returns an array of ValidationTest which did not find problems.

getOperator() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom

getOperator() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond

getOptions() - Method in class org.openscience.cdk.io.setting.OptionIOSetting

Returns a Vector of Strings containing all possible options.

getOrder() - Method in class org.openscience.cdk.Bond

Returns the bond order of this bond.

getOrder() - Method in class org.openscience.cdk.debug.DebugBond

getOrder() - Method in interface org.openscience.cdk.interfaces.IBond

Returns the bond order of this bond.

getOrder() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTValence

Returns valence order.

getOrder2ndErrorApproximateEnergyGradient() - Method in class org.openscience.cdk.modeling.forcefield.MMFF94EnergyFunction

Get the 2nd order error approximate gradient for the MMFF94 energy function.

getOrder5thErrorApproximateEnergyGradient() - Method in class org.openscience.cdk.modeling.forcefield.MMFF94EnergyFunction

Get the 5th order error approximate gradient for the MMFF94 energy function.

getOtherBondAtom(IAtom, IBond) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

Returns the other atom of the bond.

getOverlaps(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester

Returns all the maximal common substructure between twp atom containers.

getOverlapScore(IAtomContainer, Vector, Vector) - Method in class org.openscience.cdk.layout.OverlapResolver

Calculates a score based on the overlap of atoms and intersection of bonds.

getOxt() - Method in class org.openscience.cdk.debug.DebugPDBAtom

getOxt() - Method in interface org.openscience.cdk.interfaces.IPDBAtom

getOxt() - Method in class org.openscience.cdk.protein.data.PDBAtom

getParameterClass() - Method in class org.openscience.cdk.dict.EntryReact

Get the IParameterReact's of the reaction.

getParameterClass(Class<?>) - Method in interface org.openscience.cdk.reaction.IReactionProcess

Return the IParameterReact if it exists given the class.

getParameterClass(Class<?>) - Method in class org.openscience.cdk.reaction.ReactionEngine

Return the IParameterReact if it exists given the class.

getParameterList() - Method in interface org.openscience.cdk.reaction.IReactionProcess

Returns the current parameter values.

getParameterList() - Method in class org.openscience.cdk.reaction.ReactionEngine

Returns the current parameter values.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor

Gets the parameterNames attribute of the AtomDegreeDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor

Gets the parameterNames attribute of the VdWRadiusDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor

Gets the parameterNames attribute of the AtomHybridizationVSEPRDescriptor object

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor

Gets the parameterNames attribute of the VdWRadiusDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor

Gets the parameterNames attribute of the BondsToAtomDescriptor object

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor

Gets the parameterNames attribute of the VdWRadiusDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor

Gets the parameterNames attribute of the DistanceToAtomDescriptor object

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor

Gets the parameterNames attribute of the EffectiveAtomPolarizabilityDescriptor object

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor

Gets the parameterNames attribute of the InductiveAtomicHardnessDescriptor object

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor

Gets the parameterNames attribute of the InductiveAtomicSoftnessDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor

Gets the parameterNames attribute of the IPAtomicHOSEDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor

Gets the parameterNames attribute of the IPAtomicLearningDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor

Gets the parameterNames attribute of the IsProtonInAromaticSystemDescriptor object

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInConjugatedPiSystemDescriptor

Gets the parameterNames attribute of the IsProtonInConjugatedPiSystemDescriptor object

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor

Gets the parameterNames attribute of the PartialPiChargeDescriptor object

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor

Gets the parameterNames attribute of the PartialSigmaChargeDescriptor object

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor

Gets the parameterNames attribute of the PartialTChargeMMFF94Descriptor object

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor

Gets the parameterNames attribute of the PartialTChargePEOEDescriptor object

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor

Gets the parameterNames attribute of the PeriodicTablePositionDescriptor object

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor

Gets the parameterNames attribute of the SigmaElectronegativityDescriptor object

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor

Gets the parameterNames attribute of the ProtonAffinityDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor

Gets the parameterNames attribute of the ProtonTotalPartialChargeDescriptor object

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R

Gets the parameterNames attribute of the RDFProtonDescriptor object

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR

Gets the parameterNames attribute of the RDFProtonDescriptor object

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR

Gets the parameterNames attribute of the RDFProtonDescriptor object

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol

Gets the parameterNames attribute of the RDFProtonDescriptor object

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR

Gets the parameterNames attribute of the RDFProtonDescriptor object

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor

Gets the parameterNames attribute of the SigmaElectronegativityDescriptor object

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor

Gets the parameterNames attribute of the StabilizationPlusChargeDescriptor object

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor

Gets the parameterNames attribute of the VdWRadiusDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor

Gets the parameterNames attribute of the PiContactDetectionDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptor

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor

Gets the parameterNames attribute of the BondPartialPiChargeDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor

Gets the parameterNames attribute of the BondPartialSigmaChargeDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor

Gets the parameterNames attribute of the BondPartialTChargeDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor

Gets the parameterNames attribute of the BondSigmaElectronegativityDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor

Gets the parameterNames attribute of the IPBondLearningDescriptor object.

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.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.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.IPMolecularLearningDescriptor

Gets the parameterNames attribute of the IPMolecularLearningDescriptor object

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor

Gets the parameterNames attribute of the KappaShapeIndicesDescriptor object

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor

Gets the parameterNames attribute of the descriptor.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor

Gets the parameterNames attribute of the LargestPiSystemDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor

Gets the parameterNames attribute of the LargestPiSystemDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor

Gets the parameterNames attribute of the PetitjeanNumberDescriptor object

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor

Gets the parameterNames attribute of the LongestAliphaticChainDescriptor object.

getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.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.TPSADescriptor

Gets the parameterNames attribute of the TPSADescriptor object.

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.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.formula.rules.ChargeRule

Gets the parameters attribute of the ChargeRule object.

getParameters() - Method in class org.openscience.cdk.formula.rules.ElementRule

Gets the parameters attribute of the ElementRule object.

getParameters() - Method in interface org.openscience.cdk.formula.rules.IRule

Returns the current parameter values.

getParameters() - Method in class org.openscience.cdk.formula.rules.IsotopePatternRule

Gets the parameters attribute of the IsotopePatternRule object.

getParameters() - Method in class org.openscience.cdk.formula.rules.MMElementRule

Gets the parameters attribute of the MMElementRule object.

getParameters() - Method in class org.openscience.cdk.formula.rules.NitrogenRule

Gets the parameters attribute of the NitrogenRule object.

getParameters() - Method in class org.openscience.cdk.formula.rules.RDBERule

Gets the parameters attribute of the RDBRule object.

getParameters() - Method in class org.openscience.cdk.formula.rules.ToleranceRangeRule

Gets the parameters attribute of the ToleranceRangeRule object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor

Gets the parameters attribute of the AtomDegreeDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor

Gets the parameters attribute of the VdWRadiusDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor

Gets the parameters attribute of the AtomHybridizationVSEPRDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor

Gets the parameters attribute of the VdWRadiusDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor

Gets the parameters attribute of the BondsToAtomDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor

Gets the parameters attribute of the VdWRadiusDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor

Gets the parameters attribute of the DistanceToAtomDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor

Gets the parameters attribute of the EffectiveAtomPolarizabilityDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor

Gets the parameters attribute of the InductiveAtomicHardnessDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor

Gets the parameters attribute of the InductiveAtomicSoftnessDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor

Gets the parameters attribute of the IPAtomicHOSEDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor

Gets the parameters attribute of the IPAtomicLearningDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor

Gets the parameters attribute of the IsProtonInAromaticSystemDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInConjugatedPiSystemDescriptor

Gets the parameters attribute of the IsProtonInConjugatedPiSystemDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor

Gets the parameters attribute of the PartialPiChargeDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor

Gets the parameters attribute of the PartialSigmaChargeDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor

Gets the parameters attribute of the PartialTChargeMMFF94Descriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor

Gets the parameters attribute of the PartialTChargePEOEDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor

Gets the parameters attribute of the PeriodicTablePositionDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor

Gets the parameters attribute of the PiElectronegativityDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor

Gets the parameters attribute of the ProtonAffinityDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor

Gets the parameters attribute of the ProtonTotalPartialChargeDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R

Gets the parameters attribute of the RDFProtonDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR

Gets the parameters attribute of the RDFProtonDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR

Gets the parameters attribute of the RDFProtonDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol

Gets the parameters attribute of the RDFProtonDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR

Gets the parameters attribute of the RDFProtonDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor

Gets the parameters attribute of the SigmaElectronegativityDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor

Gets the parameters attribute of the StabilizationPlusChargeDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor

Gets the parameters attribute of the VdWRadiusDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor

Gets the parameters attribute of the PiContactDetectionDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptor

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor

Gets the parameters attribute of the BondPartialPiChargeDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor

Gets the parameters attribute of the BondPartialSigmaChargeDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor

Gets the parameters attribute of the BondPartialTChargeDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor

Gets the parameters attribute of the BondSigmaElectronegativityDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor

Gets the parameters attribute of the IPBondLearningDescriptor object.

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.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.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.IPMolecularLearningDescriptor

Gets the parameters attribute of the IPMolecularLearningDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor

Gets the parameters attribute of the KappaShapeIndicesDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor

Gets the parameters attribute of the descriptor.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor

Gets the parameters attribute of the LargestChainDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor

Gets the parameters attribute of the LargestPiSystemDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor

Gets the parameters attribute of the PetitjeanNumberDescriptor object

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor

Gets the parameters attribute of the LongestAliphaticChainDescriptor object.

getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.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.TPSADescriptor

Gets the parameters attribute of the TPSADescriptor object.

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.DescriptorValue

getParameters() - Method in interface org.openscience.cdk.qsar.IDescriptor

Returns the current parameter values.

getParameterSet() - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator

Gets the parameterSet attribute of the ForceFieldConfigurator object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor

Gets the parameterType attribute of the AtomDegreeDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor

Gets the parameterType attribute of the VdWRadiusDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor

Gets the parameterType attribute of the AtomHybridizationVSEPRDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor

Gets the parameterType attribute of the VdWRadiusDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor

Gets the parameterType attribute of the BondsToAtomDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor

Gets the parameterType attribute of the VdWRadiusDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor

Gets the parameterType attribute of the DistanceToAtomDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor

Gets the parameterType attribute of the EffectiveAtomPolarizabilityDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor

Gets the parameterType attribute of the InductiveAtomicHardnessDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor

Gets the parameterType attribute of the InductiveAtomicSoftnessDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor

Gets the parameterType attribute of the IPAtomicHOSEDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor

Gets the parameterType attribute of the IPAtomicLearningDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor

Gets the parameterType attribute of the IsProtonInAromaticSystemDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInConjugatedPiSystemDescriptor

Gets the parameterType attribute of the IsProtonInConjugatedPiSystemDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor

Gets the parameterType attribute of the PartialPiChargeDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor

Gets the parameterType attribute of the PartialSigmaChargeDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor

Gets the parameterType attribute of the PartialTChargeMMFF94Descriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor

Gets the parameterType attribute of the PartialTChargePEOEDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor

Gets the parameterType attribute of the PeriodicTablePositionDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor

Gets the parameterType attribute of the SigmaElectronegativityDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor

Gets the parameterType attribute of the ProtonAffinityDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor

Gets the parameterType attribute of the ProtonTotalPartialChargeDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R

Gets the parameterType attribute of the RDFProtonDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR

Gets the parameterType attribute of the RDFProtonDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR

Gets the parameterType attribute of the RDFProtonDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol

Gets the parameterType attribute of the RDFProtonDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR

Gets the parameterType attribute of the RDFProtonDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor

Gets the parameterType attribute of the SigmaElectronegativityDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor

Gets the parameterType attribute of the StabilizationPlusChargeDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor

Gets the parameterType attribute of the VdWRadiusDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor

Gets the parameterType attribute of the PiContactDetectionDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptor

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor

Gets the parameterType attribute of the BondPartialPiChargeDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor

Gets the parameterType attribute of the BondPartialSigmaChargeDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor

Gets the parameterType attribute of the BondPartialTChargeDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor

Gets the parameterType attribute of the BondSigmaElectronegativityDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor

Gets the parameterType attribute of the IPBondLearningDescriptor object.

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.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.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.IPMolecularLearningDescriptor

Gets the parameterType attribute of the IPMolecularLearningDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor

Gets the parameterType attribute of the KappaShapeIndicesDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor

Gets the parameterType attribute of the descriptor.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor

Gets the parameterType attribute of the LargestChainDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor

Gets the parameterType attribute of the LargestPiSystemDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor

Gets the parameterType attribute of the PetitjeanNumberDescriptor object

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor

Gets the parameterType attribute of the LongestAliphaticChainDescriptor object.

getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.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.TPSADescriptor

Gets the parameterType attribute of the TPSADescriptor object.

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 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

getParity() - Method in class org.openscience.cdk.AtomParity

Returns the parity value.

getParity() - Method in class org.openscience.cdk.debug.DebugAtomParity

getParity() - Method in interface org.openscience.cdk.interfaces.IAtomParity

Returns the parity value.

getParser() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleNode

getPath(IAtomContainer, IAtom, IAtom) - Method in class org.openscience.cdk.graph.SpanningTree

getPathsOfLength(IAtomContainer, IAtom, int) - Static method in class org.openscience.cdk.graph.PathTools

Get the paths starting from an atom of specified length.

getPathsOfLengthUpto(IAtomContainer, IAtom, int) - Static method in class org.openscience.cdk.graph.PathTools

Get all the paths starting from an atom of length 0 upto the specified length.

getPaulingElectronegativities(IAtomContainer, boolean) - Method in class org.openscience.cdk.charges.InductivePartialCharges

Gets the paulingElectronegativities attribute of the InductivePartialCharges object

getPaulingElectronegativity(String) - Static method in class org.openscience.cdk.tools.PeriodicTable

getPaulingEneg(PeriodicTableElement) - Method in class org.openscience.cdk.config.ElementPTFactory

Gets the Pauling Electronegativity radios of this element in the periodic table.

getPaulingEneg() - Method in class org.openscience.cdk.PeriodicTableElement

Get the Pauling electronegativity of this element.

getPeriod(PeriodicTableElement) - Method in class org.openscience.cdk.config.ElementPTFactory

Gets the period of this element in the periodic table.

getPeriod() - Method in class org.openscience.cdk.PeriodicTableElement

Returns the period which this element belongs.

getPeriod(String) - Static method in class org.openscience.cdk.tools.PeriodicTable

getPharmacophoreQuery() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher

Get the query pharmacophore

getPhase(PeriodicTableElement) - Method in class org.openscience.cdk.config.ElementPTFactory

Gets the phase of this element in the periodic table.

getPhase() - Method in class org.openscience.cdk.PeriodicTableElement

Returns the phase which this element find.

getPhase(String) - Static method in class org.openscience.cdk.tools.PeriodicTable

getPlacedAtoms(IAtomContainer) - Method in class org.openscience.cdk.layout.AtomPlacer

Get all the placed atoms in an AtomContainer

getPlacedAtomsInAtomContainer(IAtom, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

Gets all placed neighbouring atoms of a atom

getPlacedHeavyAtom(IAtomContainer, IAtom) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D

Returns a placed atom connected to a given atom

getPlacedHeavyAtom(IAtomContainer, IAtom, IAtom) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D

Gets the first placed Heavy Atom around atomA which is not atomB

getPlacedHeavyAtomInAtomContainer(IAtom, IAtom, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

Returns a placed neighbouring atom of a central atom atomA, which is not atomB

getPlacedHeavyAtoms(IAtomContainer, IAtom) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D

Gets the placed Heavy Atoms connected to an atom.

getPockets() - Method in class org.openscience.cdk.protein.ProteinPocketFinder

getPocketSize() - Method in class org.openscience.cdk.protein.ProteinPocketFinder

getPoint2d() - Method in class org.openscience.cdk.Atom

Returns a point specifying the location of this atom in a 2D space.

getPoint2d() - Method in class org.openscience.cdk.debug.DebugAtom

getPoint2d() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

getPoint2d() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

getPoint2d() - Method in interface org.openscience.cdk.interfaces.IAtom

Returns a point specifying the location of this atom in a 2D space.

getPoint3d() - Method in class org.openscience.cdk.Atom

Returns a point specifying the location of this atom in a 3D space.

getPoint3d() - Method in class org.openscience.cdk.debug.DebugAtom

getPoint3d() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

getPoint3d() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

getPoint3d() - Method in interface org.openscience.cdk.interfaces.IAtom

Returns a point specifying the location of this atom in a 3D space.

getPoint3dCoordinates(IAtomContainer) - Static method in class org.openscience.cdk.modeling.forcefield.ForceFieldTools

Get the set of N coordinates 3d of a molecule of N atoms from its atom container

getPolarizabilitiyFactorForAtom(IAtomContainer, IAtom) - Method in class org.openscience.cdk.charges.Polarizability

Gets the polarizabilitiyFactorForAtom

getPolarizability(String) - Method in class org.openscience.cdk.tools.AtomicProperties

getPosition(int) - Method in class org.openscience.cdk.math.qm.GaussiansBasis

Gets the position of a base.

getPotentialParameterSet() - Method in class org.openscience.cdk.modeling.forcefield.GeometricMinimizer

getPredictDF() - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModel

Deprecated. Returns the degrees of freedom for residual.

getPredicted() - Method in class org.openscience.cdk.qsar.model.R.CNNRegressionModelPredict

Deprecated. Get the predicted values.

getPredicted() - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModelPredict

Deprecated. Get predicted values.

getPredictedClass() - Method in class org.openscience.cdk.qsar.model.R.CNNClassificationModelPredict

Deprecated. Get the predicted classes.

getPredictedRaw() - Method in class org.openscience.cdk.qsar.model.R.CNNClassificationModelPredict

Deprecated. Get the raw probabilities of the classification result.

getPredictions() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModelPredict

Deprecated. Get the predicted values.

getPredictions() - Method in class org.openscience.cdk.qsar.model.R2.CNNRegressionModel

Get the matrix of predicted values obtained from predict.nnet.

getPredictLowerBound() - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModel

Deprecated. Returns the lower prediction bounds.

getPredictPredicted() - Method in class org.openscience.cdk.qsar.model.R.CNNRegressionModel

Deprecated. Gets predicted values for new data using a previously built model.

getPredictPredicted() - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModel

Deprecated. Returns the predicted values for the prediction set.

getPredictPredicted() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModel

Deprecated. Returns the predicted values for the prediction set.

getPredictPredictedClass() - Method in class org.openscience.cdk.qsar.model.R.CNNClassificationModel

Deprecated. Gets predicted values for new data using a previously built model.

getPredictPredictedRaw() - Method in class org.openscience.cdk.qsar.model.R.CNNClassificationModel

Deprecated. Gets predicted values for new data using a previously built model.

getPredictResidualScale() - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModel

Deprecated. Returns the residual standard deviations.

getPredictSEPredictions() - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModel

Deprecated. Returns the standard error of predictions.

getPredictUpperBound() - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModel

Deprecated. Returns the upper prediction bounds.

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ABINITFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Aces2Format

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ADFFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.AlchemyFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.BGFFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.BSFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CACheFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CIFFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CMLFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CRK2DFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CRK3DFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CrystClustFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CTXFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.DaltonFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.DMol3Format

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.DOCK5Format

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.FingerprintFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.GamessFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian03Format

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian90Format

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian92Format

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian94Format

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian95Format

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian98Format

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.GROMOS96Format

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.HINFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.INChIFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat

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

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.JMEFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MacroModelFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MDLFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MDLV2000Format

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MDLV3000Format

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MMODFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Mol2Format

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC7Format

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC93Format

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC97Format

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MPQCFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.NWChemFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PCModelFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PDBFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PDBMLFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PMPFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.POVRayFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PQSChemFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.QChemFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.RawCopyFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SDFFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ShelXFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SMARTSFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SMILESFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SpartanFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SVGFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.VASPFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ViewmolFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.XEDFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.XYZFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.YasaraFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ZindoFormat

getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat

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

Returns the i-th prime number in the sequence of all prime numbers below 19700.

getProductCoefficient(IMolecule) - Method in class org.openscience.cdk.debug.DebugReaction

getProductCoefficient(IMolecule) - Method in interface org.openscience.cdk.interfaces.IReaction

Returns the stoichiometry coefficient of the given product.

getProductCoefficient(IMolecule) - Method in class org.openscience.cdk.Reaction

Returns the stoichiometry coefficient of the given product.

getProductCoefficients() - Method in class org.openscience.cdk.debug.DebugReaction

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.

getProductCount() - Method in class org.openscience.cdk.debug.DebugReaction

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.

getProducts() - Method in class org.openscience.cdk.debug.DebugReaction

getProducts() - Method in interface org.openscience.cdk.interfaces.IReaction

Returns a IMoleculeSet containing the products of this reaction.

getProducts() - Method in class org.openscience.cdk.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

getProperties() - Method in class org.openscience.cdk.debug.DebugAtom

getProperties() - Method in class org.openscience.cdk.debug.DebugAtomContainer

getProperties() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet

getProperties() - Method in class org.openscience.cdk.debug.DebugAtomType

getProperties() - Method in class org.openscience.cdk.debug.DebugBioPolymer

getProperties() - Method in class org.openscience.cdk.debug.DebugBond

getProperties() - Method in class org.openscience.cdk.debug.DebugChemFile

getProperties() - Method in class org.openscience.cdk.debug.DebugChemModel

getProperties() - Method in class org.openscience.cdk.debug.DebugChemObject

getProperties() - Method in class org.openscience.cdk.debug.DebugChemSequence

getProperties() - Method in class org.openscience.cdk.debug.DebugCrystal

getProperties() - Method in class org.openscience.cdk.debug.DebugElectronContainer

getProperties() - Method in class org.openscience.cdk.debug.DebugElement

getProperties() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

getProperties() - Method in class org.openscience.cdk.debug.DebugIsotope

getProperties() - Method in class org.openscience.cdk.debug.DebugLonePair

getProperties() - Method in class org.openscience.cdk.debug.DebugMapping

getProperties() - Method in class org.openscience.cdk.debug.DebugMolecularFormula

getProperties() - Method in class org.openscience.cdk.debug.DebugMolecule

getProperties() - Method in class org.openscience.cdk.debug.DebugMoleculeSet

getProperties() - Method in class org.openscience.cdk.debug.DebugMonomer

getProperties() - Method in class org.openscience.cdk.debug.DebugPolymer

getProperties() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

getProperties() - Method in class org.openscience.cdk.debug.DebugReaction

getProperties() - Method in class org.openscience.cdk.debug.DebugReactionScheme

getProperties() - Method in class org.openscience.cdk.debug.DebugReactionSet

getProperties() - Method in class org.openscience.cdk.debug.DebugRing

getProperties() - Method in class org.openscience.cdk.debug.DebugSingleElectron

getProperties() - Method in class org.openscience.cdk.debug.DebugStrand

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.

getProperty(Object) - Method in class org.openscience.cdk.ChemObject

Returns a property for the IChemObject.

getProperty(Object) - Method in class org.openscience.cdk.debug.DebugAminoAcid

getProperty(Object) - Method in class org.openscience.cdk.debug.DebugAtom

getProperty(Object) - Method in class org.openscience.cdk.debug.DebugAtomContainer

getProperty(Object) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet

getProperty(Object) - Method in class org.openscience.cdk.debug.DebugAtomType

getProperty(Object) - Method in class org.openscience.cdk.debug.DebugBioPolymer

getProperty(Object) - Method in class org.openscience.cdk.debug.DebugBond

getProperty(Object) - Method in class org.openscience.cdk.debug.DebugChemFile

getProperty(Object) - Method in class org.openscience.cdk.debug.DebugChemModel

getProperty(Object) - Method in class org.openscience.cdk.debug.DebugChemObject

getProperty(Object) - Method in class org.openscience.cdk.debug.DebugChemSequence

getProperty(Object) - Method in class org.openscience.cdk.debug.DebugCrystal

getProperty(Object) - Method in class org.openscience.cdk.debug.DebugElectronContainer

getProperty(Object) - Method in class org.openscience.cdk.debug.DebugElement

getProperty(Object) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

getProperty(Object) - Method in class org.openscience.cdk.debug.DebugIsotope

getProperty(Object) - Method in class org.openscience.cdk.debug.DebugLonePair

getProperty(Object) - Method in class org.openscience.cdk.debug.DebugMapping

getProperty(Object) - Method in class org.openscience.cdk.debug.DebugMolecularFormula

getProperty(Object) - Method in class org.openscience.cdk.debug.DebugMolecule

getProperty(Object) - Method in class org.openscience.cdk.debug.DebugMoleculeSet

getProperty(Object) - Method in class org.openscience.cdk.debug.DebugMonomer

getProperty(Object) - Method in class org.openscience.cdk.debug.DebugPolymer

getProperty(Object) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

getProperty(Object) - Method in class org.openscience.cdk.debug.DebugReaction

getProperty(Object) - Method in class org.openscience.cdk.debug.DebugReactionScheme

getProperty(Object) - Method in class org.openscience.cdk.debug.DebugReactionSet

getProperty(Object) - Method in class org.openscience.cdk.debug.DebugRing

getProperty(Object) - Method in class org.openscience.cdk.debug.DebugSingleElectron

getProperty(Object) - Method in class org.openscience.cdk.debug.DebugStrand

getProperty(Object) - Method in class org.openscience.cdk.formula.MolecularFormula

Returns a property for the IChemObject.

getProperty(Object) - Method in interface org.openscience.cdk.interfaces.IChemObject

Returns a property for the IChemObject.

getProperty(Object) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula

Returns a property for the IChemObject.

getProtein() - Method in class org.openscience.cdk.protein.ProteinPocketFinder

getProteinInterior() - Method in class org.openscience.cdk.protein.ProteinPocketFinder

getQr() - Method in class org.openscience.cdk.qsar.model.R2.LinearRegressionModel

Gets the qr field of an 'lm' object.

getQSARs(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.tools.IonizationPotentialTool

Get the results of 7 qsar descriptors been applied.

getQSARs(IAtomContainer, IBond) - Static method in class org.openscience.cdk.tools.IonizationPotentialTool

Get the results of 7 qsar descriptors been applied.

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.

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.qsar.model.R.LinearRegressionModelFit

Deprecated. Get the rank of the fit.

getRank() - Method in class org.openscience.cdk.qsar.model.R2.LinearRegressionModel

Gets the rank field of an 'lm' object.

getRAtom() - Method in class org.openscience.cdk.protein.ProteinPocketFinder

getRawContent() - Method in class org.openscience.cdk.dict.Entry

getRDBEValue(IMolecularFormula) - Method in class org.openscience.cdk.formula.rules.RDBERule

Method to extract the Ring Double Bond Equivalents (RDB) value.

getReactantCoefficient(IMolecule) - Method in class org.openscience.cdk.debug.DebugReaction

getReactantCoefficient(IMolecule) - Method in interface org.openscience.cdk.interfaces.IReaction

Returns the stoichiometry coefficient of the given reactant.

getReactantCoefficient(IMolecule) - Method in class org.openscience.cdk.Reaction

Returns the stoichiometry coefficient of the given reactant.

getReactantCoefficients() - Method in class org.openscience.cdk.debug.DebugReaction

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.

getReactantCount() - Method in class org.openscience.cdk.debug.DebugReaction

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.

getReactants() - Method in class org.openscience.cdk.debug.DebugReaction

getReactants() - Method in interface org.openscience.cdk.interfaces.IReaction

Returns a IMoleculeSet containing the reactants in this reaction.

getReactants() - Method in class org.openscience.cdk.Reaction

Returns a MoleculeSet containing the reactants in this reaction.

getReaction(int) - Method in class org.openscience.cdk.debug.DebugReactionSet

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.

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

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.

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

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.

getReactionSet() - Method in class org.openscience.cdk.ChemModel

Gets the ReactionSet contained in this ChemModel.

getReactionSet() - Method in class org.openscience.cdk.debug.DebugChemModel

getReactionSet() - Method in interface org.openscience.cdk.interfaces.IChemModel

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

getReaderClassName() - Method in class org.openscience.cdk.io.formats.Aces2Format

getReaderClassName() - Method in class org.openscience.cdk.io.formats.ADFFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.AlchemyFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.BGFFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.BSFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.CACheFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format

getReaderClassName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format

getReaderClassName() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.CIFFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.CMLFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.CRK2DFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.CRK3DFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.CrystClustFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.CTXFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.DaltonFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.DMol3Format

getReaderClassName() - Method in class org.openscience.cdk.io.formats.DOCK5Format

getReaderClassName() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.FingerprintFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.GamessFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian03Format

getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian90Format

getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian92Format

getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian94Format

getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian95Format

getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian98Format

getReaderClassName() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.GROMOS96Format

getReaderClassName() - Method in class org.openscience.cdk.io.formats.HINFormat

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

getReaderClassName() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.JaguarFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.JMEFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.MacroModelFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.MDLFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format

getReaderClassName() - Method in class org.openscience.cdk.io.formats.MDLV2000Format

getReaderClassName() - Method in class org.openscience.cdk.io.formats.MDLV3000Format

getReaderClassName() - Method in class org.openscience.cdk.io.formats.MMODFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.Mol2Format

getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format

getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC7Format

getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC93Format

getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC97Format

getReaderClassName() - Method in class org.openscience.cdk.io.formats.MPQCFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.NWChemFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.PCModelFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.PDBFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.PDBMLFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.PMPFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.PQSChemFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.QChemFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.RawCopyFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.SDFFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.ShelXFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.SMARTSFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.SMILESFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.SpartanFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format

getReaderClassName() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.VASPFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.ViewmolFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.XEDFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.XYZFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.YasaraFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.ZindoFormat

getReaderClassName() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat

getRealPart() - Method in class org.openscience.cdk.math.Complex

Gets the real part of this complex value

getRecord() - Method in class org.openscience.cdk.debug.DebugPDBAtom

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.

getRecursiveQuery() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RecursiveSmartsAtom

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(IMoleculeSet, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator

getRelevantAtomContainer(IMoleculeSet, 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.

getRengine() - Static method in class org.openscience.cdk.qsar.model.R2.RModel

Get the instance of the Rengine.

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

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Aces2Format

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ADFFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.AlchemyFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.BGFFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.BSFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CACheFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CIFFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CMLFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CRK2DFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CRK3DFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CrystClustFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CTXFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.DaltonFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.DMol3Format

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.DOCK5Format

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.FingerprintFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.GamessFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian03Format

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian90Format

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian92Format

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian94Format

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian95Format

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian98Format

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.GROMOS96Format

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.HINFormat

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

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.JaguarFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.JMEFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MacroModelFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLV2000Format

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLV3000Format

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MMODFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Mol2Format

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC7Format

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC93Format

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC97Format

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MPQCFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.NWChemFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PCModelFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PDBFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PDBMLFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PMPFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PQSChemFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.QChemFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.RawCopyFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SDFFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ShelXFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SMARTSFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SMILESFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SpartanFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.VASPFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ViewmolFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.XEDFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.XYZFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.YasaraFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ZindoFormat

getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat

getResiduals() - Method in class org.openscience.cdk.qsar.model.R.CNNClassificationModelFit

Deprecated. Get the residuals of the fit.

getResiduals() - Method in class org.openscience.cdk.qsar.model.R.CNNRegressionModelFit

Deprecated. Get the residuals of the fit.

getResiduals() - Method in class org.openscience.cdk.qsar.model.R.CNNRegressionModelSummary

Deprecated. Return the residuals of the fit.

getResiduals() - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModelFit

Deprecated. Get the residuals of the fit.

getResiduals() - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModelSummary

Deprecated. Return the residuals of the fit.

getResiduals() - Method in class org.openscience.cdk.qsar.model.R2.CNNRegressionModel

Gets the residuals field of an 'nnet' object.

getResiduals() - Method in class org.openscience.cdk.qsar.model.R2.LinearRegressionModel

Gets the residuals field of an 'lm' object.

getResidualScale() - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModelPredict

Deprecated. Get the scale of residuals.

getResidues() - Method in class org.openscience.cdk.libio.md.MDMolecule

getResName() - Method in class org.openscience.cdk.debug.DebugPDBAtom

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.

getResSeq() - Method in class org.openscience.cdk.debug.DebugPDBAtom

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

getRestrictions() - Method in class org.openscience.cdk.formula.MassToFormulaTool

Get the restrictions that must be presents in the molecular formula.

getReturnStatus() - Method in class org.openscience.cdk.inchi.InChIGenerator

Gets return status from InChI process.

getReturnStatus() - Method in class org.openscience.cdk.inchi.InChIToStructure

Gets return status from InChI process.

getRight() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom

getRight() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond

getRingBond() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RingIdentifierAtom

getRingFinder() - Method in class org.openscience.cdk.smiles.SmilesGenerator

Returns the current AllRingsFinder instance

getRingFragments() - Method in class org.openscience.cdk.tools.GenerateFragments

getRingFragmentsAsSmileArray() - Method in class org.openscience.cdk.tools.GenerateFragments

getRingId() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTRingIdentifier

Returns the ring identifier.

getRings(IBond) - Method in class org.openscience.cdk.debug.DebugRingSet

getRings(IAtom) - Method in class org.openscience.cdk.debug.DebugRingSet

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.

getRingSet() - Method in class org.openscience.cdk.ChemModel

Returns the RingSet of this ChemModel.

getRingSet() - Method in class org.openscience.cdk.debug.DebugChemModel

getRingSet() - Method in interface org.openscience.cdk.interfaces.IChemModel

Returns the RingSet of this ChemModel.

getRingSize() - Method in class org.openscience.cdk.debug.DebugRing

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.

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.

getRoot(Node) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

getRotationMatrix() - Method in class org.openscience.cdk.geometry.alignment.KabschAlignment

Returns the rotation matrix (u).

getRows() - Method in class org.openscience.cdk.math.IMatrix

Returns the count of rows

getRows() - Method in class org.openscience.cdk.math.Matrix

Returns the number of rows.

getRSolvent() - Method in class org.openscience.cdk.protein.ProteinPocketFinder

getRSQ() - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModelSummary

Deprecated. Returns the R^2 value.

getRules() - Method in class org.openscience.cdk.formula.MolecularFormulaChecker

Get the IRules to be applied to validate the IMolecularFormula.

getScaleFactor(IAtomContainer, double) - Static method in class org.openscience.cdk.geometry.GeometryTools

Determines the scale factor for displaying a structure loaded from disk in a frame.

getSearchDepth() - Method in class org.openscience.cdk.fingerprint.Fingerprinter

getSecondGraphSize() - Method in class org.openscience.cdk.isomorphism.mcss.RGraph

Returns the size of the second of the two compared graphs.

getSEFit() - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModelPredict

Deprecated. Get the standard errors of prediction.

getSegID() - Method in class org.openscience.cdk.debug.DebugPDBAtom

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.

getSerial() - Method in class org.openscience.cdk.debug.DebugPDBAtom

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.

getSetting() - Method in class org.openscience.cdk.io.setting.IOSetting

Sets the setting for a certain question.

getSettingValue() - Method in class org.openscience.cdk.io.setting.IntegerIOSetting

getShortestPath(IAtomContainer, IAtom, IAtom) - Static method in class org.openscience.cdk.graph.PathTools

Returns a list of atoms in the shortest path between two atoms.

getSID(XmlPullParser) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper

getSigma() - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModelSummary

Deprecated. Return the residual standard error.

getSingleBondEquivalentSum(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator

Returns the sum of bond orders, where a single bond counts as one single bond equivalent, a double as two, etc.

getSingleBondEquivalentSum(List<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator

Get the single bond equivalent (SBE) of a list of bonds.

getSingleBondEquivalentSum(Iterator<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator

Get the single bond equivalent (SBE) of a list of bonds, given an iterator to the list.

getSingleElectron(int) - Method in class org.openscience.cdk.AtomContainer

Get the single electron at position number in [0,..].

getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid

getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer

getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer

getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugCrystal

getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugMolecule

getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugMonomer

getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugPolymer

getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugRing

getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugStrand

getSingleElectron(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Get the single electron at position number in [0,..].

getSingleElectronCount() - Method in class org.openscience.cdk.AtomContainer

Returns the number of the single electrons in this container,

getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugAminoAcid

getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugAtomContainer

getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer

getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugCrystal

getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugMolecule

getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugMonomer

getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugPolymer

getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugRing

getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugStrand

getSingleElectronCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

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

getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAtomContainer

getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugBioPolymer

getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugCrystal

getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugMolecule

getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugMonomer

getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugPolymer

getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugRing

getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugStrand

getSingleElectronNumber(ISingleElectron) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the position of a given single electron in the single electron array.

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.ElementPTFactory

Returns the number of elements defined by this class.

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.EStateFingerprinter

getSize() - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter

getSize() - Method in class org.openscience.cdk.fingerprint.Fingerprinter

getSize() - Method in interface org.openscience.cdk.fingerprint.IFingerprinter

Returns the size of the fingerprints calculated.

getSize() - Method in class org.openscience.cdk.fingerprint.MACCSFingerprinter

getSize() - Method in class org.openscience.cdk.fingerprint.SubstructureFingerprinter

getSize() - Method in class org.openscience.cdk.math.IVector

Return the size from this vector

getSize() - Method in class org.openscience.cdk.math.qm.FourierGridBasis

getSize() - Method in class org.openscience.cdk.math.qm.GaussiansBasis

Gets the number of base vectors.

getSize() - Method in interface org.openscience.cdk.math.qm.IBasis

Gets the number of base vectors

getSize() - Method in class org.openscience.cdk.math.Vector

Returns the size of this vector

getSize() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTSmallestRingSize

Returns the smallest SSSR size.

getSmarts() - Static method in class org.openscience.cdk.config.fragments.EStateFragments

Get the SMARTS patterns.

getSmarts() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom

Get the SMARTS for the group.

getSmarts() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryAtom

Get the SMARTS pattern for this pharmacophore group.

getSmarts() - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool

Returns the current SMARTS pattern being used.

getSmoothingFunction() - Method in class org.openscience.cdk.modeling.forcefield.SmoothingFunctions

Get the smoothing function value for every atom distance.

getSoftmax() - Method in class org.openscience.cdk.qsar.model.R.CNNRegressionModelSummary

Deprecated. Return whether softmax was used.

getSoftmax() - Method in class org.openscience.cdk.qsar.model.R2.CNNRegressionModel

Gets the softmax field of an 'nnet' object.

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 class org.openscience.cdk.controller.CDKPopupMenu

getSource() - Method in interface org.openscience.cdk.interfaces.IChemObjectChangeEvent

IChemObject that fired the event.

getSource(ActionEvent) - Method in class org.openscience.cdk.renderer.JCPAction2D

Gets the source attribute of the JCPAction object

getSpaceGroup() - Method in class org.openscience.cdk.Crystal

Gets the space group of this crystal.

getSpaceGroup() - Method in class org.openscience.cdk.debug.DebugCrystal

getSpaceGroup() - Method in interface org.openscience.cdk.interfaces.ICrystal

Gets the space group of this crystal.

getSpanningTree() - Method in class org.openscience.cdk.graph.SpanningTree

getSpanningTreeSize() - Method in class org.openscience.cdk.graph.SpanningTree

getSpatproduct(Vector3d, Vector3d, Vector3d) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

Gets the spatproduct of three vectors

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor

Gets the specification attribute of the AtomHybridizationDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor

Gets the specification attribute of the AtomHybridizationVSEPRDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor

Gets the specification attribute of the AtomValenceDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor

Gets the specification attribute of the BondsToAtomDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor

Returns a Map which specifies which descriptor is implemented by this class.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor

Gets the specification attribute of the DistanceToAtomDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor

Gets the specification attribute of the EffectiveAtomPolarizabilityDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor

Gets the specification attribute of the InductiveAtomicHardnessDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor

Gets the specification attribute of the InductiveAtomicSoftnessDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor

Gets the specification attribute of the IPAtomicHOSEDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor

Gets the specification attribute of the IPAtomicLearningDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor

Gets the specification attribute of the IsProtonInAromaticSystemDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInConjugatedPiSystemDescriptor

Gets the specification attribute of the IsProtonInConjugatedPiSystemDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor

Gets the specification attribute of the PartialPiChargeDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor

Gets the specification attribute of the PartialSigmaChargeDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor

Gets the specification attribute of the PartialTChargeMMFF94Descriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor

Gets the specification attribute of the PartialTChargePEOEDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor

Gets the specification attribute of the PeriodicTablePositionDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor

Gets the specification attribute of the PiElectronegativityDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor

Gets the specification attribute of the ProtonAffinityDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor

Gets the specification attribute of the ProtonTotalPartialChargeDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R

Gets the specification attribute of the RDFProtonDescriptor_G3R object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR

Gets the specification attribute of the RDFProtonDescriptor_GDR object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR

Gets the specification attribute of the RDFProtonDescriptor_GHR object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol

Gets the specification attribute of the RDFProtonDescriptor_GHR_topol object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR

Gets the specification attribute of the RDFProtonDescriptor_GSR object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor

Gets the specification attribute of the SigmaElectronegativityDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor

Gets the specification attribute of the StabilizationPlusChargeDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor

Returns a Map which specifies which descriptor is implemented by this class.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor

Gets the specification attribute of the PiContactDetectionDescriptor object.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptor

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor

Gets the specification attribute of the BondPartialPiChargeDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor

Gets the specification attribute of the BondPartialSigmaChargeDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor

Gets the specification attribute of the BondPartialTChargeDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor

Gets the specification attribute of the BondSigmaElectronegativityDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor

Gets the specification attribute of the IPBondLearningDescriptor object

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.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.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.IPMolecularLearningDescriptor

Gets the specification attribute of the IPMolecularLearningDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor

Gets the specification attribute of the KappaShapeIndicesDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor

Returns a Map which specifies which descriptor is implemented by this class.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor

Returns a Map which specifies which descriptor is implemented by this class.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor

Returns a Map which specifies which descriptor is implemented by this class.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor

Gets the specification attribute of the PetitjeanNumberDescriptor object

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor

Returns a Map which specifies which descriptor is implemented by this class.

getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.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.TPSADescriptor

Gets the specification attribute of the TPSADescriptor object.

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.DescriptorValue

getSpecification() - Method in interface org.openscience.cdk.qsar.IDescriptor

Returns a Map 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(IMolecule, IAtom, int, boolean) - Method in class org.openscience.cdk.tools.HOSECodeGenerator

This method is intended to be used to get the atoms around an atom in spheres.

getSpinVector(double, double) - Method in class org.openscience.cdk.math.qm.AngularMomentum

Calculates a spin vector by a direction specified by theta and phi

getSSSRWeightVector() - Method in class org.openscience.cdk.ringsearch.SSSRFinder

Returns a vector containing the lengths of the rings in a SSSR.

getStartChainID() - Method in class org.openscience.cdk.debug.DebugPDBStructure

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.

getStartInsertionCode() - Method in class org.openscience.cdk.debug.DebugPDBStructure

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.

getStartSequenceNumber() - Method in class org.openscience.cdk.debug.DebugPDBStructure

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.

getSteepestDescentsMinimum() - Method in class org.openscience.cdk.modeling.forcefield.GeometricMinimizer

Gets the steepestDescentsMinimum attribute of the GeometricMinimizer object

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

getStepSize() - Method in class org.openscience.cdk.modeling.forcefield.LineSearch

Gets the stepSize attribute of the LineSearch object

getStereo() - Method in class org.openscience.cdk.Bond

Returns the stereo descriptor for this bond.

getStereo() - Method in class org.openscience.cdk.debug.DebugBond

getStereo() - Method in interface org.openscience.cdk.interfaces.IBond

Returns the stereo descriptor for this bond.

getStereoParity() - Method in class org.openscience.cdk.Atom

Returns the stereo parity of this atom.

getStereoParity() - Method in class org.openscience.cdk.debug.DebugAtom

getStereoParity() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

getStereoParity() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

getStereoParity() - Method in interface org.openscience.cdk.interfaces.IAtom

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

getStrand(String) - Method in interface org.openscience.cdk.interfaces.IBioPolymer

Retrieve 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

getStrandCount() - Method in interface org.openscience.cdk.interfaces.IBioPolymer

Return the number of strands present in the BioPolymer.

getStrandName() - Method in class org.openscience.cdk.debug.DebugStrand

getStrandName() - Method in interface org.openscience.cdk.interfaces.IStrand

Retrieve 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

getStrandNames() - Method in interface org.openscience.cdk.interfaces.IBioPolymer

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

getStrands() - Method in interface org.openscience.cdk.interfaces.IBioPolymer

Returns a Map containing the strands in the Polymer.

getStrandType() - Method in class org.openscience.cdk.debug.DebugStrand

getStrandType() - Method in interface org.openscience.cdk.interfaces.IStrand

Retrieve the strand type.

getStrandType() - Method in class org.openscience.cdk.Strand

Retrieves the strand type.

getString(IMolecularFormula, String[], boolean) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator

Returns the string representation of the molecule formula.

getString(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator

Returns the string representation of the molecule formula.

getString(IMolecularFormula, boolean) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator

Returns the string representation of the molecule formula.

getStructures() - Method in class org.openscience.cdk.debug.DebugPDBPolymer

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(IMolecule) - Method in class org.openscience.cdk.tools.StructureResonanceGenerator

Get the resonance structures from an IMolecule.

getStructureType() - Method in class org.openscience.cdk.debug.DebugPDBStructure

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.

getSubgraph() - Method in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph

getSubgraphAtomsMap(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester

Returns the first subgraph 'atom mapping' found for g2 in g1.

getSubgraphAtomsMaps(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester

Returns all subgraph 'atom mappings' found for g2 in g1.

getSubgraphMap(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester

Returns the first subgraph 'bond mapping' found for g2 in g1.

getSubgraphMaps(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester

Returns all the subgraph 'bond mappings' found for g2 in g1.

GetSuffix(int) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream

GetSuffix(int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.CDKSourceCodeWriter

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ABINITFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Aces2Format

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ADFFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.AlchemyFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.BGFFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.BSFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CACheFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CIFFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CMLFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CRK2DFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CRK3DFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CrystClustFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CTXFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.DaltonFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.DMol3Format

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.DOCK5Format

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.FingerprintFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.GamessFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian03Format

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian90Format

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian92Format

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian94Format

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian95Format

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian98Format

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.GROMOS96Format

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.HINFormat

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

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.JaguarFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.JMEFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MacroModelFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLV2000Format

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLV3000Format

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MMODFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Mol2Format

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC7Format

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC93Format

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC97Format

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MPQCFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.NWChemFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PCModelFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PDBFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PDBMLFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PMPFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PQSChemFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.QChemFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.RawCopyFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SDFFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ShelXFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SMARTSFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SMILESFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SpartanFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.VASPFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ViewmolFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.XEDFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.XYZFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.YasaraFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ZindoFormat

getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat

getSupportedDataFeatures(IMolecule) - Static method in class org.openscience.cdk.tools.DataFeaturesTool

Determines the features present in the given IMolecule.

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.

getSurroundingAtoms() - Method in class org.openscience.cdk.AtomParity

Returns the four atoms that define the stereochemistry for this parity.

getSurroundingAtoms() - Method in class org.openscience.cdk.debug.DebugAtomParity

getSurroundingAtoms() - Method in interface org.openscience.cdk.interfaces.IAtomParity

Returns the four atoms that define the stereochemistry for this parity.

getSwitchingAtom() - Method in class org.openscience.cdk.libio.md.ChargeGroup

getSymbol() - Method in class org.openscience.cdk.debug.DebugAtom

getSymbol() - Method in class org.openscience.cdk.debug.DebugAtomType

getSymbol() - Method in class org.openscience.cdk.debug.DebugElement

getSymbol() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

getSymbol() - Method in class org.openscience.cdk.debug.DebugIsotope

getSymbol() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

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.smiles.smarts.parser.ASTElement

Returns the element symbol.

getSymbol() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTExplicitAtom

Returns the element symbol.

getSymbolSet() - Method in class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom

Retrieve the Set of symbols

getSymbolSet() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom

Retrieve the Set of symbols

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.

getTC(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.TotalConnectionAtom

This returns the total connection of an atom.

getTempFactor() - Method in class org.openscience.cdk.debug.DebugPDBAtom

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.

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

Gets the templateHandler attribute of the StructureDiagramGenerator object

getTessAsPoint3ds() - Method in class org.openscience.cdk.geometry.surface.Tessellate

getTessAsTriangles() - Method in class org.openscience.cdk.geometry.surface.Tessellate

getTimeout() - Method in class org.openscience.cdk.ringsearch.AllRingsFinder

Gets the timeout values in milliseconds of the AllRingsFinder object

getTitle() - Method in class org.openscience.cdk.ConformerContainer

Get the title of the conformers.

getTitle() - Method in class org.openscience.cdk.renderer.GraphRendererModel

Get the main title

getTitlemap() - Method in class org.openscience.cdk.io.RssWriter

getToken(int) - Method in class org.openscience.cdk.iupac.parser.NomParser

getToken(int) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

getTolerance() - Method in class org.openscience.cdk.formula.IsotopePatternSimilarity

Get the tolerance of the mass accuracy.

getTopoEquivClassbyHuXu(AtomContainer) - 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(IMoleculeSet) - 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

getTotalFormalCharge(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator

getTotalFormalCharge(IMoleculeSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator

getTotalHydrogenCount(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator

getTotalHydrogenCount(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator

getTotalHydrogenCount(IMoleculeSet) - 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

getTotalPositiveFormalCharge(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator

getTotalSurfaceArea() - Method in class org.openscience.cdk.geometry.surface.NumericalSurface

Get the total surface area for the AtomContainer.

getTrainingRMS() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModelFit

getTrainingYPred() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModelFit

getType() - Method in class org.openscience.cdk.dict.DictRef

getType() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTNotBond

getType() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTNotExpression

getUniqueMatchingAtoms() - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool

Get the atoms in the target molecule that match the query pattern.

getUniqueMatchingPharmacophoreAtoms() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher

Get the uniue matching pharmacophore groups.

getUniqueVariableName(String) - Method in class org.openscience.cdk.qsar.model.R2.RModel

Get a unique String value.

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

getUpper() - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModelPredict

Deprecated. Get the upper confidence bounds.

getUseTemplates() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

Returns whether the use of templates is enabled or disabled.

getValence(IAtom) - Static method in class org.openscience.cdk.qsar.AtomValenceTool

getValency() - Method in class org.openscience.cdk.AtomType

Gets the the exact electron valency of the AtomType object.

getValency() - Method in class org.openscience.cdk.debug.DebugAtom

getValency() - Method in class org.openscience.cdk.debug.DebugAtomType

getValency() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

getValency() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

getValency() - Method in interface org.openscience.cdk.interfaces.IAtomType

Gets the the exact electron valency of the AtomType object.

getValidationIter() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModel

Deprecated. The number of iterations used during CV.

getValidationIter() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModelFit

getValidationLV() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModel

Deprecated. The number of latent variables suggested by CV.

getValidationLV() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModelFit

getValidationR2() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModel

Deprecated. Get the R^2 value for validation.

getValidationR2() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModelFit

getValidationRMS() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModel

Deprecated. Get the RMS value for validation.

getValidationRMS() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModelFit

getValidationRMSsd() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModel

Deprecated. Get the standard deviation of the RMS errrors for validation.

getValidationRMSSD() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModelFit

getValidationYPred() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModel

Deprecated. Get the predicted Y values from validation.

getValidationYPred() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModelFit

getValue(double, double, double) - Method in interface org.openscience.cdk.math.IFunction

Return the function value at (x,y,z)

getValue(int, double, double, double) - Method in class org.openscience.cdk.math.qm.FourierGridBasis

getValue(int, double, double, double) - Method in class org.openscience.cdk.math.qm.GaussiansBasis

Calculates the function value an (x,y,z).

getValue(int, double, double, double) - Method in interface org.openscience.cdk.math.qm.IBasis

Calculates the function value an (x,y,z).

getValue(int, double, double, double) - Method in class org.openscience.cdk.math.qm.Orbitals

Get the function value of a orbital at the position (x,y,z)

getValue() - Method in class org.openscience.cdk.qsar.DescriptorValue

getValue() - Method in class org.openscience.cdk.qsar.model.R.CNNClassificationModelFit

Deprecated. Get the final value of the cost function.

getValue() - Method in class org.openscience.cdk.qsar.model.R.CNNRegressionModelFit

Deprecated. Get the final value of the cost function.

getValue() - Method in class org.openscience.cdk.qsar.model.R.CNNRegressionModelSummary

Deprecated. Return the final value of the convergence criterion.

getValue() - Method in class org.openscience.cdk.qsar.model.R2.CNNRegressionModel

Gets the value field of an 'nnet' object.

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.

getValueAt(int, int) - Method in class org.openscience.cdk.graph.invariant.GIMatrix

Returns the value of the given element.

getValues(Matrix) - Method in interface org.openscience.cdk.math.IFunction

Return the function value The rows of the matrix x are the Parameters like x,y,z and the columns are the values which must calculated.

getValues(int, Matrix) - Method in class org.openscience.cdk.math.qm.FourierGridBasis

getValues(int, Matrix) - Method in class org.openscience.cdk.math.qm.GaussiansBasis

Calculates the function values.

getValues(int, Matrix) - Method in interface org.openscience.cdk.math.qm.IBasis

Calculates the function values.

getValues(int, Matrix) - Method in class org.openscience.cdk.math.qm.Orbitals

Get the function value of a orbital

getVanDerWaalsFile() - Method in class org.openscience.cdk.protein.ProteinPocketFinder

getVdwRadius(PeriodicTableElement) - Method in class org.openscience.cdk.config.ElementPTFactory

Gets the Vdw radios of this element in the periodic table.

getVdwRadius() - Method in class org.openscience.cdk.PeriodicTableElement

Get the VdW radius for this element.

getVdwRadius(String) - Static method in class org.openscience.cdk.tools.PeriodicTable

getVdWVolume(String) - Method in class org.openscience.cdk.tools.AtomicProperties

getVectorFromColumn(int) - Method in class org.openscience.cdk.math.IMatrix

Creates a vector with the content of a column from this matrix

getVectorFromColumn(int) - Method in class org.openscience.cdk.math.Matrix

Creates a Vector with the content of a column from this Matrix.

getVectorFromDiagonal() - Method in class org.openscience.cdk.math.IMatrix

Creates a vector with the content of the diagonal elements from this matrix

getVectorFromDiagonal() - Method in class org.openscience.cdk.math.Matrix

Creates a Vector with the content of the diagonal elements from this Matrix.

getVectorFromRow(int) - Method in class org.openscience.cdk.math.IMatrix

Creates a vector with the content of a row from this matrix

getVectorFromRow(int) - Method in class org.openscience.cdk.math.Matrix

Creates a Vector with the content of a row from this Matrix.

getVertexCountAtDistance(IAtomContainer, int) - Static method in class org.openscience.cdk.graph.PathTools

Returns the number of vertices that are a distance 'd' apart.

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.

getWeights() - Method in class org.openscience.cdk.qsar.model.R.CNNClassificationModelFit

Deprecated. Get the weights and biases of the final network.

getWeights() - Method in class org.openscience.cdk.qsar.model.R.CNNRegressionModelFit

Deprecated. Get the weights and biases of the final network.

getWriterClassName() - Method in class org.openscience.cdk.io.formats.ABINITFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.Aces2Format

getWriterClassName() - Method in class org.openscience.cdk.io.formats.ADFFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.AlchemyFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.BGFFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.BSFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.CACheFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format

getWriterClassName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format

getWriterClassName() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.CIFFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.CMLFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.CRK2DFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.CRK3DFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.CrystClustFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.CTXFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.DaltonFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.DMol3Format

getWriterClassName() - Method in class org.openscience.cdk.io.formats.DOCK5Format

getWriterClassName() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.FingerprintFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.GamessFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.Gaussian03Format

getWriterClassName() - Method in class org.openscience.cdk.io.formats.Gaussian90Format

getWriterClassName() - Method in class org.openscience.cdk.io.formats.Gaussian92Format

getWriterClassName() - Method in class org.openscience.cdk.io.formats.Gaussian94Format

getWriterClassName() - Method in class org.openscience.cdk.io.formats.Gaussian95Format

getWriterClassName() - Method in class org.openscience.cdk.io.formats.Gaussian98Format

getWriterClassName() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.GROMOS96Format

getWriterClassName() - Method in class org.openscience.cdk.io.formats.HINFormat

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

getWriterClassName() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.JaguarFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.JMEFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.MacroModelFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.MDLFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format

getWriterClassName() - Method in class org.openscience.cdk.io.formats.MDLV2000Format

getWriterClassName() - Method in class org.openscience.cdk.io.formats.MDLV3000Format

getWriterClassName() - Method in class org.openscience.cdk.io.formats.MMODFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.Mol2Format

getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format

getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC7Format

getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC93Format

getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC97Format

getWriterClassName() - Method in class org.openscience.cdk.io.formats.MPQCFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.NWChemFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.PCModelFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.PDBFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.PDBMLFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.PMPFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.PQSChemFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.QChemFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.RawCopyFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.SDFFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.ShelXFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.SMARTSFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.SMILESFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.SpartanFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format

getWriterClassName() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.VASPFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.ViewmolFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.XEDFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.XYZFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.YasaraFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.ZindoFormat

getWriterClassName() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat

getWts() - Method in class org.openscience.cdk.qsar.model.R2.CNNRegressionModel

Gets the wts field of an 'nnet' object.

getXlevels() - Method in class org.openscience.cdk.qsar.model.R2.LinearRegressionModel

Gets the xlevels field of an 'lm' object.

getXLoading() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModelFit

getXMax() - Method in class org.openscience.cdk.renderer.GraphRendererModel

Sets the function area, which will painted

getXMin() - Method in class org.openscience.cdk.renderer.GraphRendererModel

Gets the function area, which will painted

getXScores() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModelFit

getXTitle() - Method in class org.openscience.cdk.renderer.GraphRendererModel

Get the title of the x axis

getYLoading() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModelFit

getYMax() - Method in class org.openscience.cdk.renderer.GraphRendererModel

Sets the function area, which will painted

getYMin() - Method in class org.openscience.cdk.renderer.GraphRendererModel

Sets the function area, which will painted

getYScores() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModelFit

getYTitle() - Method in class org.openscience.cdk.renderer.GraphRendererModel

Get the title of the y axis

getZ() - Method in class org.openscience.cdk.Crystal

Gets the number of asymmetric parts in the unit cell.

getZ() - Method in class org.openscience.cdk.debug.DebugCrystal

getZ() - Method in interface org.openscience.cdk.interfaces.ICrystal

Gets the number of asymmetric parts in the unit cell.

GhemicalMMFormat - Class in org.openscience.cdk.io.formats

See here.

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

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, substraction, 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

globalID - Static variable in class org.openscience.cdk.qsar.model.R.CNNRegressionModel

Deprecated.

globalID - Static variable in class org.openscience.cdk.qsar.model.R2.CNNRegressionModel

GOLD - Static variable in class org.openscience.cdk.config.Elements

GOLD - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

gradientPerInverseHessian(GVector, GMatrix) - Method in class org.openscience.cdk.modeling.forcefield.NewtonRaphsonMethod

gradientSmallEnough(double, GVector) - Method in class org.openscience.cdk.modeling.forcefield.GeometricMinimizer

Analyse if the gradient is small enough, using the criteria || gradient || < 10-5 (1 + |function|)

GraphOnlyFingerprinter - Class in org.openscience.cdk.fingerprint

Specialized version of the Fingerprinter which does not take bond orders into account.

GraphOnlyFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.GraphOnlyFingerprinter

Creates a fingerprint generator of length defaultSize and with a search depth of defaultSearchDepth.

GraphOnlyFingerprinter(int) - Constructor for class org.openscience.cdk.fingerprint.GraphOnlyFingerprinter

GraphOnlyFingerprinter(int, int) - Constructor for class org.openscience.cdk.fingerprint.GraphOnlyFingerprinter

GraphRendererModel - Class in org.openscience.cdk.renderer

This class handles a set of function for the GraphRenderer

GraphRendererModel() - Constructor for class org.openscience.cdk.renderer.GraphRendererModel

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.

GroupExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

groupOneMetals() - Method in class org.openscience.cdk.iupac.parser.NomParser

groupTwoMetals() - Method in class org.openscience.cdk.iupac.parser.NomParser

guessFormat(Reader) - Method in class org.openscience.cdk.io.FormatFactory

Creates a String of the Class name of the IChemObject reader for this file format.

guessFormat(InputStream) - Method in class org.openscience.cdk.io.FormatFactory

H

H - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

h - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

H_AND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

HAFNIUM - Static variable in class org.openscience.cdk.config.Elements

HAFNIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

has2DCoordinates(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools

Determines if this AtomContainer contains 2D coordinates.

has2DCoordinates(IAtom) - Static method in class org.openscience.cdk.geometry.GeometryTools

Determines if this Atom contains 2D coordinates.

has2DCoordinates(IBond) - Static method in class org.openscience.cdk.geometry.GeometryTools

Determines if this Bond contains 2D coordinates.

has2DCoordinatesNew(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools

Determines if this AtomContainer contains 2D coordinates for some or all molecules.

has3DCoordinates(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools

Determines if this model contains 3D coordinates

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 !!!

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.

hasElementSymbols(IMolecule) - 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.

hasFormalCharges(IMolecule) - Static method in class org.openscience.cdk.tools.features.MoleculeFeaturesTool

hasGraphRepresentation(IMolecule) - Static method in class org.openscience.cdk.tools.features.MoleculeFeaturesTool

Checks whether all bonds have exactly two atoms.

hashCode() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycle

hasMoreElements() - Method in class org.openscience.cdk.formula.rules.RDBERule.Combinations

hasNext() - Method in class org.openscience.cdk.graph.AtomContainerPermutor

hasNext() - Method in class org.openscience.cdk.graph.MinimalPathIterator

hasNext() - Method in class org.openscience.cdk.io.iterator.IteratingMDLConformerReader

hasNext() - Method in class org.openscience.cdk.io.iterator.IteratingMDLReader

Returns true if another IMolecule can be read.

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.IteratingSMILESReader

Checks whether there is another molecule to read.

hasNext() - Method in class org.openscience.cdk.io.random.RandomAccessReader

hasPartialCharges(IMolecule) - 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

HASSIUM - Static variable in class org.openscience.cdk.config.Elements

HASSIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

hasSymbol(String) - Method in class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom

Check whether a symbol is already registered

hasSymbol(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom

Check whether a symbol is already registered

hasUnsetNeighbour(IAtom, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

HBondAcceptorCountDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

This descriptor calculates the number of hydrogen bond acceptors using a slightly simplified version of the PHACIR atom types.

HBondAcceptorCountDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor

Constructor for the HBondAcceptorCountDescriptor object

HBondDonorCountDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

This descriptor calculates the number of hydrogen bond donors using a slightly simplified version of the PHACIR atom types.

HBondDonorCountDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor

Constructor for the HBondDonorCountDescriptor object

HE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

height() - Method in class org.openscience.cdk.graph.invariant.GIMatrix

Returns the number of lines of the matrix.

HELIUM - Static variable in class org.openscience.cdk.config.Elements

HELIX - Static variable in class org.openscience.cdk.protein.data.PDBStructure

HEN - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

HENICOS - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

HEPT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

hessianEigenValues(double[], int) - Method in class org.openscience.cdk.modeling.forcefield.NewtonRaphsonMethod

Calculate the eigen values for the hessian matrix.

HeterolyticCleavageMechanism - Class in org.openscience.cdk.reaction.mechanism

This mechanism displaces the chemical bond to an Atom.

HeterolyticCleavageMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.HeterolyticCleavageMechanism

HeterolyticCleavagePBReaction - Class in org.openscience.cdk.reaction.type

IReactionProcess which a bond is broken displacing the electron to one of the atoms.

HeterolyticCleavagePBReaction() - Constructor for class org.openscience.cdk.reaction.type.HeterolyticCleavagePBReaction

Constructor of the HeterolyticCleavagePBReaction object.

HeterolyticCleavageSBReaction - Class in org.openscience.cdk.reaction.type

IReactionProcess which a bond is broken displacing the electron to one of the atoms.

HeterolyticCleavageSBReaction() - Constructor for class org.openscience.cdk.reaction.type.HeterolyticCleavageSBReaction

Constructor of the HeterolyticCleavageSBReaction object.

HEX - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

HF - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

HG - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

HIGH - Static variable in class org.openscience.cdk.io.setting.IOSetting

The levels available: HIGH important question MEDIUM LOW unimportant question

HINFormat - Class in org.openscience.cdk.io.formats

See here.

HINReader - Class in org.openscience.cdk.io

Reads an object from HIN formated input.

HINReader(Reader) - Constructor for class org.openscience.cdk.io.HINReader

Construct a new reader from a Reader type object

HINReader(InputStream) - Constructor for class org.openscience.cdk.io.HINReader

HINReader() - Constructor for class org.openscience.cdk.io.HINReader

HINWriter - Class in org.openscience.cdk.io

Writer that outputs in the HIN format.

HINWriter(Writer) - Constructor for class org.openscience.cdk.io.HINWriter

Constructor.

HINWriter(OutputStream) - Constructor for class org.openscience.cdk.io.HINWriter

HINWriter() - Constructor for class org.openscience.cdk.io.HINWriter

HO - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

HOLMIUM - Static variable in class org.openscience.cdk.config.Elements

HOLMIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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.

HOSECodeAnalyser - Class in org.openscience.cdk.tools

Analyses a molecular formula given in String format and builds an AtomContainer with the Atoms in the molecular formula.

HOSECodeAnalyser() - Constructor for class org.openscience.cdk.tools.HOSECodeAnalyser

HOSECodeGenerator - Class in org.openscience.cdk.tools

Generates HOSE codes [Bremser, W., HOSE - A Novel Substructure Code, Analytica Chimica Acta, 1978, 103:355-365].

HOSECodeGenerator() - Constructor for class org.openscience.cdk.tools.HOSECodeGenerator

Constructor for the HOSECodeGenerator.

HuLuIndexTool - Class in org.openscience.cdk.graph.invariant

Collection of methods for the calculation of topological indices of a molecular graph.

HuLuIndexTool() - Constructor for class org.openscience.cdk.graph.invariant.HuLuIndexTool

HX - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

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.

HybridizationNumber() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

HybridizationNumberAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts

This matcher checks the hybridization state of an atom.

HybridizationNumberAtom(int) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.HybridizationNumberAtom

Creates a new instance

HYDROGEN - Static variable in class org.openscience.cdk.config.Elements

HydrogenAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts

This matches Hydrogen atoms.

HydrogenAtom() - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.HydrogenAtom

Creates a new instance.

HydrogenPlacer - Class in org.openscience.cdk.layout

This is a wrapper class for some existing methods in AtomPlacer.

HydrogenPlacer() - Constructor for class org.openscience.cdk.layout.HydrogenPlacer

HYDROXY - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

HyperconjugationReaction - Class in org.openscience.cdk.reaction.type

HyperconjugationReaction is the stabilizing interaction that results from the interaction of the electrons in a s-bond (for our case only C-H) with an adjacent empty (or partially filled) p-orbital.

HyperconjugationReaction() - Constructor for class org.openscience.cdk.reaction.type.HyperconjugationReaction

Constructor of the HyperconjugationReaction object

I

I - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

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.

IAtomParity - Interface in org.openscience.cdk.interfaces

Represents the concept of an atom parity identifying the stereochemistry around an atom, given four neighbouring atoms.

IAtomType - Interface in org.openscience.cdk.interfaces

The base class for atom types.

IAtomType.Hybridization - Enum in org.openscience.cdk.interfaces

IAtomTypeConfigurator - Interface in org.openscience.cdk.config

Interface that allows reading atom type configuration data from some source.

IAtomTypeGuesser - Interface in org.openscience.cdk.atomtype

Classes that implement this interface are atom type guessers.

IAtomTypeMatcher - Interface in org.openscience.cdk.atomtype

Classes that implement this interface are atom type matchers.

IBasis - Interface in org.openscience.cdk.math.qm

A basis set must implement this class.

IBioPolymer - Interface in org.openscience.cdk.interfaces

A BioPolymer is a subclass of a Polymer which is supposed to store additional informations about the Polymer which are connected to BioPolymers.

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

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.

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.

IChemModel - Interface in org.openscience.cdk.interfaces

An object containig 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 IChemObject 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 class is the interface that all IO readers should implement.

IChemObjectReader.Mode - Enum in org.openscience.cdk.io

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.

ICrystal - Interface in org.openscience.cdk.interfaces

Class representing a molecular crystal.

ID - Static variable in class org.openscience.cdk.templates.AminoAcids

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.

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.

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.

IFragmentAtom - Interface in org.openscience.cdk.interfaces

Class to represent an IPseudoAtom which embeds an IAtomContainer.

IFunction - Interface in org.openscience.cdk.math

A class, which has a function value should implement this interface.

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 - Interface in org.openscience.cdk.io.iterator

Interface for an iterating molecule reader.

ILonePair - Interface in org.openscience.cdk.interfaces

A LonePair is an orbital primarily located with one Atom, containing two electrons.

imag - Variable in class org.openscience.cdk.math.Complex

The imaginary part of this value

image - Variable in class org.openscience.cdk.iupac.parser.Token

The string image of the token.

image - Variable in class org.openscience.cdk.smiles.smarts.parser.Token

The string image of the token.

imageSuffix - Static variable in class org.openscience.cdk.renderer.JCPAction2D

Description of the Field

imagmatrix - Variable in class org.openscience.cdk.math.IMatrix

the imaginary part of the content

imagvector - Variable in class org.openscience.cdk.math.IVector

The imaginary part of this vector

IMapping - Interface in org.openscience.cdk.interfaces

Represents a mapping of two atoms.

IMatrix - Class in org.openscience.cdk.math

This class contains a complex matrix.

IMatrix(int, int) - Constructor for class org.openscience.cdk.math.IMatrix

Creates a complex matrix

IMatrix(Matrix) - Constructor for class org.openscience.cdk.math.IMatrix

Creates a complex copy of a matrix

IModel - Interface in org.openscience.cdk.qsar.model

Classes that implement this interface will build statistical models.

IMolecularDescriptor - Interface in org.openscience.cdk.qsar

Classes that implement this interface are QSAR descriptor calculators for IMolecule 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.

IMolecule - Interface in org.openscience.cdk.interfaces

Represents a set of Molecules.

IMoleculeSet - Interface in org.openscience.cdk.interfaces

Represents a set of Molecules.

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

ImplicitHCount() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

ImplicitHCountAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts

This matcher checks the number of implicit hydrogens of the Atom.

ImplicitHCountAtom(int) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.ImplicitHCountAtom

Creates a new instance

ImplicitHighAndBond() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

ImplicitHighAndExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

IN - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

INCHI - Static variable in class org.openscience.cdk.CDKConstants

The IUPAC International Chemical Identifier.

INChIContentProcessorTool - Class in org.openscience.cdk.io.inchi

Tool to help process INChI 1.12beta content.

INChIContentProcessorTool() - Constructor for class org.openscience.cdk.io.inchi.INChIContentProcessorTool

INChIFormat - Class in org.openscience.cdk.io.formats

See here.

InChIGenerator - Class in org.openscience.cdk.inchi

This class generates the IUPAC International Chemical Identifier (InChI) for a CDK IAtomContainer.

InChIGeneratorFactory - Class in org.openscience.cdk.inchi

Factory providing access to InChIGenerator and InChIToStructure.

InChIGeneratorFactory() - Constructor for class org.openscience.cdk.inchi.InChIGeneratorFactory

Constructor for InChIGeneratorFactory.

INChIHandler - Class in org.openscience.cdk.io.inchi

SAX2 implementation for INChI XML fragment parsing.

INChIHandler() - Constructor for class org.openscience.cdk.io.inchi.INChIHandler

Constructor for the IChIHandler.

INChIPlainTextFormat - Class in org.openscience.cdk.io.formats

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

InChIToStructure - Class in org.openscience.cdk.inchi

This class generates a CDK IAtomContainer from an InChI string.

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.

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.

IndexOutOfBoundsException - Exception in org.openscience.cdk.graph.invariant.exception

IndexOutOfBoundsException() - Constructor for exception org.openscience.cdk.graph.invariant.exception.IndexOutOfBoundsException

INDIUM - Static variable in class org.openscience.cdk.config.Elements

INDIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

InductiveAtomicHardnessDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic

Inductive atomic hardness of an atom in a polyatomic system can be defined as the "resistance" to a change of the atomic charge.

InductiveAtomicHardnessDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor

Constructor for the InductiveAtomicHardnessDescriptor object

InductiveAtomicSoftnessDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic

Inductive atomic softness of an atom in a polyatomic system can be defined as charge delocalizing ability.

InductiveAtomicSoftnessDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor

Constructor for the InductiveAtomicSoftnessDescriptor object

InductivePartialCharges - Class in org.openscience.cdk.charges

The calculation of the inductive partial atomic charges and equalization of effective electronegativities is based on [Cherkasov, A., Inductive Electronegativity Scale. Iterative Calculation of Inductive Partial Charges, J. Chem. Inf. Comput. Sci., 2003, 43:2039-2047].

InductivePartialCharges() - Constructor for class org.openscience.cdk.charges.InductivePartialCharges

Constructor for the InductivePartialCharges object

info(Object) - Method in class org.openscience.cdk.tools.LoggingTool

Shows INFO output for the Object.

info(Object, int) - Method in class org.openscience.cdk.tools.LoggingTool

Shows INFO output for the given Object's.

info(Object, double) - Method in class org.openscience.cdk.tools.LoggingTool

Shows INFO output for the given Object's.

info(Object, boolean) - Method in class org.openscience.cdk.tools.LoggingTool

Shows INFO output for the given Object's.

info(Object, Object) - Method in class org.openscience.cdk.tools.LoggingTool

Shows INFO output for the given Object's.

info(Object, Object, Object) - Method in class org.openscience.cdk.tools.LoggingTool

Shows INFO output for the given Object's.

info(Object, Object, Object, Object) - Method in class org.openscience.cdk.tools.LoggingTool

Shows INFO output for the given Object's.

info(Object, Object, Object, Object, Object) - Method in class org.openscience.cdk.tools.LoggingTool

Shows INFO output for the given Object's.

inherit(ICMLModule) - Method in class org.openscience.cdk.io.cml.CMLCoreModule

inherit(ICMLModule) - Method in interface org.openscience.cdk.io.cml.ICMLModule

initBookkeeping() - Method in class org.openscience.cdk.graph.AtomContainerPermutor

initialize(Map<String, List>) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94ParametersCall

Initialize the AtomOrder class.

initialize(GVector) - Method in class org.openscience.cdk.modeling.forcefield.ConjugateGradientMethod

Fletcher-Reeves: uk = gk gk / gk-1 gk-1

initialize(GVector, double, GVector, GVector, double, double) - Method in class org.openscience.cdk.modeling.forcefield.LineSearchForTheWolfeConditions

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.

initializeMinimizationParameters(GVector) - Method in class org.openscience.cdk.modeling.forcefield.GeometricMinimizer

initializeSpecifications(List<IDescriptor>) - Method in class org.openscience.cdk.qsar.DescriptorEngine

initiate(IMoleculeSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in interface org.openscience.cdk.reaction.IReactionMechanism

Initiates the process for the given mechanism.

initiate(IMoleculeSet, IMoleculeSet) - Method in interface org.openscience.cdk.reaction.IReactionProcess

Initiates the process for the given Reaction.

initiate(IMoleculeSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.AdductionLPMechanism

Initiates the process for the given mechanism.

initiate(IMoleculeSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.AdductionPBMechanism

Initiates the process for the given mechanism.

initiate(IMoleculeSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.HeterolyticCleavageMechanism

Initiates the process for the given mechanism.

initiate(IMoleculeSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.HomolyticCleavageMechanism

Initiates the process for the given mechanism.

initiate(IMoleculeSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.RadicalSiteIonizationMechanism

Initiates the process for the given mechanism.

initiate(IMoleculeSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.RadicalSiteRearrangementMechanism

Initiates the process for the given mechanism.

initiate(IMoleculeSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.RearrangementChargeMechanism

Initiates the process for the given mechanism.

initiate(IMoleculeSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.RemovingSEofBMechanism

Initiates the process for the given mechanism.

initiate(IMoleculeSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.RemovingSEofNBMechanism

Initiates the process for the given mechanism.

initiate(IMoleculeSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.SharingElectronMechanism

Initiates the process for the given mechanism.

initiate(IMoleculeSet, ArrayList<IAtom>, ArrayList<IBond>) - Method in class org.openscience.cdk.reaction.mechanism.TautomerizationMechanism

Initiates the process for the given mechanism.

initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.AdductionProtonLPReaction

Initiate process.

initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.AdductionProtonPBReaction

Initiate process.

initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.AdductionSodiumLPReaction

Initiate process.

initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.CarbonylEliminationReaction

Initiate process.

initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.ElectronImpactNBEReaction

Initiate process.

initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.ElectronImpactPDBReaction

Initiate process.

initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.ElectronImpactSDBReaction

Initiate process.

initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.HeterolyticCleavagePBReaction

Initiate process.

initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.HeterolyticCleavageSBReaction

Initiate process.

initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.HomolyticCleavageReaction

Initiate process.

initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.HyperconjugationReaction

Initiate process.

initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.PiBondingMovementReaction

Initiate process.

initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.RadicalChargeSiteInitiationHReaction

Initiate process.

initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.RadicalChargeSiteInitiationReaction

Initiate process.

initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrAlphaReaction

Initiate process.

initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrBetaReaction

Initiate process.

initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrDeltaReaction

Initiate process.

initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrGammaReaction

Initiate process.

initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteInitiationHReaction

Initiate process.

initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteInitiationReaction

Initiate process.

initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrAlphaReaction

Initiate process.

initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrBetaReaction

Initiate process.

initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrDeltaReaction

Initiate process.

initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrGammaReaction

Initiate process.

initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.RearrangementAnionReaction

Initiate process.

initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.RearrangementCationReaction

Initiate process.

initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.RearrangementLonePairReaction

Initiate process.

initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.RearrangementRadicalReaction

Initiate process.

initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.SharingAnionReaction

Initiate process.

initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.SharingChargeDBReaction

Initiate process.

initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.SharingChargeSBReaction

Initiate process.

initiate(IMoleculeSet, IMoleculeSet) - Method in class org.openscience.cdk.reaction.type.SharingLonePairReaction

Initiate process.

initiate(IMoleculeSet, IMoleculeSet) - 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

initObjectArray() - Method in class org.openscience.cdk.graph.AtomContainerAtomPermutor

initObjectArray() - Method in class org.openscience.cdk.graph.AtomContainerBondPermutor

inSameAromaticRing(IAtomContainer, IAtom, IAtom, IRingSet) - Static method in class org.openscience.cdk.atomtype.EStateAtomTypeMatcher

insertLeafChild(Node) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTLowAndExpression

instantiateDescriptors(List<String>) - Method in class org.openscience.cdk.qsar.DescriptorEngine

IntegerArrayResult - Class in org.openscience.cdk.qsar.result

IntegerArrayResult() - Constructor for class org.openscience.cdk.qsar.result.IntegerArrayResult

IntegerArrayResult(int) - Constructor for class org.openscience.cdk.qsar.result.IntegerArrayResult

IntegerArrayResultType - Class in org.openscience.cdk.qsar.result

IDescriptorResult type for booleans.

IntegerArrayResultType(int) - Constructor for class org.openscience.cdk.qsar.result.IntegerArrayResultType

IntegerDifference - Class in org.openscience.cdk.tools.diff.tree

IDifference between two Integer.

IntegerIOSetting - Class in org.openscience.cdk.io.setting

An class for a reader setting which must be of type String.

IntegerIOSetting(String, int, String, String) - Constructor for class org.openscience.cdk.io.setting.IntegerIOSetting

IntegerResult - Class in org.openscience.cdk.qsar.result

Object that provides access to the calculated descriptor value.

IntegerResult(int) - Constructor for class org.openscience.cdk.qsar.result.IntegerResult

IntegerResultType - Class in org.openscience.cdk.qsar.result

IDescriptorResult type for booleans.

IntegerResultType() - Constructor for class org.openscience.cdk.qsar.result.IntegerResultType

interp - Static variable in class org.openscience.cdk.qsar.model.R.RModel

Deprecated. This object represents an instance of the R interpreter.

intValue() - Method in class org.openscience.cdk.qsar.result.IntegerResult

InvalidSmilesException - Exception in org.openscience.cdk.exception

InvalidSmilesException(String) - Constructor for exception org.openscience.cdk.exception.InvalidSmilesException

InvalidSmilesException(String, Exception) - Constructor for exception org.openscience.cdk.exception.InvalidSmilesException

INVARIANCE_PAIR - Static variable in class org.openscience.cdk.smiles.InvPair

The description used to set the invariance numbers in the atom's property

inverse() - Method in class org.openscience.cdk.graph.invariant.GIMatrix

Returns the transpose of this matrix.

InverseSymbolSetQueryAtom - Class in org.openscience.cdk.isomorphism.matchers

A QueryAtom that matches all symbols but those in this container.

InverseSymbolSetQueryAtom() - Constructor for class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom

Constructor for the InverseSymbolSetQueryAtom object

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.

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

IODINE - Static variable in class org.openscience.cdk.config.Elements

IODO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

IonizationPotentialTool - Class in org.openscience.cdk.tools

This class contains the necessary information to predict ionization potential energy.

IonizationPotentialTool() - Constructor for class org.openscience.cdk.tools.IonizationPotentialTool

IOSetting - Class in org.openscience.cdk.io.setting

An interface for reader settings.

IOSetting(String, int, String, String) - Constructor for class org.openscience.cdk.io.setting.IOSetting

The default constructor that sets this field.

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 containg lone pair electrons.

IPAtomicHOSEDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor

Constructor for the IPAtomicHOSEDescriptor object.

IPAtomicLearningDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic

This class returns the ionization potential of an atom containing lone pair electrons.

IPAtomicLearningDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor

Constructor for the IPAtomicLearningDescriptor object.

IPBondLearningDescriptor - Class in org.openscience.cdk.qsar.descriptors.bond

This class returns the ionization potential of a Bond.

IPBondLearningDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor

Constructor for the IPBondLearningDescriptor object

IPDBAtom - Interface in org.openscience.cdk.interfaces

A PDBAtom is a subclass of a Atom which is supposed to store additional informations about the Atom

IPDBMonomer - Interface in org.openscience.cdk.interfaces

Represents the idea of an protein monomer as found in PDB files.

IPDBPolymer - Interface in org.openscience.cdk.interfaces

A PDBPolymer is a subclass of a BioPolymer which is supposed to store additional informations about the BioPolymer which are connected to BioPolymers.

IPDBStructure - Interface in org.openscience.cdk.interfaces

Represents the idea of an chemical structure.

IPMolecularLearningDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

This class returns the ionization potential of a molecule.

IPMolecularLearningDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor

Constructor for the IPMolecularLearningDescriptor object

IPolymer - Interface in org.openscience.cdk.interfaces

Subclass of Molecule to store Polymer specific attributes that a Polymer has.

IPotentialFunction - Interface in org.openscience.cdk.modeling.forcefield

Interface for a potential energy function to optimise in cdk/modeling/forcefield

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.

IR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

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

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.

IResourceFormat - Interface in org.openscience.cdk.io.formats

This class is the interface that all ResourceFormat's should implement.

IRIDIUM - Static variable in class org.openscience.cdk.config.Elements

IRIDIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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 class org.openscience.cdk.config.Elements

IRON - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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.

ISALIPHATIC - Static variable in class org.openscience.cdk.CDKConstants

Flag that is set if a chemobject is part of an aliphatic chain.

isAntisymmetric() - Method in class org.openscience.cdk.graph.invariant.GIMatrix

Verifies if the matrix is antisymmetric, that is if the matrix is equal to the opposite of it's transpose.

isAromatic(IRing, IAtomContainer) - Static method in class org.openscience.cdk.aromaticity.AromaticityCalculator

Tests the ring in the molecule for aromaticity.

ISAROMATIC - Static variable in class org.openscience.cdk.CDKConstants

Flag is set if chemobject is part of an aromatic system.

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.

isCisTrans(IAtom, IAtom, IAtom, IAtom, IAtomContainer) - Static method in class org.openscience.cdk.geometry.BondTools

Says if two atoms are in cis or trans position around a double bond.

isClockwise() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom

isClockwise() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTChirality

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.

isConnectedTo(IBond) - Method in class org.openscience.cdk.Bond

Checks whether a bond is connected to another one.

isConnectedTo(IBond) - Method in class org.openscience.cdk.debug.DebugBond

isConnectedTo(IBond) - Method in interface org.openscience.cdk.interfaces.IBond

Checks whether a bond is connected to another one.

isDebugEnabled() - Method in class org.openscience.cdk.tools.LoggingTool

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

isElement(String) - Method in class org.openscience.cdk.config.IsotopeFactory

Checks whether the given element exists.

isEmpty() - Method in class org.openscience.cdk.ConformerContainer

Checks whether any conformers are stored or not.

isEnabled() - Method in class org.openscience.cdk.renderer.JCPAction2D

Is this action runnable?

isEven(int) - Static method in class org.openscience.cdk.math.MathTools

isExpanded() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

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.

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.

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 - Static variable in class org.openscience.cdk.CDKConstants

Flag that is set when the chemobject is part of a ring.

isInterrupted() - Method in class org.openscience.cdk.smiles.DeduceBondSystemTool

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) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester

Tests if g1 and g2 are isomorph.

isIsomorphic(IMolecule, IMolecule) - 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 contruction time

isIsomorphic(IMolecule) - 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 contruction 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

isOdd(int) - Static method in class org.openscience.cdk.math.MathTools

isOfClass(String, String) - Method in class org.openscience.cdk.qsar.model.R2.RModel

Checks whether the class of a named object is of the specified class.

isOK(IMolecule) - Method in class org.openscience.cdk.smiles.DeduceBondSystemTool

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(IMolecule) - Constructor for class org.openscience.cdk.isomorphism.IsomorphismTester

Constructor for the IsomorphismTester object

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.

IsotopeContainer - Class in org.openscience.cdk.formula

This class defines a isotope container.

IsotopeContainer() - Constructor for class org.openscience.cdk.formula.IsotopeContainer

Constructor of the IsotopeContainer object.

IsotopeContainer(IMolecularFormula, double) - Constructor for class org.openscience.cdk.formula.IsotopeContainer

Constructor of the IsotopeContainer object setting a IMolecularFormula object and intensity value.

IsotopeContainer(double, double) - Constructor for class org.openscience.cdk.formula.IsotopeContainer

Constructor of the IsotopeContainer object setting a mass and intensity value.

IsotopeDiff - Class in org.openscience.cdk.tools.diff

Compares two IIsotope classes.

IsotopeDiff() - Constructor for class org.openscience.cdk.tools.diff.IsotopeDiff

IsotopeFactory - Class in org.openscience.cdk.config

Used to store and return data of a particular isotope.

IsotopeHandler - Class in org.openscience.cdk.config.isotopes

Reads an isotope list in CML2 format.

IsotopeHandler(IChemObjectBuilder) - Constructor for class org.openscience.cdk.config.isotopes.IsotopeHandler

Constructs an IsotopeHandler used by the IsotopeReader.

IsotopePattern - Class in org.openscience.cdk.formula

This class defines the properties of a deisotoped pattern distribution.

IsotopePattern() - Constructor for class org.openscience.cdk.formula.IsotopePattern

Constructor of the IsotopePattern object.

IsotopePatternGenerator - Class in org.openscience.cdk.formula

Generates all Combinatorial chemical isotopes given a structure.

IsotopePatternGenerator() - Constructor for class org.openscience.cdk.formula.IsotopePatternGenerator

Constructor for the IsotopeGenerator.

IsotopePatternGenerator(double) - Constructor for class org.openscience.cdk.formula.IsotopePatternGenerator

Constructor for the IsotopeGenerator.

IsotopePatternManipulator - Class in org.openscience.cdk.formula

Class to manipulate IsotopePattern objects.

IsotopePatternManipulator() - Constructor for class org.openscience.cdk.formula.IsotopePatternManipulator

IsotopePatternRule - Class in org.openscience.cdk.formula.rules

This class validate if the Isotope Pattern from a given IMolecularFormula correspond with other to compare.

IsotopePatternRule() - Constructor for class org.openscience.cdk.formula.rules.IsotopePatternRule

Constructor for the IsotopePatternRule object.

IsotopePatternSimilarity - Class in org.openscience.cdk.formula

This class gives a score hit of similarity between two different isotope abundance pattern.

IsotopePatternSimilarity() - Constructor for class org.openscience.cdk.formula.IsotopePatternSimilarity

Constructor for the IsotopePatternSimilarity object.

IsotopeReader - Class in org.openscience.cdk.config.isotopes

Reader that instantiates an XML parser and customized handler to process the isotope information in the CML2 isotope data file.

IsotopeReader(InputStream, IChemObjectBuilder) - Constructor for class org.openscience.cdk.config.isotopes.IsotopeReader

Instantiates a new reader that parses the XML from the given input.

isotopes() - Method in class org.openscience.cdk.debug.DebugAdductFormula

isotopes() - Method in class org.openscience.cdk.debug.DebugMolecularFormula

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.

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).

isPopupAction() - Method in class org.openscience.cdk.renderer.JCPAction2D

Gets the popupAction attribute of the JCPAction object

isPositive() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTCharge

Returns true if charge is positive.

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

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.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.

isSmilesToUpperCase() - Method in class org.openscience.cdk.tools.GenerateFragments

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.

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.

isSubgraph(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester

Tests if g2 a subgraph of g1.

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.

isTetrahedral(IAtomContainer, IAtom, boolean) - Static method in class org.openscience.cdk.geometry.BondTools

Says if an atom as a center of a tetrahedral chirality.

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.

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

isUnsaturated(IBond, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker

Returns whether a bond is unsaturated.

isUnsaturated(IBond, IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker

Returns whether a bond is unsaturated.

isUnspecified() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom

isUnspecified() - Method in class org.openscience.cdk.smiles.smarts.parser.ASTChirality

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.

isValidDoubleBondConfiguration(IAtomContainer, IBond) - Method in class org.openscience.cdk.smiles.SmilesGenerator

Tells if a certain bond is center of a valid double bond configuration.

isValidSum(IMolecularFormula) - Method in class org.openscience.cdk.formula.MolecularFormulaChecker

Validate if a IMolecularFormula is valid.

isXMLBased() - Method in class org.openscience.cdk.io.formats.ABINITFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.Aces2Format

isXMLBased() - Method in class org.openscience.cdk.io.formats.ADFFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.AlchemyFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.BGFFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.BSFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.CACheFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format

isXMLBased() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format

isXMLBased() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.CIFFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.CMLFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.CRK2DFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.CRK3DFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.CrystClustFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.CTXFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.DaltonFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.DMol3Format

isXMLBased() - Method in class org.openscience.cdk.io.formats.DOCK5Format

isXMLBased() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.FingerprintFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.GamessFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.Gaussian03Format

isXMLBased() - Method in class org.openscience.cdk.io.formats.Gaussian90Format

isXMLBased() - Method in class org.openscience.cdk.io.formats.Gaussian92Format

isXMLBased() - Method in class org.openscience.cdk.io.formats.Gaussian94Format

isXMLBased() - Method in class org.openscience.cdk.io.formats.Gaussian95Format

isXMLBased() - Method in class org.openscience.cdk.io.formats.Gaussian98Format

isXMLBased() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.GROMOS96Format

isXMLBased() - Method in class org.openscience.cdk.io.formats.HINFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.INChIFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat

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

isXMLBased() - Method in class org.openscience.cdk.io.formats.JMEFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.MacroModelFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.MDLFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format

isXMLBased() - Method in class org.openscience.cdk.io.formats.MDLV2000Format

isXMLBased() - Method in class org.openscience.cdk.io.formats.MDLV3000Format

isXMLBased() - Method in class org.openscience.cdk.io.formats.MMODFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.Mol2Format

isXMLBased() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format

isXMLBased() - Method in class org.openscience.cdk.io.formats.MOPAC7Format

isXMLBased() - Method in class org.openscience.cdk.io.formats.MOPAC93Format

isXMLBased() - Method in class org.openscience.cdk.io.formats.MOPAC97Format

isXMLBased() - Method in class org.openscience.cdk.io.formats.MPQCFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.NWChemFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.PCModelFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.PDBFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.PDBMLFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.PMPFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.POVRayFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.PQSChemFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.QChemFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.RawCopyFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.SDFFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.ShelXFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.SMARTSFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.SMILESFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.SpartanFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.SVGFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format

isXMLBased() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.VASPFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.ViewmolFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.XEDFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.XYZFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.YasaraFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.ZindoFormat

isXMLBased() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat

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

IteratingMDLReader - Class in org.openscience.cdk.io.iterator

Iterating MDL SDF reader.

IteratingMDLReader(Reader, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingMDLReader

Constructs a new IteratingMDLReader that can read Molecule from a given Reader.

IteratingMDLReader(InputStream, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingMDLReader

Contructs a new IteratingMDLReader that can read Molecule from a given InputStream.

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.

IteratingSMILESReader - Class in org.openscience.cdk.io.iterator

Iterating SMILES file reader.

IteratingSMILESReader(Reader, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingSMILESReader

Contructs a new IteratingSMILESReader that can read Molecule from a given Reader.

IteratingSMILESReader(InputStream) - Constructor for class org.openscience.cdk.io.iterator.IteratingSMILESReader

Contructs a new IteratingSMILESReader that can read Molecule from a given InputStream.

IteratingSMILESReader(InputStream, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingSMILESReader

Contructs a new IteratingSMILESReader that can read Molecule from a given InputStream and IChemObjectBuilder.

iterator() - Method in class org.openscience.cdk.ConformerContainer

Gets an iterator over the conformers.

iterator() - Method in class org.openscience.cdk.debug.DebugAdductFormula

iterator() - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet

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.

IValencyChecker - Interface in org.openscience.cdk.tools

A common interface for SaturationChecker and ValencyChecker.

IValidator - Interface in org.openscience.cdk.validate

Interface that Validators need to implement to be used in validation.

IVector - Class in org.openscience.cdk.math

IVector(int) - Constructor for class org.openscience.cdk.math.IVector

Constructs a vector with "size"-elements

IViewEventRelay - Interface in org.openscience.cdk.controller

IWriterListener - Interface in org.openscience.cdk.io.listener

Allows monitoring of progress of writing activities.

J

JaguarFormat - Class in org.openscience.cdk.io.formats

See here.

JCPAction2D - Class in org.openscience.cdk.renderer

Superclass of all JChemPaint GUI actions

JCPAction2D(JFrame, String, boolean) - Constructor for class org.openscience.cdk.renderer.JCPAction2D

Constructor for the JCPAction object

JCPAction2D(JFrame, boolean) - Constructor for class org.openscience.cdk.renderer.JCPAction2D

Constructor for the JCPAction object

JCPAction2D(JFrame) - Constructor for class org.openscience.cdk.renderer.JCPAction2D

Constructor for the JCPAction object

JCPAction2D() - Constructor for class org.openscience.cdk.renderer.JCPAction2D

Constructor for the JCPAction object

jj_nt - Variable in class org.openscience.cdk.iupac.parser.NomParser

jj_nt - Variable in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

jjstrLiteralImages - Static variable in class org.openscience.cdk.iupac.parser.NomParserTokenManager

jjstrLiteralImages - Static variable in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTAliphatic

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTAnyAtom

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTAromatic

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTAtom

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTAtomicMass

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTAtomicNumber

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTCharge

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTChirality

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTElement

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTExplicitAtom

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTExplicitConnectivity

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTExplicitHighAndBond

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTExplicitHighAndExpression

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTGroup

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTHybrdizationNumber

Accept the visitor.

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTImplicitHCount

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTImplicitHighAndBond

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTImplicitHighAndExpression

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTLowAndBond

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTLowAndExpression

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTNonCHHeavyAtom

Accept the visitor.

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTNotBond

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTNotExpression

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTOrBond

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTOrExpression

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTPeriodicGroupNumber

Accept the visitor.

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTPrimitiveAtomExpression

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTReaction

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTRecursiveSmartsExpression

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTRingConnectivity

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTRingIdentifier

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTRingMembership

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTSimpleBond

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTSmallestRingSize

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTSmarts

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTStart

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTTotalConnectivity

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTTotalHCount

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTValence

jjtAccept(SMARTSParserVisitor, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.Node

Accept the visitor.

jjtAccept(SMARTSParserVisitor, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleNode

Accept the visitor.

jjtAddChild(Node, int) - Method in interface org.openscience.cdk.smiles.smarts.parser.Node

This method tells the node to add its argument to the node's list of children.

jjtAddChild(Node, int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleNode

JJTALIPHATIC - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTANYATOM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTAROMATIC - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTATOM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTATOMICMASS - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTATOMICNUMBER - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTCHARGE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTCHIRALITY - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

jjtClose() - Method in interface org.openscience.cdk.smiles.smarts.parser.Node

This method is called after all the child nodes have been added.

jjtClose() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleNode

JJTELEMENT - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTEXPLICITATOM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTEXPLICITCONNECTIVITY - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTEXPLICITHIGHANDBOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTEXPLICITHIGHANDEXPRESSION - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

jjtGetChild(int) - Method in interface org.openscience.cdk.smiles.smarts.parser.Node

This method returns a child node.

jjtGetChild(int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleNode

jjtGetNumChildren() - Method in interface org.openscience.cdk.smiles.smarts.parser.Node

Return the number of children the node has.

jjtGetNumChildren() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleNode

jjtGetParent() - Method in interface org.openscience.cdk.smiles.smarts.parser.Node

jjtGetParent() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleNode

JJTGROUP - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTHYBRDIZATIONNUMBER - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTIMPLICITHCOUNT - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTIMPLICITHIGHANDBOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTIMPLICITHIGHANDEXPRESSION - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTLOWANDBOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTLOWANDEXPRESSION - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

jjtNodeName - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTNONCHHEAVYATOM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTNOTBOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTNOTEXPRESSION - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

jjtOpen() - Method in interface org.openscience.cdk.smiles.smarts.parser.Node

This method is called after the node has been made the current node.

jjtOpen() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleNode

JJTORBOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTOREXPRESSION - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTPERIODICGROUPNUMBER - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTREACTION - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTRECURSIVESMARTSEXPRESSION - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

jjtRemoveChild(int) - Method in interface org.openscience.cdk.smiles.smarts.parser.Node

Removes a child from this node

jjtRemoveChild(int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleNode

JJTRINGCONNECTIVITY - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTRINGIDENTIFIER - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTRINGMEMBERSHIP - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

jjtSetParent(Node) - Method in interface org.openscience.cdk.smiles.smarts.parser.Node

This pair of methods are used to inform the node of its parent.

jjtSetParent(Node) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleNode

JJTSIMPLEBOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTSMALLESTRINGSIZE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTSMARTS - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTSMARTSParserState - Class in org.openscience.cdk.smiles.smarts.parser

JJTSTART - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTTOTALCONNECTIVITY - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTTOTALHCOUNT - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTVALENCE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTVOID - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JMEFormat - Class in org.openscience.cdk.io.formats

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

join(Path, Path, IAtom) - Static method in class org.openscience.cdk.ringsearch.Path

Joins two paths.

K

K - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

KabschAlignment - Class in org.openscience.cdk.geometry.alignment

Aligns two structures to minimize the RMSD using the Kabsch algorithm.

KabschAlignment(Atom[], Atom[]) - Constructor for class org.openscience.cdk.geometry.alignment.KabschAlignment

Sets up variables for the alignment algorithm.

KabschAlignment(Atom[], Atom[], 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

KierHallSmartsDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

A fragment count descriptor that uses e-state fragments.

KierHallSmartsDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor

kind - Variable in class org.openscience.cdk.iupac.parser.Token

An integer that describes the kind of this token.

kind - Variable in class org.openscience.cdk.smiles.smarts.parser.Token

An integer that describes the kind of this token.

KNOWN_ELEMENTS - Static variable in class org.openscience.cdk.config.Symbols

KR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

KRYPTON - Static variable in class org.openscience.cdk.config.Elements

L

L_AND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

L_BRACKET - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

L_PAREN - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

LA - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

labelSuffix - Static variable in class org.openscience.cdk.renderer.JCPAction2D

Description of the Field

LANTHANUM - Static variable in class org.openscience.cdk.config.Elements

LANTHANUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

LARGE_FIRST - Static variable in class org.openscience.cdk.RingSet

Flag to denote that the set is order with the largest ring first?

LARGE_FIRST - Static variable in class org.openscience.cdk.tools.manipulator.RingSizeComparator

Flag to denote that the set is order with the largest ring first

LargestChainDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

Class that returns the number of atoms in the largest chain.

LargestChainDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor

Constructor for the LargestChain object.

LargestPiSystemDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

Class that returns the number of atoms in the largest pi system.

LargestPiSystemDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor

Constructor for the LargestPiSystemDescriptor object.

last() - Method in interface org.openscience.cdk.io.random.IRandomAccessChemObjectReader

last() - Method in class org.openscience.cdk.io.random.RandomAccessReader

lastIndexOf(Object) - Method in class org.openscience.cdk.ConformerContainer

Returns the highest index at which the specific IAtomContainer appears in the list or -1 if is not found.

LAWRENCIUM - Static variable in class org.openscience.cdk.config.Elements

LAWRENCIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

LEAD - Static variable in class org.openscience.cdk.config.Elements

LEAD - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

length() - Method in class org.openscience.cdk.io.cml.CMLStack

length() - Method in class org.openscience.cdk.math.Vector

Return the length from this vector

length() - Method in class org.openscience.cdk.qsar.result.BooleanResultType

length() - Method in class org.openscience.cdk.qsar.result.DoubleArrayResult

length() - Method in class org.openscience.cdk.qsar.result.DoubleArrayResultType

length() - Method in class org.openscience.cdk.qsar.result.DoubleResult

length() - Method in class org.openscience.cdk.qsar.result.DoubleResultType

length() - Method in interface org.openscience.cdk.qsar.result.IDescriptorResult

Returns the length of this descriptor.

length() - Method in class org.openscience.cdk.qsar.result.IntegerArrayResult

length() - Method in class org.openscience.cdk.qsar.result.IntegerArrayResultType

length() - Method in class org.openscience.cdk.qsar.result.IntegerResult

length() - Method in class org.openscience.cdk.qsar.result.IntegerResultType

LengthOverBreadthDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

Evaluates length over breadth descriptors.

LengthOverBreadthDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor

Constructor for the LengthOverBreadthDescriptor object.

lexStateNames - Static variable in class org.openscience.cdk.iupac.parser.NomParserTokenManager

lexStateNames - Static variable in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager

LI - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

linearFunctionInAlphaOptimum - Variable in class org.openscience.cdk.modeling.forcefield.LineSearchForTheWolfeConditions

LinearRegressionModel - Class in org.openscience.cdk.qsar.model.R

Deprecated.

LinearRegressionModel() - Constructor for class org.openscience.cdk.qsar.model.R.LinearRegressionModel

Deprecated. Constructs a LinearRegressionModel object.

LinearRegressionModel(double[][], double[]) - Constructor for class org.openscience.cdk.qsar.model.R.LinearRegressionModel

Deprecated. Constructs a LinearRegressionModel object.

LinearRegressionModel(double[][], double[], double[]) - Constructor for class org.openscience.cdk.qsar.model.R.LinearRegressionModel

Deprecated. Constructs a LinearRegressionModel object.

LinearRegressionModel - Class in org.openscience.cdk.qsar.model.R2

A modeling class that provides a linear least squares regression model.

LinearRegressionModel() - Constructor for class org.openscience.cdk.qsar.model.R2.LinearRegressionModel

Constructs a LinearRegressionModel object.

LinearRegressionModel(double[][], double[]) - Constructor for class org.openscience.cdk.qsar.model.R2.LinearRegressionModel

Constructs a LinearRegressionModel object.

LinearRegressionModel(double[][], double[], double[]) - Constructor for class org.openscience.cdk.qsar.model.R2.LinearRegressionModel

Constructs a LinearRegressionModel object.

LinearRegressionModelFit - Class in org.openscience.cdk.qsar.model.R

Deprecated.

LinearRegressionModelFit(double[], double[], double[], int, int) - Constructor for class org.openscience.cdk.qsar.model.R.LinearRegressionModelFit

Deprecated. Construct the object to contain a linear regression fit.

LinearRegressionModelPredict - Class in org.openscience.cdk.qsar.model.R

Deprecated.

LinearRegressionModelPredict(double[], double[], double[], double[], int, double) - Constructor for class org.openscience.cdk.qsar.model.R.LinearRegressionModelPredict

Deprecated. Construct the object to contain linear regression predictions.

LinearRegressionModelPredict(double, double, double, double, int, double) - Constructor for class org.openscience.cdk.qsar.model.R.LinearRegressionModelPredict

Deprecated. Construct the object to contain linear regression predictions.

LinearRegressionModelSummary - Class in org.openscience.cdk.qsar.model.R

Deprecated.

LinearRegressionModelSummary(double[], double[], double, double, double, int, double[], String[], String[]) - Constructor for class org.openscience.cdk.qsar.model.R.LinearRegressionModelSummary

Deprecated. Constructor for an object that wraps the return value from summary.lm.

LineSearch - Class in org.openscience.cdk.modeling.forcefield

The LineSearch class include the first and second step of the line search approach: Bracket the minimum and interpolation.

LineSearch() - Constructor for class org.openscience.cdk.modeling.forcefield.LineSearch

Constructor for the LineSearch object

lineSearchAlgorithm(double) - Method in class org.openscience.cdk.modeling.forcefield.LineSearchForTheWolfeConditions

LineSearchForTheWolfeConditions - Class in org.openscience.cdk.modeling.forcefield

LineSearchForTheWolfeConditions(IPotentialFunction, String) - Constructor for class org.openscience.cdk.modeling.forcefield.LineSearchForTheWolfeConditions

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

listIterator() - Method in class org.openscience.cdk.ConformerContainer

listIterator(int) - Method in class org.openscience.cdk.ConformerContainer

listNumbers(IAtomContainer, IAtomContainer) - 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, Vector) - 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 class org.openscience.cdk.config.Elements

LITHIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

LITHO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

loadModel(String) - Method in class org.openscience.cdk.qsar.model.R.CNNClassificationModel

Deprecated. Loads a CNNRegresionModel object from disk in to the current session.

loadModel(String, String) - Method in class org.openscience.cdk.qsar.model.R.CNNClassificationModel

Deprecated. Loads an CNNClassificationModel object from a serialized string into the current session.

loadModel(String) - Method in class org.openscience.cdk.qsar.model.R.CNNRegressionModel

Deprecated. Loads a CNNRegresionModel object from disk in to the current session.

loadModel(String, String) - Method in class org.openscience.cdk.qsar.model.R.CNNRegressionModel

Deprecated. Loads an CNNRegressionModel object from a serialized string into the current session.

loadModel(String) - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModel

Deprecated. Loads an LinearRegressionModel object from disk in to the current session.

loadModel(String, String) - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModel

Deprecated. Loads an LinearRegressionModel object from a serialized string into the current session.

loadModel(String) - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModel

Deprecated. Loads a PLSRegressionModel object from disk in to the current session.

loadModel(String, String) - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModel

Deprecated. Loads an PLSRegressionModel object from a serialized string into the current session.

loadModel(String) - Method in class org.openscience.cdk.qsar.model.R.RModel

Deprecated. Abstract method to handle loading R models.

loadModel(String, String) - Method in class org.openscience.cdk.qsar.model.R.RModel

Deprecated. Abstract method to handle loading R models that were previously serialized.

loadModel(String) - Method in class org.openscience.cdk.qsar.model.R2.CNNRegressionModel

Loads a 'nnet' object from disk in to the current session.

loadModel(String, String) - Method in class org.openscience.cdk.qsar.model.R2.CNNRegressionModel

Loads a 'nnet' object from a serialized string into the current session.

loadModel(String) - Method in class org.openscience.cdk.qsar.model.R2.LinearRegressionModel

Loads an LinearRegressionModel object from disk in to the current session.

loadModel(String, String) - Method in class org.openscience.cdk.qsar.model.R2.LinearRegressionModel

Loads an LinearRegressionModel object from a serialized string into the current session.

loadModel(String) - Method in class org.openscience.cdk.qsar.model.R2.RModel

Abstract method to handle loading R models.

loadModel(String, String) - Method in class org.openscience.cdk.qsar.model.R2.RModel

Abstract method to handle loading R models that were previously serialized.

loadMolecule(String) - Static method in class org.openscience.cdk.templates.MoleculeFactory

loadTemplates(IChemObjectBuilder) - Method in class org.openscience.cdk.layout.TemplateHandler

Loads all existing templates into memory.

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.

LogicalOperatorAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts

This class matches a logical operator that connects two query atoms

LogicalOperatorAtom() - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom

LogicalOperatorBond - Class in org.openscience.cdk.isomorphism.matchers.smarts

This class matches a logical operator that connects two query bonds.

LogicalOperatorBond() - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond

LONE_PAIR_COUNT - Static variable in class org.openscience.cdk.CDKConstants

Used as property key for indicating the HOSE code for a certain atom type.

LonePair - Class in org.openscience.cdk

A LonePair is an orbital primarily located with one Atom, containing two electrons.

LonePair() - Constructor for class org.openscience.cdk.LonePair

Constructs an unconnected lone pair.

LonePair(IAtom) - Constructor for class org.openscience.cdk.LonePair

Constructs an lone pair on an Atom.

LonePairDiff - Class in org.openscience.cdk.tools.diff

Compares two ILonePair classes.

LonePairDiff() - Constructor for class org.openscience.cdk.tools.diff.LonePairDiff

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

Constructor of the LonePairElectronChecker object.

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

lonePairs() - Method in class org.openscience.cdk.debug.DebugAtomContainer

lonePairs() - Method in class org.openscience.cdk.debug.DebugBioPolymer

lonePairs() - Method in class org.openscience.cdk.debug.DebugCrystal

lonePairs() - Method in class org.openscience.cdk.debug.DebugMolecule

lonePairs() - Method in class org.openscience.cdk.debug.DebugMonomer

lonePairs() - Method in class org.openscience.cdk.debug.DebugPolymer

lonePairs() - Method in class org.openscience.cdk.debug.DebugRing

lonePairs() - Method in class org.openscience.cdk.debug.DebugStrand

lonePairs() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns an Iterable for looping over all lone pairs in this container.

LongestAliphaticChainDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

Class that returns the number of atoms in the longest aliphatic chain.

LongestAliphaticChainDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor

Constructor for the LongestAliphaticChainDescriptor object.

lookingAhead - Variable in class org.openscience.cdk.iupac.parser.NomParser

lookingAhead - Variable in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

LOW - Static variable in class org.openscience.cdk.io.setting.IOSetting

LowAndBond() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

LowAndExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

LR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

LU - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

LUTETIUM - Static variable in class org.openscience.cdk.config.Elements

LUTETIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

M

MACCSFingerprinter - Class in org.openscience.cdk.fingerprint

This fingerprinter generates 166 bit MACCS keys.

MACCSFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.MACCSFingerprinter

MacroModelFormat - Class in org.openscience.cdk.io.formats

mag() - Method in class org.openscience.cdk.math.Quaternion

mag_sq() - Method in class org.openscience.cdk.math.Quaternion

MAGNESIUM - Static variable in class org.openscience.cdk.config.Elements

MAGNESIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

main(String[]) - Static method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor

mainChainConstruct() - Method in class org.openscience.cdk.iupac.parser.NomParser

Main chains are compulsary and consist of an optional "cyclo", a length prefix and a posfix denoting functional groups.

mainChainPrefix() - Method in class org.openscience.cdk.iupac.parser.NomParser

Deal with the main chain's length.

mainChainSuffix() - Method in class org.openscience.cdk.iupac.parser.NomParser

Figure out the functional group by the main chain's suffix.

make123Triazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory

Returns 1,2,3-triazole without explicit hydrogens.

make124Triazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory

Returns 1,2,4-triazole without explicit hydrogens.

make4x3CondensedRings() - Static method in class org.openscience.cdk.templates.MoleculeFactory

makeAdenine() - Static method in class org.openscience.cdk.templates.MoleculeFactory

makeAlkane(int) - Static method in class org.openscience.cdk.templates.MoleculeFactory

Generate an Alkane (chain of carbons with no hydrogens) of a given length.

makeAlphaPinene() - Static method in class org.openscience.cdk.templates.MoleculeFactory

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.

makeAzulene() - Static method in class org.openscience.cdk.templates.MoleculeFactory

Returns azulene without explicit hydrogens.

makeBenzene() - Static method in class org.openscience.cdk.templates.MoleculeFactory

makeBicycloRings() - Static method in class org.openscience.cdk.templates.MoleculeFactory

makeBiphenyl() - Static method in class org.openscience.cdk.templates.MoleculeFactory

Returns biphenyl without explicit hydrogens.

makeBranchedAliphatic() - Static method in class org.openscience.cdk.templates.MoleculeFactory

makeBremserCompliant(String) - Method in class org.openscience.cdk.tools.HOSECodeGenerator

makeCanonicalSmileFromRingSystems(String, String) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor

makeCyclobutadiene() - Static method in class org.openscience.cdk.templates.MoleculeFactory

Returns cyclobutadiene without explicit hydrogens.

makeCyclobutane() - Static method in class org.openscience.cdk.templates.MoleculeFactory

Returns cyclobutane without explicit hydrogens.

makeCyclohexane() - Static method in class org.openscience.cdk.templates.MoleculeFactory

Returns cyclohexane without explicit hydrogens.

makeCyclohexene() - Static method in class org.openscience.cdk.templates.MoleculeFactory

Returns cyclohexene without explicit hydrogens.

makeDiamantane() - Static method in class org.openscience.cdk.templates.MoleculeFactory

makeEthylCyclohexane() - Static method in class org.openscience.cdk.templates.MoleculeFactory

makeEthylPropylPhenantren() - Static method in class org.openscience.cdk.templates.MoleculeFactory

makeFingerprintFromRingSystems(String, String, boolean, boolean) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor

makeFingerprintsFromSdf(boolean, boolean, Map, BufferedReader, int) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor

makeFusedRings() - Static method in class org.openscience.cdk.templates.MoleculeFactory

makeImidazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory

Returns imidazole without explicit hydrogens.

makeIndole() - Static method in class org.openscience.cdk.templates.MoleculeFactory

Returns indole without explicit hydrogens.

makeIsothiazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory

Returns isothiazole without explicit hydrogens.

makeIsoxazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory

Returns Isoxazole without explicit hydrogens.

makeMethylDecaline() - Static method in class org.openscience.cdk.templates.MoleculeFactory

makeOxadiazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory

Returns oxadiazole without explicit hydrogens.

makeOxazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory

Returns Oxazole without explicit hydrogens.

makePhenylAmine() - Static method in class org.openscience.cdk.templates.MoleculeFactory

makePhenylEthylBenzene() - Static method in class org.openscience.cdk.templates.MoleculeFactory

makePiperidine() - Static method in class org.openscience.cdk.templates.MoleculeFactory

makePropylCycloPropane() - Static method in class org.openscience.cdk.templates.MoleculeFactory

makePyrazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory

Returns pyrazole without explicit hydrogens.

makePyridazine() - Static method in class org.openscience.cdk.templates.MoleculeFactory

Returns pyridazine without explicit hydrogens.

makePyridine() - Static method in class org.openscience.cdk.templates.MoleculeFactory

Returns pyridine without explicit hydrogens.

makePyridineOxide() - Static method in class org.openscience.cdk.templates.MoleculeFactory

Returns pyridine oxide without explicit hydrogens.

makePyrimidine() - Static method in class org.openscience.cdk.templates.MoleculeFactory

Returns pyrimidine without explicit hydrogens.

makePyrrole() - Static method in class org.openscience.cdk.templates.MoleculeFactory

Returns pyrrole without explicit hydrogens.

makePyrroleAnion() - Static method in class org.openscience.cdk.templates.MoleculeFactory

Returns pyrrole anion without explicit hydrogens.

makeQuinone() - Static method in class org.openscience.cdk.templates.MoleculeFactory

makeReferencesExplicit(IChemObject) - Static method in class org.openscience.cdk.dict.CDKDictionaryReferences

makeSingleRing() - Static method in class org.openscience.cdk.templates.MoleculeFactory

makeSpiroRings() - Static method in class org.openscience.cdk.templates.MoleculeFactory

makeSteran() - Static method in class org.openscience.cdk.templates.MoleculeFactory

makeStereocenter(Point3d, IBond, Point3d, Point3d, Point3d[]) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

set Atoms in respect to stereoinformation.

makeTetrahydropyran() - Static method in class org.openscience.cdk.templates.MoleculeFactory

makeTetrazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory

Returns tetrazole without explicit hydrogens.

makeThiadiazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory

Returns thiadiazole without explicit hydrogens.

makeThiazole() - Static method in class org.openscience.cdk.templates.MoleculeFactory

Returns thiazole without explicit hydrogens.

makeTriazine() - Static method in class org.openscience.cdk.templates.MoleculeFactory

Returns triazine without explicit hydrogens.

makeUpDownBonds(IAtomContainer) - Static method in class org.openscience.cdk.geometry.BondTools

MANGANESE - Static variable in class org.openscience.cdk.config.Elements

MANGANESE - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

mapAtomsOfAlignedStructures(IAtomContainer, IAtomContainer, double, Map<Integer, Integer>) - Static method in class org.openscience.cdk.geometry.GeometryTools

Returns a Map with the AtomNumbers, the first number corresponds to the first (or the largest AtomContainer) atomcontainer.

mapAtomsOfAlignedStructures(IAtomContainer, IAtomContainer, 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

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.

mappings() - Method in interface org.openscience.cdk.interfaces.IReaction

Returns the mappings between the reactant and the product side.

mappings() - Method in class org.openscience.cdk.Reaction

Returns the mappings between the reactant and the product side.

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

Checks if one of the loaded templates is a substructure in the given Molecule.

markAromaticRings(IRing) - Static method in class org.openscience.cdk.tools.manipulator.RingManipulator

Marks the ring aromatic if all atoms and all bonds are aromatic.

markAromaticRings(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator

Iterates over the rings in the ring set, and marks the ring aromatic if all atoms and all bonds are aromatic.

markNotPlaced(IAtomContainer) - Method in class org.openscience.cdk.layout.AtomPlacer

Marks all the atoms in the given AtomContainer as not placed

markPlaced(IAtomContainer) - 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 (CDKConstant ISPLACED)

markWithError(IChemObject) - Static method in class org.openscience.cdk.validate.ProblemMarker

markWithWarning(IChemObject) - Static method in class org.openscience.cdk.validate.ProblemMarker

MASS_ELECTRON - Static variable in class org.openscience.cdk.PhysicalConstants

Mass of an electron.

MASS_PROTON - Static variable in class org.openscience.cdk.PhysicalConstants

Mass of a proton.

MassAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts

This class matches an atom based on the atomic mass.

MassAtom(int) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.MassAtom

Creates a new instance

MassToFormulaTool - Class in org.openscience.cdk.formula

Tool to determine molecular formula consistent with a given accurate mass.

MassToFormulaTool(IChemObjectBuilder) - Constructor for class org.openscience.cdk.formula.MassToFormulaTool

Construct an instance of MassToFormulaTool.

matches(int, String) - Method in class org.openscience.cdk.io.formats.ABINITFormat

matches(int, String) - Method in class org.openscience.cdk.io.formats.Aces2Format

matches(int, String) - Method in class org.openscience.cdk.io.formats.ADFFormat

matches(int, String) - Method in class org.openscience.cdk.io.formats.CACheFormat

matches(int, String) - Method in class org.openscience.cdk.io.formats.CIFFormat

matches(int, String) - Method in class org.openscience.cdk.io.formats.CMLFormat

matches(int, String) - Method in class org.openscience.cdk.io.formats.CrystClustFormat

matches(int, String) - Method in class org.openscience.cdk.io.formats.CTXFormat

matches(int, String) - Method in class org.openscience.cdk.io.formats.DaltonFormat

matches(int, String) - Method in class org.openscience.cdk.io.formats.GamessFormat

matches(int, String) - Method in class org.openscience.cdk.io.formats.Gaussian03Format

matches(int, String) - Method in class org.openscience.cdk.io.formats.Gaussian90Format

matches(int, String) - Method in class org.openscience.cdk.io.formats.Gaussian92Format

matches(int, String) - Method in class org.openscience.cdk.io.formats.Gaussian94Format

matches(int, String) - Method in class org.openscience.cdk.io.formats.Gaussian95Format

matches(int, String) - Method in class org.openscience.cdk.io.formats.Gaussian98Format

matches(int, String) - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat

matches(int, String) - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat

matches(int, String) - Method in class org.openscience.cdk.io.formats.HINFormat

matches(int, String) - Method in interface org.openscience.cdk.io.formats.IChemFormatMatcher

Method that checks whether the given line is part of the format read by this reader.

matches(int, String) - Method in class org.openscience.cdk.io.formats.INChIFormat

matches(int, String) - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat

matches(int, String) - Method in class org.openscience.cdk.io.formats.JaguarFormat

matches(int, String) - Method in class org.openscience.cdk.io.formats.MDLFormat

matches(int, String) - Method in class org.openscience.cdk.io.formats.MDLRXNFormat

matches(int, String) - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format

matches(int, String) - Method in class org.openscience.cdk.io.formats.MDLV2000Format

matches(int, String) - Method in class org.openscience.cdk.io.formats.MDLV3000Format

matches(int, String) - Method in class org.openscience.cdk.io.formats.Mol2Format

matches(int, String) - Method in class org.openscience.cdk.io.formats.MOPAC2002Format

matches(int, String) - Method in class org.openscience.cdk.io.formats.MOPAC7Format

matches(int, String) - Method in class org.openscience.cdk.io.formats.MOPAC93Format

matches(int, String) - Method in class org.openscience.cdk.io.formats.MOPAC97Format

matches(int, String) - Method in class org.openscience.cdk.io.formats.NWChemFormat

matches(int, String) - Method in class org.openscience.cdk.io.formats.PDBFormat

matches(int, String) - Method in class org.openscience.cdk.io.formats.PMPFormat

matches(int, String) - Method in class org.openscience.cdk.io.formats.PubChemASNFormat

matches(int, String) - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat

matches(int, String) - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat

matches(int, String) - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat

matches(int, String) - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat

matches(int, String) - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat

matches(int, String) - Method in class org.openscience.cdk.io.formats.QChemFormat

matches(int, String) - Method in class org.openscience.cdk.io.formats.SDFFormat

matches(int, String) - Method in class org.openscience.cdk.io.formats.ShelXFormat

matches(int, String) - Method in class org.openscience.cdk.io.formats.SpartanFormat

matches(int, String) - Method in class org.openscience.cdk.io.formats.VASPFormat

matches(int, String) - Method in class org.openscience.cdk.io.formats.ZMatrixFormat

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom

The matches implementation of the QueryAtom interface.

matches(IAtom) - Method in interface org.openscience.cdk.isomorphism.matchers.IQueryAtom

Returns true of the given atom matches this IQueryAtom.

matches(IBond) - Method in interface org.openscience.cdk.isomorphism.matchers.IQueryBond

Returns true of the given bond matches this IQueryBond.

matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.OrderQueryBond

matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.OrderQueryBondOrderOnly

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AliphaticAtom

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AliphaticSymbolAtom

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AnyAtom

matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AnyOrderQueryBond

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AromaticAtom

matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AromaticOrSingleQueryBond

matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AromaticQueryBond

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AromaticSymbolAtom

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AtomicNumberAtom

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ConnectionCountAtom

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.DegreeAtom

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ExplicitConnectionAtom

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.FormalChargeAtom

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.HybridizationNumberAtom

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.HydrogenAtom

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ImplicitHCountAtom

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom

matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.MassAtom

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.NonCHHeavyAtom

matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.OrderQueryBond

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.PeriodicGroupNumberAtom

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RecursiveSmartsAtom

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RingAtom

matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RingBond

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RingIdentifierAtom

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RingMembershipAtom

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.SmallestRingAtom

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom

matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.SMARTSBond

matches(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.StereoBond

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.TotalConnectionAtom

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.TotalHCountAtom

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.TotalRingConnectionAtom

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.TotalValencyAtom

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolAndChargeQueryAtom

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolChargeIDQueryAtom

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom

matches(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom

The matches implementation of the QueryAtom interface.

matches(IAtomContainer) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher

Performs the pharmacophore matching.

matches(IAtomContainer, boolean) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher

Performs the pharmacophore matching.

matches(IBond) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryAngleBond

Checks whether the query angle constraint matches a target distance.

matches(IAtom) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryAtom

Checks whether this query atom matches a target atom.

matches(IBond) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryBond

Checks whether the query distance constraint matches a target distance.

matches(IAtomContainer) - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool

Perform a SMARTS match and check whether the query is present in the target molecule.

matches(IAtomContainer, boolean) - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool

Perform a SMARTS match and check whether the query is present in the target molecule.

MathTools - Class in org.openscience.cdk.math

Class providing convenience methods for simple mathematical operations.

MathTools() - Constructor for class org.openscience.cdk.math.MathTools

Matrix - Class in org.openscience.cdk.math

This class contains a matrix.

Matrix(int, int) - Constructor for class org.openscience.cdk.math.Matrix

Creates a new Matrix.

Matrix(double[][]) - Constructor for class org.openscience.cdk.math.Matrix

Creates a Matrix with content of an array.

matrix - Variable in class org.openscience.cdk.math.Matrix

the content of this matrix

MatrixNotInvertibleException - Exception in org.openscience.cdk.graph.invariant.exception

MatrixNotInvertibleException() - Constructor for exception org.openscience.cdk.graph.invariant.exception.MatrixNotInvertibleException

max(double[]) - Static method in class org.openscience.cdk.math.MathTools

Analog of Math.max that returns the largest double value in an array of dpubles.

max(int[]) - Static method in class org.openscience.cdk.math.MathTools

Analog of Math.max that returns the largest int value in an array of ints

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.

MD - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

mdec11 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

mdec12 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

mdec13 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

mdec14 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

mdec22 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

mdec23 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

mdec24 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

mdec33 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

mdec34 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

mdec44 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

MDEDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

Calculates the Molecular Distance Edge descriptor described in [Liu, S. and Cao, C. and Li, Z. , Approach to Estimation and Prediction for Normal Boiling Point (NBP) of Alkanes Based on a Novel Molecular Distance Edge (MDE) Vector, lambda, Journal of Chemical Information and Computer Sciences, 1998, 38:387-394].

MDEDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

mden11 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

mden12 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

mden13 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

mden22 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

mden23 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

mden33 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

mdeo11 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

mdeo12 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

mdeo22 - Static variable in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

MDLFormat - Class in org.openscience.cdk.io.formats

See here.

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

Reads a molecule from the original MDL MOL or SDF file [Dalby, A. and Nourse, J. G. and Hounshell, W. D. and Gushurst, A. K. and Grier, D. L. and Leland, B. A. and Laufer, J., Description of Several Chemical Structure File Formats Used by Computer Programs Developed at Molecular Design Limited, Journal of Chemical Information and Computer Sciences, 1992, 32:244-255].

MDLReader() - Constructor for class org.openscience.cdk.io.MDLReader

MDLReader(InputStream) - Constructor for class org.openscience.cdk.io.MDLReader

Constructs a new MDLReader that can read Molecule from a given InputStream.

MDLReader(InputStream, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLReader

MDLReader(Reader) - Constructor for class org.openscience.cdk.io.MDLReader

Constructs a new MDLReader that can read Molecule from a given Reader.

MDLReader(Reader, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLReader

MDLRXNFormat - Class in org.openscience.cdk.io.formats

See here.

MDLRXNReader - Class in org.openscience.cdk.io

Reads a molecule from an MDL RXN file [Dalby, A. and Nourse, J. G. and Hounshell, W. D. and Gushurst, A. K. and Grier, D. L. and Leland, B. A. and Laufer, J., Description of Several Chemical Structure File Formats Used by Computer Programs Developed at Molecular Design Limited, Journal of Chemical Information and Computer Sciences, 1992, 32:244-255].

MDLRXNReader(Reader) - Constructor for class org.openscience.cdk.io.MDLRXNReader

Contructs a new MDLReader that can read Molecule from a given Reader.

MDLRXNReader(Reader, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLRXNReader

MDLRXNReader(InputStream) - Constructor for class org.openscience.cdk.io.MDLRXNReader

MDLRXNReader(InputStream, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLRXNReader

MDLRXNReader() - Constructor for class org.openscience.cdk.io.MDLRXNReader

MDLRXNV2000Reader - Class in org.openscience.cdk.io

Reads a molecule from an MDL RXN file [Dalby, A. and Nourse, J. G. and Hounshell, W. D. and Gushurst, A. K. and Grier, D. L. and Leland, B. A. and Laufer, J., Description of Several Chemical Structure File Formats Used by Computer Programs Developed at Molecular Design Limited, Journal of Chemical Information and Computer Sciences, 1992, 32:244-255].

MDLRXNV2000Reader(Reader) - Constructor for class org.openscience.cdk.io.MDLRXNV2000Reader

Contructs 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.

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

Contructs a new MDLWriter that can write an array of Molecules to a Writer.

MDLRXNWriter(OutputStream) - Constructor for class org.openscience.cdk.io.MDLRXNWriter

Contructs 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

MDLV2000Reader - Class in org.openscience.cdk.io

Reads a molecule from an MDL MOL or SDF file [Dalby, A. and Nourse, J. G. and Hounshell, W. D. and Gushurst, A. K. and Grier, D. L. and Leland, B. A. and Laufer, J., Description of Several Chemical Structure File Formats Used by Computer Programs Developed at Molecular Design Limited, Journal of Chemical Information and Computer Sciences, 1992, 32:244-255].

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

Contructs a new MDLReader that can read Molecule from a given Reader.

MDLV2000Reader(Reader, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLV2000Reader

MDLV3000Format - Class in org.openscience.cdk.io.formats

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

MDLWriter - Class in org.openscience.cdk.io

Writes MDL molfiles, which contains a single molecule.

MDLWriter(Writer) - Constructor for class org.openscience.cdk.io.MDLWriter

Constructs a new MDLWriter that can write an IMolecule to the MDL molfile format.

MDLWriter(OutputStream) - Constructor for class org.openscience.cdk.io.MDLWriter

Constructs a new MDLWriter that can write an IMolecule to a given OutputStream.

MDLWriter() - Constructor for class org.openscience.cdk.io.MDLWriter

MDMolecule - Class in org.openscience.cdk.libio.md

MDMolecule() - Constructor for class org.openscience.cdk.libio.md.MDMolecule

MDMolecule(IAtomContainer) - Constructor for class org.openscience.cdk.libio.md.MDMolecule

MDMoleculeConvention - Class in org.openscience.cdk.io.cml

Implements a Convention for parsing an MDMolecule from CML.

MDMoleculeConvention(IChemFile) - Constructor for class org.openscience.cdk.io.cml.MDMoleculeConvention

MDMoleculeConvention(ICMLModule) - Constructor for class org.openscience.cdk.io.cml.MDMoleculeConvention

MDMoleculeCustomizer - Class in org.openscience.cdk.libio.cml

Customize persistence of MDMolecule by adding support for residues and charge groups.

MDMoleculeCustomizer() - Constructor for class org.openscience.cdk.libio.cml.MDMoleculeCustomizer

mechanism - Variable in class org.openscience.cdk.reaction.ReactionEngine

MECURY - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

MEDIUM - Static variable in class org.openscience.cdk.io.setting.IOSetting

MEITMERIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

MEITNERIUM - Static variable in class org.openscience.cdk.config.Elements

MENDELEVIUM - Static variable in class org.openscience.cdk.config.Elements

MENDELEVIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

MERCURY - Static variable in class org.openscience.cdk.config.Elements

METH - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

MG - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

min(double[]) - Static method in class org.openscience.cdk.math.MathTools

Analog of Math.min that returns the largest double value in an array of double.

min(int[]) - Static method in class org.openscience.cdk.math.MathTools

Analog of Math.max that returns the largest int value in an array of ints

MinimalPathIterator - Class in org.openscience.cdk.graph

Iterates over all shortest paths between two vertices in an undirected, unweighted graph.

MinimalPathIterator(SimpleGraph, Object, Object) - Constructor for class org.openscience.cdk.graph.MinimalPathIterator

Creates a minimal path iterator for the specified undirected graph.

minimize() - Method in class org.openscience.cdk.modeling.forcefield.ForceField

MM2AtomTypeMatcher - Class in org.openscience.cdk.atomtype

Class implements methods to assign mmff94 atom types for a specific atom in an molecule.

MM2AtomTypeMatcher() - Constructor for class org.openscience.cdk.atomtype.MM2AtomTypeMatcher

Constructor for the MMFF94AtomTypeMatcher object.

MM2BasedAtomTypePattern - Class in org.openscience.cdk.modeling.builder3d

Class stores hose code patterns to identify mm2 force field atom types.

MM2BasedParameterSetReader - Class in org.openscience.cdk.modeling.builder3d

AtomType list configurator that uses the ParameterSet originally defined in mm2.prm from tinker.

MM2BasedParameterSetReader() - Constructor for class org.openscience.cdk.modeling.builder3d.MM2BasedParameterSetReader

Constructor for the MM2BasedParameterSetReader object.

MMElementRule - Class in org.openscience.cdk.formula.rules

This class validate if the occurrence of the IElements in the IMolecularFormula, for metabolites, are into a maximal limit according paper: .

MMElementRule() - Constructor for class org.openscience.cdk.formula.rules.MMElementRule

Constructor for the MMElementRule object.

MMElementRule.Database - Enum in org.openscience.cdk.formula.rules

A enumeration of the possible databases according the rules

MMElementRule.RangeMass - Enum in org.openscience.cdk.formula.rules

A enumeration of the possible mass range according the rules

MMFF94AtomTypeMatcher - Class in org.openscience.cdk.atomtype

Class implements methods to assign mmff94 atom types for a specific atom in an molecule.

MMFF94AtomTypeMatcher() - Constructor for class org.openscience.cdk.atomtype.MMFF94AtomTypeMatcher

Constructor for the MMFF94AtomTypeMatcher object.

MMFF94BasedAtomTypePattern - Class in org.openscience.cdk.modeling.builder3d

Class stores hose code patterns to identify mm2 force field atom types

MMFF94BasedParameterSetReader - Class in org.openscience.cdk.modeling.builder3d

AtomType list configurator that uses the ParameterSet originally defined in mmff94.prm from moe.

MMFF94BasedParameterSetReader() - Constructor for class org.openscience.cdk.modeling.builder3d.MMFF94BasedParameterSetReader

Constructor for the MM2BasedParameterSetReader object

MMFF94EnergyFunction - Class in org.openscience.cdk.modeling.forcefield

MMFF94 energy function.

MMFF94EnergyFunction(IAtomContainer, Map) - Constructor for class org.openscience.cdk.modeling.forcefield.MMFF94EnergyFunction

Constructor for the MMFF94EnergyFunction object

MMFF94ParametersCall - Class in org.openscience.cdk.modeling.builder3d

Set the right atoms order to get the parameters.

MMFF94ParametersCall() - Constructor for class org.openscience.cdk.modeling.builder3d.MMFF94ParametersCall

MMFF94PartialCharges - Class in org.openscience.cdk.charges

The calculation of the MMFF94 partial charges.

MMFF94PartialCharges() - Constructor for class org.openscience.cdk.charges.MMFF94PartialCharges

Constructor for the MMFF94PartialCharges object

MMODFormat - Class in org.openscience.cdk.io.formats

See here.

MN - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

MO - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

ModelBuilder3D - Class in org.openscience.cdk.modeling.builder3d

The main class to generate the 3D coordinates of a molecule ModelBuilder3D.

Mol2Format - Class in org.openscience.cdk.io.formats

See here.

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

Contructs 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 - Static variable in class org.openscience.cdk.qsar.DescriptorEngine

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.

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.

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

molecularFormulas() - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet

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.

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).

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 - Class in org.openscience.cdk

Represents the concept of a chemical molecule, an object composed of atoms connected by bonds.

Molecule() - Constructor for class org.openscience.cdk.Molecule

Creates an Molecule without Atoms and Bonds.

Molecule(int, int, int, int) - Constructor for class org.openscience.cdk.Molecule

Constructor for the Molecule object.

Molecule(IAtomContainer) - Constructor for class org.openscience.cdk.Molecule

Constructs a Molecule with a shallow copy of the atoms and bonds of an AtomContainer.

MoleculeBuilder - Class in org.openscience.cdk.iupac.parser

Takes in parsed Tokens from NomParser and contains rules to convert those tokens to a Molecule.

MoleculeBuilder() - Constructor for class org.openscience.cdk.iupac.parser.MoleculeBuilder

MoleculeFactory - Class in org.openscience.cdk.templates

This class contains methods for generating simple organic molecules.

MoleculeFactory() - Constructor for class org.openscience.cdk.templates.MoleculeFactory

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

MoleculeGraphs - Class in org.openscience.cdk.graph

Utility class to create a molecule graph for use with jgrapht.

molecules() - Method in class org.openscience.cdk.debug.DebugMoleculeSet

molecules() - Method in interface org.openscience.cdk.interfaces.IMoleculeSet

Returns the array of Molecules of this container.

molecules() - Method in class org.openscience.cdk.MoleculeSet

Returns the array of Molecules of this container.

MoleculeSet - Class in org.openscience.cdk

A set of molecules, for example those taking part in a reaction.

MoleculeSet() - Constructor for class org.openscience.cdk.MoleculeSet

MoleculeSetManipulator - Class in org.openscience.cdk.tools.manipulator

MoleculeSetManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator

MOLYBDENUM - Static variable in class org.openscience.cdk.config.Elements

MOLYBDENUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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.

MOPAC2002Format - Class in org.openscience.cdk.io.formats

MOPAC7Format - Class in org.openscience.cdk.io.formats

MOPAC93Format - Class in org.openscience.cdk.io.formats

MOPAC97Format - Class in org.openscience.cdk.io.formats

MorganNumbersTools - Class in org.openscience.cdk.graph.invariant

Tool for calculating Morgan numbers [Morgan, H.L., The Generation of a Unique Machine Description for Chemical Structures - A Technique Developed at Chemical Abstracts Service., J.Chem.Doc., 1965, 5:107-113].

MorganNumbersTools() - Constructor for class org.openscience.cdk.graph.invariant.MorganNumbersTools

mouseClicked(MouseEvent) - Method in class org.openscience.cdk.controller.SwingMouseEventRelay

mouseClickedDouble(int, int) - Method in interface org.openscience.cdk.controller.IMouseEventRelay

mouseClickedDown(int, int) - Method in interface org.openscience.cdk.controller.IMouseEventRelay

mouseClickedUp(int, int) - Method in interface org.openscience.cdk.controller.IMouseEventRelay

mouseDrag(int, int, int, int) - Method in interface org.openscience.cdk.controller.IMouseEventRelay

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

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

MPQCFormat - Class in org.openscience.cdk.io.formats

See here.

mul(Complex) - Method in class org.openscience.cdk.math.Complex

Multiply this value with a complex value

mul(IMatrix) - Method in class org.openscience.cdk.math.IMatrix

Multiplikation from two matrices

mul(IMatrix, IMatrix) - Method in class org.openscience.cdk.math.IMatrix

Multiplikation from two matrices

mul(IVector) - Method in class org.openscience.cdk.math.IMatrix

Multiplikation from a vector and a matrix

mul(IVector, IVector) - Method in class org.openscience.cdk.math.IMatrix

Multiplikation from a vector and a matrix

mul(Complex) - Method in class org.openscience.cdk.math.IMatrix

Multiplikation from a scalar and a matrix

mul(Complex, IMatrix) - Method in class org.openscience.cdk.math.IMatrix

Multiplikation from a scalar and a matrix

mul(double) - Method in class org.openscience.cdk.math.IVector

Multiplication from a vectors with an double

mul(double, IVector) - Method in class org.openscience.cdk.math.IVector

Multiplication from a vectors with an double

mul(Matrix) - Method in class org.openscience.cdk.math.Matrix

Multiplies this Matrix with another one.

mul(Vector) - Method in class org.openscience.cdk.math.Matrix

Multiplies a Vector with this Matrix.

mul(double) - Method in class org.openscience.cdk.math.Matrix

Multiplies a scalar with this Matrix.

mul(Quaternion) - Method in class org.openscience.cdk.math.Quaternion

mul(double) - Method in class org.openscience.cdk.math.Quaternion

mul(double) - Method in class org.openscience.cdk.math.Vector

Multiplikation from a vectors with an double

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 matricial multiplication of this matrix by another one.

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.

mutate(IAtomContainer) - Method in class org.openscience.cdk.structgen.RandomGenerator

Randomly chooses four atoms and alters the bonding pattern between them according to rules described in "Faulon, JCICS 1996, 36, 731".

N

n - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

N - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

NA - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

NAMES - Static variable in class org.openscience.cdk.CDKConstants

A List of names.

naturalAbundance - Variable in class org.openscience.cdk.Isotope

Natural abundance of this isotope.

NB - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

ND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

NE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

negate() - Method in class org.openscience.cdk.math.Quaternion

negate() - Method in class org.openscience.cdk.math.Vector

Negates this vector

NeighborList - Class in org.openscience.cdk.geometry.surface

Creates a list of atoms neighboring each atom in the molecule.

NeighborList(IAtom[], double) - Constructor for class org.openscience.cdk.geometry.surface.NeighborList

NEODYMIUM - Static variable in class org.openscience.cdk.config.Elements

NEODYMIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

NEON - Static variable in class org.openscience.cdk.config.Elements

NEPTUNIUM - Static variable in class org.openscience.cdk.config.Elements

NEPTUNIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

newAdductFormula() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newAdductFormula(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newAdductFormula() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newAdductFormula(IMolecularFormula) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newAdductFormula() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

newAdductFormula(IMolecularFormula) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

newAdductFormula() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newAdductFormula(IMolecularFormula) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newAminoAcid() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newAminoAcid() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newAminoAcid() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an completely unset IAminoAcid.

newAminoAcid() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newAtom() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newAtom(String) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newAtom(String, Point2d) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newAtom(String, Point3d) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newAtom(IElement) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newAtom() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newAtom(String) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newAtom(String, Point2d) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newAtom(String, Point3d) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newAtom(IElement) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newAtom() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an completely unset IAtom.

newAtom(IElement) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an IAtom from a String containing an element symbol.

newAtom(String) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an IAtom from a String containing an element symbol.

newAtom(String, Point2d) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an IAtom from an Element and a Point2d.

newAtom(String, Point3d) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an IAtom from an Element and a Point3d.

newAtom() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newAtom(String) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newAtom(String, Point2d) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newAtom(String, Point3d) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newAtom(IElement) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newAtomContainer() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newAtomContainer(int, int, int, int) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newAtomContainer() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newAtomContainer(int, int, int, int) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newAtomContainer() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an empty IAtomContainer.

newAtomContainer(int, int, int, int) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an empty IAtomContainer that will contain a certain number of atoms and electronContainers.

newAtomContainer(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an IAtomContainer with a copy of the atoms and electronContainers of another IAtomContainer (A shallow copy, i.e., with the same objects as in the original IAtomContainer).

newAtomContainer() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newAtomContainer(int, int, int, int) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newAtomContainerSet() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newAtomContainerSet() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newAtomContainerSet() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an empty IAtomContainerSet.

newAtomContainerSet() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newAtomParity(IAtom, IAtom, IAtom, IAtom, IAtom, int) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newAtomParity(IAtom, IAtom, IAtom, IAtom, IAtom, int) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newAtomParity(IAtom, IAtom, IAtom, IAtom, IAtom, int) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an IAtomParity.

newAtomParity(IAtom, IAtom, IAtom, IAtom, IAtom, int) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newAtomType(String) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newAtomType(String, String) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newAtomType(IElement) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newAtomType(String) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newAtomType(String, String) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newAtomType(IElement) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newAtomType(String) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructor for the IAtomType object.

newAtomType(String, String) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructor for the IAtomType object.

newAtomType(IElement) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an IAtomType from a String containing an element symbol.

newAtomType(String) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newAtomType(String, String) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newAtomType(IElement) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newBioPolymer() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newBioPolymer() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newBioPolymer() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Contructs a new IBioPolymer to store the IStrands.

newBioPolymer() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newBond() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newBond(IAtom, IAtom, IBond.Order) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newBond(IAtom, IAtom, IBond.Order, int) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newBond(IAtom[]) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newBond(IAtom[], IBond.Order) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newBond() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newBond(IAtom, IAtom) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newBond(IAtom, IAtom, IBond.Order) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newBond(IAtom, IAtom, IBond.Order, int) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newBond(IAtom[]) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newBond(IAtom[], IBond.Order) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newBond() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an empty IBond.

newBond(IAtom, IAtom) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs a IBond with a single bond order..

newBond(IAtom, IAtom, IBond.Order) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs a IBond with a given order.

newBond(IAtom, IAtom, IBond.Order, int) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs a IBond with a given order and stereo orientation from an array of atoms.

newBond(IAtom[]) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constrcts a IBond with multiple atoms and undefined order and orientation.

newBond(IAtom[], IBond.Order) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constrcts a IBond with multiple atoms and defined order and undefined orientation.

newBond() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newBond(IAtom, IAtom) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newBond(IAtom, IAtom, IBond.Order) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newBond(IAtom, IAtom, IBond.Order, int) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newBond(IAtom[]) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newBond(IAtom[], IBond.Order) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newChemFile() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newChemFile() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newChemFile() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an empty IChemFile.

newChemFile() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newChemModel() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newChemModel() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newChemModel() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an new IChemModel with a null IMoleculeSet.

newChemModel() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newChemModel(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator

Create a new ChemModel containing an IAtomContainer.

newChemObject() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newChemObject(IChemObject) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newChemObject() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newChemObject(IChemObject) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newChemObject() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an new IChemObject.

newChemObject(IChemObject) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an new IChemObject from an existing one.

newChemObject() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newChemObject(IChemObject) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newChemSequence() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newChemSequence() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newChemSequence() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an empty IChemSequence.

newChemSequence() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newCrystal() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newCrystal(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newCrystal() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newCrystal(IAtomContainer) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newCrystal() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs a new ICrystal with zero length cell axis.

newCrystal(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs a new ICrystal with zero length cell axis and adds the atoms in the IAtomContainer as cell content.

newCrystal() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newCrystal(IAtomContainer) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newElectronContainer() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newElectronContainer() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newElectronContainer() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an empty IElectronContainer.

newElectronContainer() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newElement() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newElement(String) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newElement(String, int) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newElement(IElement) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newElement() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newElement(String) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newElement(String, int) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newElement(IElement) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newElement() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an empty IElement.

newElement(IElement) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an empty IElement from an existing IElement.

newElement(String) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an IElement with a given element symbol.

newElement(String, int) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an IElement with a given element symbol, atomic number and atomic mass.

newElement() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newElement(String) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newElement(String, int) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newElement(IElement) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newFragmentAtom() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newFragmentAtom() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newFragmentAtom() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs a IFragmentAtom.

newFragmentAtom() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newIsotope(String) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newIsotope(int, String, int, double, double) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newIsotope(int, String, double, double) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newIsotope(String, int) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newIsotope(IElement) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newIsotope(String) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newIsotope(int, String, int, double, double) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newIsotope(int, String, double, double) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newIsotope(String, int) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newIsotope(IElement) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newIsotope(String) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructor for the IIsotope object.

newIsotope(IElement) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an IIsotope object from an existing IIsotope.

newIsotope(int, String, int, double, double) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructor for the IIsotope object.

newIsotope(int, String, double, double) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructor for the IIsotope object.

newIsotope(String, int) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructor for the IIsotope object.

newIsotope(String) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newIsotope(int, String, int, double, double) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newIsotope(int, String, double, double) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newIsotope(String, int) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newIsotope(IElement) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newLonePair() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newLonePair(IAtom) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newLonePair() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newLonePair(IAtom) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newLonePair() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an unconnected ILonePair.

newLonePair(IAtom) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an ILonePair on an IAtom.

newLonePair() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newLonePair(IAtom) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newMapping(IChemObject, IChemObject) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newMapping(IChemObject, IChemObject) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newMapping(IChemObject, IChemObject) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Creates a directional IMapping between IChemObject's.

newMapping(IChemObject, IChemObject) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newMolecularFormula() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newMolecularFormula() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newMolecularFormula() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

newMolecularFormula() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newMolecularFormulaSet() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newMolecularFormulaSet(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newMolecularFormulaSet() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newMolecularFormulaSet(IMolecularFormula) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newMolecularFormulaSet() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

newMolecularFormulaSet(IMolecularFormula) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

newMolecularFormulaSet() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newMolecularFormulaSet(IMolecularFormula) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newMolecule() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newMolecule(int, int, int, int) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newMolecule(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newMolecule() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newMolecule(int, int, int, int) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newMolecule(IAtomContainer) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newMolecule() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Creates an IMolecule without any IAtoms and IBonds.

newMolecule(int, int, int, int) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructor for the IMolecule object.

newMolecule(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an IMolecule with a shallow copy of the atoms and bonds of an IAtomContainer.

newMolecule() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newMolecule(int, int, int, int) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newMolecule(IAtomContainer) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newMoleculeSet() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newMoleculeSet() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newMoleculeSet() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an empty IMoleculeSet.

newMoleculeSet() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newMonomer() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newMonomer() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newMonomer() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs a new IMonomer.

newMonomer() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newPDBAtom(IElement) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newPDBAtom(String) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newPDBAtom(String, Point3d) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newPDBAtom(IElement) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newPDBAtom(String) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newPDBAtom(String, Point3d) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newPDBAtom(IElement) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an IPDBAtom from a IElement.

newPDBAtom(String) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an IPDBAtom from a String containing an element symbol.

newPDBAtom(String, Point3d) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an IPDBAtom from an Element and a Point3d.

newPDBAtom(IElement) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newPDBAtom(String) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newPDBAtom(String, Point3d) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newPDBMonomer() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newPDBMonomer() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newPDBMonomer() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an IPDBMonomer.

newPDBMonomer() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newPDBPolymer() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newPDBPolymer() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newPDBPolymer() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Contructs a new IPDBPolymer to store the IStrands.

newPDBPolymer() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newPDBStructure() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newPDBStructure() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newPDBStructure() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an IPDBStructure.

newPDBStructure() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newPolymer() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newPolymer() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newPolymer() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs a new IPolymer to store the IMonomers.

newPolymer() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newPseudoAtom() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newPseudoAtom(String) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newPseudoAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newPseudoAtom(String, Point3d) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newPseudoAtom(String, Point2d) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newPseudoAtom(IElement) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newPseudoAtom() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newPseudoAtom(String) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newPseudoAtom(IAtom) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newPseudoAtom(String, Point3d) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newPseudoAtom(String, Point2d) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newPseudoAtom(IElement) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newPseudoAtom() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an empty IPseudoAtom.

newPseudoAtom(String) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an IPseudoAtom from a label.

newPseudoAtom(IElement) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an IPseudoAtom from an existing IAtom object.

newPseudoAtom(String, Point3d) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an IPseudoAtom from a label and a Point3d.

newPseudoAtom(String, Point2d) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an IPseudoAtom from a label and a Point2d.

newPseudoAtom() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newPseudoAtom(String) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newPseudoAtom(IAtom) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newPseudoAtom(String, Point3d) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newPseudoAtom(String, Point2d) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newPseudoAtom(IElement) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newReaction() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newReaction() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newReaction() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an empty, forward IReaction.

newReaction() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newReactionScheme() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newReactionScheme() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newReactionScheme() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an empty IReactionScheme.

newReactionScheme() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newReactionSet() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newReactionSet() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newReactionSet() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an empty IReactionSet.

newReactionSet() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newRing() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newRing(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newRing(int, String) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newRing(int) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newRing() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newRing(IAtomContainer) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newRing(int, String) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newRing(int) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newRing() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an empty IRing.

newRing(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs a IRing from an IAtomContainer.

newRing(int, String) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs a ring that will have a certain number of atoms of the given elements.

newRing(int) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an empty IRing that will have a certain size.

newRing() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newRing(IAtomContainer) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newRing(int, String) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newRing(int) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newRingSet() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newRingSet() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newRingSet() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an empty IRingSet.

newRingSet() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

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

newSingleElectron() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newSingleElectron(IAtom) - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newSingleElectron() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newSingleElectron(IAtom) - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newSingleElectron() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an single electron orbital with an associated IAtom.

newSingleElectron(IAtom) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Constructs an single electron orbital on an IAtom.

newSingleElectron() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newSingleElectron(IAtom) - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newStrand() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newStrand() - Method in class org.openscience.cdk.DefaultChemObjectBuilder

newStrand() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Contructs a new IStrand.

newStrand() - Method in class org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder

newStructure() - Method in class org.openscience.cdk.debug.DebugChemObjectBuilder

newToken(int) - Static method in class org.openscience.cdk.iupac.parser.Token

Returns a new Token object, by default.

newToken(int) - Static method in class org.openscience.cdk.smiles.smarts.parser.Token

Returns a new Token object, by default.

NewtonRaphsonMethod - Class in org.openscience.cdk.modeling.forcefield

Methods of Newton-Raphson approach.

NewtonRaphsonMethod() - Constructor for class org.openscience.cdk.modeling.forcefield.NewtonRaphsonMethod

Constructor for the NR object

newtonRaphsonMinimization(GVector, IPotentialFunction) - Method in class org.openscience.cdk.modeling.forcefield.GeometricMinimizer

Minimize the potential energy function using the Newton-Raphson method

next() - Method in class org.openscience.cdk.graph.AtomContainerPermutor

next() - Method in class org.openscience.cdk.graph.MinimalPathIterator

next() - Method in class org.openscience.cdk.io.iterator.IteratingMDLConformerReader

next() - Method in class org.openscience.cdk.io.iterator.IteratingMDLReader

Returns the next IMolecule.

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.IteratingSMILESReader

Get the next molecule from the stream.

next() - Method in class org.openscience.cdk.io.random.RandomAccessReader

next - Variable in class org.openscience.cdk.iupac.parser.Token

A reference to the next regular (non-special) token from the input stream.

next - Variable in class org.openscience.cdk.smiles.smarts.parser.Token

A reference to the next regular (non-special) token from the input stream.

nextElement() - Method in class org.openscience.cdk.formula.rules.RDBERule.Combinations

nextIndex() - Method in class org.openscience.cdk.io.random.RandomAccessReader

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 begining with the *next* line.

NI - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

NICKEL - Static variable in class org.openscience.cdk.config.Elements

NICKEL - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

NIOBIUM - Static variable in class org.openscience.cdk.config.Elements

NIOBIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

NITRILE - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

NITRO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

NITROGEN - Static variable in class 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.

NNAdductFormula - Class in org.openscience.cdk.nonotify

NNAdductFormula() - Constructor for class org.openscience.cdk.nonotify.NNAdductFormula

NNAdductFormula(IMolecularFormula) - Constructor for class org.openscience.cdk.nonotify.NNAdductFormula

NNAminoAcid - Class in org.openscience.cdk.nonotify

NNAminoAcid() - Constructor for class org.openscience.cdk.nonotify.NNAminoAcid

NNAtom - Class in org.openscience.cdk.nonotify

NNAtom() - Constructor for class org.openscience.cdk.nonotify.NNAtom

NNAtom(String) - Constructor for class org.openscience.cdk.nonotify.NNAtom

NNAtom(IElement) - Constructor for class org.openscience.cdk.nonotify.NNAtom

NNAtom(String, Point3d) - Constructor for class org.openscience.cdk.nonotify.NNAtom

NNAtom(String, Point2d) - Constructor for class org.openscience.cdk.nonotify.NNAtom

NNAtomContainer - Class in org.openscience.cdk.nonotify

NNAtomContainer() - Constructor for class org.openscience.cdk.nonotify.NNAtomContainer

NNAtomContainer(IAtomContainer) - Constructor for class org.openscience.cdk.nonotify.NNAtomContainer

NNAtomContainer(int, int, int, int) - Constructor for class org.openscience.cdk.nonotify.NNAtomContainer

NNAtomContainerSet - Class in org.openscience.cdk.nonotify

NNAtomContainerSet() - Constructor for class org.openscience.cdk.nonotify.NNAtomContainerSet

NNAtomParity - Class in org.openscience.cdk.nonotify

NNAtomParity(IAtom, IAtom, IAtom, IAtom, IAtom, int) - Constructor for class org.openscience.cdk.nonotify.NNAtomParity

NNAtomType - Class in org.openscience.cdk.nonotify

NNAtomType(String) - Constructor for class org.openscience.cdk.nonotify.NNAtomType

NNAtomType(String, String) - Constructor for class org.openscience.cdk.nonotify.NNAtomType

NNAtomType(IElement) - Constructor for class org.openscience.cdk.nonotify.NNAtomType

NNBioPolymer - Class in org.openscience.cdk.nonotify

NNBioPolymer() - Constructor for class org.openscience.cdk.nonotify.NNBioPolymer

NNBond - Class in org.openscience.cdk.nonotify

NNBond() - Constructor for class org.openscience.cdk.nonotify.NNBond

NNBond(IAtom, IAtom) - Constructor for class org.openscience.cdk.nonotify.NNBond

NNBond(IAtom, IAtom, IBond.Order) - Constructor for class org.openscience.cdk.nonotify.NNBond

NNBond(IAtom, IAtom, IBond.Order, int) - Constructor for class org.openscience.cdk.nonotify.NNBond

NNBond(IAtom[]) - Constructor for class org.openscience.cdk.nonotify.NNBond

NNBond(IAtom[], IBond.Order) - Constructor for class org.openscience.cdk.nonotify.NNBond

NNChemFile - Class in org.openscience.cdk.nonotify

NNChemFile() - Constructor for class org.openscience.cdk.nonotify.NNChemFile

NNChemModel - Class in org.openscience.cdk.nonotify

NNChemModel() - Constructor for class org.openscience.cdk.nonotify.NNChemModel

NNChemObject - Class in org.openscience.cdk.nonotify

NNChemObject() - Constructor for class org.openscience.cdk.nonotify.NNChemObject

NNChemObject(IChemObject) - Constructor for class org.openscience.cdk.nonotify.NNChemObject

NNChemSequence - Class in org.openscience.cdk.nonotify

NNChemSequence() - Constructor for class org.openscience.cdk.nonotify.NNChemSequence

NNCrystal - Class in org.openscience.cdk.nonotify

NNCrystal() - Constructor for class org.openscience.cdk.nonotify.NNCrystal

NNCrystal(IAtomContainer) - Constructor for class org.openscience.cdk.nonotify.NNCrystal

NNElectronContainer - Class in org.openscience.cdk.nonotify

NNElectronContainer() - Constructor for class org.openscience.cdk.nonotify.NNElectronContainer

NNElement - Class in org.openscience.cdk.nonotify

NNElement() - Constructor for class org.openscience.cdk.nonotify.NNElement

NNElement(String) - Constructor for class org.openscience.cdk.nonotify.NNElement

NNElement(String, int) - Constructor for class org.openscience.cdk.nonotify.NNElement

NNElement(IElement) - Constructor for class org.openscience.cdk.nonotify.NNElement

NNFragmentAtom - Class in org.openscience.cdk.nonotify

Class to represent an IPseudoAtom which embeds an IAtomContainer.

NNFragmentAtom() - Constructor for class org.openscience.cdk.nonotify.NNFragmentAtom

NNIsotope - Class in org.openscience.cdk.nonotify

NNIsotope(String) - Constructor for class org.openscience.cdk.nonotify.NNIsotope

NNIsotope(int, String, int, double, double) - Constructor for class org.openscience.cdk.nonotify.NNIsotope

NNIsotope(int, String, double, double) - Constructor for class org.openscience.cdk.nonotify.NNIsotope

NNIsotope(String, int) - Constructor for class org.openscience.cdk.nonotify.NNIsotope

NNIsotope(IElement) - Constructor for class org.openscience.cdk.nonotify.NNIsotope

NNLonePair - Class in org.openscience.cdk.nonotify

NNLonePair() - Constructor for class org.openscience.cdk.nonotify.NNLonePair

NNLonePair(IAtom) - Constructor for class org.openscience.cdk.nonotify.NNLonePair

NNMapping - Class in org.openscience.cdk.nonotify

NNMapping(IChemObject, IChemObject) - Constructor for class org.openscience.cdk.nonotify.NNMapping

NNMolecularFormula - Class in org.openscience.cdk.nonotify

NNMolecularFormula() - Constructor for class org.openscience.cdk.nonotify.NNMolecularFormula

NNMolecularFormulaSet - Class in org.openscience.cdk.nonotify

NNMolecularFormulaSet() - Constructor for class org.openscience.cdk.nonotify.NNMolecularFormulaSet

NNMolecularFormulaSet(IMolecularFormula) - Constructor for class org.openscience.cdk.nonotify.NNMolecularFormulaSet

NNMolecule - Class in org.openscience.cdk.nonotify

NNMolecule() - Constructor for class org.openscience.cdk.nonotify.NNMolecule

NNMolecule(int, int, int, int) - Constructor for class org.openscience.cdk.nonotify.NNMolecule

NNMolecule(IAtomContainer) - Constructor for class org.openscience.cdk.nonotify.NNMolecule

NNMoleculeSet - Class in org.openscience.cdk.nonotify

NNMoleculeSet() - Constructor for class org.openscience.cdk.nonotify.NNMoleculeSet

NNMonomer - Class in org.openscience.cdk.nonotify

NNMonomer() - Constructor for class org.openscience.cdk.nonotify.NNMonomer

NNPDBAtom - Class in org.openscience.cdk.nonotify

NNPDBAtom(IElement) - Constructor for class org.openscience.cdk.nonotify.NNPDBAtom

NNPDBAtom(String) - Constructor for class org.openscience.cdk.nonotify.NNPDBAtom

NNPDBAtom(String, Point3d) - Constructor for class org.openscience.cdk.nonotify.NNPDBAtom

NNPDBMonomer - Class in org.openscience.cdk.nonotify

NNPDBMonomer() - Constructor for class org.openscience.cdk.nonotify.NNPDBMonomer

NNPDBPolymer - Class in org.openscience.cdk.nonotify

NNPDBPolymer() - Constructor for class org.openscience.cdk.nonotify.NNPDBPolymer

NNPDBStructure - Class in org.openscience.cdk.nonotify

NNPDBStructure() - Constructor for class org.openscience.cdk.nonotify.NNPDBStructure

NNPolymer - Class in org.openscience.cdk.nonotify

NNPolymer() - Constructor for class org.openscience.cdk.nonotify.NNPolymer

NNPseudoAtom - Class in org.openscience.cdk.nonotify

NNPseudoAtom() - Constructor for class org.openscience.cdk.nonotify.NNPseudoAtom

NNPseudoAtom(String) - Constructor for class org.openscience.cdk.nonotify.NNPseudoAtom

NNPseudoAtom(IAtom) - Constructor for class org.openscience.cdk.nonotify.NNPseudoAtom

NNPseudoAtom(String, Point3d) - Constructor for class org.openscience.cdk.nonotify.NNPseudoAtom

NNPseudoAtom(String, Point2d) - Constructor for class org.openscience.cdk.nonotify.NNPseudoAtom

NNPseudoAtom(IElement) - Constructor for class org.openscience.cdk.nonotify.NNPseudoAtom

NNReaction - Class in org.openscience.cdk.nonotify

NNReaction() - Constructor for class org.openscience.cdk.nonotify.NNReaction

NNReactionScheme - Class in org.openscience.cdk.nonotify

NNReactionScheme() - Constructor for class org.openscience.cdk.nonotify.NNReactionScheme

NNReactionSet - Class in org.openscience.cdk.nonotify

NNReactionSet() - Constructor for class org.openscience.cdk.nonotify.NNReactionSet

NNRing - Class in org.openscience.cdk.nonotify

NNRing() - Constructor for class org.openscience.cdk.nonotify.NNRing

NNRing(IAtomContainer) - Constructor for class org.openscience.cdk.nonotify.NNRing

NNRing(int, String) - Constructor for class org.openscience.cdk.nonotify.NNRing

NNRing(int) - Constructor for class org.openscience.cdk.nonotify.NNRing

NNRingSet - Class in org.openscience.cdk.nonotify

NNRingSet() - Constructor for class org.openscience.cdk.nonotify.NNRingSet

NNSingleElectron - Class in org.openscience.cdk.nonotify

NNSingleElectron(IAtom) - Constructor for class org.openscience.cdk.nonotify.NNSingleElectron

NNSingleElectron() - Constructor for class org.openscience.cdk.nonotify.NNSingleElectron

NNStrand - Class in org.openscience.cdk.nonotify

NNStrand() - Constructor for class org.openscience.cdk.nonotify.NNStrand

NO - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

NO_ATOMS - Static variable in class org.openscience.cdk.templates.AminoAcids

NO_BONDS - Static variable in class org.openscience.cdk.templates.AminoAcids

NOBELIUM - Static variable in class org.openscience.cdk.config.Elements

NOBELIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

Node - Interface in org.openscience.cdk.smiles.smarts.parser

All AST nodes must implement this interface.

NoHydrogenElement() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

NomParser - Class in org.openscience.cdk.iupac.parser

A class partly generated by JavaCC which breaks down the chemical name into computable subparts and passes these parts to the MoleculeBuilder.

NomParser(InputStream) - Constructor for class org.openscience.cdk.iupac.parser.NomParser

NomParser(Reader) - Constructor for class org.openscience.cdk.iupac.parser.NomParser

NomParser(NomParserTokenManager) - Constructor for class org.openscience.cdk.iupac.parser.NomParser

NomParserConstants - Interface in org.openscience.cdk.iupac.parser

NomParserTokenManager - Class in org.openscience.cdk.iupac.parser

NomParserTokenManager(SimpleCharStream) - Constructor for class org.openscience.cdk.iupac.parser.NomParserTokenManager

NomParserTokenManager(SimpleCharStream, int) - Constructor for class org.openscience.cdk.iupac.parser.NomParserTokenManager

NON - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

NonCHHeavyAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts

This matcher any heavy atom that is not C or H.

NonCHHeavyAtom() - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.NonCHHeavyAtom

Creates a new instance

NonCHHeavyAtom() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

NONE - Static variable in class org.openscience.cdk.tools.DataFeatures

NoNotificationChemObjectBuilder - Class in org.openscience.cdk.nonotify

A helper class to instantiate a IChemObject for a specific implementation.

NORMAL - Static variable in class org.openscience.cdk.renderer.GraphRendererModel

Paints the function normal

normalize(IsotopePattern) - Static method in class org.openscience.cdk.formula.IsotopePatternManipulator

Return the isotope pattern normalized to the highest abundance

normalize(Point3d) - Static method in class org.openscience.cdk.geometry.GeometryTools

Normalizes a point.

normalize(Matrix) - Method in class org.openscience.cdk.math.Matrix

Normalizes the vectors of this matrix.

normalize() - Method in class org.openscience.cdk.math.Quaternion

normalize() - Method in class org.openscience.cdk.math.Vector

Normalize this vector

normalize(IAtomContainer, Document) - Static method in class org.openscience.cdk.tools.Normalizer

The method takes an xml files like the following:
<replace-set>
<replace>O=N=O</replace>
<replacement>[O-][N+]=O</replacement>
</replace-set>
All parts in ac which are the same as replace will be changed according to replacement.

Normalizer - Class in org.openscience.cdk.tools

Adjusts parts of an AtomContainer to the congiguratin of a fragment.

Normalizer() - Constructor for class org.openscience.cdk.tools.Normalizer

NoSuchAtomException - Exception in org.openscience.cdk.exception

Exception that is thrown when an Atom is requested or required that does not exist in the relevant environment.

NoSuchAtomException(String) - Constructor for exception org.openscience.cdk.exception.NoSuchAtomException

Constructs a new NoSuchAtomException with the given message.

NoSuchAtomTypeException - Exception in org.openscience.cdk.exception

Exception that may be thrown when an atom type is looked up or perceived but no such atom type was found.

NoSuchAtomTypeException(String) - Constructor for exception org.openscience.cdk.exception.NoSuchAtomTypeException

Constructs a new NoSuchAtomTypeException.

NOT - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

NotBond() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

NotExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

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

notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugAminoAcid

notifyChanged() - Method in class org.openscience.cdk.debug.DebugAtom

notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugAtom

notifyChanged() - Method in class org.openscience.cdk.debug.DebugAtomContainer

notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugAtomContainer

notifyChanged() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet

notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet

notifyChanged() - Method in class org.openscience.cdk.debug.DebugAtomType

notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugAtomType

notifyChanged() - Method in class org.openscience.cdk.debug.DebugBioPolymer

notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugBioPolymer

notifyChanged() - Method in class org.openscience.cdk.debug.DebugBond

notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugBond

notifyChanged() - Method in class org.openscience.cdk.debug.DebugChemFile

notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugChemFile

notifyChanged() - Method in class org.openscience.cdk.debug.DebugChemModel

notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugChemModel

notifyChanged() - Method in class org.openscience.cdk.debug.DebugChemObject

notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugChemObject

notifyChanged() - Method in class org.openscience.cdk.debug.DebugChemSequence

notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugChemSequence

notifyChanged() - Method in class org.openscience.cdk.debug.DebugCrystal

notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugCrystal

notifyChanged() - Method in class org.openscience.cdk.debug.DebugElectronContainer

notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugElectronContainer

notifyChanged() - Method in class org.openscience.cdk.debug.DebugElement

notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugElement

notifyChanged() - Method in class org.openscience.cdk.debug.DebugFragmentAtom

notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

notifyChanged() - Method in class org.openscience.cdk.debug.DebugIsotope

notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugIsotope

notifyChanged() - Method in class org.openscience.cdk.debug.DebugLonePair

notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugLonePair

notifyChanged() - Method in class org.openscience.cdk.debug.DebugMapping

notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugMapping

notifyChanged() - Method in class org.openscience.cdk.debug.DebugMolecule

notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugMolecule

notifyChanged() - Method in class org.openscience.cdk.debug.DebugMoleculeSet

notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugMoleculeSet

notifyChanged() - Method in class org.openscience.cdk.debug.DebugMonomer

notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugMonomer

notifyChanged() - Method in class org.openscience.cdk.debug.DebugPolymer

notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugPolymer

notifyChanged() - Method in class org.openscience.cdk.debug.DebugPseudoAtom

notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

notifyChanged() - Method in class org.openscience.cdk.debug.DebugReaction

notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugReaction

notifyChanged() - Method in class org.openscience.cdk.debug.DebugReactionScheme

notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugReactionScheme

notifyChanged() - Method in class org.openscience.cdk.debug.DebugReactionSet

notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugReactionSet

notifyChanged() - Method in class org.openscience.cdk.debug.DebugRing

notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugRing

notifyChanged() - Method in class org.openscience.cdk.debug.DebugSingleElectron

notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugSingleElectron

notifyChanged() - Method in class org.openscience.cdk.debug.DebugStrand

notifyChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugStrand

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.

notionalToCartesian(double, double, double, double, double, double) - Static method in class org.openscience.cdk.geometry.CrystalGeometryTools

Calculates cartesian vectors for unit cell axes from axes lengths and angles between axes.

NP - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

NS_CML - Static variable in class org.openscience.cdk.libio.cml.Convertor

NULLVECTOR - Static variable in class org.openscience.cdk.math.Vector

Null vector in 3 dimensional space

numberOfUnplacedHeavyAtoms(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D

Gets numberOfUnplacedHeavyAtoms (no Flag ISPLACED, no Hydrogens)

NumericalSurface - Class in org.openscience.cdk.geometry.surface

A class representing the solvent acessible 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.

NWChemFormat - Class in org.openscience.cdk.io.formats

See here.

O

o - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

O - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

OATE - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

OBJECT_UNIQUE_POLICY - Static variable in class org.openscience.cdk.tools.IDCreator

New ID generation policy - to generate IDs unique only in a molecule

OCT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

OICACID - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

OL - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

ONE - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

oneAttachLocation() - Method in class org.openscience.cdk.iupac.parser.NomParser

Only one attach location specified, should be followed by a dash.

OneElectronJob - Class in org.openscience.cdk.math.qm

Calculates the orbitals and orbital energies of electron systems without electron electron interactions

OneElectronJob(Orbitals) - Constructor for class org.openscience.cdk.math.qm.OneElectronJob

Constructs a one electron job

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, int, String, List<String>, String) - Constructor for class org.openscience.cdk.io.setting.OptionIOSetting

OptionIOSetting is IOSetting for which the value must be in the list of possible options.

OR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

Orbitals - Class in org.openscience.cdk.math.qm

This class represents a set of orbitals

Orbitals(IBasis) - Constructor for class org.openscience.cdk.math.qm.Orbitals

Constructs orbitals with a specified base set

Orbitals(IBasis, Matrix) - Constructor for class org.openscience.cdk.math.qm.Orbitals

Constructs orbitals with a specified base set and a coefficient matrix

OrBond() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

OrderQueryBond - Class in org.openscience.cdk.isomorphism.matchers

OrderQueryBond() - Constructor for class org.openscience.cdk.isomorphism.matchers.OrderQueryBond

OrderQueryBond(IQueryAtom, IQueryAtom, IBond.Order) - Constructor for class org.openscience.cdk.isomorphism.matchers.OrderQueryBond

OrderQueryBond - Class in org.openscience.cdk.isomorphism.matchers.smarts

This matches a bond with a certain bond order.

OrderQueryBond(IBond.Order) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.OrderQueryBond

Creates a new instance

OrderQueryBondOrderOnly - Class in org.openscience.cdk.isomorphism.matchers

IQueryBond that matches IBond object only based on bond order, and disregarding any aromaticity flag.

OrderQueryBondOrderOnly() - Constructor for class org.openscience.cdk.isomorphism.matchers.OrderQueryBondOrderOnly

OrderQueryBondOrderOnly(IQueryAtom, IQueryAtom, IBond.Order) - Constructor for class org.openscience.cdk.isomorphism.matchers.OrderQueryBondOrderOnly

OrExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

org.openscience.cdk - package org.openscience.cdk

org.openscience.cdk.annotations - package org.openscience.cdk.annotations

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.elements - package org.openscience.cdk.config.elements

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.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.formula - package org.openscience.cdk.formula

org.openscience.cdk.formula.rules - package org.openscience.cdk.formula.rules

org.openscience.cdk.geometry - package org.openscience.cdk.geometry

org.openscience.cdk.geometry.alignment - package org.openscience.cdk.geometry.alignment

org.openscience.cdk.geometry.surface - package org.openscience.cdk.geometry.surface

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.inchi - package org.openscience.cdk.inchi

org.openscience.cdk.index - package org.openscience.cdk.index

org.openscience.cdk.interfaces - package org.openscience.cdk.interfaces

org.openscience.cdk.io - package org.openscience.cdk.io

org.openscience.cdk.io.cml - package org.openscience.cdk.io.cml

org.openscience.cdk.io.formats - package org.openscience.cdk.io.formats

org.openscience.cdk.io.inchi - package org.openscience.cdk.io.inchi

org.openscience.cdk.io.iterator - package org.openscience.cdk.io.iterator

org.openscience.cdk.io.iterator.event - package org.openscience.cdk.io.iterator.event

org.openscience.cdk.io.listener - package org.openscience.cdk.io.listener

org.openscience.cdk.io.program - package org.openscience.cdk.io.program

org.openscience.cdk.io.pubchemxml - package org.openscience.cdk.io.pubchemxml

org.openscience.cdk.io.random - package org.openscience.cdk.io.random

org.openscience.cdk.io.setting - package org.openscience.cdk.io.setting

org.openscience.cdk.isomorphism - package org.openscience.cdk.isomorphism

org.openscience.cdk.isomorphism.matchers - package org.openscience.cdk.isomorphism.matchers

org.openscience.cdk.isomorphism.matchers.smarts - package org.openscience.cdk.isomorphism.matchers.smarts

org.openscience.cdk.isomorphism.mcss - package org.openscience.cdk.isomorphism.mcss

org.openscience.cdk.iupac.parser - package org.openscience.cdk.iupac.parser

The core classes of the ChemNomParse project, an open source attempt of a chemical nomenclature parser, call via generate (name).

org.openscience.cdk.layout - package org.openscience.cdk.layout

org.openscience.cdk.libio.cml - package org.openscience.cdk.libio.cml

org.openscience.cdk.libio.md - package org.openscience.cdk.libio.md

org.openscience.cdk.math - package org.openscience.cdk.math

org.openscience.cdk.math.qm - package org.openscience.cdk.math.qm

org.openscience.cdk.modeling.builder3d - package org.openscience.cdk.modeling.builder3d

org.openscience.cdk.modeling.forcefield - package org.openscience.cdk.modeling.forcefield

org.openscience.cdk.nonotify - package org.openscience.cdk.nonotify

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.model - package org.openscience.cdk.qsar.model

org.openscience.cdk.qsar.model.R - package org.openscience.cdk.qsar.model.R

org.openscience.cdk.qsar.model.R2 - package org.openscience.cdk.qsar.model.R2

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.ringsearch - package org.openscience.cdk.ringsearch

org.openscience.cdk.ringsearch.cyclebasis - package org.openscience.cdk.ringsearch.cyclebasis

org.openscience.cdk.similarity - package org.openscience.cdk.similarity

org.openscience.cdk.smiles - package org.openscience.cdk.smiles

org.openscience.cdk.smiles.smarts - package org.openscience.cdk.smiles.smarts

org.openscience.cdk.smiles.smarts.parser - package org.openscience.cdk.smiles.smarts.parser

org.openscience.cdk.smiles.smarts.parser.visitor - package org.openscience.cdk.smiles.smarts.parser.visitor

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.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.validate - package org.openscience.cdk.validate

orthonormalize(Matrix) - Method in class org.openscience.cdk.math.Matrix

Orthonormalize the vectors of this matrix by Gram-Schmidt.

OS - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

OSMIUM - Static variable in class org.openscience.cdk.config.Elements

OSMIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

OVERAREA - Static variable in class org.openscience.cdk.renderer.GraphRendererModel

Paints the area over the function

OverlapResolver - Class in org.openscience.cdk.layout

Helper class for Structure Diagram Generation.

OverlapResolver() - Constructor for class org.openscience.cdk.layout.OverlapResolver

OverlapResolver.OverlapPair - Class in org.openscience.cdk.layout

A little helper class to store pairs of overlapping atoms.

OverlapResolver.OverlapPair(IChemObject, IChemObject) - Constructor for class org.openscience.cdk.layout.OverlapResolver.OverlapPair

Constructor for the OverlapPair object.

OWLAtomTypeHandler - Class in org.openscience.cdk.config.atomtypes

SAX Handler for the OWLAtomTypeReader.

OWLAtomTypeHandler(IChemObjectBuilder) - Constructor for class org.openscience.cdk.config.atomtypes.OWLAtomTypeHandler

Constructs a new AtomTypeHandler and will create IAtomType implementations using the given IChemObjectBuilder.

OWLAtomTypeMappingHandler - Class in org.openscience.cdk.config.atomtypes

SAX Handler for the OWLAtomTypeMappingReader.

OWLAtomTypeMappingHandler() - Constructor for class org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingHandler

Constructs a new OWLAtomTypeMappingHandler.

OWLAtomTypeMappingReader - Class in org.openscience.cdk.config.atomtypes

XML Reader for the OWLBasedAtomTypeConfigurator.

OWLAtomTypeMappingReader(Reader) - Constructor for class org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingReader

Instantiates the XML based AtomTypeReader.

OWLAtomTypeReader - Class in org.openscience.cdk.config.atomtypes

XML Reader for the OWLBasedAtomTypeConfigurator.

OWLAtomTypeReader(Reader) - Constructor for class org.openscience.cdk.config.atomtypes.OWLAtomTypeReader

Instantiates the XML based AtomTypeReader.

OWLBasedAtomTypeConfigurator - Class in org.openscience.cdk.config

AtomType resource that reads the atom type configuration from an OWL file.

OWLBasedAtomTypeConfigurator() - Constructor for class org.openscience.cdk.config.OWLBasedAtomTypeConfigurator

OWLFile - Class in org.openscience.cdk.dict

Dictionary with entries build from an OWL file.

OWLFile() - Constructor for class org.openscience.cdk.dict.OWLFile

OWLReact - Class in org.openscience.cdk.dict

Dictionary with entries build from an OWL React.

OWLReact() - Constructor for class org.openscience.cdk.dict.OWLReact

Constructor of the OWLReact object.

OXO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

OXYGEN - Static variable in class org.openscience.cdk.config.Elements

OYLCHLORIDE - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

P

p - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

P - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

PA - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

PALLADIUM - Static variable in class org.openscience.cdk.config.Elements

PALLADIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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

parse(BitSet, BitSet, boolean, boolean) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph

Parsing of the RGraph.

parse(String) - Static method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

This method parses a Smarts String and returns an instance of QueryAtomContainer

parseAtomCharges(XmlPullParser, IMolecule) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper

parseAtomElements(XmlPullParser, IMolecule) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper

parseCompoundsBlock(XmlPullParser) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper

ParseException - Exception in org.openscience.cdk.iupac.parser

This exception is thrown when parse errors are encountered.

ParseException(Token, int[][], String[]) - Constructor for exception org.openscience.cdk.iupac.parser.ParseException

This constructor is used by the method "generateParseException" in the generated parser.

ParseException() - Constructor for exception org.openscience.cdk.iupac.parser.ParseException

The following constructors are for use by you for whatever purpose you can think of.

ParseException(String) - Constructor for exception org.openscience.cdk.iupac.parser.ParseException

ParseException - Exception in org.openscience.cdk.smiles.smarts.parser

This exception is thrown when parse errors are encountered.

ParseException(Token, int[][], String[]) - Constructor for exception org.openscience.cdk.smiles.smarts.parser.ParseException

This constructor is used by the method "generateParseException" in the generated parser.

ParseException() - Constructor for exception org.openscience.cdk.smiles.smarts.parser.ParseException

The following constructors are for use by you for whatever purpose you can think of.

ParseException(String) - Constructor for exception org.openscience.cdk.smiles.smarts.parser.ParseException

parseMolecule(XmlPullParser, IChemObjectBuilder) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper

parserAtomBlock(XmlPullParser, IMolecule) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper

parserBondBlock(XmlPullParser, IMolecule) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper

parserCompoundInfoData(XmlPullParser, IMolecule) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper

parserCoordBlock(XmlPullParser, IMolecule) - 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 Molecule object.

parseSubstance(XmlPullParser) - 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

PartialFilledStructureMerger - Class in org.openscience.cdk.structgen.stochastic

Randomly generates a single, connected, correctly bonded structure for a given molecular formula.

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

partitionIntoMolecules(IAtomContainer) - Static method in class org.openscience.cdk.graph.ConnectivityChecker

Partitions the atoms in an AtomContainer into covalently connected components.

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.

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

Path - Class in org.openscience.cdk.ringsearch

Implementation of a Path as needed by [Hanser, Th. and Jauffret, Ph. and Kaufmann, G., A New Algorithm for Exhaustive Ring Perception in a Molecular Graph, J. Chem. Inf. Comput. Sci., 1996, 36:1146-1152].

Path() - Constructor for class org.openscience.cdk.ringsearch.Path

Constructs an empty path

Path(IAtom, IAtom) - Constructor for class org.openscience.cdk.ringsearch.Path

Constructs a new Path with two Atoms

PathTools - Class in org.openscience.cdk.graph

Tools class with methods for handling molecular graphs.

PathTools() - Constructor for class org.openscience.cdk.graph.PathTools

PB - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

pBlockMetals() - Method in class org.openscience.cdk.iupac.parser.NomParser

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.

PCSubstanceXMLReader - Class in org.openscience.cdk.io

Reads an object from ASN formated input for PubChem Compound entries.

PCSubstanceXMLReader(Reader) - Constructor for class org.openscience.cdk.io.PCSubstanceXMLReader

Construct a new reader from a Reader type object.

PCSubstanceXMLReader(InputStream) - Constructor for class org.openscience.cdk.io.PCSubstanceXMLReader

PCSubstanceXMLReader() - Constructor for class org.openscience.cdk.io.PCSubstanceXMLReader

PD - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

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.

PDBAtomCustomizer - Class in org.openscience.cdk.libio.cml

Customizer for the libio-cml Convertor to be able to export details for PDBAtom'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.

PDBMLFormat - Class in org.openscience.cdk.io.formats

XML version of the PDB format.

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

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.

PDBReader - Class in org.openscience.cdk.io

Reads the contents of a PDBFile.

PDBReader(InputStream) - Constructor for class org.openscience.cdk.io.PDBReader

Contructs a new PDBReader that can read Molecules from a given InputStream.

PDBReader(Reader) - Constructor for class org.openscience.cdk.io.PDBReader

Contructs 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

Contructs 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

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

PENT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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.

PeriodicGroupNumber() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

PeriodicGroupNumberAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts

This matcher checks the periodic group number of an atom.

PeriodicGroupNumberAtom(int) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.PeriodicGroupNumberAtom

Creates a new instance

periodicTable - Variable in class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor

PeriodicTable - Class in org.openscience.cdk.tools

Represents elements of the Periodic Table.

PeriodicTable() - Constructor for class org.openscience.cdk.tools.PeriodicTable

PeriodicTableElement - Class in org.openscience.cdk

An PeriodicTableElement class is instantiated with at least the atom symbol:

PeriodicTableElement(String) - Constructor for class org.openscience.cdk.PeriodicTableElement

Constructor for the PeriodicTableElement object.

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

PeriodicTablePositionDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor

Constructor for the PeriodicTablePositionDescriptor object

PetitjeanNumberDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

According to the Petitjean definition, the eccentricity of a vertex corresponds to the distance from that vertex to the most remote vertex in the graph.

PetitjeanNumberDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor

Constructor for the PetitjeanNumberDescriptor object

PetitjeanShapeIndexDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

Evaluates the Petitjean shape indices,

These original Petitjean number was described by Petitjean ([ Petitjean, M. , Applications of the radius-diameter diagram to the classification of topological and geometrical shapes of chemical compounds, Journal of Chemical Information and Computer Science, 1992, 32:331-337]) and considered the molecular graph.

PetitjeanShapeIndexDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor

PharmacophoreAngleBond - Class in org.openscience.cdk.pharmacophore

Represents an angle relationship between three pharmacophore groups.

PharmacophoreAngleBond(PharmacophoreAtom, PharmacophoreAtom, PharmacophoreAtom) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreAngleBond

Create a pharmacophore distance constraint.

PharmacophoreAtom - Class in org.openscience.cdk.pharmacophore

A representation of a pharmacophore group.

PharmacophoreAtom(String, String, Point3d) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreAtom

Create a pharmacophore group.

PharmacophoreAtom(PharmacophoreAtom) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreAtom

Create a pharmacophore group.

PharmacophoreBond - Class in org.openscience.cdk.pharmacophore

Represents a distance relationship between two pharmacophore groups.

PharmacophoreBond(PharmacophoreAtom, PharmacophoreAtom) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreBond

Create a pharmacophore distance constraint.

PharmacophoreMatcher - Class in org.openscience.cdk.pharmacophore

Identifies atoms whose 3D arrangement matches a specified pharmacophore query.

PharmacophoreMatcher() - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreMatcher

An empty constructor.

PharmacophoreMatcher(IQueryAtomContainer) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreMatcher

Initialize the matcher with a query.

PharmacophoreQueryAngleBond - Class in org.openscience.cdk.pharmacophore

Represents a pharmacophore query angle constraint.

PharmacophoreQueryAngleBond() - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreQueryAngleBond

PharmacophoreQueryAngleBond(PharmacophoreQueryAtom, PharmacophoreQueryAtom, PharmacophoreQueryAtom, double, double) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreQueryAngleBond

Create a query angle constraint between three query groups.

PharmacophoreQueryAngleBond(PharmacophoreQueryAtom, PharmacophoreQueryAtom, PharmacophoreQueryAtom, double) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreQueryAngleBond

Create a query angle constraint between three query groups.

PharmacophoreQueryAtom - Class in org.openscience.cdk.pharmacophore

Represents a query pharmacophore group.

PharmacophoreQueryAtom(String, String) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreQueryAtom

Creat a new query pharmacophore group

PharmacophoreQueryBond - Class in org.openscience.cdk.pharmacophore

Represents a pharmacophore query distance constraint.

PharmacophoreQueryBond() - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreQueryBond

PharmacophoreQueryBond(PharmacophoreQueryAtom, PharmacophoreQueryAtom, double, double) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreQueryBond

Create a query distance constraint between two query groups.

PharmacophoreQueryBond(PharmacophoreQueryAtom, PharmacophoreQueryAtom, double) - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreQueryBond

Create a query distance constraint between two query groups.

PharmacophoreUtils - Class in org.openscience.cdk.pharmacophore

Provides some utility methods for pharmacophore handling.

PharmacophoreUtils() - Constructor for class org.openscience.cdk.pharmacophore.PharmacophoreUtils

PHENYL - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

PHOSPHORUS - Static variable in class 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

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 neighboors 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)

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 3Dcoordinates to the heavy atoms in an aliphatic chain

placeFusedRing(IRing, IAtomContainer, Point2d, 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

placeHydrogens2D(IAtomContainer, IAtom) - Method in class org.openscience.cdk.layout.HydrogenPlacer

placeHydrogens2D(IAtomContainer, IAtom, double) - Method in class org.openscience.cdk.layout.HydrogenPlacer

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

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.

PLATINUM - Static variable in class org.openscience.cdk.config.Elements

PLATINUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

PLSRegressionModel - Class in org.openscience.cdk.qsar.model.R

Deprecated.

PLSRegressionModel() - Constructor for class org.openscience.cdk.qsar.model.R.PLSRegressionModel

Deprecated. Constructs a PLSRegressionModel object.

PLSRegressionModel(double[][], double[]) - Constructor for class org.openscience.cdk.qsar.model.R.PLSRegressionModel

Deprecated. Constructs a PLSRegressionModel object.

PLSRegressionModel(double[][], double[][]) - Constructor for class org.openscience.cdk.qsar.model.R.PLSRegressionModel

Deprecated. Constructs a PLSRegressionModel object.

PLSRegressionModelFit - Class in org.openscience.cdk.qsar.model.R

PLSRegressionModelFit(int, int, int, int[], String) - Constructor for class org.openscience.cdk.qsar.model.R.PLSRegressionModelFit

PLSRegressionModelPredict - Class in org.openscience.cdk.qsar.model.R

Deprecated.

PLSRegressionModelPredict(int, double[]) - Constructor for class org.openscience.cdk.qsar.model.R.PLSRegressionModelPredict

Deprecated. Constructor to contain the results of a PLS prediction.

PLUTONIUM - Static variable in class org.openscience.cdk.config.Elements

PLUTONIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

PM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

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

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

PO - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

Point - Class in org.openscience.cdk.graph.rebond

Point(double, double, double) - Constructor for class org.openscience.cdk.graph.rebond.Point

Point2dDifference - Class in org.openscience.cdk.tools.diff.tree

Difference between two boolean[]'s.

Point3dDifference - Class in org.openscience.cdk.tools.diff.tree

Difference between two boolean[]'s.

Polarizability - Class in org.openscience.cdk.charges

Calculation of the polarizability of a molecule by the method of Kang and Jhon and Gasteiger based on [Kang, Y.K. and Jhon, M.S., Additivity of Atomic Static Polarizabilities and Dispersion Coefficients, Theoretica Chimica Acta, 1982, 61:41-48] and [Gasteiger, J. and Hutchings, M.G., Quantitative Models of Gas-Phase Proton Transfer Reactions Involving Alcohols, Ethers, and their Thio analogs. Correlation Analyses Based on Residual Electronegativity and Effective Polarizability, J. Amer. Chem. Soc., 1984, 106:6489-6495] Limitations in parameterization of atoms: H, Csp3, Csp2, Csp2arom, Csp3, Nsp3, Nsp2, Nsp3, P, Osp3 and Osp2.

Polarizability() - Constructor for class org.openscience.cdk.charges.Polarizability

Constructor for the Polarizability object

POLONIUM - Static variable in class org.openscience.cdk.config.Elements

POLONIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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.

pop() - Method in class org.openscience.cdk.io.cml.CMLStack

Retrieves and deletes to last added entry.

pop() - Method in class org.openscience.cdk.ringsearch.Queue

Returns an Object from the queue

pop() - Method in class org.openscience.cdk.tools.FixedSizeStack

Returns the last object that was pushed onto the stack

populatePolygonCorners(List<IAtom>, Point2d, double, double, double) - Method in class org.openscience.cdk.layout.AtomPlacer

Populates the corners of a polygon with atoms.

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 class org.openscience.cdk.config.Elements

POTASSIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

POVRayFormat - Class in org.openscience.cdk.io.formats

See here.

PQSChemFormat - Class in org.openscience.cdk.io.formats

See here.

PR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

PRASEODYMIUM - Static variable in class org.openscience.cdk.config.Elements

PRASEODYMIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

predict() - Method in interface org.openscience.cdk.qsar.model.IModel

Makes predictions using a previously built model.

predict() - Method in class org.openscience.cdk.qsar.model.R.CNNClassificationModel

Deprecated. Uses a fitted model to predict the response for new observations.

predict() - Method in class org.openscience.cdk.qsar.model.R.CNNRegressionModel

Deprecated. Uses a fitted model to predict the response for new observations.

predict() - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModel

Deprecated. Uses a fitted model to predict the response for new observations.

predict() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModel

Deprecated. Uses a fitted model to predict the response for new observations.

predict() - Method in class org.openscience.cdk.qsar.model.R.RModel

Deprecated.

predict() - Method in class org.openscience.cdk.qsar.model.R2.CNNRegressionModel

Uses a fitted model to predict the response for new observations.

predict() - Method in class org.openscience.cdk.qsar.model.R2.LinearRegressionModel

Uses a fitted model to predict the response for new observations.

predict() - Method in class org.openscience.cdk.qsar.model.R2.RModel

predict(String) - Method in class org.openscience.cdk.tools.BremserOneSphereHOSECodePredictor

predictFull(String) - Method in class org.openscience.cdk.tools.BremserOneSphereHOSECodePredictor

predictIP(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.tools.IonizationPotentialTool

Method which is predict the Ionization Potential from given atom.

predictIP(IAtomContainer, IBond) - Static method in class org.openscience.cdk.tools.IonizationPotentialTool

Method which is predict the Ionization Potential from given atom.

prefixConstruct() - Method in class org.openscience.cdk.iupac.parser.NomParser

Allows 1 or more prefixes

prefixFunctionalGroups() - Method in class org.openscience.cdk.iupac.parser.NomParser

prefixType() - Method in class org.openscience.cdk.iupac.parser.NomParser

prepareNode(AtomContainer) - 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

Primes() - Constructor for class org.openscience.cdk.math.Primes

PrimitiveAtomExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

printInt2D(int[][]) - Static method in class org.openscience.cdk.tools.SwissArmyKnife

Returns a string representation of a 2D int matrix for printing or listing to the console

prioritySubstituents() - Method in class org.openscience.cdk.iupac.parser.NomParser

Things which have sub chains branching off them but the molecule has no main chain.

prioritySubstituentsFunGroups() - Method in class org.openscience.cdk.iupac.parser.NomParser

Things which have sub chains branching off them and the molecule does have a main chain.

ProblemMarker - Class in org.openscience.cdk.validate

Tool to mark IChemObject's as having a problem.

ProblemMarker() - Constructor for class org.openscience.cdk.validate.ProblemMarker

process() - Method in class org.openscience.cdk.io.iterator.event.EventCMLReader

Starts the reading of the CML file.

process(IAtomContainer) - Method in class org.openscience.cdk.qsar.DescriptorEngine

Calculates all available (or only those specified) descriptors for a molecule.

processConnections(String, IAtomContainer, int) - Method in class org.openscience.cdk.io.inchi.INChIContentProcessorTool

Processes the content from the connections field of the INChI.

processFormula(IAtomContainer, String) - Method in class org.openscience.cdk.io.inchi.INChIContentProcessorTool

Processes the content from the formula field of the INChI.

processIOSettingQuestion(IOSetting) - Method in class org.openscience.cdk.io.iterator.IteratingMDLReader

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.

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) - 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.

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 class org.openscience.cdk.config.Elements

PROMETHIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

PROP - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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 class org.openscience.cdk.config.Elements

PROTACTINIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

ProteinBuilderTool - Class in org.openscience.cdk.tools

Class that facilitates building protein structures.

ProteinBuilderTool() - Constructor for class org.openscience.cdk.tools.ProteinBuilderTool

proteinGridToPmesh(String) - Method in class org.openscience.cdk.protein.ProteinPocketFinder

Method writes the protein grid points to pmesh format.

ProteinPocketFinder - Class in org.openscience.cdk.protein

The detection of pocket and cavities in a bioPolymer is done similar to the program LIGSITE [Hendlich, M. and Rippmann, F. and Bernickel, G. , LIGSITE: Automatic and efficient detection of potential small molecule-binding sites in proteins, Journal of Molecular Graphics and Modelling, 1997, 15:359-363].

ProteinPocketFinder(String, boolean) - Constructor for class org.openscience.cdk.protein.ProteinPocketFinder

ProteinPocketFinder(String, double, boolean) - Constructor for class org.openscience.cdk.protein.ProteinPocketFinder

ProteinPocketFinder(String, double[][][]) - Constructor for class org.openscience.cdk.protein.ProteinPocketFinder

ProteinPocketFinder(IBioPolymer, double[][][]) - Constructor for class org.openscience.cdk.protein.ProteinPocketFinder

ProtonAffinityHOSEDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic

This class returns the proton affinity of an atom containing.

ProtonAffinityHOSEDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor

Constructor for the ProtonAffinityDescriptor object.

ProtonTotalPartialChargeDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic

The calculation of partial charges of an heavy atom and its protons is based on Gasteiger Marsili (PEOE).

ProtonTotalPartialChargeDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor

Constructor for the ProtonTotalPartialChargeDescriptor object

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.

pspGridToPmesh(String) - Method in class org.openscience.cdk.protein.ProteinPocketFinder

Method writes the PSP points (>=minPSPocket) to pmesh format.

PT - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

PU - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

PubChemASNFormat - Class in org.openscience.cdk.io.formats

PubChemCompoundsXMLFormat - Class in org.openscience.cdk.io.formats

PubChemCompoundXMLFormat - Class in org.openscience.cdk.io.formats

PubChemFormat - Class in org.openscience.cdk.io.formats

See here.

PubChemSubstancesASNFormat - Class in org.openscience.cdk.io.formats

PubChemSubstancesXMLFormat - Class in org.openscience.cdk.io.formats

PubChemSubstanceXMLFormat - Class in org.openscience.cdk.io.formats

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(String) - Method in class org.openscience.cdk.io.cml.CMLStack

Adds an entry to the stack.

push(Object) - Method in class org.openscience.cdk.ringsearch.Queue

Places an Object into the queue

push(Object) - Method in class org.openscience.cdk.tools.FixedSizeStack

Pushes an object onto the stack.

putInOrder(String[], IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator

Q

Q_MARK - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

QChemFormat - Class in org.openscience.cdk.io.formats

See here.

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

QSARModelException - Exception in org.openscience.cdk.qsar.model

Exception that is thrown by model routines when a problem has occured.

QSARModelException(String) - Constructor for exception org.openscience.cdk.qsar.model.QSARModelException

Constructs a new QSARModelException with the given message.

Quaternion - Class in org.openscience.cdk.math

This class handles quaternions.

Quaternion() - Constructor for class org.openscience.cdk.math.Quaternion

Quaternion(double, double, double, double) - Constructor for class org.openscience.cdk.math.Quaternion

Quaternion(Vector, double) - Constructor for class org.openscience.cdk.math.Quaternion

Generate a quaternion from a rotation axis and an angle

Quaternion(double, double, double) - Constructor for class org.openscience.cdk.math.Quaternion

Generate a quaternion from spherical coordinates and a rotation angle

QueryAtomContainer - Class in org.openscience.cdk.isomorphism.matchers

QueryAtomContainer() - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

QueryAtomContainerCreator - Class in org.openscience.cdk.isomorphism.matchers

QueryAtomContainerCreator() - Constructor for class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator

Queue - Class in org.openscience.cdk.ringsearch

Implementation of a Queue (FIFO stack).

Queue() - Constructor for class org.openscience.cdk.ringsearch.Queue

Constructs an empty Queue

R

R - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

r - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

R_BOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

R_BRACKET - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

R_PAREN - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

RA - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

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

RadicalSiteHrAlphaReaction - Class in org.openscience.cdk.reaction.type

This reaction could be represented as [A*]-(C)_2-C3[H] => A([H])-(C_2)-[C3*].

RadicalSiteHrAlphaReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalSiteHrAlphaReaction

Constructor of the RadicalSiteHrAlphaReaction object

RadicalSiteHrBetaReaction - Class in org.openscience.cdk.reaction.type

This reaction could be represented as [A*]-(C)_3-C4[H] => A([H])-(C_3)-[C4*].

RadicalSiteHrBetaReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalSiteHrBetaReaction

Constructor of the RadicalSiteHrBetaReaction object

RadicalSiteHrDeltaReaction - Class in org.openscience.cdk.reaction.type

This reaction could be represented as [A*]-(C)_4-C5[H] => A([H])-(C_4)-[C5*].

RadicalSiteHrDeltaReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalSiteHrDeltaReaction

Constructor of the RadicalSiteHrDeltaReaction object

RadicalSiteHrGammaReaction - Class in org.openscience.cdk.reaction.type

This reaction could be represented as [A*]-C1-C2-C3[H] => A([H])-C1-C2-[C3*].

RadicalSiteHrGammaReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalSiteHrGammaReaction

Constructor of the RadicalSiteHrGammaReaction object

RadicalSiteInitiationHReaction - Class in org.openscience.cdk.reaction.type

IReactionProcess which participate mass spectrum process.

RadicalSiteInitiationHReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalSiteInitiationHReaction

Constructor of the RadicalSiteInitiationHReaction object

RadicalSiteInitiationReaction - Class in org.openscience.cdk.reaction.type

IReactionProcess which participate mass spectrum process.

RadicalSiteInitiationReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalSiteInitiationReaction

Constructor of the RadicalSiteInitiationReaction object

RadicalSiteIonizationMechanism - Class in org.openscience.cdk.reaction.mechanism

This mechanism extracts an atom because of the stabilization of a radical.

RadicalSiteIonizationMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.RadicalSiteIonizationMechanism

RadicalSiteRearrangementMechanism - Class in org.openscience.cdk.reaction.mechanism

This mechanism displaces an Atom or substructure (R) from one position to an other.

RadicalSiteRearrangementMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.RadicalSiteRearrangementMechanism

RadicalSiteRrAlphaReaction - Class in org.openscience.cdk.reaction.type

This reaction could be represented as [A*]-(C)_2-C3[R] => A([RH])-(C_2)-[C3*].

RadicalSiteRrAlphaReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalSiteRrAlphaReaction

Constructor of the RadicalSiteRrAlphaReaction object

RadicalSiteRrBetaReaction - Class in org.openscience.cdk.reaction.type

This reaction could be represented as [A*]-(C)_3-C4[R] => A([R])-(C_3)-[C4*].

RadicalSiteRrBetaReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalSiteRrBetaReaction

Constructor of the RadicalSiteRrBetaReaction object

RadicalSiteRrDeltaReaction - Class in org.openscience.cdk.reaction.type

This reaction could be represented as [A*]-(C)_4-C5[R] => A([R])-(C_4)-[C5*].

RadicalSiteRrDeltaReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalSiteRrDeltaReaction

Constructor of the RadicalSiteRrDeltaReaction object

RadicalSiteRrGammaReaction - Class in org.openscience.cdk.reaction.type

This reaction could be represented as [A*]-(C)_5-C6[R] => A([R])-(C_5)-[C6*].

RadicalSiteRrGammaReaction() - Constructor for class org.openscience.cdk.reaction.type.RadicalSiteRrGammaReaction

Constructor of the RadicalSiteRrGammaReaction object

RADIUM - Static variable in class org.openscience.cdk.config.Elements

RADIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

RADON - Static variable in class org.openscience.cdk.config.Elements

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(IMolecule) - 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.

RandomNumbersTool - Class in org.openscience.cdk.math

Class supplying useful methods to generate random numbers.

RandomNumbersTool() - Constructor for class org.openscience.cdk.math.RandomNumbersTool

RawCopyFormat - Class in org.openscience.cdk.io.formats

See here.

RB - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

RDBERule - Class in org.openscience.cdk.formula.rules

Ring Double Bond Equivalents (RDBE) or Double Bond Equivalents (DBE) are calculated from valence values of elements contained in a formula and should tell the number of bonds - or rings.

RDBERule() - Constructor for class org.openscience.cdk.formula.rules.RDBERule

Constructor for the RDBE object.

RDBERule.Combinations - Class in org.openscience.cdk.formula.rules

RDBERule.Combinations(Object[], int) - Constructor for class org.openscience.cdk.formula.rules.RDBERule.Combinations

Create a Combination to enumerate through all subsets of the supplied Object array, selecting m at a time.

RDFCalculator - Class in org.openscience.cdk.geometry

Calculator of radial distribution functions.

RDFCalculator(double, double, double, double) - Constructor for class org.openscience.cdk.geometry.RDFCalculator

Constructs a RDF calculator that calculates a unweighted, digitized RDF function.

RDFCalculator(double, double, double, double, IRDFWeightFunction) - Constructor for class org.openscience.cdk.geometry.RDFCalculator

Constructs a RDF calculator that calculates a digitized RDF function.

rdFields - Variable in class org.openscience.cdk.io.MDLRXNWriter

RDFProtonDescriptor_G3R - Class in org.openscience.cdk.qsar.descriptors.atomic

This class calculates G3R proton descriptors used in neural networks for H1 NMR shift.

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.

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.

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.

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.

RDFProtonDescriptor_GSR() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR

Constructor for the RDFProtonDescriptor object

RE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

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.

ReactionChain - Class in org.openscience.cdk.reaction

Classes that extends the definition of reaction to a chain reaction.

ReactionChain() - Constructor for class org.openscience.cdk.reaction.ReactionChain

ReactionEngine - Class in org.openscience.cdk.reaction

The base class for all chemical reactions objects in this cdk.

ReactionEngine() - Constructor for class org.openscience.cdk.reaction.ReactionEngine

Constructor of the ReactionEngine object.

ReactionExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

ReactionManipulator - Class in org.openscience.cdk.tools.manipulator

ReactionManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.ReactionManipulator

reactions() - Method in class org.openscience.cdk.debug.DebugReactionSet

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.

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.

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

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.

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.

ReactionSetManipulator - Class in org.openscience.cdk.tools.manipulator

ReactionSetManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.ReactionSetManipulator

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(IChemObject) - Method in class org.openscience.cdk.io.CIFReader

Read a ChemFile from input

read(IChemObject) - Method in class org.openscience.cdk.io.CMLReader

Read a IChemObject from input

read(IChemObject) - Method in class org.openscience.cdk.io.CrystClustReader

read(IChemObject) - Method in class org.openscience.cdk.io.CTXReader

read(IChemObject) - Method in class org.openscience.cdk.io.GamessReader

read(IChemObject) - Method in class org.openscience.cdk.io.Gaussian03Reader

read(IChemObject) - Method in class org.openscience.cdk.io.Gaussian98Reader

read(IChemObject) - Method in class org.openscience.cdk.io.GhemicalMMReader

read(IChemObject) - Method in class org.openscience.cdk.io.HINReader

Reads the content from a HIN input.

read(IChemObject) - Method in class org.openscience.cdk.io.INChIPlainTextReader

Reads a IChemObject of type object from input.

read(IChemObject) - Method in class org.openscience.cdk.io.INChIReader

Reads a IChemObject of type object from input.

read(IChemObject) - Method in interface org.openscience.cdk.io.ISimpleChemObjectReader

Reads an IChemObject of type "object" from input.

read(IChemObject) - Method in class org.openscience.cdk.io.MDLReader

Takes an object which subclasses IChemObject, e.g.

read(IChemObject) - Method in class org.openscience.cdk.io.MDLRXNReader

Takes an object which subclasses IChemObject, e.g.Molecule, and will read this (from file, database, internet etc).

read(IChemObject) - 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(IChemObject) - Method in class org.openscience.cdk.io.MDLRXNV3000Reader

read(IChemObject) - Method in class org.openscience.cdk.io.MDLV2000Reader

Takes an object which subclasses IChemObject, e.g.

read(IChemObject) - Method in class org.openscience.cdk.io.MDLV3000Reader

read(IChemObject) - Method in class org.openscience.cdk.io.Mol2Reader

Takes an object which subclasses IChemObject, e.g.Molecule, and will read this from from the Reader.

read(IChemObject) - Method in class org.openscience.cdk.io.PCCompoundASNReader

read(IChemObject) - Method in class org.openscience.cdk.io.PCCompoundXMLReader

read(IChemObject) - Method in class org.openscience.cdk.io.PCSubstanceXMLReader

read(IChemObject) - Method in class org.openscience.cdk.io.PDBReader

Takes an object which subclasses IChemObject, e.g.

read(IChemObject) - Method in class org.openscience.cdk.io.PMPReader

reads the content from a PMP input.

read(IChemObject) - Method in class org.openscience.cdk.io.ShelXReader

Read a ChemFile from input

read(IChemObject) - Method in class org.openscience.cdk.io.SMILESReader

reads the content from a XYZ input.

read(IChemObject) - Method in class org.openscience.cdk.io.VASPReader

read(IChemObject) - Method in class org.openscience.cdk.io.XYZReader

reads the content from a XYZ input.

read(IChemObject) - Method in class org.openscience.cdk.io.ZMatrixReader

Returns a IChemObject of type object bye reading from the input.

readAtomBlock(IAtomContainer) - Method in class org.openscience.cdk.io.MDLV3000Reader

Reads the atoms, coordinates and charges.

readAtomTypeMappings() - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingReader

Reads the atom type mappings from the data file.

readAtomTypes(IChemObjectBuilder) - Method in class org.openscience.cdk.config.atomtypes.AtomTypeReader

Reads the atom types from the data file.

readAtomTypes(IChemObjectBuilder) - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeReader

Reads the atom types from the data file.

readAtomTypes(IChemObjectBuilder) - Method in class org.openscience.cdk.config.CDKBasedAtomTypeConfigurator

Reads the atom types from the CDK based atom type list.

readAtomTypes(IChemObjectBuilder) - Method in interface org.openscience.cdk.config.IAtomTypeConfigurator

Reads a set of configured AtomType's into a List.

readAtomTypes(IChemObjectBuilder) - Method in class org.openscience.cdk.config.OWLBasedAtomTypeConfigurator

Reads the atom types from the OWL based atom type list.

readAtomTypes(IChemObjectBuilder) - Method in class org.openscience.cdk.config.TXTBasedAtomTypeConfigurator

Reads a text based configuration file.

readBondBlock(IAtomContainer) - Method in class org.openscience.cdk.io.MDLV3000Reader

Reads the bond atoms, order and stereo configuration.

readChar() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream

readChar() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream

readConnectionTable(IChemObjectBuilder) - Method in class org.openscience.cdk.io.MDLV3000Reader

readDictionary(Reader, String) - Method in class org.openscience.cdk.dict.DictionaryDatabase

Reads a custom dictionary into the database.

readElements() - Method in class org.openscience.cdk.config.elements.ElementPTReader

Triggers the XML parsing of the data file and returns the read Isotopes.

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() - Method in class org.openscience.cdk.modeling.builder3d.MM2BasedParameterSetReader

The main method which parses through the force field configuration file

readParameterSets() - Method in class org.openscience.cdk.modeling.builder3d.MMFF94BasedParameterSetReader

The main method which parses through the force field configuration file

readPharmacophoreDefinitions(String) - Static method in class org.openscience.cdk.pharmacophore.PharmacophoreUtils

Read in a set of pharmacophore definitions to create pharmacophore queries.

readPharmacophoreDefinitions(InputStream) - Static method in class org.openscience.cdk.pharmacophore.PharmacophoreUtils

Read in a set of pharmacophore definitions to create pharmacophore queries.

readRecord(int) - Method in interface org.openscience.cdk.io.random.IRandomAccessChemObjectReader

readRecord(int) - Method in class org.openscience.cdk.io.random.RandomAccessReader

Returns the object at given record No.

readSGroup(IAtomContainer) - Method in class org.openscience.cdk.io.MDLV3000Reader

Reads labels.

real - Variable in class org.openscience.cdk.math.Complex

The real part of this value

realmatrix - Variable in class org.openscience.cdk.math.IMatrix

the real part of the content

realvector - Variable in class org.openscience.cdk.math.IVector

The real part of this vector

RearrangementAnionReaction - Class in org.openscience.cdk.reaction.type

IReactionProcess which participate in movement resonance.

RearrangementAnionReaction() - Constructor for class org.openscience.cdk.reaction.type.RearrangementAnionReaction

Constructor of the RearrangementAnionReaction object

RearrangementCationReaction - Class in org.openscience.cdk.reaction.type

IReactionProcess which participate in movement resonance.

RearrangementCationReaction() - Constructor for class org.openscience.cdk.reaction.type.RearrangementCationReaction

Constructor of the RearrangementCharge2Reaction object

RearrangementChargeMechanism - Class in org.openscience.cdk.reaction.mechanism

This mechanism displaces the charge(radical, charge + or charge -) because of a double bond which is associated.

RearrangementChargeMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.RearrangementChargeMechanism

RearrangementLonePairReaction - Class in org.openscience.cdk.reaction.type

IReactionProcess which participate in movement resonance.

RearrangementLonePairReaction() - Constructor for class org.openscience.cdk.reaction.type.RearrangementLonePairReaction

Constructor of the RearrangementLonePairReaction object

RearrangementRadicalReaction - Class in org.openscience.cdk.reaction.type

IReactionProcess which participate in movement resonance.

RearrangementRadicalReaction() - Constructor for class org.openscience.cdk.reaction.type.RearrangementRadicalReaction

Constructor of the RearrangementRadicalReaction object

rebond(IAtomContainer) - Method in class org.openscience.cdk.graph.rebond.RebondTool

Rebonding using a Binary Space Partition Tree.

RebondTool - Class in org.openscience.cdk.graph.rebond

Provides tools to rebond a molecule from 3D coordinates only.

RebondTool(double, double, double) - Constructor for class org.openscience.cdk.graph.rebond.RebondTool

RecursiveSmartsAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts

This matches recursive smarts atoms.

RecursiveSmartsAtom(IQueryAtomContainer) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.RecursiveSmartsAtom

Creates a new instance

RecursiveSmartsExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

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

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.

registerWriter(Class<?>) - Method in class org.openscience.cdk.io.WriterFactory

ReInit(InputStream) - Method in class org.openscience.cdk.iupac.parser.NomParser

ReInit(Reader) - Method in class org.openscience.cdk.iupac.parser.NomParser

ReInit(NomParserTokenManager) - Method in class org.openscience.cdk.iupac.parser.NomParser

ReInit(SimpleCharStream) - Method in class org.openscience.cdk.iupac.parser.NomParserTokenManager

ReInit(SimpleCharStream, int) - Method in class org.openscience.cdk.iupac.parser.NomParserTokenManager

ReInit(Reader, int, int, int) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream

ReInit(Reader, int, int) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream

ReInit(Reader) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream

ReInit(InputStream, int, int, int) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream

ReInit(InputStream) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream

ReInit(InputStream, int, int) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream

ReInit(Reader, int, int, int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream

ReInit(Reader, int, int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream

ReInit(Reader) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream

ReInit(InputStream, int, int, int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream

ReInit(InputStream) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream

ReInit(InputStream, int, int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream

ReInit(InputStream) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

ReInit(Reader) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

ReInit(SMARTSParserTokenManager) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

ReInit(SimpleCharStream) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager

ReInit(SimpleCharStream, int) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager

relatedChemObjects() - Method in class org.openscience.cdk.debug.DebugMapping

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.

RELEVANT_RINGS - Static variable in class org.openscience.cdk.CDKConstants

The relevant rings computed for this molecule.

relevantCycles() - Method in class org.openscience.cdk.ringsearch.cyclebasis.CycleBasis

Returns the essential cycles of this cycle basis.

relevantCycles() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis

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

remove(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainer

remove(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugBioPolymer

remove(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugCrystal

remove(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugMolecule

remove(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugMonomer

remove(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugPolymer

remove(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugRing

remove(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugStrand

remove() - Method in class org.openscience.cdk.graph.AtomContainerPermutor

remove() - Method in class org.openscience.cdk.graph.MinimalPathIterator

remove(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Removes all atoms and electronContainers of a given atomcontainer from this container.

remove() - Method in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader

File IO generally does not support removing of entries.

remove() - Method in class org.openscience.cdk.io.iterator.event.DefaultEventChemObjectReader

File IO generally does not support removing of entries.

remove() - Method in class org.openscience.cdk.io.iterator.IteratingMDLConformerReader

remove() - Method in class org.openscience.cdk.io.iterator.IteratingMDLReader

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.IteratingSMILESReader

remove() - Method in class org.openscience.cdk.io.random.RandomAccessSDFReader

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

removeAllAtomContainers() - Method in class org.openscience.cdk.debug.DebugMoleculeSet

removeAllAtomContainers() - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet

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

removeAllBonds() - Method in class org.openscience.cdk.debug.DebugAtomContainer

removeAllBonds() - Method in class org.openscience.cdk.debug.DebugBioPolymer

removeAllBonds() - Method in class org.openscience.cdk.debug.DebugCrystal

removeAllBonds() - Method in class org.openscience.cdk.debug.DebugMolecule

removeAllBonds() - Method in class org.openscience.cdk.debug.DebugMonomer

removeAllBonds() - Method in class org.openscience.cdk.debug.DebugPolymer

removeAllBonds() - Method in class org.openscience.cdk.debug.DebugRing

removeAllBonds() - Method in class org.openscience.cdk.debug.DebugStrand

removeAllBonds() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

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

removeAllElectronContainers() - Method in class org.openscience.cdk.debug.DebugAtomContainer

removeAllElectronContainers() - Method in class org.openscience.cdk.debug.DebugBioPolymer

removeAllElectronContainers() - Method in class org.openscience.cdk.debug.DebugCrystal

removeAllElectronContainers() - Method in class org.openscience.cdk.debug.DebugMolecule

removeAllElectronContainers() - Method in class org.openscience.cdk.debug.DebugMonomer

removeAllElectronContainers() - Method in class org.openscience.cdk.debug.DebugPolymer

removeAllElectronContainers() - Method in class org.openscience.cdk.debug.DebugRing

removeAllElectronContainers() - Method in class org.openscience.cdk.debug.DebugStrand

removeAllElectronContainers() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Removes electronContainers from this container.

removeAllElements() - Method in class org.openscience.cdk.AtomContainer

Removes all atoms and bond from this container.

removeAllElements() - Method in class org.openscience.cdk.debug.DebugAminoAcid

removeAllElements() - Method in class org.openscience.cdk.debug.DebugAtomContainer

removeAllElements() - Method in class org.openscience.cdk.debug.DebugBioPolymer

removeAllElements() - Method in class org.openscience.cdk.debug.DebugCrystal

removeAllElements() - Method in class org.openscience.cdk.debug.DebugMolecule

removeAllElements() - Method in class org.openscience.cdk.debug.DebugMonomer

removeAllElements() - Method in class org.openscience.cdk.debug.DebugPolymer

removeAllElements() - Method in class org.openscience.cdk.debug.DebugRing

removeAllElements() - Method in class org.openscience.cdk.debug.DebugStrand

removeAllElements() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Removes all atoms and bond from this container.

removeAllIsotopes() - Method in class org.openscience.cdk.debug.DebugMolecularFormula

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.

removeAllMolecularFormulas() - Method in class org.openscience.cdk.debug.DebugAdductFormula

removeAllMolecularFormulas() - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet

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.

removeAllReactions() - Method in class org.openscience.cdk.debug.DebugReactionSet

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.

removeAllReactionSchemes() - Method in class org.openscience.cdk.debug.DebugReactionScheme

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.

removeAromaticityFlagsFromHoseCode(String) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator

removeAtom(int) - Method in class org.openscience.cdk.AtomContainer

Removes the atom at the given position from the AtomContainer.

removeAtom(IAtom) - Method in class org.openscience.cdk.AtomContainer

Removes the given atom from the AtomContainer.

removeAtom(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid

removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid

removeAtom(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer

removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer

removeAtom(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer

removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer

removeAtom(int) - Method in class org.openscience.cdk.debug.DebugCrystal

removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal

removeAtom(int) - Method in class org.openscience.cdk.debug.DebugMolecule

removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule

removeAtom(int) - Method in class org.openscience.cdk.debug.DebugMonomer

removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer

removeAtom(int) - Method in class org.openscience.cdk.debug.DebugPolymer

removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer

removeAtom(int) - Method in class org.openscience.cdk.debug.DebugRing

removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugRing

removeAtom(int) - Method in class org.openscience.cdk.debug.DebugStrand

removeAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand

removeAtom(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Removes the atom at the given position from the AtomContainer.

removeAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Removes the given atom from the AtomContainer.

removeAtomAndConnectedElectronContainers(IAtom) - Method in class org.openscience.cdk.AtomContainer

Removes the given atom and all connected electronContainers from the AtomContainer.

removeAtomAndConnectedElectronContainers(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid

removeAtomAndConnectedElectronContainers(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer

removeAtomAndConnectedElectronContainers(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer

removeAtomAndConnectedElectronContainers(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal

removeAtomAndConnectedElectronContainers(IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule

removeAtomAndConnectedElectronContainers(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer

removeAtomAndConnectedElectronContainers(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer

removeAtomAndConnectedElectronContainers(IAtom) - Method in class org.openscience.cdk.debug.DebugRing

removeAtomAndConnectedElectronContainers(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand

removeAtomAndConnectedElectronContainers(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Removes the given atom and all connected electronContainers from the AtomContainer.

removeAtomAndConnectedElectronContainers(IAtomContainerSet, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator

removeAtomAndConnectedElectronContainers(IChemModel, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator

Remove an Atom and the connected ElectronContainers from all AtomContainers inside an IChemModel.

removeAtomAndConnectedElectronContainers(IMoleculeSet, 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

removeAtomContainer(int) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet

removeAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugMoleculeSet

removeAtomContainer(int) - Method in class org.openscience.cdk.debug.DebugMoleculeSet

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.

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

removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid

removeBond(IBond) - Method in class org.openscience.cdk.debug.DebugAminoAcid

removeBond(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer

removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer

removeBond(IBond) - Method in class org.openscience.cdk.debug.DebugAtomContainer

removeBond(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer

removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer

removeBond(IBond) - Method in class org.openscience.cdk.debug.DebugBioPolymer

removeBond(int) - Method in class org.openscience.cdk.debug.DebugCrystal

removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal

removeBond(IBond) - Method in class org.openscience.cdk.debug.DebugCrystal

removeBond(int) - Method in class org.openscience.cdk.debug.DebugMolecule

removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule

removeBond(IBond) - Method in class org.openscience.cdk.debug.DebugMolecule

removeBond(int) - Method in class org.openscience.cdk.debug.DebugMonomer

removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer

removeBond(IBond) - Method in class org.openscience.cdk.debug.DebugMonomer

removeBond(int) - Method in class org.openscience.cdk.debug.DebugPolymer

removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer

removeBond(IBond) - Method in class org.openscience.cdk.debug.DebugPolymer

removeBond(int) - Method in class org.openscience.cdk.debug.DebugRing

removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugRing

removeBond(IBond) - Method in class org.openscience.cdk.debug.DebugRing

removeBond(int) - Method in class org.openscience.cdk.debug.DebugStrand

removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugStrand

removeBond(IBond) - Method in class org.openscience.cdk.debug.DebugStrand

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.

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

removeChemModel(int) - Method in interface org.openscience.cdk.interfaces.IChemSequence

Remove a ChemModel from this ChemSequence.

removeChemObjectIOListener(IChemObjectIOListener) - Method in class org.openscience.cdk.io.DefaultChemObjectReader

removeChemObjectIOListener(IChemObjectIOListener) - Method in class org.openscience.cdk.io.DefaultChemObjectWriter

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.iterator.DefaultIteratingChemObjectReader

removeChemObjectIOListener(IChemObjectIOListener) - Method in class org.openscience.cdk.io.iterator.event.DefaultEventChemObjectReader

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

removeChemSequence(int) - Method in interface org.openscience.cdk.interfaces.IChemFile

Removes the IChemSequence at the given position 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

removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugAminoAcid

removeElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer

removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainer

removeElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer

removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugBioPolymer

removeElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugCrystal

removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugCrystal

removeElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugMolecule

removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugMolecule

removeElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugMonomer

removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugMonomer

removeElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugPolymer

removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugPolymer

removeElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugRing

removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugRing

removeElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugStrand

removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugStrand

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(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(IMoleculeSet, 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

Produces an AtomContainer without explicit Hs but with H count from one with Hs.

removeHydrogensPreserveMultiplyBonded(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator

Produces an AtomContainer without explicit Hs but with H count from one with Hs.

removeIsotope(IIsotope) - Method in class org.openscience.cdk.debug.DebugMolecularFormula

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.

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

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAtom

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAtomContainer

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugAtomType

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugBioPolymer

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugBond

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugChemFile

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugChemModel

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugChemObject

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugChemSequence

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugCrystal

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugElectronContainer

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugElement

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugIsotope

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugLonePair

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugMapping

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugMolecule

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugMoleculeSet

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugMonomer

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugPolymer

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugReaction

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugReactionScheme

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugReactionSet

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugRing

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugSingleElectron

removeListener(IChemObjectListener) - Method in class org.openscience.cdk.debug.DebugStrand

removeListener(IChemObjectListener) - Method in interface org.openscience.cdk.interfaces.IChemObject

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

removeLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugAminoAcid

removeLonePair(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer

removeLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugAtomContainer

removeLonePair(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer

removeLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugBioPolymer

removeLonePair(int) - Method in class org.openscience.cdk.debug.DebugCrystal

removeLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugCrystal

removeLonePair(int) - Method in class org.openscience.cdk.debug.DebugMolecule

removeLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugMolecule

removeLonePair(int) - Method in class org.openscience.cdk.debug.DebugMonomer

removeLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugMonomer

removeLonePair(int) - Method in class org.openscience.cdk.debug.DebugPolymer

removeLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugPolymer

removeLonePair(int) - Method in class org.openscience.cdk.debug.DebugRing

removeLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugRing

removeLonePair(int) - Method in class org.openscience.cdk.debug.DebugStrand

removeLonePair(ILonePair) - Method in class org.openscience.cdk.debug.DebugStrand

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.

removeLoopBonds(IMolecule, 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.

removeMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugAdductFormula

removeMolecularFormula(int) - Method in class org.openscience.cdk.debug.DebugAdductFormula

removeMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet

removeMolecularFormula(int) - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet

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.

removeMolecule(IAtomContainer) - Method in class org.openscience.cdk.layout.TemplateHandler

removeMonomer(String) - Method in class org.openscience.cdk.debug.DebugBioPolymer

removeMonomer(String) - Method in class org.openscience.cdk.debug.DebugPolymer

removeMonomer(String) - Method in class org.openscience.cdk.debug.DebugStrand

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.Strand

Removes a particular monomer, specified by its name.

removeObject(String) - Method in class org.openscience.cdk.qsar.model.R2.RModel

Removes an object from the R session.

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

removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugAtom

removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugAtomContainer

removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet

removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugAtomType

removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugBioPolymer

removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugBond

removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugChemFile

removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugChemModel

removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugChemObject

removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugChemSequence

removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugCrystal

removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugElectronContainer

removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugElement

removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugIsotope

removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugLonePair

removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugMapping

removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugMolecularFormula

removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugMolecule

removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugMoleculeSet

removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugMonomer

removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugPolymer

removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugReaction

removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugReactionScheme

removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugReactionSet

removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugRing

removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugSingleElectron

removeProperty(Object) - Method in class org.openscience.cdk.debug.DebugStrand

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.

removeReaction(IReaction) - Method in class org.openscience.cdk.debug.DebugReactionSet

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

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.

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

removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAminoAcid

removeSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer

removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAtomContainer

removeSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer

removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugBioPolymer

removeSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugCrystal

removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugCrystal

removeSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugMolecule

removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugMolecule

removeSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugMonomer

removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugMonomer

removeSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugPolymer

removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugPolymer

removeSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugRing

removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugRing

removeSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugStrand

removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugStrand

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.

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

removeStrand(String) - Method in interface org.openscience.cdk.interfaces.IBioPolymer

Removes a particular strand, specified by its name.

removeSymbol(String) - Method in class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom

Remove a symbol from this QueryAtom

removeSymbol(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom

Remove a symbol from this QueryAtom

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

replaceAtomByAtom(IAtomContainer, IAtom, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator

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

replaceAtomContainer(int, IAtomContainer) - Method in class org.openscience.cdk.debug.DebugMoleculeSet

replaceAtomContainer(int, IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet

Replace the AtomContainer at a specific position (array has to be large enough).

reportErrors - Variable in class org.openscience.cdk.io.cml.CMLErrorHandler

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(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) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor

reshape(int, int) - Method in class org.openscience.cdk.math.IMatrix

Resize the matrix

reshape(int) - Method in class org.openscience.cdk.math.IVector

Resize this vector

Residue - Class in org.openscience.cdk.libio.md

A residue is a named, numbered collection of atoms in an MDMolecule.

Residue() - Constructor for class org.openscience.cdk.libio.md.Residue

Empty constructor

Residue(IAtomContainer, int, MDMolecule) - Constructor for class org.openscience.cdk.libio.md.Residue

Constructor to create a Residue based on an AC, a number, and a MDMolecule.

RESIDUE_NAME - Static variable in class org.openscience.cdk.templates.AminoAcids

RESIDUE_NAME_SHORT - Static variable in class org.openscience.cdk.templates.AminoAcids

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

Main method to be called to resolve overlap situations.

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

revaluator - Static variable in class org.openscience.cdk.qsar.model.R.RModel

Deprecated. The object that performs the calls to the R engine.

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.

RH - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

RHENIUM - Static variable in class org.openscience.cdk.config.Elements

RHENIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

RHODIUM - Static variable in class org.openscience.cdk.config.Elements

RHODIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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_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.

RingAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts

This matches an atom in a specific size ring.

RingAtom(int) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.RingAtom

Creates a new instance

RingBond - Class in org.openscience.cdk.isomorphism.matchers.smarts

This smarts bond matches any bond that is in a ring.

RingBond() - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.RingBond

Creates a new instance

RingConnectivity() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

RingIdentifier() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

RingIdentifierAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts

This encapsulates an atom with a ring identifier, with an optional ring bond specified.

RingIdentifierAtom() - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.RingIdentifierAtom

RingManipulator - Class in org.openscience.cdk.tools.manipulator

RingManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.RingManipulator

RingMembership() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

RingMembershipAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts

This query atom matches any atom with a certain number of SSSR.

RingMembershipAtom(int) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.RingMembershipAtom

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.

RingSet - Class in org.openscience.cdk

Maintains a set of Ring objects.

RingSet() - Constructor for class org.openscience.cdk.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

RModel - Class in org.openscience.cdk.qsar.model.R

Deprecated.

RModel(String[]) - Constructor for class org.openscience.cdk.qsar.model.R.RModel

Deprecated. Initializes SJava and R with the specified command line arguments (see R documentation).

RModel() - Constructor for class org.openscience.cdk.qsar.model.R.RModel

Deprecated. Initializes SJava with the --vanilla, -q, --slave flags.

RModel - Class in org.openscience.cdk.qsar.model.R2

Base class for the R-CDK interface.

RModel() - Constructor for class org.openscience.cdk.qsar.model.R2.RModel

Initializes R with the --vanilla, --quiet, --slave flags.

RN - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

RNode - Class in org.openscience.cdk.isomorphism.mcss

Node of the resolution graphe (RGraph) An RNode represents an association betwwen 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

ROENTGENIUM - Static variable in class org.openscience.cdk.config.Elements

rootMeanSquareGradient(GVector) - Method in class org.openscience.cdk.modeling.forcefield.GeometricMinimizer

Calculate the Root Mean Square gradient (RMS)

rootNode - Variable in class org.openscience.cdk.tools.HOSECodeGenerator

RotatableBondsCountDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

The number of rotatable bonds is given by the SMARTS specified by Daylight on SMARTS tutorial

RotatableBondsCountDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor

Constructor for the RotatableBondsCountDescriptor object

rotate(IAtomContainer, Point2d, double) - Static method in class org.openscience.cdk.geometry.GeometryTools

Rotates a molecule around a given center by a given angle

rotate(IAtom, Point3d, Point3d, double) - Static method in class org.openscience.cdk.geometry.GeometryTools

Rotates a 3D point about a specified line segment by a specified angle.

rotate(Vector3d, Vector3d, double) - Static method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

Rotates a vector around an axis

rotateAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.geometry.alignment.KabschAlignment

Rotates the IAtomContainer coordinates by the rotation matrix.

rows - Variable in class org.openscience.cdk.math.IMatrix

the count of rows of the matrix

rows - Variable in class org.openscience.cdk.math.Matrix

the number of rows of this matrix

RssWriter - Class in org.openscience.cdk.io

Generates an RSS feed.

RssWriter() - Constructor for class org.openscience.cdk.io.RssWriter

RU - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

RUBIDIUM - Static variable in class org.openscience.cdk.config.Elements

RUBIDIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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 class org.openscience.cdk.config.Elements

RUTHENIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

RUTHERFORDIUM - Static variable in class org.openscience.cdk.config.Elements

RUTHERFORDIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

S

s - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

S - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

S_BOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

SAMARIUM - Static variable in class org.openscience.cdk.config.Elements

sample(IMolecule) - Static method in class org.openscience.cdk.structgen.VicinitySampler

Choose any possible quadruple of the set of atoms in ac and establish all of the possible bonding schemes according to Faulon's equations.

SANARIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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

saveModel(String, String) - Static method in class org.openscience.cdk.qsar.model.R.RModel

Deprecated. Saves a R model to disk.

saveModel(String, String) - Method in class org.openscience.cdk.qsar.model.R2.RModel

Saves a R model to disk.

SB - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

SC - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

scaleMolecule(IAtomContainer, Dimension, double) - Static method in class org.openscience.cdk.geometry.GeometryTools

Scales a molecule such that it fills a given percentage of a given dimension See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets

scaleMolecule(IAtomContainer, double) - Static method in class org.openscience.cdk.geometry.GeometryTools

Multiplies all the coordinates of the atoms of the given molecule with the scalefactor.

SCANDIUM - Static variable in class org.openscience.cdk.config.Elements

SCANDIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

SDFFormat - Class in org.openscience.cdk.io.formats

See here.

SDFWriter - Class in org.openscience.cdk.io

Writes MDL SD files ([Dalby, A. and Nourse, J. G. and Hounshell, W. D. and Gushurst, A. K. and Grier, D. L. and Leland, B. A. and Laufer, J., Description of Several Chemical Structure File Formats Used by Computer Programs Developed at Molecular Design Limited, Journal of Chemical Information and Computer Sciences, 1992, 32:244-255]).

SDFWriter(Writer) - Constructor for class org.openscience.cdk.io.SDFWriter

Constructs a new SDFWriter that writes to the given Writer.

SDFWriter(OutputStream) - Constructor for class org.openscience.cdk.io.SDFWriter

Constructs a new MDLWriter that can write to a given OutputStream.

SDFWriter() - Constructor for class org.openscience.cdk.io.SDFWriter

se - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

SE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

SEABORGIUM - Static variable in class org.openscience.cdk.config.Elements

SEABORGIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

search(IAtomContainer, IAtomContainer, BitSet, BitSet, boolean, boolean) - Static 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.

SELENIUM - Static variable in class org.openscience.cdk.config.Elements

SELENIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

set(int, IAtomContainer) - Method in class org.openscience.cdk.ConformerContainer

set(IChemObject) - Method in class org.openscience.cdk.io.random.RandomAccessReader

set2ndOrderErrorApproximateGradientMMFF94SumEA(GVector) - Method in class org.openscience.cdk.modeling.forcefield.AngleBending

Evaluate a 2nd order approximation of the gradient, of the angle bending term, for a given atoms coordinates

set2ndOrderErrorApproximateGradientMMFF94SumEBA(GVector) - Method in class org.openscience.cdk.modeling.forcefield.StretchBendInteractions

Evaluate a 2nd order approximation of the gradient for the stretch-bend interaction term, given the atoms coordinates.

set2ndOrderErrorApproximateGradientMMFF94SumET(GVector) - Method in class org.openscience.cdk.modeling.forcefield.Torsions

Evaluate a 2nd order error approximation of the gradient, for the torsion term, given the atoms coordinates.

set2ndOrderErrorApproximateGradientMMFF94SumEvdW(GVector) - Method in class org.openscience.cdk.modeling.forcefield.VanDerWaalsInteractions

Evaluate a 2nd order error approximation of the gradient, for the Van Der Waals interaction term, given the atoms coordinates

set2ndOrderErrorApproximateHessianMMFF94SumEA(GVector) - Method in class org.openscience.cdk.modeling.forcefield.AngleBending

Evaluate a 2nd order approximation of the Hessian, for the angle bending energy term, given the atoms coordinates.

set2ndOrderErrorApproximateHessianMMFF94SumEB(GVector) - Method in class org.openscience.cdk.modeling.forcefield.BondStretching

Evaluate a 2nd order approximation of the Hessian, for the bond stretching energy term, given the atoms coordinates.

set2ndOrderErrorApproximateHessianMMFF94SumET(GVector) - Method in class org.openscience.cdk.modeling.forcefield.Torsions

Evaluate a 2nd order approximation of the Hessian, for the torsion energy term, given the atoms coordinates.

set5thOrderApproximateGradientMMFF94SumET(GVector) - Method in class org.openscience.cdk.modeling.forcefield.Torsions

Evaluate an 5 order approximation of the gradient, of the torsion term, given the atoms coordinates

set5thOrderErrorApproximateGradientMMFF94SumEA(GVector) - Method in class org.openscience.cdk.modeling.forcefield.AngleBending

Evaluate a 5th order error approximation of the gradient, of the angle bending term, for a given atoms coordinates

set5thOrderErrorApproximateGradientMMFF94SumEBA(GVector) - Method in class org.openscience.cdk.modeling.forcefield.StretchBendInteractions

Evaluate a 5th order error approximation of the gradient, of the stretch-bend interaction term, for a given atoms coordinates

set5thOrderErrorApproximateGradientMMFF94SumEvdW(GVector) - Method in class org.openscience.cdk.modeling.forcefield.VanDerWaalsInteractions

Evaluate a 5th order error approximation of the gradient, for the Van Der Waals interaction term, given the atoms coordinates

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

setA(Vector3d) - Method in interface org.openscience.cdk.interfaces.ICrystal

Sets the A unit cell axes in carthesian coordinates in a eucledian space.

setAbout(String) - Method in class org.openscience.cdk.io.RssWriter

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

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.

setAngleBending2ndOrderErrorApproximateGradient(GVector) - Method in class org.openscience.cdk.modeling.forcefield.AngleBending

Set a 2nd order approximation of the gradient, for the angle bending, given the atoms coordinates

setAngleBending2ndOrderErrorApproximateHessian(GVector) - Method in class org.openscience.cdk.modeling.forcefield.AngleBending

Evaluate a 2nd order approximation of the Hessian, for the angle bending, given the atoms coordinates.

setAngleBendingFirstDerivative(GVector) - Method in class org.openscience.cdk.modeling.forcefield.AngleBending

Calculate the angle bending first derivative respect to the cartesian coordinates of the atoms.

setAngleBendingFlag(boolean) - Method in class org.openscience.cdk.modeling.forcefield.AngleBending

setAngleBendingSecondDerivative(GVector) - Method in class org.openscience.cdk.modeling.forcefield.AngleBending

Calculate the angle bending second derivative respect to the cartesian coordinates of the atoms.

setArrayValue(double[][]) - Method in class org.openscience.cdk.graph.invariant.GIMatrix

Resets the value of the matrix to the given array of double numbers

setAtom(int, IAtom) - Method in class org.openscience.cdk.AtomContainer

Sets the atom at position number in [0,..].

setAtom(IAtom, int) - Method in class org.openscience.cdk.Bond

Sets an Atom in this bond.

setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid

setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer

setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer

setAtom(IAtom, int) - Method in class org.openscience.cdk.debug.DebugBond

setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal

setAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugLonePair

setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugMolecule

setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer

setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer

setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugRing

setAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugSingleElectron

setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugStrand

setAtom(int, IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Set the atom at position number in [0,..].

setAtom(IAtom, int) - Method in interface org.openscience.cdk.interfaces.IBond

Sets an Atom in this bond.

setAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.ILonePair

Sets the associated Atom.

setAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.ISingleElectron

Sets the associated Atom.

setAtom(IQueryAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RingIdentifierAtom

setAtom(IAtom) - Method in class org.openscience.cdk.LonePair

Sets the associated Atom.

setAtom(IAtom) - Method in class org.openscience.cdk.SingleElectron

Sets the associated Atom.

setAtom(IAtom) - Method in class org.openscience.cdk.smiles.InvPair

setAtomAt(IAtom, int) - Method in class org.openscience.cdk.Association

Sets an Atom in this Association.

setAtomAt(IAtom, int) - Method in class org.openscience.cdk.isomorphism.matchers.OrderQueryBond

setAtomAt(IAtom, int) - Method in class org.openscience.cdk.isomorphism.matchers.OrderQueryBondOrderOnly

setAtomCheckRadius(double) - Method in class org.openscience.cdk.protein.ProteinPocketFinder

setAtomContainer(AtomContainer) - Method in class org.openscience.cdk.graph.AtomContainerPermutor

setAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.HydrogenAtom

Sets IAtomContainer.

setAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RecursiveSmartsAtom

setAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.structgen.SingleStructureRandomGenerator

Sets the AtomContainer attribute of the SingleStructureRandomGenerator object.

setAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.structgen.stochastic.PartialFilledStructureMerger

Sets the AtomContainer attribute of the PartialFilledStructureMerger object

setAtomDistance(GVector) - Method in class org.openscience.cdk.modeling.forcefield.VanDerWaalsInteractions

Calculate the actual Rij

setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugAtom

setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugAtomType

setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugElement

setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugIsotope

setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

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.

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(IMoleculeSet, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator

setAtomProperties(IReaction, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator

setAtomProperties(IReactionSet, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator

setAtoms(IAtom[]) - Method in class org.openscience.cdk.Association

Sets the array of atoms making up this Association.

setAtoms(IAtom[]) - Method in class org.openscience.cdk.AtomContainer

Sets the array of atoms of this AtomContainer.

setAtoms(IAtom[]) - Method in class org.openscience.cdk.Bond

Sets the array of atoms making up this bond.

setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugAminoAcid

setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugAtomContainer

setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugBioPolymer

setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugBond

setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugCrystal

setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugMolecule

setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugMonomer

setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugPolymer

setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugRing

setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugStrand

setAtoms(IAtom[]) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Sets the array of atoms of this AtomContainer.

setAtoms(IAtom[]) - Method in interface org.openscience.cdk.interfaces.IBond

Sets the array of atoms making up this bond.

setAtoms(IAtom[]) - Method in class org.openscience.cdk.isomorphism.matchers.OrderQueryBond

setAtoms(IAtom[]) - Method in class org.openscience.cdk.isomorphism.matchers.OrderQueryBondOrderOnly

setAtoms(IAtom[]) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond

setAtomsDistancesFirstOrderDerivative(GVector) - Method in class org.openscience.cdk.modeling.forcefield.VanDerWaalsInteractions

Calculate the atoms distances (Rij) first derivative respect to the cartesian coordinates of the atoms.

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

setAtomTypeName(String) - Method in class org.openscience.cdk.debug.DebugAtomType

setAtomTypeName(String) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

setAtomTypeName(String) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

setAtomTypeName(String) - Method in interface org.openscience.cdk.interfaces.IAtomType

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

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

setB(Vector3d) - Method in interface org.openscience.cdk.interfaces.ICrystal

Sets the B unit cell axes in carthesian coordinates.

setBondLength(double) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

Set the bond length used for laying out the molecule.

setBondLengthsFirstDerivative(GVector, double[], int[][]) - Method in class org.openscience.cdk.modeling.forcefield.BondStretching

Set the bond lengths first derivative respect to the cartesian coordinates of the atoms.

setBondLengthsSecondDerivative(GVector, double[], int[][]) - Method in class org.openscience.cdk.modeling.forcefield.BondStretching

Calculate the bond lengths second derivative respect to the cartesian coordinates of the atoms.

setBondLengthsSecondDerivative(GVector) - Method in class org.openscience.cdk.modeling.forcefield.VanDerWaalsInteractions

Calculate the bond lengths second derivative respect to the cartesian coordinates of the atoms.

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

setBondOrderSum(Double) - Method in class org.openscience.cdk.debug.DebugAtomType

setBondOrderSum(Double) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

setBondOrderSum(Double) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

setBondOrderSum(Double) - Method in interface org.openscience.cdk.interfaces.IAtomType

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.

setBondType(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTSimpleBond

Sets type of bond.

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

setC(Vector3d) - Method in interface org.openscience.cdk.interfaces.ICrystal

Sets the C unit cell axes in carthesian coordinates.

setCASid(String) - Method in class org.openscience.cdk.PeriodicTableElement

Sets the CAS (Chemical Abstracts Service), which this element has.

setChainID(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom

setChainID(String) - Method in class org.openscience.cdk.debug.DebugPDBMonomer

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

setCharge(Double) - Method in class org.openscience.cdk.Atom

Sets the partial charge of this atom.

setCharge(Integer) - Method in class org.openscience.cdk.debug.DebugAdductFormula

setCharge(Double) - Method in class org.openscience.cdk.debug.DebugAtom

setCharge(Double) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

setCharge(Integer) - Method in class org.openscience.cdk.debug.DebugMolecularFormula

setCharge(Double) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

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 partial charge of this IMolecularFormula.

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 partial charge of this IMolecularFormula.

setCharge(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTCharge

Sets the charge value.

setChargeGroups(List) - 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 +1 for cationic atom types -1 for anionic atom types carboxylic oxygen -0.5 phosphorylic oxygen -0.66 sulfanilic oxygen -0.5 or to formal charge (which must be determined elsewhere or set manually) polycations are not handled by this approach

setChemicalSerie(String) - Method in class org.openscience.cdk.PeriodicTableElement

Sets the chemical series of this element.

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

setClockwise(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom

setClockwise(boolean) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTChirality

setCoefficients(Matrix) - Method in class org.openscience.cdk.math.qm.Orbitals

Set a coefficient matrix

setCoefficients(double[]) - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModelFit

Deprecated. Set the fitted coefficients.

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.

setConvergenceParametersForCGM(int, double) - Method in class org.openscience.cdk.modeling.forcefield.GeometricMinimizer

Set convergence parameters for Conjugate Gradient Method

setConvergenceParametersForNRM(int, double) - Method in class org.openscience.cdk.modeling.forcefield.GeometricMinimizer

Set convergence parameters for Newton-Raphson Method

setConvergenceParametersForSDM(int, double) - Method in class org.openscience.cdk.modeling.forcefield.GeometricMinimizer

Set convergence parameters for Steepest Decents Method

setCount(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTImplicitHCount

Set the value of implicit H count.

setCount(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTTotalHCount

Sets total H count.

setCountElectrons(int) - Method in class org.openscience.cdk.math.qm.Orbitals

Sets the count of electrons, which occupies the orbitals

setCovalentRadius(Double) - Method in class org.openscience.cdk.AtomType

Sets the covalent radius for this AtomType.

setCovalentRadius(Double) - Method in class org.openscience.cdk.debug.DebugAtom

setCovalentRadius(Double) - Method in class org.openscience.cdk.debug.DebugAtomType

setCovalentRadius(Double) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

setCovalentRadius(Double) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

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.PeriodicTableElement

Set the covalent radius.

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

setCrystal(ICrystal) - Method in interface org.openscience.cdk.interfaces.IChemModel

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

setDebugStream(PrintStream) - Method in class org.openscience.cdk.iupac.parser.NomParserTokenManager

setDebugStream(PrintStream) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager

setDefaultReactions() - Method in class org.openscience.cdk.tools.StructureResonanceGenerator

Set the default reactions that must be presents to generate the resonance.

setDefaultRestrictions() - Method in class org.openscience.cdk.formula.MassToFormulaTool

Set the default restrictions that must be presents in the molecular formula.

setDefinition(String) - Method in class org.openscience.cdk.dict.Entry

setDegree(int) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom

setDegree(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTChirality

setDeltarijAndDeltarkj(GVector) - Method in class org.openscience.cdk.modeling.forcefield.StretchBendInteractions

Calculate the current bond distances rij and rkj for each angle j, and the difference with the reference bonds.

setDeltav(GVector) - Method in class org.openscience.cdk.modeling.forcefield.AngleBending

Calculate the actual bond angles vijk and the difference with the reference angles.

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<DescriptorSpecification>) - Method in class org.openscience.cdk.qsar.DescriptorEngine

Set the list of DescriptorSpecification objects.

setDetails(String) - Method in class org.openscience.cdk.validate.ValidationTest

setDF(int) - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModelPredict

Deprecated. Set the degrees of freedom.

setdfResidual(int) - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModelFit

Deprecated. Set the DOF of the residuals.

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

setDirection(IReaction.Direction) - Method in interface org.openscience.cdk.interfaces.IReaction

Sets the direction of the reaction.

setDirection(GVector, GVector) - Method in class org.openscience.cdk.modeling.forcefield.ConjugateGradientMethod

Calculate the conjugate gradient direction.

setDirection(IReaction.Direction) - Method in class org.openscience.cdk.Reaction

Sets the direction of the reaction.

setDisplayMode(int) - Method in class org.openscience.cdk.renderer.GraphRendererModel

Set the display mode

setDocumentProperty(String, String) - Method in class org.openscience.cdk.io.iterator.event.EventCMLHandler

Procedure required by the CDOInterface.

setElectronCount(Integer) - Method in class org.openscience.cdk.debug.DebugBond

setElectronCount(Integer) - Method in class org.openscience.cdk.debug.DebugElectronContainer

setElectronCount(Integer) - Method in class org.openscience.cdk.debug.DebugLonePair

setElectronCount(Integer) - Method in class org.openscience.cdk.debug.DebugSingleElectron

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.

setEndChainID(Character) - Method in class org.openscience.cdk.debug.DebugPDBStructure

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.

setEndInsertionCode(Character) - Method in class org.openscience.cdk.debug.DebugPDBStructure

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.

setEndSequenceNumber(Integer) - Method in class org.openscience.cdk.debug.DebugPDBStructure

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.

setEnergyGradient(GVector) - Method in interface org.openscience.cdk.modeling.forcefield.IPotentialFunction

Evaluate the gradient of the potential energy function in a given point.

setEnergyGradient(GVector) - Method in class org.openscience.cdk.modeling.forcefield.MMFF94EnergyFunction

Evaluate the gradient for the MMFF94 energy function in a given 3xN point

setEnergyHessian(GVector) - Method in interface org.openscience.cdk.modeling.forcefield.IPotentialFunction

Evaluate the hessian of the potential energy function in a given point.

setEnergyHessian(GVector) - Method in class org.openscience.cdk.modeling.forcefield.MMFF94EnergyFunction

Evaluate the hessian for the MMFF94 energy function in a given 3xN point

setExactMass(Double) - Method in class org.openscience.cdk.debug.DebugAtom

setExactMass(Double) - Method in class org.openscience.cdk.debug.DebugAtomType

setExactMass(Double) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

setExactMass(Double) - Method in class org.openscience.cdk.debug.DebugIsotope

setExactMass(Double) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

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.Isotope

Sets the ExactMass attribute of the Isotope object.

setExpanded(boolean) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

setExpanded(boolean) - Method in class org.openscience.cdk.FragmentAtom

setExpanded(boolean) - Method in interface org.openscience.cdk.interfaces.IFragmentAtom

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

setFirstGraphSize(int) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph

Sets the size of the first of the two compared graphs.

setFitted(double[][]) - Method in class org.openscience.cdk.qsar.model.R.CNNClassificationModelFit

Deprecated. Set the fitted values.

setFitted(double[][]) - Method in class org.openscience.cdk.qsar.model.R.CNNRegressionModelFit

Deprecated. Set the fitted values.

setFitted(double[]) - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModelFit

Deprecated. Set the fitted values.

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

setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugAtom

setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugAtomContainer

setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet

setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugAtomType

setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugBioPolymer

setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugBond

setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugChemFile

setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugChemModel

setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugChemObject

setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugChemSequence

setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugCrystal

setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugElectronContainer

setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugElement

setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugIsotope

setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugLonePair

setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugMapping

setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugMolecule

setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugMoleculeSet

setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugMonomer

setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugPolymer

setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugReaction

setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugReactionScheme

setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugReactionSet

setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugRing

setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugSingleElectron

setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugStrand

setFlag(int, boolean) - Method in interface org.openscience.cdk.interfaces.IChemObject

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

setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugAtom

setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugAtomContainer

setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet

setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugAtomType

setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugBioPolymer

setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugBond

setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugChemFile

setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugChemModel

setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugChemObject

setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugChemSequence

setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugCrystal

setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugElectronContainer

setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugElement

setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugIsotope

setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugLonePair

setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugMapping

setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugMolecule

setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugMoleculeSet

setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugMonomer

setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugPolymer

setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugReaction

setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugReactionScheme

setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugReactionSet

setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugRing

setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugSingleElectron

setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugStrand

setFlags(boolean[]) - Method in interface org.openscience.cdk.interfaces.IChemObject

Sets the whole set of flags.

setFletcherReeves_uk(GVector, GVector) - Method in class org.openscience.cdk.modeling.forcefield.ConjugateGradientMethod

Fletcher-Reeves: uk = gk gk / gk-1 gk-1

setForbidden(BitSet) - Method in class org.openscience.cdk.isomorphism.mcss.RNode

Sets the forbidden attribute of the RNode object

setForceFieldConfigurator(String) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator

Constructor for the ForceFieldConfigurator object

setFormalCharge(Integer) - Method in class org.openscience.cdk.AtomType

Sets the formal charge of this atom.

setFormalCharge(Integer) - Method in class org.openscience.cdk.debug.DebugAtom

setFormalCharge(Integer) - Method in class org.openscience.cdk.debug.DebugAtomType

setFormalCharge(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

setFormalCharge(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

setFormalCharge(Integer) - Method in interface org.openscience.cdk.interfaces.IAtomType

Sets the formal charge of this atom.

setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.AtomType

Sets the formal neighbour count of this atom.

setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.debug.DebugAtom

setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.debug.DebugAtomType

setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

setFormalNeighbourCount(Integer) - Method in interface org.openscience.cdk.interfaces.IAtomType

Sets the formal neighbour count of this atom.

setFormula(IMolecularFormula) - Method in class org.openscience.cdk.formula.IsotopeContainer

Set IMolecularFormula object of this container.

setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.Atom

Sets a point specifying the location of this atom in a Crystal unit cell.

setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugAtom

setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

setFractionalPoint3d(Point3d) - Method in interface org.openscience.cdk.interfaces.IAtom

Sets a point specifying the location of this atom in a Crystal unit cell.

setFragment(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

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.

setFunctionMMFF94SumEBA(GVector) - Method in class org.openscience.cdk.modeling.forcefield.StretchBendInteractions

Set the MMFF94 stretch-bend interaction term given the atoms cartesian coordinates.

setFunctionMMFF94SumEvdW(GVector) - Method in class org.openscience.cdk.modeling.forcefield.VanDerWaalsInteractions

Evaluate the MMFF94 Van Der Waals interaction energy given the atoms cartesian coordinates.

setGradientMMFF94SumEA(GVector) - Method in class org.openscience.cdk.modeling.forcefield.AngleBending

Evaluate the gradient of the angle bending term for a given atoms coordinates

setGradientMMFF94SumEB(GVector) - Method in class org.openscience.cdk.modeling.forcefield.BondStretching

Evaluate the first order partial derivative for the bond stretching given the atoms coordinates

setGradientMMFF94SumEBA(GVector) - Method in class org.openscience.cdk.modeling.forcefield.StretchBendInteractions

Evaluate the gradient of the stretch-bend interaction term.

setGradientMMFF94SumEQ(GVector) - Method in class org.openscience.cdk.modeling.forcefield.ElectrostaticInteractions

Set the gradient of the MMFF94 Electrostatic interaction term.

setGradientMMFF94SumET(GVector) - Method in class org.openscience.cdk.modeling.forcefield.Torsions

Evaluate the gradient of the torsions term.

setGradientMMFF94SumEvdW(GVector) - Method in class org.openscience.cdk.modeling.forcefield.VanDerWaalsInteractions

Set the gradient of the MMFF94 Van Der Waals interaction term.

setGrid(double[][][]) - Method in class org.openscience.cdk.protein.ProteinPocketFinder

setGrid(double[][][]) - Method in class org.openscience.cdk.tools.GridGenerator

setGroup(Integer) - Method in class org.openscience.cdk.PeriodicTableElement

Sets the group, which this element belongs.

setGroupNumber(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTPeriodicGroupNumber

Set the periodic table group number for this element.

setHCount(int) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom

setHessian(double[][]) - Method in class org.openscience.cdk.qsar.model.R.CNNClassificationModelFit

Deprecated. Set the Hessian for the final network.

setHessian(double[][]) - Method in class org.openscience.cdk.qsar.model.R.CNNRegressionModelFit

Deprecated. Set the Hessian for the final network.

setHessianMMFF94SumEA(GVector) - Method in class org.openscience.cdk.modeling.forcefield.AngleBending

Evaluate the hessian for the angle bending.

setHessianMMFF94SumEB(GVector) - Method in class org.openscience.cdk.modeling.forcefield.BondStretching

Evaluate the second order partial derivative (hessian) for the bond stretching given the atoms coordinates

setHessianMMFF94SumEBA(GVector) - Method in class org.openscience.cdk.modeling.forcefield.StretchBendInteractions

Evaluate the hessian of the stretch-bend interaction.

setHessianMMFF94SumEQ(GVector) - Method in class org.openscience.cdk.modeling.forcefield.ElectrostaticInteractions

Evaluate the second order partial derivative (hessian) for the Electrostatic interaction energy given the atoms coordinates

setHessianMMFF94SumET(GVector) - Method in class org.openscience.cdk.modeling.forcefield.Torsions

Evaluate the hessian of the torsions.

setHessianMMFF94SumEvdW(GVector) - Method in class org.openscience.cdk.modeling.forcefield.VanDerWaalsInteractions

Evaluate the second order partial derivative (hessian) for the van der Waals interactions given the atoms coordinates

setHetAtom(Boolean) - Method in class org.openscience.cdk.debug.DebugPDBAtom

setHetAtom(Boolean) - Method in interface org.openscience.cdk.interfaces.IPDBAtom

setHetAtom(Boolean) - Method in class org.openscience.cdk.protein.data.PDBAtom

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

setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.debug.DebugAtomType

setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

setHybridization(IAtomType.Hybridization) - Method in interface org.openscience.cdk.interfaces.IAtomType

Sets the hybridization of this atom.

setHybridizationNumber(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTHybrdizationNumber

setHydrogenCount(Integer) - Method in class org.openscience.cdk.Atom

Sets the number of implicit hydrogen count of this atom.

setHydrogenCount(Integer) - Method in class org.openscience.cdk.debug.DebugAtom

setHydrogenCount(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

setHydrogenCount(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

setHydrogenCount(Integer) - Method in interface org.openscience.cdk.interfaces.IAtom

Sets the implicit hydrogen count of this atom.

setICode(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom

setICode(String) - Method in class org.openscience.cdk.debug.DebugPDBMonomer

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

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

setID(String) - Method in class org.openscience.cdk.debug.DebugAtom

setID(String) - Method in class org.openscience.cdk.debug.DebugAtomContainer

setID(String) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet

setID(String) - Method in class org.openscience.cdk.debug.DebugAtomType

setID(String) - Method in class org.openscience.cdk.debug.DebugBioPolymer

setID(String) - Method in class org.openscience.cdk.debug.DebugBond

setID(String) - Method in class org.openscience.cdk.debug.DebugChemFile

setID(String) - Method in class org.openscience.cdk.debug.DebugChemModel

setID(String) - Method in class org.openscience.cdk.debug.DebugChemObject

setID(String) - Method in class org.openscience.cdk.debug.DebugChemSequence

setID(String) - Method in class org.openscience.cdk.debug.DebugCrystal

setID(String) - Method in class org.openscience.cdk.debug.DebugElectronContainer

setID(String) - Method in class org.openscience.cdk.debug.DebugElement

setID(String) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

setID(String) - Method in class org.openscience.cdk.debug.DebugIsotope

setID(String) - Method in class org.openscience.cdk.debug.DebugLonePair

setID(String) - Method in class org.openscience.cdk.debug.DebugMapping

setID(String) - Method in class org.openscience.cdk.debug.DebugMolecule

setID(String) - Method in class org.openscience.cdk.debug.DebugMoleculeSet

setID(String) - Method in class org.openscience.cdk.debug.DebugMonomer

setID(String) - Method in class org.openscience.cdk.debug.DebugPolymer

setID(String) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

setID(String) - Method in class org.openscience.cdk.debug.DebugReaction

setID(String) - Method in class org.openscience.cdk.debug.DebugReactionScheme

setID(String) - Method in class org.openscience.cdk.debug.DebugReactionSet

setID(String) - Method in class org.openscience.cdk.debug.DebugRing

setID(String) - Method in class org.openscience.cdk.debug.DebugSingleElectron

setID(String) - Method in class org.openscience.cdk.debug.DebugStrand

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(int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleNode

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.

setImagelink(String) - Method in class org.openscience.cdk.io.RssWriter

setImaginaryPart(double) - Method in class org.openscience.cdk.math.Complex

Sets the imaginary part of this value

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

setInputStream(InputStream) - Method in interface org.openscience.cdk.config.IAtomTypeConfigurator

Sets the file containing the config data.

setInputStream(InputStream) - Method in class org.openscience.cdk.config.OWLBasedAtomTypeConfigurator

setInputStream(InputStream) - Method in class org.openscience.cdk.config.TXTBasedAtomTypeConfigurator

Sets the file containing the config 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.

setInternuclearSeparation(GVector) - Method in class org.openscience.cdk.modeling.forcefield.ElectrostaticInteractions

Calculate the internuclear separation Rij

setInternuclearSeparationFirstOrderDerivative(GVector) - Method in class org.openscience.cdk.modeling.forcefield.ElectrostaticInteractions

Calculate the internuclear separation (Rij) first derivative respect to the cartesian coordinates of the atoms.

setInternuclearSeparationSecondDerivative(GVector) - Method in class org.openscience.cdk.modeling.forcefield.ElectrostaticInteractions

Calculate the internuclear separation second derivative respect to the cartesian coordinates of the atoms.

setInterrupted(boolean) - Method in class org.openscience.cdk.smiles.DeduceBondSystemTool

setIsPopupAction(boolean) - Method in class org.openscience.cdk.renderer.JCPAction2D

Sets the isPopupAction attribute of the JCPAction object

setJChemPaintPanel(JFrame) - Method in class org.openscience.cdk.renderer.JCPAction2D

Sets the jChemPaintPanel attribute of the JCPAction object

setkplus1Coordinates(GVector, double) - Method in class org.openscience.cdk.modeling.forcefield.GeometricMinimizer

setLabel(String) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

setLabel(String) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

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.

setLast(long) - Method in class org.openscience.cdk.smiles.InvPair

setLatticeConstant(double) - Method in class org.openscience.cdk.protein.ProteinPocketFinder

setLatticeConstant(double) - Method in class org.openscience.cdk.tools.GridGenerator

setLeft(IQueryAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom

setLeft(IQueryBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond

setLength(int) - Method in class org.openscience.cdk.iupac.parser.AttachedGroup

Setter for property length.

setLevel(int) - Method in class org.openscience.cdk.io.listener.SwingGUIListener

setLevel(int) - Method in class org.openscience.cdk.io.listener.TextGUIListener

setLine(int, GIMatrix) - Method in class org.openscience.cdk.graph.invariant.GIMatrix

Sets the line of the matrix at the specified index to a new value.

setLineStep(GVector, GVector, IPotentialFunction) - Method in class org.openscience.cdk.modeling.forcefield.LineSearch

Given the atom coordinates and a direction where decrease the energy function, Bracket a local minimum in this direction and find the minimum, that determine the direction movement.

setLink(String) - Method in class org.openscience.cdk.io.RssWriter

setLinkageRadius(double) - Method in class org.openscience.cdk.protein.ProteinPocketFinder

setLinkmap(Map) - Method in class org.openscience.cdk.io.RssWriter

setLocations(Vector) - Method in class org.openscience.cdk.iupac.parser.AttachedGroup

Setter for property locations.

setLower(double[]) - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModelPredict

Deprecated. Set the lower confidence bounds.

setMass(double) - Method in class org.openscience.cdk.formula.IsotopeContainer

Set the mass value of this container.

setMass(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTAtomicMass

Sets the mass value.

setMassNumber(Integer) - Method in class org.openscience.cdk.debug.DebugAtom

setMassNumber(Integer) - Method in class org.openscience.cdk.debug.DebugAtomType

setMassNumber(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

setMassNumber(Integer) - Method in class org.openscience.cdk.debug.DebugIsotope

setMassNumber(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

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.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.AtomType

Sets the MaxBondOrder attribute of the AtomType object.

setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.debug.DebugAtom

setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.debug.DebugAtomType

setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

setMaxBondOrder(IBond.Order) - Method in interface org.openscience.cdk.interfaces.IAtomType

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 maximal number of Iterations.

setMaxIterations(int) - Method in class org.openscience.cdk.charges.PiElectronegativity

set the maximal number of Iterations.

setMaxResonStruc(int) - Method in class org.openscience.cdk.charges.Electronegativity

set the maximal number of resonance structures.

setMaxResonStruc(int) - Method in class org.openscience.cdk.charges.PiElectronegativity

set the maximal 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.

setMinPSCluster(int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder

setMinPSPocket(int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder

setMM2Parameters() - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator

Sets the parameters attribute of the ForceFieldConfigurator object, default is mm2 force field

setMMFF94AngleBendingParameters(IAtomContainer, Map, boolean) - Method in class org.openscience.cdk.modeling.forcefield.AngleBending

Set MMFF94 reference angle v0IJK and the constants k2, k3, k4 for each i-j-k angle in the molecule.

setMMFF94BondStretchingParameters(IAtomContainer, Map) - Method in class org.openscience.cdk.modeling.forcefield.BondStretching

Set MMFF94 reference bond lengths r0IJ and the constants k2, k3, k4 for each i-j bond in the molecule.

setMMFF94ElectrostaticParameters(IAtomContainer, Map) - Method in class org.openscience.cdk.modeling.forcefield.ElectrostaticInteractions

Set CCG Electrostatic parameters for the molecule.

setMMFF94Parameters() - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator

setMMFF94StretchBendParameters(IAtomContainer, Map, boolean) - Method in class org.openscience.cdk.modeling.forcefield.StretchBendInteractions

Set MMFF94 reference bond lengths r0IJ and r0JK and stretch-bend interaction constants kbaIJK and kbaKJI for each i-j-k angle in the molecule.

setMMFF94Tables(IAtomContainer) - Method in class org.openscience.cdk.modeling.forcefield.GeometricMinimizer

Assign MMFF94 atom types to the molecule.

setMMFF94TorsionsParameters(IAtomContainer, Map) - Method in class org.openscience.cdk.modeling.forcefield.Torsions

Set MMFF94 constants V1, V2 and V3 for each i-j, j-k and k-l bonded pairs in the molecule.

setMMFF94VanDerWaalsParameters(IAtomContainer, Map) - Method in class org.openscience.cdk.modeling.forcefield.VanDerWaalsInteractions

Set CCG Van Der Waals parameters for the molecule.

setModelName(String) - Method in class org.openscience.cdk.qsar.model.R.RModel

Deprecated. Set the name of the model.

setModelName(String) - Method in class org.openscience.cdk.qsar.model.R2.RModel

Set the name of the model.

setMolecule(IAtomContainer) - Method in class org.openscience.cdk.layout.AtomPlacer

Sets the molecule the AtomPlacer currently works with

setMolecule(IMolecule) - Method in class org.openscience.cdk.layout.RingPlacer

setMolecule(IMolecule, boolean) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

Assings a molecule to be layed out.

setMolecule(IMolecule) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

Assings a molecule to be layed out.

setMolecule(IMolecule, boolean) - Method in class org.openscience.cdk.modeling.forcefield.GeometricMinimizer

setMolecule(IMolecule) - Method in class org.openscience.cdk.structgen.RandomGenerator

Assigns a starting structure to this generator.

setMolecules(IMolecule[]) - Method in class org.openscience.cdk.debug.DebugMoleculeSet

setMolecules(IMolecule[]) - Method in interface org.openscience.cdk.interfaces.IMoleculeSet

Sets the molecules in the IMoleculeSet, removing previously added IMolecule's.

setMolecules(IMolecule[]) - Method in class org.openscience.cdk.MoleculeSet

setMoleculeSet(IMoleculeSet) - Method in class org.openscience.cdk.ChemModel

Sets the MoleculeSet of this ChemModel.

setMoleculeSet(IMoleculeSet) - Method in class org.openscience.cdk.debug.DebugChemModel

setMoleculeSet(IMoleculeSet) - Method in interface org.openscience.cdk.interfaces.IChemModel

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

setMonomerName(String) - Method in class org.openscience.cdk.debug.DebugMonomer

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.

setMonomerType(String) - Method in class org.openscience.cdk.debug.DebugAminoAcid

setMonomerType(String) - Method in class org.openscience.cdk.debug.DebugMonomer

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.

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

setMultiplier(int, Double) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet

setMultiplier(IAtomContainer, Double) - Method in class org.openscience.cdk.debug.DebugMoleculeSet

setMultiplier(int, Double) - Method in class org.openscience.cdk.debug.DebugMoleculeSet

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.

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

setMultipliers(Double[]) - Method in class org.openscience.cdk.debug.DebugMoleculeSet

setMultipliers(Double[]) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet

Sets the multipliers of the AtomContainers.

setName(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom

setName(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom

set the Atom name of this atom.

setName(String) - Method in class org.openscience.cdk.iupac.parser.AttachedGroup

Setter for property name.

setName(String) - Method in class org.openscience.cdk.libio.md.Residue

setName(String) - Method in class org.openscience.cdk.PeriodicTableElement

Sets the name of this element.

setName(String) - Method in class org.openscience.cdk.protein.data.PDBAtom

set the Atom name of this atom.

setNaturalAbundance(Double) - Method in class org.openscience.cdk.debug.DebugAtom

setNaturalAbundance(Double) - Method in class org.openscience.cdk.debug.DebugAtomType

setNaturalAbundance(Double) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

setNaturalAbundance(Double) - Method in class org.openscience.cdk.debug.DebugIsotope

setNaturalAbundance(Double) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

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.Isotope

Sets the NaturalAbundance attribute of the Isotope object.

setNotification(boolean) - Method in class org.openscience.cdk.ChemObject

setNotification(boolean) - Method in class org.openscience.cdk.debug.DebugChemObject

setNotification(boolean) - Method in interface org.openscience.cdk.interfaces.IChemObject

Set a flag to use or not use notification.

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

setNumber(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTAtomicNumber

Sets the atomic number.

setNumOfConnection(int) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ExplicitConnectionAtom

Sets number of explicit connections.

setNumOfConnection(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTExplicitConnectivity

Sets the number of explicit connections.

setNumOfConnection(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTRingConnectivity

Sets the number of ring connections.

setNumOfConnection(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTTotalConnectivity

Sets the number of total connections.

setNumOfMembership(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTRingMembership

Sets the number of SSSR rings this atom is in.

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

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.

seTolerance(double) - Method in class org.openscience.cdk.formula.IsotopePatternSimilarity

Set the tolerance of the mass accuracy.

setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom

setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom

setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond

setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolAndChargeQueryAtom

setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolChargeIDQueryAtom

setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom

setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom

setOperator(String) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryAtom

setOrder(IBond.Order) - Method in class org.openscience.cdk.Bond

Sets the bond order of this bond.

setOrder(IBond.Order) - Method in class org.openscience.cdk.debug.DebugBond

setOrder(IBond.Order) - Method in interface org.openscience.cdk.interfaces.IBond

Sets the bond order of this bond.

setOrder(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTValence

Sets valence order.

setOrder2ndErrorApproximateEnergyGradient(GVector) - Method in class org.openscience.cdk.modeling.forcefield.MMFF94EnergyFunction

Evaluate the 2nd order error approximate gradient for the MMFF94 energy function in a given 3xN point.

setOrder5thErrorApproximateEnergyGradient(GVector) - Method in class org.openscience.cdk.modeling.forcefield.MMFF94EnergyFunction

Evaluate the 5th order error approximate gradient for the MMFF94 energy function, given a 3xN point

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.

setOxt(Boolean) - Method in class org.openscience.cdk.debug.DebugPDBAtom

setOxt(Boolean) - Method in interface org.openscience.cdk.interfaces.IPDBAtom

setOxt(Boolean) - Method in class org.openscience.cdk.protein.data.PDBAtom

setParameter(boolean) - Method in interface org.openscience.cdk.reaction.type.parameters.IParameterReact

Set the parameter to take account.

setParameter(boolean) - Method in class org.openscience.cdk.reaction.type.parameters.ParameterReact

Set the parameter to take account.

setParameterList(List<IParameterReact>) - Method in interface org.openscience.cdk.reaction.IReactionProcess

Sets the parameters for this reaction.

setParameterList(List<IParameterReact>) - Method in class org.openscience.cdk.reaction.ReactionEngine

Returns the current parameter Map for this reaction.

setParameters(String, String, String) - Method in class org.openscience.cdk.dict.EntryReact

Set the parameters of the reaction.

setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.ChargeRule

Sets the parameters attribute of the ChargeRule object.

setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.ElementRule

Sets the parameters attribute of the ElementRule object.

setParameters(Object[]) - Method in interface org.openscience.cdk.formula.rules.IRule

Sets the parameters for this rule.

setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.IsotopePatternRule

Sets the parameters attribute of the IsotopePatternRule object.

setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.MMElementRule

Sets the parameters attribute of the MMElementRule object.

setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.NitrogenRule

Sets the parameters attribute of the NitrogenRule object.

setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.RDBERule

Sets the parameters attribute of the RDBE object.

setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.ToleranceRangeRule

Sets the parameters attribute of the ToleranceRangeRule object.

setParameters(Map<String, Object>) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator

Sets the parameters attribute of the ForceFieldConfigurator object

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor

This descriptor does not have any parameter to be set.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor

This descriptor does have any parameter.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor

This descriptor does have any parameter.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor

This descriptor does have any parameter.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor

Sets the parameters attribute of the BondsToAtomDescriptor object

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor

This descriptor does have any parameter.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor

Sets the parameters attribute of the DistanceToAtomDescriptor object

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor

This descriptor does have any parameter.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor

This descriptor does have any parameter.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor

This descriptor does have any parameter.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor

This descriptor does have any parameter.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor

This descriptor does have any parameter.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor

Sets the parameters attribute of the IsProtonInAromaticSystemDescriptor object

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IsProtonInConjugatedPiSystemDescriptor

Sets the parameters attribute of the IsProtonInConjugatedPiSystemDescriptor object

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor

Sets the parameters attribute of the PartialPiChargeDescriptor object

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor

Sets the parameters attribute of the PartialSigmaChargeDescriptor object

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor

This descriptor does not have any parameter to be set.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor

This descriptor does not have any parameter to be set.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor

This descriptor does not have any parameter to be set.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor

Sets the parameters attribute of the PiElectronegativityDescriptor object

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor

This descriptor does have any parameter.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor

This descriptor does not have any parameter to be set.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R

Sets the parameters attribute of the RDFProtonDescriptor object

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR

Sets the parameters attribute of the RDFProtonDescriptor object

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR

Sets the parameters attribute of the RDFProtonDescriptor object

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol

Sets the parameters attribute of the RDFProtonDescriptor object

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR

Sets the parameters attribute of the RDFProtonDescriptor object

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor

Sets the parameters attribute of the SigmaElectronegativityDescriptor object

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor

Sets the parameters attribute of the StabilizationPlusChargeDescriptor object

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor

This descriptor does have any parameter.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor

Sets the parameters attribute of the PiContactDetectionDescriptor object.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptor

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor

This descriptor does have any parameter.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor

This descriptor does have any parameter.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor

This descriptor does have any parameter.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor

This descriptor does have any parameter.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor

This descriptor does have any parameter.

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.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.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.IPMolecularLearningDescriptor

Sets the parameters attribute of the IPMolecularLearningDescriptor object

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor

Sets the parameters attribute of the KappaShapeIndicesDescriptor object

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor

Sets the parameters attribute of the descriptor.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor

Sets the parameters attribute of the LargestChain object.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor

Sets the parameters attribute of the LargestPiSystemDescriptor object.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor

Sets the parameters attribute of the PetitjeanNumberDescriptor object

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor

Sets the parameters attribute of the LongestAliphaticChainDescriptor object.

setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.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.TPSADescriptor

Sets the parameters attribute of the TPSADescriptor object.

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 interface org.openscience.cdk.qsar.IDescriptor

Sets the parameters for this descriptor.

setParameters(String, Object) - Method in class org.openscience.cdk.qsar.model.R.CNNClassificationModel

Deprecated. Sets parameters required for building a linear model or using one for prediction.

setParameters(String, Object) - Method in class org.openscience.cdk.qsar.model.R.CNNRegressionModel

Deprecated. Sets parameters required for building a linear model or using one for prediction.

setParameters(String, Object) - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModel

Deprecated. Sets parameters required for building a linear model or using one for prediction.

setParameters(String, Object) - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModel

Deprecated. Sets parameters required for building a PLS model or using one for prediction.

setParameters(String, Object) - Method in class org.openscience.cdk.qsar.model.R.RModel

Deprecated. Specifies the parameters value.

setParameters(String, Object) - Method in class org.openscience.cdk.qsar.model.R2.CNNRegressionModel

Sets parameters required for building a CNN model or using one for prediction.

setParameters(String, Object) - Method in class org.openscience.cdk.qsar.model.R2.LinearRegressionModel

Sets parameters required for building a linear model or using one for prediction.

setParameters(String, Object) - Method in class org.openscience.cdk.qsar.model.R2.RModel

Specifies the parameters value.

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

setParser(SMARTSParser) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleNode

setPaulingEneg(Double) - Method in class org.openscience.cdk.PeriodicTableElement

Set the Pauling electronegativity for this element.

setPeriod(Integer) - Method in class org.openscience.cdk.PeriodicTableElement

Sets the chemical series of this element.

setPharmacophoreQuery(IQueryAtomContainer) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher

Set a pharmacophore query

setPhase(String) - Method in class org.openscience.cdk.PeriodicTableElement

Sets the phase, which this element finds.

setPhi(GVector) - Method in class org.openscience.cdk.modeling.forcefield.Torsions

Calculate the actual phi

setPocketSize(int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder

setPoint2d(Point2d) - Method in class org.openscience.cdk.Atom

Sets a point specifying the location of this atom in a 2D space.

setPoint2d(Point2d) - Method in class org.openscience.cdk.debug.DebugAtom

setPoint2d(Point2d) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

setPoint2d(Point2d) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

setPoint2d(Point2d) - Method in interface org.openscience.cdk.interfaces.IAtom

Sets a point specifying the location of this atom in a 2D space.

setPoint3d(Point3d) - Method in class org.openscience.cdk.Atom

Sets a point specifying the location of this atom in 3D space.

setPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugAtom

setPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

setPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

setPoint3d(Point3d) - Method in interface org.openscience.cdk.interfaces.IAtom

Sets a point specifying the location of this atom in 3D space.

setPolankRibierePlus_uk(GVector, GVector) - Method in class org.openscience.cdk.modeling.forcefield.ConjugateGradientMethod

Polak-Ribiere plus: uk = Max(0, (gk - gk-1) gk / gk-1 gk-1)

setPositive(boolean) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTCharge

Sets whether the charge is positive.

setPotentialFunction(String) - Method in class org.openscience.cdk.modeling.forcefield.ForceField

setPredicted(double[][]) - Method in class org.openscience.cdk.qsar.model.R.CNNRegressionModelPredict

Deprecated. Set the predicted values.

setPredicted(double[]) - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModelPredict

Deprecated. Set the predicted values.

setPredictedRaw(double[][]) - Method in class org.openscience.cdk.qsar.model.R.CNNClassificationModelPredict

Deprecated. Get the raw probabilities of the classification result.

setPrime() - Method in class org.openscience.cdk.smiles.InvPair

Sets the prime number based on the current seed.

setProductCoefficient(IMolecule, Double) - Method in class org.openscience.cdk.debug.DebugReaction

setProductCoefficient(IMolecule, Double) - Method in interface org.openscience.cdk.interfaces.IReaction

Sets the coefficient of a a product to a given value.

setProductCoefficient(IMolecule, Double) - Method in class org.openscience.cdk.Reaction

Sets the coefficient of a a product to a given value.

setProductCoefficients(Double[]) - Method in class org.openscience.cdk.debug.DebugReaction

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.

setProducts(IMoleculeSet) - Method in class org.openscience.cdk.debug.DebugReaction

setProducts(IMoleculeSet) - Method in interface org.openscience.cdk.interfaces.IReaction

Assigns a IMoleculeSet to the products of this reaction.

setProducts(IMoleculeSet) - Method in class org.openscience.cdk.Reaction

Assigns a MoleculeSet to the products of this reaction.

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.ChemObject

Sets the properties of this object.

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugAminoAcid

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugAtom

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugAtomContainer

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugAtomType

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugBioPolymer

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugBond

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugChemFile

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugChemModel

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugChemObject

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugChemSequence

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugCrystal

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugElectronContainer

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugElement

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugIsotope

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugLonePair

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugMapping

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugMolecularFormula

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugMolecule

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugMoleculeSet

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugMonomer

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugPolymer

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugReaction

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugReactionScheme

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugReactionSet

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugRing

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugSingleElectron

setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugStrand

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

Sets the properties of this object.

setProperties(Map<Object, Object>) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula

Sets the properties of this object.I should integrate into ChemObject.

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

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugAtom

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugAtomContainer

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugAtomType

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugBioPolymer

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugBond

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugChemFile

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugChemModel

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugChemObject

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugChemSequence

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugCrystal

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugElectronContainer

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugElement

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugIsotope

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugLonePair

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugMapping

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugMolecularFormula

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugMolecule

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugMoleculeSet

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugMonomer

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugPolymer

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugReaction

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugReactionScheme

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugReactionSet

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugRing

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugSingleElectron

setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugStrand

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.

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.qsar.model.R.LinearRegressionModelFit

Deprecated. Set the rank of the fit.

setRAtom(double) - Method in class org.openscience.cdk.protein.ProteinPocketFinder

setRawContent(Object) - Method in class org.openscience.cdk.dict.Entry

setRdFields(Map) - 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(IMolecule, Double) - Method in class org.openscience.cdk.debug.DebugReaction

setReactantCoefficient(IMolecule, Double) - Method in interface org.openscience.cdk.interfaces.IReaction

Sets the coefficient of a a reactant to a given value.

setReactantCoefficient(IMolecule, Double) - Method in class org.openscience.cdk.Reaction

Sets the coefficient of a a reactant to a given value.

setReactantCoefficients(Double[]) - Method in class org.openscience.cdk.debug.DebugReaction

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.

setReactants(IMoleculeSet) - Method in class org.openscience.cdk.debug.DebugReaction

setReactants(IMoleculeSet) - Method in interface org.openscience.cdk.interfaces.IReaction

Assigns a IMoleculeSet to the reactants in this reaction.

setReactants(IMoleculeSet) - Method in class org.openscience.cdk.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

setReactionSet(IReactionSet) - Method in interface org.openscience.cdk.interfaces.IChemModel

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.IteratingMDLReader

setReader(InputStream) - Method in class org.openscience.cdk.io.iterator.IteratingMDLReader

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.IteratingSMILESReader

setReader(InputStream) - Method in class org.openscience.cdk.io.iterator.IteratingSMILESReader

setReader(Reader) - Method in class org.openscience.cdk.io.MDLReader

setReader(InputStream) - Method in class org.openscience.cdk.io.MDLReader

setReader(Reader) - Method in class org.openscience.cdk.io.MDLRXNReader

setReader(InputStream) - Method in class org.openscience.cdk.io.MDLRXNReader

setReader(Reader) - Method in class org.openscience.cdk.io.MDLRXNV2000Reader

setReader(InputStream) - Method in class org.openscience.cdk.io.MDLRXNV2000Reader

setReader(Reader) - Method in class org.openscience.cdk.io.MDLRXNV3000Reader

setReader(InputStream) - Method in class org.openscience.cdk.io.MDLRXNV3000Reader

setReader(Reader) - Method in class org.openscience.cdk.io.MDLV2000Reader

setReader(InputStream) - Method in class org.openscience.cdk.io.MDLV2000Reader

setReader(Reader) - Method in class org.openscience.cdk.io.MDLV3000Reader

setReader(InputStream) - Method in class org.openscience.cdk.io.MDLV3000Reader

setReader(Reader) - Method in class org.openscience.cdk.io.Mol2Reader

setReader(InputStream) - Method in class org.openscience.cdk.io.Mol2Reader

setReader(Reader) - Method in class org.openscience.cdk.io.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.ShelXReader

setReader(InputStream) - Method in class org.openscience.cdk.io.ShelXReader

setReader(Reader) - Method in class org.openscience.cdk.io.SMILESReader

setReader(InputStream) - Method in class org.openscience.cdk.io.SMILESReader

setReader(Reader) - Method in class org.openscience.cdk.io.VASPReader

setReader(InputStream) - Method in class org.openscience.cdk.io.VASPReader

setReader(Reader) - Method in class org.openscience.cdk.io.XYZReader

setReader(InputStream) - Method in class org.openscience.cdk.io.XYZReader

setReader(Reader) - Method in class org.openscience.cdk.io.ZMatrixReader

setReader(InputStream) - Method in class org.openscience.cdk.io.ZMatrixReader

setReaderMode(IChemObjectReader.Mode) - Method in class org.openscience.cdk.io.DefaultChemObjectReader

setReaderMode(IChemObjectReader.Mode) - Method in interface org.openscience.cdk.io.IChemObjectReader

Sets the reader mode.

setReaderMode(IChemObjectReader.Mode) - Method in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader

setReaderMode(IChemObjectReader.Mode) - Method in class org.openscience.cdk.io.random.DefaultRandomAccessChemObjectReader

setRealPart(double) - Method in class org.openscience.cdk.math.Complex

Sets the real part of this complex value

setRecord(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom

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.

setRecursiveQuery(IQueryAtomContainer) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RecursiveSmartsAtom

setRepresentation(String) - Method in class org.openscience.cdk.dict.EntryReact

Set the representation of the reaction.

setResiduals(double[][]) - Method in class org.openscience.cdk.qsar.model.R.CNNClassificationModelFit

Deprecated. Set the residuals of the fit.

setResiduals(double[][]) - Method in class org.openscience.cdk.qsar.model.R.CNNRegressionModelFit

Deprecated. Set the residuals of the fit.

setResiduals(double[]) - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModelFit

Deprecated. Set the residuals of the fit.

setResidualScale(double) - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModelPredict

Deprecated. Set the scale of the residuals.

setResidues(List) - Method in class org.openscience.cdk.libio.md.MDMolecule

setResName(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom

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.

setResSeq(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom

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

setRestrictions(List<IRule>) - Method in class org.openscience.cdk.formula.MassToFormulaTool

Set the restrictions that must be presents in the molecular formula.

setRight(IQueryAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom

setRight(IQueryBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond

setRingBond(IQueryBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RingIdentifierAtom

setRingFinder(AllRingsFinder) - Method in class org.openscience.cdk.smiles.SmilesGenerator

Sets the current AllRingsFinder instance Use this if you want to customize the timeout for the AllRingsFinder.

setRingId(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTRingIdentifier

Sets the ring identifier.

setRings(IRingSet) - Method in class org.openscience.cdk.smiles.SmilesGenerator

Provide a reference to a RingSet that holds ALL rings of the molecule.
During creation of a SMILES the aromaticity of the molecule has to be detected.

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

setRingSet(IRingSet) - Method in interface org.openscience.cdk.interfaces.IChemModel

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

setRSolvent(double) - Method in class org.openscience.cdk.protein.ProteinPocketFinder

setSecondGraphSize(int) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph

Returns the size of the second of the two compared graphs.

setSEFit(double[]) - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModelPredict

Deprecated. Set the standard errors of predictions.

setSegID(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom

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.

setSerial(Integer) - Method in class org.openscience.cdk.debug.DebugPDBAtom

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.

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.

setSize(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTSmallestRingSize

Sets the smallest SSSR size.

setSk(GVector) - Method in class org.openscience.cdk.modeling.forcefield.SteepestDescentsMethod

sk=-gK/|gk|

setSmarts(String) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom

Set the SMARTS for the group.

setSmarts(String) - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool

Set a new SMARTS pattern.

setSmilesToUpperCase(boolean) - Method in class org.openscience.cdk.tools.GenerateFragments

setSmoothingFunction(double[]) - Method in class org.openscience.cdk.modeling.forcefield.SmoothingFunctions

Calculate the smoothing function from atom distances.

setSolvantValue(int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder

setSource(IChemObject) - Method in class org.openscience.cdk.controller.CDKPopupMenu

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

setSpaceGroup(String) - Method in interface org.openscience.cdk.interfaces.ICrystal

Sets the space group of this crystal.

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).

setStartChainID(Character) - Method in class org.openscience.cdk.debug.DebugPDBStructure

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.

setStartInsertionCode(Character) - Method in class org.openscience.cdk.debug.DebugPDBStructure

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.

setStartSequenceNumber(Integer) - Method in class org.openscience.cdk.debug.DebugPDBStructure

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.

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(int) - Method in class org.openscience.cdk.Bond

Sets the stereo descriptor for this bond.

setStereo(int) - Method in class org.openscience.cdk.debug.DebugBond

setStereo(int) - Method in interface org.openscience.cdk.interfaces.IBond

Sets the stereo descriptor for this bond.

setStereoParity(Integer) - Method in class org.openscience.cdk.Atom

Sets the stereo parity for this atom.

setStereoParity(Integer) - Method in class org.openscience.cdk.debug.DebugAtom

setStereoParity(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

setStereoParity(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

setStereoParity(Integer) - Method in interface org.openscience.cdk.interfaces.IAtom

Sets the stereo parity for this atom.

setStereoParity(Integer) - Method in class org.openscience.cdk.PseudoAtom

Dummy method: the stereo parity is undefined, final.

setStrandName(String) - Method in class org.openscience.cdk.debug.DebugStrand

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.Strand

Sets the name of the Strand object.

setStrandType(String) - Method in class org.openscience.cdk.debug.DebugStrand

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.Strand

Sets the type of the Strand object.

setStructureType(String) - Method in class org.openscience.cdk.debug.DebugPDBStructure

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.

setSubgraph(List) - Method in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph

setSwitchingAtom(IAtom) - Method in class org.openscience.cdk.libio.md.ChargeGroup

setSymbol(String) - Method in class org.openscience.cdk.debug.DebugAtom

setSymbol(String) - Method in class org.openscience.cdk.debug.DebugAtomType

setSymbol(String) - Method in class org.openscience.cdk.debug.DebugElement

setSymbol(String) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

setSymbol(String) - Method in class org.openscience.cdk.debug.DebugIsotope

setSymbol(String) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

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.smiles.smarts.parser.ASTElement

Sets the element symbol.

setSymbol(String) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTExplicitAtom

Sets the element symbol.

setTempFactor(Double) - Method in class org.openscience.cdk.debug.DebugPDBAtom

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.

setTemplateHandler(TemplateHandler) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

Sets the templateHandler attribute of the StructureDiagramGenerator object

setTimeout(long) - Method in class org.openscience.cdk.ringsearch.AllRingsFinder

Sets the timeout value in milliseconds of the AllRingsFinder object This is used to prevent this AllRingsFinder to run for ages in certain rare cases with ring systems of large size or special topology

setTimezone(String) - Method in class org.openscience.cdk.io.RssWriter

setTitle(String) - Method in class org.openscience.cdk.io.RssWriter

setTitle(String) - Method in class org.openscience.cdk.renderer.GraphRendererModel

Set the main title

setTitlemap(Map) - Method in class org.openscience.cdk.io.RssWriter

setTrainingData(double[], double[], double[], double[], double[], double[], double[]) - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModelFit

setType(String) - Method in class org.openscience.cdk.renderer.JCPAction2D

Sets the type attribute of the JCPAction object

setType(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTNotBond

setType(int) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTNotExpression

setUnspecified(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom

setUnspecified(boolean) - Method in class org.openscience.cdk.smiles.smarts.parser.ASTChirality

setUpper(double[]) - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModelPredict

Deprecated. Set the upper confidence bounds.

setUseAromaticityFlag(boolean) - Method in class org.openscience.cdk.smiles.SmilesGenerator

Indicates whether output should be an aromatic SMILES.

setUsedGMMethods(boolean, boolean, boolean) - Method in class org.openscience.cdk.modeling.forcefield.ForceField

setUseTemplates(boolean) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator

Sets whether to use templates or not.

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

setValency(Integer) - Method in class org.openscience.cdk.debug.DebugAtomType

setValency(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom

setValency(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom

setValency(Integer) - Method in interface org.openscience.cdk.interfaces.IAtomType

Sets the the exact electron valency of the AtomType object.

setValidationData(int, int, double[], double[], double[], double[]) - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModelFit

setValue(double) - Method in class org.openscience.cdk.qsar.model.R.CNNClassificationModelFit

Deprecated. Set the final value of the cost function.

setValue(double) - Method in class org.openscience.cdk.qsar.model.R.CNNRegressionModelFit

Deprecated. Set the final value of the cost function.

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.

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

setVdwRadius(Double) - Method in class org.openscience.cdk.PeriodicTableElement

Set the VdW radius of this element.

setWeights(double[]) - Method in class org.openscience.cdk.qsar.model.R.CNNClassificationModelFit

Deprecated. Set the weights and biases of the final network.

setWeights(double[]) - Method in class org.openscience.cdk.qsar.model.R.CNNRegressionModelFit

Deprecated. Set the weights and biases of the final network.

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.MDLWriter

setWriter(OutputStream) - Method in class org.openscience.cdk.io.MDLWriter

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(Writer) - Method in class org.openscience.cdk.io.RssWriter

setWriter(OutputStream) - Method in class org.openscience.cdk.io.RssWriter

setWriter(Writer) - Method in class org.openscience.cdk.io.SDFWriter

setWriter(OutputStream) - Method in class org.openscience.cdk.io.SDFWriter

setWriter(Writer) - Method in class org.openscience.cdk.io.ShelXWriter

setWriter(OutputStream) - Method in class org.openscience.cdk.io.ShelXWriter

setWriter(Writer) - Method in class org.openscience.cdk.io.SMILESWriter

setWriter(OutputStream) - Method in class org.openscience.cdk.io.SMILESWriter

setWriter(Writer) - Method in class org.openscience.cdk.io.XYZWriter

setWriter(OutputStream) - Method in class org.openscience.cdk.io.XYZWriter

setX(double, double) - Method in class org.openscience.cdk.renderer.GraphRendererModel

Sets the function area, which will painted

setXTitle(String) - Method in class org.openscience.cdk.renderer.GraphRendererModel

Set the title of the x axis

setY(double, double) - Method in class org.openscience.cdk.renderer.GraphRendererModel

Sets the function area, which will painted

setYTitle(String) - Method in class org.openscience.cdk.renderer.GraphRendererModel

Set the title of the y axis

setZ(Integer) - Method in class org.openscience.cdk.Crystal

Sets the number of asymmetric parts in the unit cell.

setZ(Integer) - Method in class org.openscience.cdk.debug.DebugCrystal

setZ(Integer) - Method in interface org.openscience.cdk.interfaces.ICrystal

Sets the number of assymmetric parts in the unit cell.

shallowCopy() - Method in class org.openscience.cdk.ChemObject

Clones this IChemObject, but preserves references to Objects.

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

ShelXFormat - Class in org.openscience.cdk.io.formats

See here.

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

shouldBeLinear(IAtom, IAtomContainer) - Method in class org.openscience.cdk.layout.AtomPlacer

SI - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

SigmaElectronegativityDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic

Sigma electronegativity is given by X = a + bq + c(q*q)

SigmaElectronegativityDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor

Constructor for the SigmaElectronegativityDescriptor object

sign(double, double) - Method in class org.openscience.cdk.modeling.forcefield.LineSearch

SILICON - Static variable in class org.openscience.cdk.config.Elements

SILVER - Static variable in class org.openscience.cdk.config.Elements

SILVER - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

similar(IMatrix) - Method in class org.openscience.cdk.math.IMatrix

Similar transformation Ut * M * U

similar(IMatrix, IMatrix) - Method in class org.openscience.cdk.math.IMatrix

Similar transformation Ut * M * U

similar(Matrix) - Method in class org.openscience.cdk.math.Matrix

Similar transformation Ut * M * U

SimpleBasisSet - Class in org.openscience.cdk.math.qm

This class will generate a simple base set for a atom container.

SimpleBasisSet(IAtom[]) - Constructor for class org.openscience.cdk.math.qm.SimpleBasisSet

Create a base set

SimpleBond() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

SimpleCharStream - Class in org.openscience.cdk.iupac.parser

An implementation of interface CharStream, where the stream is assumed to contain only ASCII characters (without unicode processing).

SimpleCharStream(Reader, int, int, int) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream

SimpleCharStream(Reader, int, int) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream

SimpleCharStream(Reader) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream

SimpleCharStream(InputStream, int, int, int) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream

SimpleCharStream(InputStream, int, int) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream

SimpleCharStream(InputStream) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream

SimpleCharStream - Class in org.openscience.cdk.smiles.smarts.parser

An implementation of interface CharStream, where the stream is assumed to contain only ASCII characters (without unicode processing).

SimpleCharStream(Reader, int, int, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream

SimpleCharStream(Reader, int, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream

SimpleCharStream(Reader) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream

SimpleCharStream(InputStream, int, int, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream

SimpleCharStream(InputStream, int, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream

SimpleCharStream(InputStream) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream

SimpleCycle - Class in org.openscience.cdk.ringsearch.cyclebasis

A cycle in a graph G is a subgraph in which every vertex has even degree.

SimpleCycle(UndirectedGraph, Collection) - Constructor for class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycle

Constructs a cycle in a graph consisting of the specified edges.

SimpleCycle(UndirectedGraph, Set) - Constructor for class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycle

Constructs a cycle in a graph consisting of the specified edges.

SimpleCycleBasis - Class in org.openscience.cdk.ringsearch.cyclebasis

Auxiliary class for CycleBasis.

SimpleCycleBasis(List, List, UndirectedGraph) - Constructor for class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis

SimpleCycleBasis(UndirectedGraph) - Constructor for class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis

SimpleNode - Class in org.openscience.cdk.smiles.smarts.parser

Basic implementation of AST nodes.

SimpleNode(int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleNode

SimpleNode(SMARTSParser, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleNode

simplifyMolecularFormula(String) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator

Simplify the molecular formula.

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.

SingleElectronDiff - Class in org.openscience.cdk.tools.diff

Compares two ISingleElectron classes.

SingleElectronDiff() - Constructor for class org.openscience.cdk.tools.diff.SingleElectronDiff

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

singleElectrons() - Method in class org.openscience.cdk.debug.DebugAtomContainer

singleElectrons() - Method in class org.openscience.cdk.debug.DebugBioPolymer

singleElectrons() - Method in class org.openscience.cdk.debug.DebugCrystal

singleElectrons() - Method in class org.openscience.cdk.debug.DebugMolecule

singleElectrons() - Method in class org.openscience.cdk.debug.DebugMonomer

singleElectrons() - Method in class org.openscience.cdk.debug.DebugPolymer

singleElectrons() - Method in class org.openscience.cdk.debug.DebugRing

singleElectrons() - Method in class org.openscience.cdk.debug.DebugStrand

singleElectrons() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

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

size() - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet

size() - Method in class org.openscience.cdk.dict.Dictionary

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 interface org.openscience.cdk.interfaces.IMolecularFormulaSet

Returns the number of MolecularFormulas in this IMolecularFormulaSet.

size() - Method in interface org.openscience.cdk.io.random.IRandomAccessChemObjectReader

size() - Method in class org.openscience.cdk.io.random.RandomAccessReader

size - Variable in class org.openscience.cdk.math.IVector

Size of this vector

size - Variable in class org.openscience.cdk.math.Vector

The size of this vector

SM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

SMALL_FIRST - Static variable in class org.openscience.cdk.RingSet

Flag to denote that the set is order with the smallest ring first?

SMALL_FIRST - Static variable in class org.openscience.cdk.tools.manipulator.RingSizeComparator

Flag to denote that the set is order with the smallest ring first

SMALLEST_RINGS - Static variable in class org.openscience.cdk.CDKConstants

A smallest set of smallest rings computed for this molecule.

SmallestRingAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts

This smarts atom matches any atom with the smallest SSSR size being a certain value.

SmallestRingAtom(int) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.SmallestRingAtom

SmallestRingSize() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

Smarts2MQLVisitor - Class in org.openscience.cdk.smiles.smarts.parser.visitor

An AST tree visitor.

Smarts2MQLVisitor() - Constructor for class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

SMARTSAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts

Abstract smarts atom.

SMARTSAtom() - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom

SMARTSBond - Class in org.openscience.cdk.isomorphism.matchers.smarts

Abstract smarts bond.

SMARTSBond() - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.SMARTSBond

SMARTSBond(IQueryAtom, IQueryAtom, IBond.Order) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.SMARTSBond

SmartsDumpVisitor - Class in org.openscience.cdk.smiles.smarts.parser.visitor

An AST Tree visitor.

SmartsDumpVisitor() - Constructor for class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

SmartsExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

SMARTSFormat - Class in org.openscience.cdk.io.formats

See here.

SMARTSParser - Class in org.openscience.cdk.smiles.smarts.parser

This parser implements a nearly complete subset of the SMARTS syntax as defined on the Daylight website.

SMARTSParser(InputStream) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

SMARTSParser(Reader) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

SMARTSParser(SMARTSParserTokenManager) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

SMARTSParserConstants - Interface in org.openscience.cdk.smiles.smarts.parser

SMARTSParserTokenManager - Class in org.openscience.cdk.smiles.smarts.parser

SMARTSParserTokenManager(SimpleCharStream) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager

SMARTSParserTokenManager(SimpleCharStream, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager

SMARTSParserTreeConstants - Interface in org.openscience.cdk.smiles.smarts.parser

SMARTSParserVisitor - Interface in org.openscience.cdk.smiles.smarts.parser

SMARTSQueryTool - Class in org.openscience.cdk.smiles.smarts

This class provides a easy to use wrapper around SMARTS matching functionality.

SMARTSQueryTool(String) - Constructor for class org.openscience.cdk.smiles.smarts.SMARTSQueryTool

SmartsQueryVisitor - Class in org.openscience.cdk.smiles.smarts.parser.visitor

An AST tree visitor.

SmartsQueryVisitor() - Constructor for class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

Creates a new instance

SMILES - Static variable in class org.openscience.cdk.CDKConstants

The Daylight SMILES.

SMILESFIXFormat - Class in org.openscience.cdk.io.formats

SMILESFormat - Class in org.openscience.cdk.io.formats

See here.

SmilesGenerator - Class in org.openscience.cdk.smiles

Generates SMILES strings [Weininger, David, SMILES, a Chemical Language and Information System. 1. Introduction to Methodology and Encoding Rules, Journal of Chemical Information and Computer Sciences, 1988, 28:31-36, Weininger, David and Weininger, Arthur and Weininger, Joseph L., SMILES 2. Algorithm for Generation of Unique SMILES Notation, Journal of Chemical Information and Computer Sciences, 1989, 29:97-101].

SmilesGenerator() - Constructor for class org.openscience.cdk.smiles.SmilesGenerator

Create the SMILES generator.

SmilesParser - Class in org.openscience.cdk.smiles

Parses a SMILES [?Authors?, SMILES Tutorial] string and an AtomContainer.

SmilesParser(IChemObjectBuilder) - Constructor for class org.openscience.cdk.smiles.SmilesParser

Constructor for the SmilesParser object.

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

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

Contructs 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

Contructs a new SMILESWriter that can write an list of SMILES to a given OutputStream

SmoothingFunctions - Class in org.openscience.cdk.modeling.forcefield

Cutoffs and Smoothing Functions.

SmoothingFunctions() - Constructor for class org.openscience.cdk.modeling.forcefield.SmoothingFunctions

Constructor for the SmoothingFunctions object

SN - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

SODIUM - Static variable in class org.openscience.cdk.config.Elements

SODIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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.

sortBy2DDistance(IAtom[], Point2d) - Static method in class org.openscience.cdk.geometry.GeometryTools

Sorts a Vector of atoms such that the 2D distances of the atom locations from a given point are smallest for the first atoms in the vector See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets

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.

SPACE - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

SpanningTree - Class in org.openscience.cdk.graph

Spanning tree of a molecule.

SpanningTree(IAtomContainer) - Constructor for class org.openscience.cdk.graph.SpanningTree

SpartanFormat - Class in org.openscience.cdk.io.formats

specialCase() - Method in class org.openscience.cdk.iupac.parser.NomParser

Deal with special cases where the rules don't apply.

specialToken - Variable in class org.openscience.cdk.iupac.parser.Token

This field is used to access special tokens that occur prior to this token, but after the immediately preceding regular (non-special) token.

specialToken - Variable in class org.openscience.cdk.smiles.smarts.parser.Token

This field is used to access special tokens that occur prior to this token, but after the immediately preceding regular (non-special) token.

SPHERICAL_MATCHER - Static variable in class org.openscience.cdk.CDKConstants

Used as property key for indicating the HOSE code for a certain atom type.

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.

sqrt() - Method in class org.openscience.cdk.math.Quaternion

SR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

SSSRFinder - Class in org.openscience.cdk.ringsearch

Finds the Smallest Set of Smallest Rings.

SSSRFinder(IAtomContainer) - Constructor for class org.openscience.cdk.ringsearch.SSSRFinder

Constructs a SSSRFinder for a specified molecule.

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

StandardSubstructureSets - Class in org.openscience.cdk.fingerprint

Default sets of atom containers aimed for use with the substructure

StandardSubstructureSets() - Constructor for class org.openscience.cdk.fingerprint.StandardSubstructureSets

Start() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

Start ::= ReactionExpression ::= (">>" )? | ">" ">" | ">>" GroupExpression ::= ["("] [")"] ( "." ["("] [")"] )* SmartsExpression ::= ( ( [ ] ( | ) ) | ( "(" [ ] ")" ) )* AtomExpression ::= ( "[" [ ] "]" ) | LowAndBond ::= [ ";" ] OrBond ::= [ "," ] ExplicitHighAndBond ::= [ "&" ] ImplicitHighAndBond ::= [ ] NotBond ::= [ "!" ] SimpleBond ::= "/" | "\\" | "/?" | "\\?" | "=" | "#" | "~" | "@" ExplicitAtomExpression ::= [ "B" | "C" | "N" | "O" | "P" | "S" | "F" | "CL" | "BR" | "I" | "c" | "o" | "n" | "*" | "A" | "a" | "p" | "as" | "se" ] LowAndExpression ::= ( ";" )? OrExpression ::= ( "," ) ? ExplicitHighAndExpression ::= ( "&" )? ImplicitHighAndExpression ::= ( ) ? NotExpression ::= "!" ( | ) RecursiveSmartsExpression ::= "$" "(" ")" PrimitiveAtomExpression ::= | "*" | "A" | "a" | "D" ()? | "H" ()? | "h" ()? | "R" (+)? | "r" (+)? | "v" (+)? | "#X" | "G" (+) | "X" (+)? | "x" (+)? | "^" () | ("+" | "-") (+)? | "#" (+) | "@" | "@@" | + Digit ::= ( "0" - "9") NonHydrogenElement ::= [ "HE" | "LI" | "BE" | "NE" | "NA" | "MG" | "AL" | "SI" | "AR" | "CA" | "SC" | "TI" | "CR" | "MN" | "FE" | "CO" | "NI" | "CU" | "ZN" | "GA" | "GE" | "AS" | "SE" | "BR" | "KR" | "RB" | "SR" | "ZR" | "NB" | "MO" | "TC" | "RU" | "RH" | "PD" | "AG" | "CD" | "IN" | "SN" | "SB" | "TE" | "XE" | "CS" | "BA" | "LA" | "HF" | "TA" | "RE" | "OS" | "IR" | "PT" | "AU" | "HG" | "TL" | "PB" | "BI" | "PO" | "AT" | "RN" | "FR" | "RA" | "AC" | "TH" | "PA" | "B" | "C" | "N" | "O" | "F" | "P" | "S" | "K" | "V" | "Y" | "I" | "U" | "c" | "o" | "n" | "p" | "as" | "se" ]

startDocument() - Method in class org.openscience.cdk.config.atomtypes.AtomTypeHandler

startDocument() - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeHandler

startDocument() - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingHandler

startDocument() - Method in class org.openscience.cdk.config.elements.ElementPTHandler

startDocument() - Method in class org.openscience.cdk.config.isotopes.IsotopeHandler

startDocument() - Method in class org.openscience.cdk.dict.DictionaryHandler

startDocument() - Method in class org.openscience.cdk.io.cml.CDKConvention

startDocument() - Method in class org.openscience.cdk.io.cml.CMLCoreModule

startDocument() - Method in class org.openscience.cdk.io.cml.CMLHandler

startDocument() - Method in interface org.openscience.cdk.io.cml.ICMLModule

startDocument() - Method in class org.openscience.cdk.io.cml.MDLMolConvention

startDocument() - Method in class org.openscience.cdk.io.cml.PMPConvention

startDocument() - Method in class org.openscience.cdk.io.inchi.INChIHandler

startDocument() - Method in class org.openscience.cdk.io.iterator.event.EventCMLHandler

Procedure required by the CDOInterface.

startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.config.atomtypes.AtomTypeHandler

startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeHandler

startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingHandler

startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.config.elements.ElementPTHandler

startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.config.isotopes.IsotopeHandler

startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.dict.DictionaryHandler

startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.CDKConvention

startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.CMLCoreModule

startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.CMLHandler

startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.CMLReactionModule

startElement(CMLStack, String, String, String, Attributes) - Method in interface org.openscience.cdk.io.cml.ICMLModule

startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.JMOLANIMATIONConvention

startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.MDLMolConvention

startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.MDMoleculeConvention

Add parsing of elements in mdmolecule: mdmolecule chargeGroup id cgNumber atomArray switchingAtom residue id title resNumber atomArray

startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.PDBConvention

startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.PMPConvention

startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.QSARConvention

startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.io.inchi.INChIHandler

Implementation of the startElement() procedure overwriting the DefaultHandler interface.

startObject(String) - Method in class org.openscience.cdk.io.iterator.event.EventCMLHandler

Procedure required by the CDOInterface.

stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.AtomContainer

Called by objects to which this object has registered as a listener.

stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.AtomContainerSet

Called by objects to which this object has registered as a listener.

stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.ChemFile

Called by objects to which this object has registered as a listener.

stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.ChemModel

Called by objects to which this object has registered as a listener.

stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.ChemSequence

Called by objects to which this object has registered as a listener.

stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugAminoAcid

stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugBioPolymer

stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugCrystal

stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugMonomer

stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugPolymer

stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugRing

stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugStrand

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.MoleculeSet

Called by objects to which this object has registered as a listener.

stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.ReactionSet

stateChanged(List) - Method in interface org.openscience.cdk.structgen.IStructureGenerationListener

staticFlag - Static variable in class org.openscience.cdk.iupac.parser.SimpleCharStream

staticFlag - Static variable in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream

SteepestDescentsMethod - Class in org.openscience.cdk.modeling.forcefield

Find a direction from a point of the coordinates space using the steepest descents approach.

SteepestDescentsMethod() - Constructor for class org.openscience.cdk.modeling.forcefield.SteepestDescentsMethod

SteepestDescentsMethod(GVector) - Constructor for class org.openscience.cdk.modeling.forcefield.SteepestDescentsMethod

Constructor for the SteepestDescentsMethod object

steepestDescentsMinimization(GVector, IPotentialFunction) - Method in class org.openscience.cdk.modeling.forcefield.GeometricMinimizer

Minimize the potential energy function using steepest descents method

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.

STEREO_BOND_DOWN - Static variable in class org.openscience.cdk.CDKConstants

A bonds which end is below the drawing plane.

STEREO_BOND_DOWN_INV - Static variable in class org.openscience.cdk.CDKConstants

A bonds which end is below the drawing plane.

STEREO_BOND_NONE - Static variable in class org.openscience.cdk.CDKConstants

A bonds for which there is no stereochemistry.

STEREO_BOND_UNDEFINED - Static variable in class org.openscience.cdk.CDKConstants

A bonds for which the stereochemistry is undefined.

STEREO_BOND_UP - Static variable in class org.openscience.cdk.CDKConstants

A bonds which end is above the drawing plane.

STEREO_BOND_UP_INV - Static variable in class org.openscience.cdk.CDKConstants

A bonds which start is above the drawing plane.

StereoBond - Class in org.openscience.cdk.isomorphism.matchers.smarts

This query bond matches bonds with specific stereo type.

StereoBond() - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.StereoBond

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.

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.

StretchBendInteractions - Class in org.openscience.cdk.modeling.forcefield

Stretch-Bend Interaction calculator for the potential energy function.

StretchBendInteractions() - Constructor for class org.openscience.cdk.modeling.forcefield.StretchBendInteractions

Constructor for the StretchBendInteractions object

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, int, String, String) - Constructor for class org.openscience.cdk.io.setting.StringIOSetting

STRONTIUM - Static variable in class org.openscience.cdk.config.Elements

STRONTIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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(IMolecule) - Constructor for class org.openscience.cdk.layout.StructureDiagramGenerator

Creates an instance of this class while assigning a molecule to be layed out.

StructureResonanceGenerator - Class in org.openscience.cdk.tools

This class try to generate resonance structure for a determinate molecule.

StructureResonanceGenerator() - Constructor for class org.openscience.cdk.tools.StructureResonanceGenerator

Construct an instance of StructureResonanceGenerator.

StructureResonanceGenerator(boolean) - Constructor for class org.openscience.cdk.tools.StructureResonanceGenerator

Construct an instance of StructureResonanceGenerator.

sub(Complex) - Method in class org.openscience.cdk.math.Complex

Subtracs a complex value

sub(IMatrix) - Method in class org.openscience.cdk.math.IMatrix

Subtraktion from two matrices

sub(IMatrix, IMatrix) - Method in class org.openscience.cdk.math.IMatrix

Subtraktion from two matrices

sub(IVector) - Method in class org.openscience.cdk.math.IVector

Subtraction from two vectors

sub(IVector, IVector) - Method in class org.openscience.cdk.math.IVector

Subtraction from two vectors

sub(Matrix) - Method in class org.openscience.cdk.math.Matrix

Subtracts from two matrices.

sub(Quaternion) - Method in class org.openscience.cdk.math.Quaternion

sub(Vector) - Method in class org.openscience.cdk.math.Vector

Subtraktion from two vectors

subChain() - Method in class org.openscience.cdk.iupac.parser.NomParser

The substituent part of the prefix

subList(int, int) - Method in class org.openscience.cdk.ConformerContainer

SubstructureFingerprinter - Class in org.openscience.cdk.fingerprint

IFingerprinter that gives a bit set which has a size equal to the number of substructures it was constructed from.

SubstructureFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.SubstructureFingerprinter

Set up the fingerprinter to use the fragments from StandardSubstructureSets.

SubstructureFingerprinter(String[]) - Constructor for class org.openscience.cdk.fingerprint.SubstructureFingerprinter

Set up the fingerprinter to use a user-defined set of fragments.

SULFUR - Static variable in class org.openscience.cdk.config.Elements

summary() - Method in class org.openscience.cdk.qsar.model.R.CNNRegressionModel

Deprecated. Returns an object summarizing the CNN regression model.

summary() - Method in class org.openscience.cdk.qsar.model.R.LinearRegressionModel

Deprecated. Returns an object summarizing the linear regression model.

summary() - Method in class org.openscience.cdk.qsar.model.R2.CNNRegressionModel

Returns an RList object summarizing the nnet regression model.

summary() - Method in class org.openscience.cdk.qsar.model.R2.LinearRegressionModel

Returns an RList object summarizing the linear regression model.

SVGFormat - Class in org.openscience.cdk.io.formats

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, int) - Constructor for class org.openscience.cdk.io.listener.SwingGUIListener

0 = ask no questions 3 = ask all questions

SwingMouseEventRelay - Class in org.openscience.cdk.controller

SwingMouseEventRelay(IMouseEventRelay) - Constructor for class org.openscience.cdk.controller.SwingMouseEventRelay

SwissArmyKnife - Class in org.openscience.cdk.tools

A set of utilities which did not really fit into any other category

SwissArmyKnife() - Constructor for class org.openscience.cdk.tools.SwissArmyKnife

SwitchTo(int) - Method in class org.openscience.cdk.iupac.parser.NomParserTokenManager

SwitchTo(int) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager

SybylAtomTypeMatcher - Class in org.openscience.cdk.atomtype

Atom Type matcher for Sybyl atom types.

SybylDescriptorFormat - Class in org.openscience.cdk.io.formats

See here.

SymbolAndChargeQueryAtom - Class in org.openscience.cdk.isomorphism.matchers

SymbolAndChargeQueryAtom() - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolAndChargeQueryAtom

SymbolAndChargeQueryAtom(IAtom) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolAndChargeQueryAtom

SymbolChargeIDQueryAtom - Class in org.openscience.cdk.isomorphism.matchers

SymbolChargeIDQueryAtom() - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolChargeIDQueryAtom

SymbolChargeIDQueryAtom(IAtom) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolChargeIDQueryAtom

SymbolQueryAtom - Class in org.openscience.cdk.isomorphism.matchers

SymbolQueryAtom() - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom

SymbolQueryAtom(IAtom) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom

Symbols - Class in org.openscience.cdk.config

List of element symbols.

Symbols() - Constructor for class org.openscience.cdk.config.Symbols

SymbolSetQueryAtom - Class in org.openscience.cdk.isomorphism.matchers

A QueryAtom that matches all symbols in this container.

SymbolSetQueryAtom() - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom

Constructor for the SymbolSetQueryAtom object

T

T_BOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

TA - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

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.

Tanimoto() - Constructor for class org.openscience.cdk.similarity.Tanimoto

TANTALUM - Static variable in class org.openscience.cdk.config.Elements

TANTALUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

TautomerizationMechanism - Class in org.openscience.cdk.reaction.mechanism

This mechanism produces the tautomerization chemical reaction between two tautomers.

TautomerizationMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.TautomerizationMechanism

TautomerizationReaction - Class in org.openscience.cdk.reaction.type

IReactionProcess which produces a tautomerization chemical reaction.

TautomerizationReaction() - Constructor for class org.openscience.cdk.reaction.type.TautomerizationReaction

Constructor of the TautomerizationReaction object.

TB - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

TC - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

TE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

TECHNETIUM - Static variable in class org.openscience.cdk.config.Elements

TECHNETIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

TELLURIUM - Static variable in class org.openscience.cdk.config.Elements

TELLURIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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.

TemplateHandler3D - Class in org.openscience.cdk.modeling.builder3d

Helper class for ModelBuilder3D.

tensNoUnits() - Method in class org.openscience.cdk.iupac.parser.NomParser

Deal with fragments refering to the positioning of the base numbers (denoting their magnitude)

tensWithUnits() - Method in class org.openscience.cdk.iupac.parser.NomParser

Deals with numbers above 30 where the base numbers set appear twice.

TERBIUM - Static variable in class org.openscience.cdk.config.Elements

TERBIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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

TestClass - Annotation Type in org.openscience.cdk.annotations

An annotation for source classes to indicate the JUnit test class tests the functionality.

TestMethod - Annotation Type in org.openscience.cdk.annotations

An annotation for source classes to indicate the specific test class and method that tests the source class.

TETR - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

TETRAHEDRAL_ANGLE - Static variable in class org.openscience.cdk.geometry.AtomTools

TETRAHEDRAL_ANGLE - Static variable in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D

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(int) - Constructor for class org.openscience.cdk.io.listener.TextGUIListener

0 = ask no questions 3 = ask all questions

TH - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

THALLIUM - Static variable in class org.openscience.cdk.config.Elements

THALLIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

THORIUM - Static variable in class org.openscience.cdk.config.Elements

THORIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

THULIUM - Static variable in class org.openscience.cdk.config.Elements

THULIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

TI - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

timeout - Static variable in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester

TIN - Static variable in class org.openscience.cdk.config.Elements

TIN - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

TinkerMM2Format - Class in org.openscience.cdk.io.formats

See here.

TinkerXYZFormat - Class in org.openscience.cdk.io.formats

See here.

TITANIUM - Static variable in class org.openscience.cdk.config.Elements

TITANIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

TITLE - Static variable in class org.openscience.cdk.CDKConstants

The title for a IChemObject.

TL - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

TM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

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

toDegrees(double) - Static method in class org.openscience.cdk.modeling.forcefield.ForceFieldTools

token - Variable in class org.openscience.cdk.iupac.parser.NomParser

Token - Class in org.openscience.cdk.iupac.parser

Describes the input token stream.

Token() - Constructor for class org.openscience.cdk.iupac.parser.Token

token - Variable in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

Token - Class in org.openscience.cdk.smiles.smarts.parser

Describes the input token stream.

Token() - Constructor for class org.openscience.cdk.smiles.smarts.parser.Token

token_source - Variable in class org.openscience.cdk.iupac.parser.NomParser

token_source - Variable in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

tokenImage - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

tokenImage - Variable in exception org.openscience.cdk.iupac.parser.ParseException

This is a reference to the "tokenImage" array of the generated parser within which the parse error occurred.

tokenImage - Variable in exception org.openscience.cdk.smiles.smarts.parser.ParseException

This is a reference to the "tokenImage" array of the generated parser within which the parse error occurred.

tokenImage - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

TokenMgrError - Error in org.openscience.cdk.iupac.parser

TokenMgrError() - Constructor for error org.openscience.cdk.iupac.parser.TokenMgrError

TokenMgrError(String, int) - Constructor for error org.openscience.cdk.iupac.parser.TokenMgrError

TokenMgrError(boolean, int, int, int, String, char, int) - Constructor for error org.openscience.cdk.iupac.parser.TokenMgrError

TokenMgrError - Error in org.openscience.cdk.smiles.smarts.parser

TokenMgrError() - Constructor for error org.openscience.cdk.smiles.smarts.parser.TokenMgrError

TokenMgrError(String, int) - Constructor for error org.openscience.cdk.smiles.smarts.parser.TokenMgrError

TokenMgrError(boolean, int, int, int, String, char, int) - Constructor for error org.openscience.cdk.smiles.smarts.parser.TokenMgrError

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.

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

toRotationMatrix() - Method in class org.openscience.cdk.math.Quaternion

torsionAngle(IAtom, IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.modeling.forcefield.ForceFieldTools

Calculate the torsion angle from 4 atoms i,j,k and l, where i-j, j-k, and k-l are bonded pairs.

torsionAngleFrom3xNCoordinates(GVector, int, int, int, int) - Static method in class org.openscience.cdk.modeling.forcefield.ForceFieldTools

Calculate the torsion angle from 4 atoms i,j,k and l positions, where i-j, j-k, and k-l are bonded pairs.

Torsions - Class in org.openscience.cdk.modeling.forcefield

Torsions calculator for the potential energy function.

Torsions() - Constructor for class org.openscience.cdk.modeling.forcefield.Torsions

Constructor for the Torsions object

toString() - Method in class org.openscience.cdk.AminoAcid

toString() - Method in class org.openscience.cdk.Association

Returns a one line string representation of this Container.

toString() - Method in class org.openscience.cdk.Atom

Returns a one line string representation of this Atom.

toString() - Method in class org.openscience.cdk.AtomContainer

Returns a one line string representation of this Container.

toString() - Method in class org.openscience.cdk.AtomContainerSet

Returns the String representation of this AtomContainerSet.

toString() - Method in class org.openscience.cdk.AtomParity

Returns a one line string representation of this AtomParity.

toString() - Method in class org.openscience.cdk.AtomType

toString() - Method in class org.openscience.cdk.BioPolymer

toString() - Method in class org.openscience.cdk.Bond

Returns a one line string representation of this Container.

toString() - Method in class org.openscience.cdk.ChemFile

Returns a String representation of this class.

toString() - Method in class org.openscience.cdk.ChemModel

Returns a String representation of the contents of this IChemObject.

toString() - Method in class org.openscience.cdk.ChemSequence

toString() - Method in class org.openscience.cdk.Crystal

Returns a String representation of this crystal.

toString() - Method in class org.openscience.cdk.dict.DictRef

toString() - Method in class org.openscience.cdk.dict.Entry

toString() - Method in class org.openscience.cdk.ElectronContainer

toString() - Method in class org.openscience.cdk.Element

toString() - Method in class org.openscience.cdk.FragmentAtom

toString() - Method in class org.openscience.cdk.graph.rebond.Bspt

toString() - Method in class org.openscience.cdk.graph.rebond.Point

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.CMLStack

Returns a String representation of the stack.

toString() - Method in class org.openscience.cdk.io.random.RandomAccessReader

toString() - Method in class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom

The toString method

toString() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer

toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AliphaticAtom

toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AliphaticSymbolAtom

toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AnyAtom

toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AnyOrderQueryBond

toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AromaticAtom

toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AromaticOrSingleQueryBond

toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AromaticQueryBond

toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.AromaticSymbolAtom

toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ConnectionCountAtom

toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.DegreeAtom

toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.FormalChargeAtom

toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.HybridizationNumberAtom

toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ImplicitHCountAtom

toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.MassAtom

toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.NonCHHeavyAtom

toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.OrderQueryBond

toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.PeriodicGroupNumberAtom

toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RingAtom

toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.TotalHCountAtom

toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.TotalRingConnectionAtom

toString() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.TotalValencyAtom

toString() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolAndChargeQueryAtom

toString() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolChargeIDQueryAtom

toString() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom

toString() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom

The toString method

toString() - Method in class org.openscience.cdk.isomorphism.mcss.RGraph

Returns a string representation of the RGraph.

toString() - Method in class org.openscience.cdk.isomorphism.mcss.RNode

Returns a string representation of the RNode

toString() - Method in class org.openscience.cdk.Isotope

A string representation of this isotope.

toString() - Method in class org.openscience.cdk.iupac.parser.AttachedGroup

A debug string which represents the contents of the class.

toString() - Method in class org.openscience.cdk.iupac.parser.Token

Returns the image.

toString() - Method in class org.openscience.cdk.LonePair

Returns a one line string representation of this LonePair.

toString() - Method in class org.openscience.cdk.math.Complex

Create a string of the content of this class

toString() - Method in class org.openscience.cdk.math.IMatrix

Return a matrix as a string

toString() - Method in class org.openscience.cdk.math.IVector

Return a vector as a string

toString() - Method in class org.openscience.cdk.math.Matrix

Return a matrix as a String.

toString() - Method in class org.openscience.cdk.math.Quaternion

toString() - Method in class org.openscience.cdk.math.Vector

Return a vector as a string

toString() - Method in class org.openscience.cdk.Molecule

Returns a one line string representation of this Atom.

toString() - Method in class org.openscience.cdk.MoleculeSet

toString() - Method in class org.openscience.cdk.Monomer

toString() - Method in class org.openscience.cdk.PeriodicTableElement

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.Ring

toString() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycle

toString(IAtomContainer) - Method in class org.openscience.cdk.ringsearch.Path

toString() - Method in class org.openscience.cdk.RingSet

Returns the String representation of this RingSet.

toString() - Method in class org.openscience.cdk.SingleElectron

Returns a one line string representation of this SingleElectron.

toString() - Method in class org.openscience.cdk.smiles.InvPair

String representation.

toString() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleNode

toString(String) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleNode

toString() - Method in class org.openscience.cdk.smiles.smarts.parser.Token

Returns the image.

toString() - Method in class org.openscience.cdk.Strand

toString() - Method in class org.openscience.cdk.tools.diff.tree.AtomTypeHybridizationDifference

toString() - Method in class org.openscience.cdk.tools.diff.tree.BondOrderDifference

toString() - Method in class org.openscience.cdk.tools.diff.tree.BooleanArrayDifference

toString() - Method in class org.openscience.cdk.tools.diff.tree.BooleanDifference

toString() - Method in class org.openscience.cdk.tools.diff.tree.ChemObjectDifference

toString() - Method in class org.openscience.cdk.tools.diff.tree.DoubleDifference

toString() - Method in class org.openscience.cdk.tools.diff.tree.IntegerDifference

toString() - Method in class org.openscience.cdk.tools.diff.tree.Point2dDifference

toString() - Method in class org.openscience.cdk.tools.diff.tree.Point3dDifference

toString() - Method in class org.openscience.cdk.tools.diff.tree.StringDifference

toString() - Method in class org.openscience.cdk.tools.FormatStringBuffer

Get the result of the formatting.

toString() - Method in class org.openscience.cdk.tools.GridGenerator

TOTAL_CONNECTIONS - Static variable in class org.openscience.cdk.CDKConstants

TOTAL_H_COUNT - Static variable in class org.openscience.cdk.CDKConstants

TotalConnectionAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts

This matches an atom using total number of connections.

TotalConnectionAtom(int) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.TotalConnectionAtom

Creates a new instance.

TotalConnectivity() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

TotalHCount() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

TotalHCountAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts

This matcher checks the formal charge of the Atom.

TotalHCountAtom(int) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.TotalHCountAtom

TotalRingConnectionAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts

This matcher checks the number of ring connections of the checked Atom with other Atom's.

TotalRingConnectionAtom(int) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.TotalRingConnectionAtom

Creates a new instance

TotalValencyAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts

This matcher checks the total valency of the Atom.

TotalValencyAtom(int) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.TotalValencyAtom

TPSADescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

Calculation of topological polar surface area based on fragment contributions (TPSA) [Ertl, P. and Rohde, B. and Selzer, P., Fast Calculation of Molecular Polar Surface Area as a Sum of Fragment-Based Contributions and Its Application to the Prediction of Drug Transport Properties, J. Med. Chem., 2000, 43:3714-3717].

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.

translate2D(IAtomContainer, double, double) - Static method in class org.openscience.cdk.geometry.GeometryTools

Translates the given molecule by the given Vector.

translate2D(IAtomContainer, Vector2d) - Static method in class org.openscience.cdk.geometry.GeometryTools

Translates a molecule from the origin to a new point denoted by a vector.

translate2DCenterTo(IAtomContainer, Point2d) - Static method in class org.openscience.cdk.geometry.GeometryTools

Translates the geometric 2DCenter of the given AtomContainer container to the specified Point2d p.

translate2DCentreOfMassTo(IAtomContainer, Point2d) - Static method in class org.openscience.cdk.geometry.GeometryTools

Translates a molecule from the origin to a new point denoted by a vector.

translateAllPositive(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools

Adds an automatically calculated offset to the coordinates of all atoms such that all coordinates are positive and the smallest x or y coordinate is exactly zero.

transpose() - Method in class org.openscience.cdk.graph.invariant.GIMatrix

Returns the transpose of this matrix.

transpose() - Method in class org.openscience.cdk.math.IMatrix

Transpose a matrix

transpose(IMatrix) - Method in class org.openscience.cdk.math.IMatrix

Transpose a matrix

transpose() - Method in class org.openscience.cdk.math.Matrix

Transposes a matrix.

TRI - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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

TUNGSTEN - Static variable in class org.openscience.cdk.config.Elements

TUNGSTEN - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

TurboMoleFormat - Class in org.openscience.cdk.io.formats

See here.

TURN - Static variable in class org.openscience.cdk.protein.data.PDBStructure

twoOrThreeAttachLocations() - Method in class org.openscience.cdk.iupac.parser.NomParser

Two or three attach locations specidied, handle the second and if needed, the third one here.

TXTBasedAtomTypeConfigurator - Class in org.openscience.cdk.config

AtomType list configurator that uses the AtomTypes originally defined in Jmol v5.

TXTBasedAtomTypeConfigurator() - Constructor for class org.openscience.cdk.config.TXTBasedAtomTypeConfigurator

U

U - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

UNDEC - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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

UniversalIsomorphismTester - Class in org.openscience.cdk.isomorphism

This class implements a multipurpose structure comparison tool.

UniversalIsomorphismTester() - Constructor for class org.openscience.cdk.isomorphism.UniversalIsomorphismTester

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

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 class org.openscience.cdk.config.Elements

UNUNHEXIUM - Static variable in class org.openscience.cdk.config.Elements

UNUNPENTIUM - Static variable in class org.openscience.cdk.config.Elements

UNUNQUADIUM - Static variable in class org.openscience.cdk.config.Elements

UNUNTRIUM - Static variable in class org.openscience.cdk.config.Elements

UP_OR_UNSPECIFIED_S_BOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

UP_S_BOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

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 class org.openscience.cdk.config.Elements

URANIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

V

V - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

v - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

VAdjMaDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

Vertex adjacency information (magnitude): 1 + log2 m where m is the number of heavy-heavy bonds.

VAdjMaDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor

Constructor for the VAdjMaDescriptor object

Valence() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser

validate(IMolecularFormula) - Method in class org.openscience.cdk.formula.rules.ChargeRule

Validate the charge of this IMolecularFormula.

validate(IMolecularFormula) - Method in class org.openscience.cdk.formula.rules.ElementRule

Validate the occurrence of this IMolecularFormula.

validate(IMolecularFormula) - Method in interface org.openscience.cdk.formula.rules.IRule

Analyze the validity for the given IMolecularFormula.

validate(IMolecularFormula) - Method in class org.openscience.cdk.formula.rules.IsotopePatternRule

Validate the isotope pattern of this IMolecularFormula.

validate(IMolecularFormula) - Method in class org.openscience.cdk.formula.rules.MMElementRule

Validate the occurrence of this IMolecularFormula.

validate(IMolecularFormula) - Method in class org.openscience.cdk.formula.rules.NitrogenRule

Validate the nitrogen rule of this IMolecularFormula.

validate(IMolecularFormula) - Method in class org.openscience.cdk.formula.rules.RDBERule

Validate the RDBRule of this IMolecularFormula.

validate(IMolecularFormula, double) - Method in class org.openscience.cdk.formula.rules.RDBERule

Validate the ion state.

validate(IMolecularFormula) - Method in class org.openscience.cdk.formula.rules.ToleranceRangeRule

Validate the Tolerance Range of this IMolecularFormula.

validateAtom(IAtom) - Method in class org.openscience.cdk.validate.AbstractValidator

validateAtom(Atom) - 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(Bond) - 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

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

validateMolecule(IMolecule) - Method in class org.openscience.cdk.validate.AbstractValidator

validateMolecule(Molecule) - Method in class org.openscience.cdk.validate.BasicValidator

validateMolecule(IMolecule) - Method in interface org.openscience.cdk.validate.IValidator

validateMolecule(IMolecule) - Method in class org.openscience.cdk.validate.ValidatorEngine

validateMoleculeSet(IMoleculeSet) - Method in class org.openscience.cdk.validate.AbstractValidator

validateMoleculeSet(IMoleculeSet) - Method in interface org.openscience.cdk.validate.IValidator

validateMoleculeSet(IMoleculeSet) - Method in class org.openscience.cdk.validate.ValidatorEngine

validateReaction(IReaction) - Method in class org.openscience.cdk.validate.AbstractValidator

validateReaction(Reaction) - 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

ValidationReport - Class in org.openscience.cdk.validate

A report on validation of chemical semantics.

ValidationReport() - Constructor for class org.openscience.cdk.validate.ValidationReport

Constructs a new empty ValidationReport.

ValidationTest - Class in org.openscience.cdk.validate

Error found during sematical validation of a IChemObject.

ValidationTest(IChemObject, String) - Constructor for class org.openscience.cdk.validate.ValidationTest

ValidationTest(IChemObject, String, String) - Constructor for class org.openscience.cdk.validate.ValidationTest

ValidatorEngine - Class in org.openscience.cdk.validate

Engine that performs the validation by traversing the IChemObject hierarchy.

ValidatorEngine() - Constructor for class org.openscience.cdk.validate.ValidatorEngine

valueOf(String) - Static method in enum org.openscience.cdk.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.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.IReaction.Direction

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.

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.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.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.io.IChemObjectReader.Mode

Returns an array containing the constants of this enum type, in the order they are declared.

VANADIUM - Static variable in class org.openscience.cdk.config.Elements

VANADIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

VanDerWaalsInteractions - Class in org.openscience.cdk.modeling.forcefield

Van Der Waals Interactions calculator for the potential energy function.

VanDerWaalsInteractions() - Constructor for class org.openscience.cdk.modeling.forcefield.VanDerWaalsInteractions

Constructor for the VanDerWaalsInteractions object

VASPFormat - Class in org.openscience.cdk.io.formats

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

VdWRadiusDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic

This class return the VdW radius of a given atom.

VdWRadiusDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor

Constructor for the VdWRadiusDescriptor object.

Vector - Class in org.openscience.cdk.math

This class handles vectors.

Vector(int) - Constructor for class org.openscience.cdk.math.Vector

Constructs a Vector with "size" elements

Vector(double[]) - Constructor for class org.openscience.cdk.math.Vector

Constructs a vector with the content of a array

Vector(Tuple3d) - Constructor for class org.openscience.cdk.math.Vector

Constructs a Vector with a Tuple3d, Vector3d or Point3d

vector - Variable in class org.openscience.cdk.math.Vector

The content of this vector

vertexAdded(GraphVertexChangeEvent) - Method in class org.openscience.cdk.graph.BiconnectivityInspector

vertexList() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycle

Returns a list of the vertices contained in this cycle.

vertexRemoved(GraphVertexChangeEvent) - Method in class org.openscience.cdk.graph.BiconnectivityInspector

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.

visit(SimpleNode, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTStart, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTReaction, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTGroup, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTSmarts, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTAtom, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTLowAndBond, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTOrBond, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTExplicitHighAndBond, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTImplicitHighAndBond, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTNotBond, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTSimpleBond, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTExplicitAtom, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTLowAndExpression, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTOrExpression, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTExplicitHighAndExpression, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTImplicitHighAndExpression, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTNotExpression, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTRecursiveSmartsExpression, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTTotalHCount, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTImplicitHCount, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTExplicitConnectivity, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTAtomicNumber, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTHybrdizationNumber, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTCharge, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTRingConnectivity, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTPeriodicGroupNumber, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTTotalConnectivity, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTValence, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTRingMembership, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTSmallestRingSize, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTAliphatic, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTNonCHHeavyAtom, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTAromatic, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTAnyAtom, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTAtomicMass, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTRingIdentifier, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTChirality, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTElement, Object) - Method in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor

visit(ASTRingIdentifier, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(SimpleNode, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTStart, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTReaction, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTGroup, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTSmarts, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTLowAndBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTOrBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTExplicitHighAndBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTImplicitHighAndBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTNotBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTSimpleBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTExplicitAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTLowAndExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTOrExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTExplicitHighAndExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTImplicitHighAndExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTNotExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTRecursiveSmartsExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTTotalHCount, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTImplicitHCount, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTExplicitConnectivity, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTAtomicNumber, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTHybrdizationNumber, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTCharge, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTRingConnectivity, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTPeriodicGroupNumber, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTTotalConnectivity, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTValence, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTRingMembership, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTSmallestRingSize, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTAliphatic, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTNonCHHeavyAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTAromatic, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTAnyAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTAtomicMass, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTChirality, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTElement, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.Smarts2MQLVisitor

visit(ASTRingIdentifier, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(SimpleNode, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTStart, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTReaction, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTGroup, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTSmarts, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTNotBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTSimpleBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTImplicitHighAndBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTLowAndBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTOrBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTExplicitHighAndBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTElement, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTRecursiveSmartsExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTPrimitiveAtomExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTTotalHCount, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTImplicitHCount, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTExplicitConnectivity, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTAtomicNumber, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTHybrdizationNumber, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTCharge, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTRingConnectivity, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTPeriodicGroupNumber, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTTotalConnectivity, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTValence, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTRingMembership, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTSmallestRingSize, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTAliphatic, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTNonCHHeavyAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTAromatic, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTAnyAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTAtomicMass, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTChirality, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTLowAndExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTOrExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTNotExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTExplicitHighAndExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTImplicitHighAndExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTExplicitAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsDumpVisitor

visit(ASTRingIdentifier, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(SimpleNode, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTStart, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTReaction, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTGroup, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTSmarts, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTNotBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTImplicitHighAndBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTLowAndBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTOrBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTExplicitHighAndBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTSimpleBond, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTRecursiveSmartsExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTElement, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTTotalHCount, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTImplicitHCount, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTExplicitConnectivity, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTAtomicNumber, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTHybrdizationNumber, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTCharge, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTRingConnectivity, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTPeriodicGroupNumber, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTTotalConnectivity, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTValence, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTRingMembership, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTSmallestRingSize, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTAliphatic, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTNonCHHeavyAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTAromatic, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTAnyAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTAtomicMass, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTChirality, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTLowAndExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTOrExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTNotExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTExplicitHighAndExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTImplicitHighAndExpression, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

visit(ASTExplicitAtom, Object) - Method in class org.openscience.cdk.smiles.smarts.parser.visitor.SmartsQueryVisitor

VISITED - Static variable in class org.openscience.cdk.CDKConstants

Flag is set if chemobject has been visited.

W

W - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

warn(Object) - Method in class org.openscience.cdk.tools.LoggingTool

Shows WARN output for the Object.

warn(Object, int) - Method in class org.openscience.cdk.tools.LoggingTool

Shows WARN output for the given Object's.

warn(Object, boolean) - Method in class org.openscience.cdk.tools.LoggingTool

Shows WARN output for the given Object's.

warn(Object, double) - Method in class org.openscience.cdk.tools.LoggingTool

Shows WARN output for the given Object's.

warn(Object, Object) - Method in class org.openscience.cdk.tools.LoggingTool

Shows WARN output for the given Object's.

warn(Object, Object, Object) - Method in class org.openscience.cdk.tools.LoggingTool

Shows WARN output for the given Object's.

warn(Object, Object, Object, Object) - Method in class org.openscience.cdk.tools.LoggingTool

Shows WARN output for the given Object's.

warn(Object, Object, Object, Object, Object) - Method in class org.openscience.cdk.tools.LoggingTool

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

wasValidated() - Method in class org.openscience.cdk.qsar.model.R.PLSRegressionModelFit

weight() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycle

Returns the sum of the weights of all edges in this cycle.

WeightDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

IDescriptor based on the weight of atoms of a certain element type.

WeightDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor

Constructor for the WeightDescriptor object.

WeightedPathDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

Evaluates the weighted path descriptors.

WeightedPathDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor

weightVector() - Method in class org.openscience.cdk.ringsearch.cyclebasis.CycleBasis

weightVector() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis

WHIMDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

Holistic descriptors described by Todeschini et al [Todeschini, R. and Gramatica, P., New 3D Molecular Descriptors: The WHIM theory and QAR Applications, Persepectives in Drug Discovery and Design, 1998, ?:355-380].

WHIMDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor

width() - Method in class org.openscience.cdk.graph.invariant.GIMatrix

Returns the number of columns of the matrix.

WienerNumbersDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular

This descriptor calculates the Wiener numbers.

WienerNumbersDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor

Constructor for the WienerNumbersDescriptor object.

WILDCARD - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

wolfeConditions(double) - Method in class org.openscience.cdk.modeling.forcefield.LineSearch

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.MDLWriter

Writes a IChemObject to the MDL molfile formated output.

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.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

writeAtom(IAtom) - Method in class org.openscience.cdk.io.CDKSourceCodeWriter

writeAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.io.CDKSourceCodeWriter

writeBond(IBond) - Method in class org.openscience.cdk.io.CDKSourceCodeWriter

writeChemModel(IMoleculeSet, 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(IMolecule) - Method in class org.openscience.cdk.io.CDKSourceCodeWriter

writeMolecule(IAtomContainer) - Method in class org.openscience.cdk.io.MDLWriter

Writes a Molecule to an OutputStream in MDL sdf format.

writeMolecule(IMolecule) - Method in class org.openscience.cdk.io.Mol2Writer

Writes a single frame in XYZ format to the Writer.

writeMolecule(IMolecule) - Method in class org.openscience.cdk.io.PDBWriter

Writes a single frame in PDB format to the Writer.

writeMolecule(IMolecule) - Method in class org.openscience.cdk.io.program.GaussianInputWriter

Writes a molecule for input for Gaussian.

writeMolecule(IMolecule) - Method in class org.openscience.cdk.io.SMILESWriter

Writes the content from molecule to output.

writeMolecule(IMolecule) - Method in class org.openscience.cdk.io.XYZWriter

writes a single frame in XYZ format to the Writer.

writeMoleculeSet(IMoleculeSet) - Method in class org.openscience.cdk.io.SMILESWriter

Writes a list of molecules to an OutputStream

writePharmacophoreDefinition(IQueryAtomContainer, OutputStream) - Static method in class org.openscience.cdk.pharmacophore.PharmacophoreUtils

Write out one or more pharmacophore queries in the CDK XML format.

writePharmacophoreDefinition(List<IQueryAtomContainer>, OutputStream) - Static method in class org.openscience.cdk.pharmacophore.PharmacophoreUtils

Write out one or more pharmacophore queries in the CDK XML format.

writePharmacophoreDefinition(IQueryAtomContainer[], 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.

X

X - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

x - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

XE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

XEDFormat - Class in org.openscience.cdk.io.formats

XENON - Static variable in class org.openscience.cdk.config.Elements

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.

XYZFormat - Class in org.openscience.cdk.io.formats

XYZReader - Class in org.openscience.cdk.io

Reads an object from XYZ formated input.

XYZReader(Reader) - Constructor for class org.openscience.cdk.io.XYZReader

Construct a new reader from a Reader type object.

XYZReader(InputStream) - Constructor for class org.openscience.cdk.io.XYZReader

XYZReader() - Constructor for class org.openscience.cdk.io.XYZReader

XYZWriter - Class in org.openscience.cdk.io

XYZWriter(Writer) - Constructor for class org.openscience.cdk.io.XYZWriter

Constructor.

XYZWriter(OutputStream) - Constructor for class org.openscience.cdk.io.XYZWriter

XYZWriter() - Constructor for class org.openscience.cdk.io.XYZWriter

Y

Y - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

YasaraFormat - Class in org.openscience.cdk.io.formats

See here.

YB - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

YL - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

YN - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

YTTERBIUM - Static variable in class org.openscience.cdk.config.Elements

YTTERBIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

YTTRIUM - Static variable in class org.openscience.cdk.config.Elements

YTTRIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

Z

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.

ZINC - Static variable in class org.openscience.cdk.config.Elements

ZINC - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

ZindoFormat - Class in org.openscience.cdk.io.formats

See here.

ZIRCONIUM - Static variable in class org.openscience.cdk.config.Elements

ZIRCONIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants

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

ZMatrixReader - Class in org.openscience.cdk.io

It reads Z matrices like in Gaussian input files.

ZMatrixReader(Reader) - Constructor for class org.openscience.cdk.io.ZMatrixReader

Constructs a ZMatrixReader from a Reader that contains the data to be parsed.

ZMatrixReader(InputStream) - Constructor for class org.openscience.cdk.io.ZMatrixReader

ZMatrixReader() - Constructor for class org.openscience.cdk.io.ZMatrixReader

zmatrixToCartesian(double[], int[], double[], int[], double[], int[]) - Static method in class org.openscience.cdk.geometry.ZMatrixTools

Takes the given Z Matrix coordinates and converts them to cartesian coordinates.

ZMatrixTools - Class in org.openscience.cdk.geometry

A set of static utility classes for dealing with Z matrices.

ZMatrixTools() - Constructor for class org.openscience.cdk.geometry.ZMatrixTools

ZN - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

ZR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

_

_WS - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

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