- c - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- C - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- CA - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- CacaoCartesianFormat - Class in org.openscience.cdk.io.formats
-
- CacaoCartesianFormat() - Constructor for class org.openscience.cdk.io.formats.CacaoCartesianFormat
-
- CacaoInternalFormat - Class in org.openscience.cdk.io.formats
-
- CacaoInternalFormat() - Constructor for class org.openscience.cdk.io.formats.CacaoInternalFormat
-
- cachedDiagram - Variable in class org.openscience.cdk.renderer.AbstractRenderer
-
Used when repainting an unchanged model.
- cacheDescriptorValue(IAtom, IAtomContainer, IDescriptorResult) - Method in class org.openscience.cdk.qsar.AbstractAtomicDescriptor
-
Caches a DescriptorValue for a given IAtom.
- cacheDescriptorValue(IBond, IAtomContainer, IDescriptorResult) - Method in class org.openscience.cdk.qsar.AbstractBondDescriptor
-
Caches a DescriptorValue for a given IBond.
- CACheFormat - Class in org.openscience.cdk.io.formats
-
- CACheFormat() - Constructor for class org.openscience.cdk.io.formats.CACheFormat
-
- CADMIUM - Static variable in enum org.openscience.cdk.config.Elements
-
- CADMIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- CAESIUM - Static variable in enum org.openscience.cdk.config.Elements
-
- calcD(double, double, double, double, Vector, Vector) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
- calcG(int, double, double, double, double, double, double) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Transfer equation for the calculation of core potentials
- calcG(int, int, double, double, double, double, double, double, double, double, double) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Transfer equation for a four center integral.
- calcI(int, int, int, int) - Method in class org.openscience.cdk.math.qm.FourierGridBasis
-
- calcI(int, int, int, int, double, double, double, double, double, double, double, double, double) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Transfer equation for a four center integral.
- calcI(int, int, int, int) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
- calcI(int, int, int, int) - Method in interface org.openscience.cdk.math.qm.IBasis
-
Calculates a two eletron fout center integral
I = <chi_i chi_j | 1/r12 | chi_k chi_l >.
- calcInvertedAxes(Vector3d, Vector3d, Vector3d) - Static method in class org.openscience.cdk.geometry.CrystalGeometryTools
-
Inverts three cell axes.
- CALCIUM - Static variable in enum org.openscience.cdk.config.Elements
-
- CALCIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- calcJ(int, int) - Method in class org.openscience.cdk.math.qm.FourierGridBasis
-
- calcJ(int, int, double, double, double, double) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Transfer equation the the calculation of the impulse
- calcJ(int, int) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
- calcJ(int, int) - Method in interface org.openscience.cdk.math.qm.IBasis
-
Calculates the impulse J = -<d/dr chi_i | d/dr chi_j>.
- calcS(int, int) - Method in class org.openscience.cdk.math.qm.FourierGridBasis
-
- calcS(int, int) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
- calcS(int, int) - Method in interface org.openscience.cdk.math.qm.IBasis
-
Calculate the overlap integral S = <phi_i|phi_j>.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter
-
Calculates the fingerprints for the given
IAtomContainer
, and stores them for subsequent retrieval.
- calculate(IAtom, IAtom) - Method in interface org.openscience.cdk.geometry.IRDFWeightFunction
-
Calculates the weight for the interaction between the two atoms.
- calculate(IAtomContainer, IAtom) - Method in class org.openscience.cdk.geometry.RDFCalculator
-
Calculates a RDF for Atom
atom in the environment
of the atoms in the AtomContainer
.
- calculate(IAtomContainer) - Static method in class org.openscience.cdk.geometry.volume.VABCVolume
-
- 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.AcidicGroupCountDescriptor
-
Calculates the descriptor value for the given IAtomContainer.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
-
The AlogP descriptor.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor
-
Determine the number of amino acids groups the supplied
IAtomContainer
.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor
-
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor
-
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor
-
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor
-
This method calculate the number of atoms of a given type in an
IAtomContainer
.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
-
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
-
This method calculate the ATS Autocorrelation descriptor.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
-
This method calculate the ATS Autocorrelation descriptor.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor
-
Calculates the descriptor value for the given IAtomContainer.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor
-
Calculates the three classes of BCUT descriptors.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor
-
This method calculate the number of bonds of a given type in an atomContainer
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor
-
This method calculate the sum of the absolute value of
the difference between atomic polarizabilities of all bonded atoms in the molecule
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor
-
Calculates the 9 carbon types descriptors
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
-
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
-
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
-
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
-
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor
-
Evaluates the 29 CPSA descriptors using Gasteiger-Marsilli charges.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor
-
Calculates the eccentric connectivity
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor
-
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor
-
Calculates the topological polar surface area and expresses it as a ratio to molecule size.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor
-
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor
-
Calculates the 9 gravitational indices.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor
-
Calculates the number of H bond acceptors.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor
-
Calculates the number of H bond donors.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor
-
- calculate(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
IAtomContainer
.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor
-
Evaluate the descriptor for the molecule.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor
-
Calculate the count of atoms of the longest aliphatic chain in the supplied
IAtomContainer
.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor
-
Calculates the Mannhold LogP for an atom container.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
-
Calculate the weight of specified element type in the supplied
IAtomContainer
.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor
-
Calculates the 3 MI's, 3 ration and the R_gyr value.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor
-
Evaluate the descriptor for the molecule.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor
-
Calculates the two Petitjean shape indices.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor
-
The method calculates the number of rotatable bonds of an atom container.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor
-
the method take a boolean checkAromaticity: if the boolean is true, it means that
aromaticity has to be checked.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor
-
Performs the calculation: the graph will be analyzed and ring information will be determined and wrapped
up into descriptors.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor
-
Calculates the TPSA for an atom container.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor
-
Calculates the descriptor value using the
VABCVolume
class.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor
-
calculates the VAdjMa descriptor for an atom container
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor
-
Calculate the weight of specified element type in the supplied
IAtomContainer
.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor
-
Calculates the weighted path descriptors.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor
-
Calculates 11 directional and 6 non-directional WHIM descriptors for.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor
-
Calculate the Wiener numbers.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor
-
Calculates the xlogP for an atom container.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor
-
Evaluate the Zagreb Index for a molecule.
- calculate(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor
-
Calculates the 147 TAE descriptors for amino acids.
- calculate(IAtom, IAtomContainer) - Method in interface org.openscience.cdk.qsar.IAtomicDescriptor
-
Calculates the descriptor value for the given IAtom.
- calculate(IAtom, IAtom, IAtomContainer) - Method in interface org.openscience.cdk.qsar.IAtomPairDescriptor
-
Calculates the descriptor value for the given IAtom.
- calculate(IBond, IAtomContainer) - Method in interface org.openscience.cdk.qsar.IBondDescriptor
-
Calculates the descriptor value for the given IBond.
- calculate(IAtomContainer) - Method in interface org.openscience.cdk.qsar.IMolecularDescriptor
-
Calculates the descriptor value for the given IAtomContainer.
- calculate(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.similarity.DistanceMoment
-
Evaluate the 3D similarity between two molecules.
- calculate(Map<String, Integer>, Map<String, Integer>) - Static method in class org.openscience.cdk.similarity.LingoSimilarity
-
Evaluate the LINGO similarity between two key,value sty;e fingerprints.
- calculate(BitSet, BitSet) - Static method in class org.openscience.cdk.similarity.Tanimoto
-
Evaluates Tanimoto coefficient for two bit sets.
- calculate(IBitFingerprint, IBitFingerprint) - Static method in class org.openscience.cdk.similarity.Tanimoto
-
Evaluates Tanimoto coefficient for two IBitFingerprint
.
- calculate(double[], double[]) - Static method in class org.openscience.cdk.similarity.Tanimoto
-
Evaluates the continuous Tanimoto coefficient for two real valued vectors.
- calculate(Map<String, Integer>, Map<String, Integer>) - Static method in class org.openscience.cdk.similarity.Tanimoto
-
Evaluate continuous Tanimoto coefficient for two feature,count fingerprint representations.
- calculate(ICountFingerprint, ICountFingerprint) - Static method in class org.openscience.cdk.similarity.Tanimoto
-
Evaluate continuous Tanimoto coefficient for two feature,count fingerprint representations.
- calculate3DCoordinates0(Point3d, int, double) - Static method in class org.openscience.cdk.geometry.AtomTools
-
Calculates substituent points.
- calculate3DCoordinates0(Point3d, int, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Calculates substituent points.
- calculate3DCoordinates1(Point3d, Point3d, Point3d, int, double, double) - Static method in class org.openscience.cdk.geometry.AtomTools
-
Calculate new point(s) X in a B-A system to form B-A-X.
- calculate3DCoordinates1(Point3d, Point3d, Point3d, int, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Calculate new point(s) X in a B-A system to form B-A-X.
- calculate3DCoordinates2(Point3d, Point3d, Point3d, int, double, double) - Static method in class org.openscience.cdk.geometry.AtomTools
-
Calculate new point(s) X in a B-A-C system.
- calculate3DCoordinates2(Point3d, Point3d, Point3d, int, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Calculate new point(s) X in a B-A-C system, it forms a B-A(-C)-X
system.
- calculate3DCoordinates3(Point3d, Point3d, Point3d, Point3d, double) - Static method in class org.openscience.cdk.geometry.AtomTools
-
Calculate new point X in a B-A(-D)-C system.
- calculate3DCoordinates3(Point3d, Point3d, Point3d, Point3d, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Calculate new point X in a B-A(-D)-C system.
- calculate3DCoordinatesForLigands(IAtomContainer, IAtom, int, double, double) - Static method in class org.openscience.cdk.geometry.AtomTools
-
Adds 3D coordinates for singly-bonded ligands of a reference atom (A).
- calculate3DCoordinatesSP2_1(Point3d, Point3d, Point3d, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Calculate new point in B-A-C system.
- calculate3DCoordinatesSP2_2(Point3d, Point3d, Point3d, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Calculate two new points in B-A system.
- calculateAverageBondLength(IReaction) - Static method in class org.openscience.cdk.renderer.AverageBondLengthCalculator
-
Calculate the average bond length for the bonds in a reaction.
- calculateAverageBondLength(IAtomContainerSet) - Static method in class org.openscience.cdk.renderer.AverageBondLengthCalculator
-
Calculate the average bond length for the bonds in a molecule set.
- calculateAverageBondLength(IChemModel) - Static method in class org.openscience.cdk.renderer.AverageBondLengthCalculator
-
Calculate the average bond length for the bonds in a chem model.
- calculateAverageBondLength(IReactionSet) - Static method in class org.openscience.cdk.renderer.AverageBondLengthCalculator
-
Calculate the average bond length for the bonds in a reaction set.
- calculateBondPolarizability(IAtomContainer, IBond) - Method in class org.openscience.cdk.charges.Polarizability
-
calculate bond polarizability.
- calculateBounds(IChemModel) - Static method in class org.openscience.cdk.renderer.BoundsCalculator
-
Calculate the bounding rectangle for a chem model.
- calculateBounds(IReactionSet) - Static method in class org.openscience.cdk.renderer.BoundsCalculator
-
Calculate the bounding rectangle for a reaction set.
- calculateBounds(IReaction) - Static method in class org.openscience.cdk.renderer.BoundsCalculator
-
Calculate the bounding rectangle for a reaction.
- calculateBounds(IAtomContainerSet) - Static method in class org.openscience.cdk.renderer.BoundsCalculator
-
Calculate the bounding rectangle for a molecule set.
- calculateBounds(IAtomContainer) - Static method in class org.openscience.cdk.renderer.BoundsCalculator
-
Calculate the bounding rectangle for an atom container.
- calculateCharges(IAtomContainer) - Method in class org.openscience.cdk.charges.AtomTypeCharges
-
- calculateCharges(IAtomContainer) - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
-
- calculateCharges(IAtomContainer) - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges
-
- calculateCharges(IAtomContainer) - Method in interface org.openscience.cdk.charges.IElectronicPropertyCalculator
-
- calculateCharges(IAtomContainer) - Method in class org.openscience.cdk.charges.InductivePartialCharges
-
- calculateCharges(IAtomContainer) - Method in class org.openscience.cdk.charges.MMFF94PartialCharges
-
- calculateDiagramBounds(IAtomContainer) - Method in class org.openscience.cdk.renderer.AtomContainerRenderer
-
Given a
IChemObject
, calculates the bounding rectangle in screen
space.
- calculateDiagramBounds(IChemModel) - Method in class org.openscience.cdk.renderer.ChemModelRenderer
-
Given a chem model, calculates the bounding rectangle in screen space.
- calculateDiagramBounds(T) - Method in interface org.openscience.cdk.renderer.IRenderer
-
Given a
IChemObject
, calculates the bounding rectangle in screen
space.
- calculateDiagramBounds(IAtomContainerSet) - Method in class org.openscience.cdk.renderer.MoleculeSetRenderer
-
Given a
IChemObject
, calculates the bounding rectangle in screen
space.
- calculateDiagramBounds(IReaction) - Method in class org.openscience.cdk.renderer.ReactionRenderer
-
Given a
IChemObject
, calculates the bounding rectangle in screen
space.
- calculateDiagramBounds(IReactionSet) - Method in class org.openscience.cdk.renderer.ReactionSetRenderer
-
Given a
IChemObject
, calculates the bounding rectangle in screen
space.
- calculateGHEffectiveAtomPolarizability(IAtomContainer, IAtom, int, boolean) - Method in class org.openscience.cdk.charges.Polarizability
-
calculate effective atom polarizability.
- calculateGHEffectiveAtomPolarizability(IAtomContainer, IAtom, boolean, int[][]) - Method in class org.openscience.cdk.charges.Polarizability
-
calculate effective atom polarizability.
- calculateIsomorphs(IAtomContainer, IAtomContainer, boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
-
This function calculates only one solution (exact) because we are looking at the
molecules which are exactly same in terms of the bonds and atoms determined by the
Fingerprint
- calculateKJMeanMolecularPolarizability(IAtomContainer) - Method in class org.openscience.cdk.charges.Polarizability
-
calculates the mean molecular polarizability as described in paper of Kang and Jhorn.
- calculateMaxRank() - Method in class org.openscience.cdk.graph.Permutor
-
Calculate the max possible rank for permutations of N numbers.
- calculateMaxRank() - Method in class org.openscience.cdk.smsd.labelling.Permutor
-
Calculate the max possible rank for permutations of N numbers.
- calculateNumberOfImplicitHydrogens(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker
-
Calculate the number of missing hydrogens by subtracting the number of
bonds for the atom from the expected number of bonds.
- calculateNumberOfImplicitHydrogens(IAtom) - Method in class org.openscience.cdk.tools.SaturationChecker
-
- calculateNumberOfImplicitHydrogens(IAtom, IAtomContainer, boolean) - Method in class org.openscience.cdk.tools.SaturationChecker
-
- calculateNumberOfImplicitHydrogens(IAtom, double, double, List<IBond>, boolean) - Method in class org.openscience.cdk.tools.SaturationChecker
-
Calculate the number of missing hydrogens by subtracting the number of
bonds for the atom from the expected number of bonds.
- calculateNumberOfImplicitHydrogens(IAtom, double, IBond.Order, int) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
-
Calculates the number of hydrogens that can be added to the given atom to fullfil
the atom's valency.
- calculateNumberOfImplicitHydrogens(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
-
- calculateOrbits() - Method in class org.openscience.cdk.signature.MoleculeSignature
-
Calculates the orbits of the atoms of the molecule.
- calculateOverlapsAndReduce(IAtomContainer, IAtomContainer, boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
-
This function calculates all the possible combinations of MCS
- calculateOverlapsAndReduceExactMatch(IAtomContainer, IAtomContainer, boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
-
This function calculates only one solution (exact) because we are looking at the
molecules which are exactly same in terms of the bonds and atoms determined by the
Fingerprint
- calculatePerpendicularUnitVector(Point2d, Point2d) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Determines the normalized vector orthogonal on the vector p1->p2.
- calculatePerpendicularUnitVector(Point2d, Point2d) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Determines the normalized vector orthogonal on the vector p1->p2.
- calculatePiElectronegativity(IAtomContainer, IAtom) - Method in class org.openscience.cdk.charges.PiElectronegativity
-
calculate the electronegativity of orbitals pi.
- calculatePiElectronegativity(IAtomContainer, IAtom, int, int) - Method in class org.openscience.cdk.charges.PiElectronegativity
-
calculate the electronegativity of orbitals pi.
- calculatePlus(IAtomContainer) - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor
-
It calculates the 1,2,..
- calculatePositive(IAtomContainer, IAtom) - Method in class org.openscience.cdk.charges.StabilizationCharges
-
calculate the stabilization of orbitals when they contain deficiency of charge.
- calculateScaleForBondLength(double) - Method in class org.openscience.cdk.renderer.AbstractRenderer
-
Calculate the scale to convert the model bonds into bonds of the length
supplied.
- calculateScaleForBondLength(double) - Method in class org.openscience.cdk.renderer.AtomContainerRenderer
-
Given a bond length for a model, calculate the scale that will transform
this length to the on screen bond length in RendererModel.
- calculateScaleForBondLength(double) - Method in class org.openscience.cdk.renderer.ChemModelRenderer
-
Given a bond length for a model, calculate the scale that will transform
this length to the on screen bond length in RendererModel.
- calculateScaleForBondLength(double) - Method in class org.openscience.cdk.renderer.MoleculeSetRenderer
-
Given a bond length for a model, calculate the scale that will transform
this length to the on screen bond length in RendererModel.
- calculateScaleForBondLength(double) - Method in class org.openscience.cdk.renderer.ReactionRenderer
-
Given a bond length for a model, calculate the scale that will transform
this length to the on screen bond length in RendererModel.
- calculateScaleForBondLength(double) - Method in class org.openscience.cdk.renderer.ReactionSetRenderer
-
Given a bond length for a model, calculate the scale that will transform
this length to the on screen bond length in RendererModel.
- calculateScreenBounds(Rectangle2D) - Method in class org.openscience.cdk.renderer.AbstractRenderer
-
Converts a bounding rectangle in 'model space' into the equivalent
bounds in 'screen space'.
- calculateSigmaElectronegativity(IAtomContainer, IAtom) - Method in class org.openscience.cdk.charges.Electronegativity
-
calculate the electronegativity of orbitals sigma.
- calculateSigmaElectronegativity(IAtomContainer, IAtom, int, int) - Method in class org.openscience.cdk.charges.Electronegativity
-
calculate the electronegativity of orbitals sigma.
- calculateSubGraphs(IAtomContainer, IAtomContainer, boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
-
This function calculates only one solution (exact) because we are looking at the
molecules which are exactly same in terms of the bonds and atoms determined by the
Fingerprint
- calculateSurface() - Method in class org.openscience.cdk.geometry.surface.NumericalSurface
-
Evaluate the surface.
- calcV(int, int) - Method in class org.openscience.cdk.math.qm.FourierGridBasis
-
- calcV(int, int, Vector, double) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Calculates the core potential.
- calcV(int, int) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Calculates the core potential.
- calcV(int, int) - Method in interface org.openscience.cdk.math.qm.IBasis
-
Calculates the potential V = <chi_i | 1/r | chi_j>.
- CALIFORNIUM - Static variable in enum org.openscience.cdk.config.Elements
-
- CALIFORNIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- cancel() - Method in class org.openscience.cdk.formula.MolecularFormulaGenerator
-
Cancel the current search.
- canDraw(IAtom, IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator
-
Checks an atom to see if it should be drawn.
- Canon - Class in org.openscience.cdk.graph.invariant
-
An implementation based on the canon algorithm [Weininger, David and Weininger, Arthur and Weininger, Joseph
L., SMILES 2. Algorithm for Generation of Unique SMILES
Notation, Journal of Chemical Information and Computer
Sciences, 1989, 29:97-101].
- CANONICAL_LABEL - Static variable in class org.openscience.cdk.smiles.InvPair
-
- canonicalizeAtoms(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.SimpleAtomCanonicalizer
-
- CanonicalLabeler - Class in org.openscience.cdk.graph.invariant
-
Deprecated.
this labeller uses slow data structures and has been replaced - Canon
- CanonicalLabeler() - Constructor for class org.openscience.cdk.graph.invariant.CanonicalLabeler
-
Deprecated.
- CanonicalLabellingAdaptor - Class in org.openscience.cdk.smsd.labelling
-
- CanonicalLabellingAdaptor() - Constructor for class org.openscience.cdk.smsd.labelling.CanonicalLabellingAdaptor
-
- canonLabel(IAtomContainer) - Method in class org.openscience.cdk.graph.invariant.CanonicalLabeler
-
Deprecated.
Canonically label the fragment.
- CARBON - Static variable in enum org.openscience.cdk.config.Elements
-
- CarbonTypesDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
-
Topological descriptor characterizing the carbon connectivity.
- CarbonTypesDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor
-
- CarbonylEliminationReaction - Class in org.openscience.cdk.reaction.type
-
IReactionProcess which participate mass spectrum process.
- CarbonylEliminationReaction() - Constructor for class org.openscience.cdk.reaction.type.CarbonylEliminationReaction
-
Constructor of the CarbonylEliminationReaction object.
- cardinality() - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
-
- cardinality() - Method in interface org.openscience.cdk.fingerprint.IBitFingerprint
-
Returns the number of bits set to true in the fingerprint.
- cardinality() - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
-
- CARET - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- cartesianToFractional(Vector3d, Vector3d, Vector3d, Point3d) - Static method in class org.openscience.cdk.geometry.CrystalGeometryTools
-
- cartesianToNotional(Vector3d, Vector3d, Vector3d) - Static method in class org.openscience.cdk.geometry.CrystalGeometryTools
-
- case1(int, int, int, int, int, int, int) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
-
- case2(int, int, int, int, int, int, int) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
-
- case3(int, int, int, int, int, int, int) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
-
- case4(int, int, int, int, int, int, int) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
-
- cases(int, int, int, int, int, int, int, int) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
-
- CASNumber - Class in org.openscience.cdk.index
-
Tools to work with CAS registry numbers.
- CASNumber() - Constructor for class org.openscience.cdk.index.CASNumber
-
- CASRN - Static variable in class org.openscience.cdk.CDKConstants
-
The CAS Registry Number.
- CD - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- cdk() - Static method in class org.openscience.cdk.aromaticity.ElectronDonation
-
Use the preset CDK atom types to determine the electron contribution of
atoms.
- CDK - Class in org.openscience.cdk
-
Helper class to provide general information about this CDK library.
- CDK() - Constructor for class org.openscience.cdk.CDK
-
- CDK - Class in org.openscience.cdk.libio.jena
-
Helper class to provide a Java API to the CDK OWL ontology, following the design of similar namespace
classes in the Jena library, like RDF
.
- CDK() - Constructor for class org.openscience.cdk.libio.jena.CDK
-
- CDK2DAtomColors - Class in org.openscience.cdk.renderer.color
-
Gives a short table of atom colors for 2D display.
- CDK2DAtomColors() - Constructor for class org.openscience.cdk.renderer.color.CDK2DAtomColors
-
- cdkAllowingExocyclic() - Static method in class org.openscience.cdk.aromaticity.ElectronDonation
-
Use the preset CDK atom types to determine the electron contribution of
atoms.
- cdkAromaticSet() - Static method in class org.openscience.cdk.graph.Cycles
-
Create a cycle finder which will compute a set of cycles traditionally
used by the CDK to test for aromaticity.
- CDKAtomColors - Class in org.openscience.cdk.renderer.color
-
Gives a short table of atom colors for 3D display.
- CDKAtomColors() - Constructor for class org.openscience.cdk.renderer.color.CDKAtomColors
-
- cdkAtomContainerSetToCMLList(IAtomContainerSet) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- cdkAtomContainerToCMLMolecule(IAtomContainer) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- cdkAtomToCMLAtom(IAtom) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- cdkAtomToCMLAtom(IAtomContainer, IAtom) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- CDKAtomTypeMatcher - Class in org.openscience.cdk.atomtype
-
Atom Type matcher that perceives atom types as defined in the CDK atom type list
org/openscience/cdk/dict/data/cdk-atom-types.owl
.
- CDKBasedAtomTypeConfigurator - Class in org.openscience.cdk.config
-
AtomType resource that reads the atom type configuration from an XML file.
- CDKBasedAtomTypeConfigurator() - Constructor for class org.openscience.cdk.config.CDKBasedAtomTypeConfigurator
-
- cdkBondToCMLBond(IBond) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- cdkChemFileToCMLList(IChemFile) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- cdkChemModelToCMLList(IChemModel) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- cdkChemSequenceToCMLList(IChemSequence) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- CDKConstants - Class in org.openscience.cdk
-
An interface providing predefined values for a number of
constants used throughout the CDK.
- CDKConstants() - Constructor for class org.openscience.cdk.CDKConstants
-
- CDKConvention - Class in org.openscience.cdk.io.cml
-
This is an implementation for the CDK convention.
- CDKConvention(IChemFile) - Constructor for class org.openscience.cdk.io.cml.CDKConvention
-
- CDKConvention(ICMLModule) - Constructor for class org.openscience.cdk.io.cml.CDKConvention
-
- cdkCrystalToCMLMolecule(ICrystal) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- CDKDictionaryReferences - Class in org.openscience.cdk.dict
-
This class transforms implicit references to dictionary of CDK
objects into explicit references.
- CDKDictionaryReferences() - Constructor for class org.openscience.cdk.dict.CDKDictionaryReferences
-
- CDKException - Exception in org.openscience.cdk.exception
-
Exception that is thrown by CDK classes when some problem has 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
-
- CDKHueckelAromaticityDetector() - Constructor for class org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector
-
Deprecated.
- CDKHydrogenAdder - Class in org.openscience.cdk.tools
-
Adds implicit hydrogens based on atom type definitions.
- cdkLegacy() - Static method in class org.openscience.cdk.aromaticity.Aromaticity
-
Access an aromaticity instance that replicates the previously utilised -
CDKHueckelAromaticityDetector.
- CDKMCS - Class in org.openscience.cdk.smsd.algorithm.rgraph
-
This class implements atom multipurpose structure comparison tool.
- CDKMCS() - Constructor for class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
-
- CDKMCSHandler - Class in org.openscience.cdk.smsd.algorithm.rgraph
-
This class acts as a handler class for
CDKMCS
algorithm.
- CDKMCSHandler() - Constructor for class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler
-
- cdkMonomerToCMLMolecule(IMonomer) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- CDKOWLFormat - Class in org.openscience.cdk.io.formats
-
Serializes a CDK model into the Web Ontology Language using the
N3 format.
- CDKOWLFormat() - Constructor for class org.openscience.cdk.io.formats.CDKOWLFormat
-
- CDKOWLReader - Class in org.openscience.cdk.io.rdf
-
Reads content from a CDK OWL serialization.
- CDKOWLReader(Reader) - Constructor for class org.openscience.cdk.io.rdf.CDKOWLReader
-
Creates a new CDKOWLReader sending output to the given Writer.
- CDKOWLReader() - Constructor for class org.openscience.cdk.io.rdf.CDKOWLReader
-
Creates a new CDKOWLReader with an undefined input.
- CDKOWLWriter - Class in org.openscience.cdk.io.rdf
-
Serializes the data model into CDK OWL.
- CDKOWLWriter(Writer) - Constructor for class org.openscience.cdk.io.rdf.CDKOWLWriter
-
Creates a new CDKOWLWriter sending output to the given Writer.
- CDKOWLWriter() - Constructor for class org.openscience.cdk.io.rdf.CDKOWLWriter
-
Creates a new CDKOWLWriter with an undefined output.
- cdkPDBPolymerToCMLMolecule(IPDBPolymer) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- cdkReactionSchemeToCMLReactionScheme(IReactionScheme) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- cdkReactionSchemeToCMLReactionSchemeAndMoleculeList(IReactionScheme) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- cdkReactionSetToCMLReactionList(IReactionSet) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- cdkReactionToCMLReaction(IReaction) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- cdkReactionToCMLReactionStep(IReaction) - Method in class org.openscience.cdk.libio.cml.Convertor
-
- CDKRGraph - Class in org.openscience.cdk.smsd.algorithm.rgraph
-
This class implements the Resolution Graph (CDKRGraph).
- CDKRGraph() - Constructor for class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
-
Constructor for the CDKRGraph object and creates an empty CDKRGraph.
- CDKRMap - Class in org.openscience.cdk.smsd.algorithm.rgraph
-
An CDKRMap 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.
- CDKRMap(int, int) - Constructor for class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMap
-
Constructor for the CDKRMap
- CDKRMapHandler - Class in org.openscience.cdk.smsd.algorithm.rgraph
-
This algorithm derives from the algorithm described in
[Tonnelier, C.
- CDKRMapHandler() - Constructor for class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
-
- CDKRNode - Class in org.openscience.cdk.smsd.algorithm.rgraph
-
Node of the resolution graphe (RGraph) An CDKRNode represents an association
betwwen two edges of the source graphs G1 and G2 that are compared.
- CDKRNode(int, int) - Constructor for class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode
-
Constructor for the RNode object
- CDKSourceCodeFormat - Class in org.openscience.cdk.io.formats
-
- CDKSourceCodeFormat() - Constructor for class org.openscience.cdk.io.formats.CDKSourceCodeFormat
-
- CDKSourceCodeWriter - Class in org.openscience.cdk.io
-
Converts a Molecule into CDK source code that would build the same
molecule.
- CDKSourceCodeWriter(Writer) - Constructor for class org.openscience.cdk.io.CDKSourceCodeWriter
-
Constructs a new CDKSourceCodeWriter.
- CDKSourceCodeWriter(OutputStream) - Constructor for class org.openscience.cdk.io.CDKSourceCodeWriter
-
- CDKSourceCodeWriter() - Constructor for class org.openscience.cdk.io.CDKSourceCodeWriter
-
- CDKSubGraphHandler - Class in org.openscience.cdk.smsd.algorithm.rgraph
-
This class acts as a handler class for
CDKMCS
algorithm.
- CDKSubGraphHandler() - Constructor for class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler
-
- 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 data structures, and
tries to detect inconsistencies in it.
- CDKValidator() - Constructor for class org.openscience.cdk.validate.CDKValidator
-
- CE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- center(IAtomContainer, Dimension) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Centers the molecule in the given area.
- center(IAtomContainer, double[]) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Centers the molecule in the given area.
- centerCode - Variable in class org.openscience.cdk.tools.HOSECodeGenerator
-
- CERIUM - Static variable in enum org.openscience.cdk.config.Elements
-
- CERIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- CESIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- CF - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- chainPrefix() - Method in class org.openscience.cdk.iupac.parser.NomParser
-
Deprecated.
A list of known tokens denoting a chain's length.
- changeBase(Permutation) - Method in class org.openscience.cdk.group.PermutationGroup
-
Change the base of the group to the new base newBase
.
- changeCharBonds(int, String, int, IAtomContainer, List<String>) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
-
- changeCharBonds(int, String, int, List<Integer>, List<String>) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
-
- characterData(CMLStack, char[], int, int) - Method in class org.openscience.cdk.io.cml.CDKConvention
-
- characterData(CMLStack, char[], int, int) - Method in class org.openscience.cdk.io.cml.CMLCoreModule
-
- characterData(CMLStack, char[], int, int) - Method in interface org.openscience.cdk.io.cml.ICMLModule
-
- characterData(CMLStack, char[], int, int) - Method in class org.openscience.cdk.io.cml.JMOLANIMATIONConvention
-
- characterData(CMLStack, char[], int, int) - Method in class org.openscience.cdk.io.cml.MDLMolConvention
-
- characterData(CMLStack, char[], int, int) - Method in class org.openscience.cdk.io.cml.PDBConvention
-
- characterData(CMLStack, char[], int, int) - Method in class org.openscience.cdk.io.cml.PMPConvention
-
- characters(char[], int, int) - Method in class org.openscience.cdk.config.atomtypes.AtomTypeHandler
- characters(char[], int, int) - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeHandler
- characters(char[], int, int) - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingHandler
- characters(char[], int, int) - Method in class org.openscience.cdk.config.isotopes.IsotopeHandler
- characters(char[], int, int) - Method in class org.openscience.cdk.dict.DictionaryHandler
-
- characters(char[], int, int) - Method in class org.openscience.cdk.io.cml.CMLHandler
-
Implementation of the characters() procedure overwriting the DefaultHandler interface.
- characters(char[], int, int) - Method in class org.openscience.cdk.io.inchi.INChIHandler
-
Implementation of the characters() procedure overwriting the
DefaultHandler interface.
- charge - Variable in class org.openscience.cdk.Atom
-
The partial charge of the atom.
- charge - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
The partial charge of the atom.
- charge - Variable in class org.openscience.cdk.silent.Atom
-
The partial charge of the atom.
- Charge() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
- charged() - Method in class org.openscience.cdk.hash.HashGeneratorMaker
-
Discriminate protonation states.
- ChargeGroup - Class in org.openscience.cdk.libio.md
-
A ChargeGroup (CG) is a numbered collection of atoms in an MDMolecule.
- ChargeGroup() - Constructor for class org.openscience.cdk.libio.md.ChargeGroup
-
Empty constructor.
- ChargeGroup(IAtomContainer, int, MDMolecule) - Constructor for class org.openscience.cdk.libio.md.ChargeGroup
-
Constructor to create a ChargeGroup based on an AC, a number, and a MDMolecule.
- ChargeRule - Class in org.openscience.cdk.formula.rules
-
This class validate if the charge in the IMolecularFormula correspond with
a specific value.
- ChargeRule() - Constructor for class org.openscience.cdk.formula.rules.ChargeRule
-
Constructor for the ChargeRule object.
- checkAndCleanMolecule(IAtomContainer) - Static method in class org.openscience.cdk.smsd.tools.MoleculeSanityCheck
-
Modules for cleaning a molecule
- checkAndMarkPlaced(IRingSet) - Method in class org.openscience.cdk.layout.RingPlacer
-
Walks throught the atoms of each ring in a ring set and marks
a ring as PLACED if all of its atoms have been placed.
- checkConsistency() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycle
-
- checkDiffNumber(double[]) - Method in class org.openscience.cdk.graph.invariant.EquivalentClassPartitioner
-
Get different number of the given number.
- checkForceFieldType(String) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
-
Sets the forceFieldType attribute of the ForceFieldConfigurator object
- checkIfAllLigandsAreDifferent(ILigand[]) - Static method in class org.openscience.cdk.geometry.cip.CIPTool
-
- checkSingleAtomCases(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
-
Checks for single atom cases before doing subgraph/isomorphism search.
- checkSingleAtomCases(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
-
Checks for single atom cases before doing subgraph/isomorphism search
- checkTimeout() - Method in class org.openscience.cdk.ringsearch.AllRingsFinder
-
Deprecated.
timeout not used
- Chem3D_Cartesian_1Format - Class in org.openscience.cdk.io.formats
-
- Chem3D_Cartesian_1Format() - Constructor for class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
-
- Chem3D_Cartesian_2Format - Class in org.openscience.cdk.io.formats
-
- Chem3D_Cartesian_2Format() - Constructor for class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
-
- ChemDrawFormat - Class in org.openscience.cdk.io.formats
-
- ChemDrawFormat() - Constructor for class org.openscience.cdk.io.formats.ChemDrawFormat
-
- ChemFile - Class in org.openscience.cdk
-
A Object containing a number of ChemSequences.
- ChemFile() - Constructor for class org.openscience.cdk.ChemFile
-
Constructs an empty ChemFile.
- ChemFile - Class in org.openscience.cdk.silent
-
A Object containing a number of ChemSequences.
- ChemFile() - Constructor for class org.openscience.cdk.silent.ChemFile
-
Constructs an empty ChemFile.
- ChemFileManipulator - Class in org.openscience.cdk.tools.manipulator
-
Class with convenience methods that provide methods from
methods from ChemObjects within the ChemFile.
- ChemFileManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.ChemFileManipulator
-
- ChemGraph - Class in org.openscience.cdk.structgen.stochastic.operator
-
- ChemGraph(IAtomContainer) - Constructor for class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
-
- CHEMICAL_GROUP_CONSTANT - Static variable in class org.openscience.cdk.CDKConstants
-
Used as property key for indicating the chemical group of a certain atom type.
- ChemicalFilters - Class in org.openscience.cdk.smsd.filters
-
Class that ranks MCS final solution according to the chemical rules.
- ChemicalFilters(List<Map<Integer, Integer>>, List<Map<IAtom, IAtom>>, Map<Integer, Integer>, Map<IAtom, IAtom>, IAtomContainer, IAtomContainer) - Constructor for class org.openscience.cdk.smsd.filters.ChemicalFilters
-
This class has all the three chemical filters supported by the SMSD.
- ChemModel - Class in org.openscience.cdk
-
An object containing multiple MoleculeSet and
the other lower level concepts like rings, sequences,
fragments, etc.
- ChemModel() - Constructor for class org.openscience.cdk.ChemModel
-
Constructs an new ChemModel with a null setOfMolecules.
- ChemModel - Class in org.openscience.cdk.silent
-
An object containing multiple MoleculeSet and
the other lower level concepts like rings, sequences,
fragments, etc.
- ChemModel() - Constructor for class org.openscience.cdk.silent.ChemModel
-
Constructs an new ChemModel with a null setOfMolecules.
- chemModelCount - Variable in class org.openscience.cdk.ChemSequence
-
Number of ChemModels contained by this container.
- chemModelCount - Variable in class org.openscience.cdk.silent.ChemSequence
-
Number of ChemModels contained by this container.
- ChemModelManipulator - Class in org.openscience.cdk.tools.manipulator
-
Class with convenience methods that provide methods from
methods from ChemObjects within the ChemModel.
- ChemModelManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.ChemModelManipulator
-
- ChemModelRenderer - Class in org.openscience.cdk.renderer
-
- ChemModelRenderer(List<IGenerator<IAtomContainer>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.ChemModelRenderer
-
A renderer that generates diagrams using the specified
generators and manages fonts with the supplied font manager.
- ChemModelRenderer(List<IGenerator<IAtomContainer>>, List<IGenerator<IReaction>>, IFontManager) - Constructor for class org.openscience.cdk.renderer.ChemModelRenderer
-
- chemModels - Variable in class org.openscience.cdk.ChemSequence
-
Array of ChemModels.
- chemModels() - Method in class org.openscience.cdk.ChemSequence
-
Returns an Iterable to ChemModels in this container.
- chemModels() - Method in class org.openscience.cdk.debug.DebugChemSequence
-
Returns an Iterable to ChemModels in this container.
- chemModels() - Method in interface org.openscience.cdk.interfaces.IChemSequence
-
Returns an Iterable to ChemModels in this container.
- chemModels - Variable in class org.openscience.cdk.silent.ChemSequence
-
Array of ChemModels.
- chemModels() - Method in class org.openscience.cdk.silent.ChemSequence
-
Returns an Iterable to ChemModels in this container.
- ChemObject - Class in org.openscience.cdk
-
The base class for all chemical objects in this cdk.
- ChemObject() - Constructor for class org.openscience.cdk.ChemObject
-
Constructs a new IChemObject.
- ChemObject(IChemObject) - Constructor for class org.openscience.cdk.ChemObject
-
Constructs a new IChemObject by copying the flags, and the
identifier.
- CHEMOBJECT - Static variable in class org.openscience.cdk.libio.jena.CDK
-
- ChemObject - Class in org.openscience.cdk.silent
-
The base class for all chemical objects in this cdk.
- ChemObject() - Constructor for class org.openscience.cdk.silent.ChemObject
-
Constructs a new IChemObject.
- ChemObject(IChemObject) - Constructor for class org.openscience.cdk.silent.ChemObject
-
Constructs a new IChemObject by copying the flags, and the
identifier.
- ChemObjectChangeEvent - Class in org.openscience.cdk.event
-
Event fired by cdk classes to their registered listeners
in case something changes within them.
- ChemObjectChangeEvent(Object) - Constructor for class org.openscience.cdk.event.ChemObjectChangeEvent
-
Constructs a ChemObjectChangeEvent with a reference
to the object where it originated.
- ChemObjectDiff - Class in org.openscience.cdk.tools.diff
-
- ChemObjectDifference - Class in org.openscience.cdk.tools.diff.tree
-
- ChemObjectDifference(String) - Constructor for class org.openscience.cdk.tools.diff.tree.ChemObjectDifference
-
- ChemObjectIO - Class in org.openscience.cdk.io
-
Provides some basic functionality for readers and writers.
- ChemObjectIO() - Constructor for class org.openscience.cdk.io.ChemObjectIO
-
- chemObjectReader - Variable in class org.openscience.cdk.io.random.RandomAccessReader
-
- ChemSequence - Class in org.openscience.cdk
-
A sequence of ChemModels, which can, for example, be used to
store the course of a reaction.
- ChemSequence() - Constructor for class org.openscience.cdk.ChemSequence
-
Constructs an empty ChemSequence.
- ChemSequence - Class in org.openscience.cdk.silent
-
A sequence of ChemModels, which can, for example, be used to
store the course of a reaction.
- ChemSequence() - Constructor for class org.openscience.cdk.silent.ChemSequence
-
Constructs an empty ChemSequence.
- chemSequenceCount - Variable in class org.openscience.cdk.ChemFile
-
Number of ChemSequences contained by this container.
- chemSequenceCount - Variable in class org.openscience.cdk.silent.ChemFile
-
Number of ChemSequences contained by this container.
- ChemSequenceManipulator - Class in org.openscience.cdk.tools.manipulator
-
Class with convenience methods that provide methods from
methods from ChemObjects within the ChemSequence.
- ChemSequenceManipulator() - Constructor for class org.openscience.cdk.tools.manipulator.ChemSequenceManipulator
-
- chemSequences - Variable in class org.openscience.cdk.ChemFile
-
Array of ChemSquences.
- chemSequences() - Method in class org.openscience.cdk.ChemFile
-
Returns the Iterable to ChemSequences of this container.
- chemSequences() - Method in class org.openscience.cdk.debug.DebugChemFile
-
Returns the Iterable to ChemSequences of this container.
- chemSequences() - Method in interface org.openscience.cdk.interfaces.IChemFile
-
Returns the
Iterable
to ChemSequences of this container.
- chemSequences - Variable in class org.openscience.cdk.silent.ChemFile
-
Array of ChemSquences.
- chemSequences() - Method in class org.openscience.cdk.silent.ChemFile
-
Returns the Iterable to ChemSequences of this container.
- ChemtoolFormat - Class in org.openscience.cdk.io.formats
-
- ChemtoolFormat() - Constructor for class org.openscience.cdk.io.formats.ChemtoolFormat
-
- ChiChainDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
-
Evaluates chi chain descriptors.
- ChiChainDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
-
- ChiClusterDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
-
Evaluates chi cluster descriptors.
- ChiClusterDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
-
- childCount() - Method in class org.openscience.cdk.tools.diff.tree.AbstractDifferenceList
-
- childCount() - Method in interface org.openscience.cdk.tools.diff.tree.IDifferenceList
-
- children - Variable in class org.openscience.cdk.renderer.elements.TextGroupElement
-
The child text elements.
- ChiPathClusterDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
-
Evaluates chi path cluster descriptors.
- ChiPathClusterDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
-
- ChiPathDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
-
Evaluates chi path descriptors.
- ChiPathDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
-
- chiral() - Method in class org.openscience.cdk.hash.HashGeneratorMaker
-
Generate different hash codes for stereoisomers.
- Chirality() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
- ChiralityAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
-
This matches an atom with chirality property.
- ChiralityAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom
-
Creates a new instance
- chiralityMatches(IAtom, int, int) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom
-
- chiralityMatches(IAtom, int, int) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom
-
Check if the atom-based chirality of the target matches.
- CHLORINE - Static variable in enum org.openscience.cdk.config.Elements
-
- CHLORO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- CHROMIUM - Static variable in enum org.openscience.cdk.config.Elements
-
- CHROMIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- CIFFormat - Class in org.openscience.cdk.io.formats
-
- CIFFormat() - Constructor for class org.openscience.cdk.io.formats.CIFFormat
-
- CIFReader - Class in org.openscience.cdk.io
-
This is not a reader for the CIF and mmCIF crystallographic formats.
- CIFReader(Reader) - Constructor for class org.openscience.cdk.io.CIFReader
-
Create an CIF like file reader.
- CIFReader(InputStream) - Constructor for class org.openscience.cdk.io.CIFReader
-
- CIFReader() - Constructor for class org.openscience.cdk.io.CIFReader
-
- CIP_DESCRIPTOR - Static variable in class org.openscience.cdk.CDKConstants
-
Property key to store the CIP descriptor label for an atom / bond.
- CIPLigandRule - Class in org.openscience.cdk.geometry.cip.rules
-
Compares to
ILigand
s based on CIP sequences sub rules.
- CIPLigandRule() - Constructor for class org.openscience.cdk.geometry.cip.rules.CIPLigandRule
-
- CIPTool - Class in org.openscience.cdk.geometry.cip
-
Tool to help determine the R,S and stereochemistry definitions of a subset of the
CIP rules [Cahn, R.S. and Ingold, C. and Prelog, V., Specification of Molecular Chirality, Angew. Chem. Int. Ed., 1966, 5:385-415].
- CIPTool() - Constructor for class org.openscience.cdk.geometry.cip.CIPTool
-
- CIPTool.CIP_CHIRALITY - Enum in org.openscience.cdk.geometry.cip
-
Enumeration with the two tetrahedral chiralities defined by the CIP schema.
- CircularFingerprinter - Class in org.openscience.cdk.fingerprint
-
Circular fingerprints: for generating fingerprints that are functionally equivalent to ECFP-2/4/6 and FCFP-2/4/6
fingerprints, which are partially described by Rogers et al.
- CircularFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.CircularFingerprinter
-
Default constructor: uses the ECFP6 type.
- CircularFingerprinter(int) - Constructor for class org.openscience.cdk.fingerprint.CircularFingerprinter
-
Specific constructor: initializes with descriptor class type, one of ECFP_{p} or FCFP_{p}, where ECFP is
for the extended-connectivity fingerprints, FCFP is for the functional class version, and {p} is the
path diameter, and may be 0, 2, 4 or 6.
- CircularFingerprinter(int, int) - Constructor for class org.openscience.cdk.fingerprint.CircularFingerprinter
-
Specific constructor: initializes with descriptor class type, one of ECFP_{p} or FCFP_{p}, where ECFP is
for the extended-connectivity fingerprints, FCFP is for the functional class version, and {p} is the
path diameter, and may be 0, 2, 4 or 6.
- CircularFingerprinter.FP - Class in org.openscience.cdk.fingerprint
-
- CircularFingerprinter.FP(int, int, int[]) - Constructor for class org.openscience.cdk.fingerprint.CircularFingerprinter.FP
-
- CL - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- CLASS_ECFP0 - Static variable in class org.openscience.cdk.fingerprint.CircularFingerprinter
-
- CLASS_ECFP2 - Static variable in class org.openscience.cdk.fingerprint.CircularFingerprinter
-
- CLASS_ECFP4 - Static variable in class org.openscience.cdk.fingerprint.CircularFingerprinter
-
- CLASS_ECFP6 - Static variable in class org.openscience.cdk.fingerprint.CircularFingerprinter
-
- CLASS_FCFP0 - Static variable in class org.openscience.cdk.fingerprint.CircularFingerprinter
-
- CLASS_FCFP2 - Static variable in class org.openscience.cdk.fingerprint.CircularFingerprinter
-
- CLASS_FCFP4 - Static variable in class org.openscience.cdk.fingerprint.CircularFingerprinter
-
- CLASS_FCFP6 - Static variable in class org.openscience.cdk.fingerprint.CircularFingerprinter
-
- cleanDataSet(String) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor
-
- clear() - Method in class org.openscience.cdk.ConformerContainer
-
Get rid of all the conformers but keeps atom and bond information.
- clear() - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
-
Reinitialisation of the TGraph.
- clear() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
- clear() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
-
Reinitialisation of the TGraph.
- clear() - Method in class org.openscience.cdk.smsd.helper.FinalMappings
-
clear the mapping
- clear() - Method in interface org.openscience.cdk.smsd.interfaces.IFinalMapping
-
clear the mapping
- clearAtomConfigurations(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
This method will reset all atom configuration to UNSET.
- clearCEgdes() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
- clearCompGraphNodes() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
- clearCompGraphNodesCZero() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
- clearDEgdes() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
- clearNodeScope(Node) - Method in class org.openscience.cdk.smiles.smarts.parser.JJTSMARTSParserState
-
- clone() - Method in class org.openscience.cdk.AminoAcid
-
Clones this AminoAcid object.
- clone() - Method in class org.openscience.cdk.Atom
-
Clones this atom object and its content.
- clone() - Method in class org.openscience.cdk.AtomContainer
-
Clones this AtomContainer object and its content.
- clone() - Method in class org.openscience.cdk.AtomContainerSet
-
Clones this AtomContainerSet and its content.
- clone() - Method in class org.openscience.cdk.AtomType
-
- clone() - Method in class org.openscience.cdk.BioPolymer
-
- clone() - Method in class org.openscience.cdk.Bond
-
Clones this bond object, including clones of the atoms between which the
bond is defined.
- clone() - Method in class org.openscience.cdk.ChemFile
-
Allows for getting an clone of this object.
- clone() - Method in class org.openscience.cdk.ChemModel
-
Clones this ChemModel
and its content.
- clone() - Method in class org.openscience.cdk.ChemObject
-
Clones this IChemObject
.
- clone() - Method in class org.openscience.cdk.ChemSequence
-
- clone() - Method in class org.openscience.cdk.Crystal
-
Makes a clone of this crystal.
- clone() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Clones this AminoAcid object.
- clone() - Method in class org.openscience.cdk.debug.DebugAtom
-
Clones this atom object and its content.
- clone() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Clones this AtomContainer object and its content.
- clone() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
Clones this AtomContainerSet and its content.
- clone() - Method in class org.openscience.cdk.debug.DebugAtomType
-
Clones this IChemObject
.
- clone() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Clones this AtomContainer object and its content.
- clone() - Method in class org.openscience.cdk.debug.DebugBond
-
Clones this bond object, including clones of the atoms between which the
bond is defined.
- clone() - Method in class org.openscience.cdk.debug.DebugChemFile
-
Allows for getting an clone of this object.
- clone() - Method in class org.openscience.cdk.debug.DebugChemModel
-
Clones this ChemModel
and its content.
- clone() - Method in class org.openscience.cdk.debug.DebugChemObject
-
Clones this IChemObject
.
- clone() - Method in class org.openscience.cdk.debug.DebugChemSequence
-
Clones this IChemObject
.
- clone() - Method in class org.openscience.cdk.debug.DebugCrystal
-
Makes a clone of this crystal.
- clone() - Method in class org.openscience.cdk.debug.DebugElectronContainer
-
Clones this IChemObject
.
- clone() - Method in class org.openscience.cdk.debug.DebugElement
-
Clones this IChemObject
.
- clone() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Clones this atom object and its content.
- clone() - Method in class org.openscience.cdk.debug.DebugIsotope
-
Clones this IChemObject
.
- clone() - Method in class org.openscience.cdk.debug.DebugLonePair
-
Clones this LonePair object, including a clone of the atom for which the
lone pair is defined.
- clone() - Method in class org.openscience.cdk.debug.DebugMapping
-
Clones this Mapping
and the mapped IChemObject
s.
- clone() - Method in class org.openscience.cdk.debug.DebugMonomer
-
Clones this AtomContainer object and its content.
- clone() - Method in class org.openscience.cdk.debug.DebugPolymer
-
Clones this AtomContainer object and its content.
- clone() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Clones this atom object and its content.
- clone() - Method in class org.openscience.cdk.debug.DebugReaction
-
Clones this Reaction
and its content.
- clone() - Method in class org.openscience.cdk.debug.DebugReactionScheme
-
Clones this ReactionScheme object and its content.
- clone() - Method in class org.openscience.cdk.debug.DebugReactionSet
-
Clones this ReactionSet
and the contained Reaction
s
too.
- clone() - Method in class org.openscience.cdk.debug.DebugRing
-
Clones this AtomContainer object and its content.
- clone() - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
Clones this SingleElectron object, including a clone of the atom for which the
SingleElectron is defined.
- clone() - Method in class org.openscience.cdk.debug.DebugStrand
-
Clones this AtomContainer object and its content.
- clone() - Method in class org.openscience.cdk.debug.DebugSubstance
-
Clones this AtomContainerSet and its content.
- clone() - Method in class org.openscience.cdk.ElectronContainer
-
- clone() - Method in class org.openscience.cdk.Element
-
- clone() - Method in class org.openscience.cdk.formula.AdductFormula
-
Clones this AdductFormula object and its content.
- clone() - Method in class org.openscience.cdk.formula.IsotopeContainer
-
Clones this IsotopeContainer object and its content.
- clone() - Method in class org.openscience.cdk.formula.IsotopePattern
-
Clones this IsotopePattern object and its content.
- clone() - Method in class org.openscience.cdk.formula.MolecularFormula
-
Clones this MolecularFormula object and its content.
- clone() - Method in class org.openscience.cdk.formula.MolecularFormulaRange
-
Clones this MolecularFormulaExpand object and its content.
- clone() - Method in class org.openscience.cdk.formula.MolecularFormulaSet
-
Clones this MolecularFormulaSet object and its content.
- clone() - Method in class org.openscience.cdk.FragmentAtom
-
- clone() - Method in interface org.openscience.cdk.interfaces.IAdductFormula
-
Clones this IAdductFormula object and its content.
- clone() - Method in interface org.openscience.cdk.interfaces.IAminoAcid
-
- clone() - Method in interface org.openscience.cdk.interfaces.IAtom
-
- clone() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
- clone() - Method in interface org.openscience.cdk.interfaces.IBioPolymer
-
- clone() - Method in interface org.openscience.cdk.interfaces.IBond
-
- clone() - Method in interface org.openscience.cdk.interfaces.IChemObject
-
Returns a deep clone of this IChemObject.
- clone() - Method in interface org.openscience.cdk.interfaces.ICrystal
-
- clone() - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
-
Clones this MolecularFormula object and its content.
- clone() - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet
-
Clones this IMolecularFormulaSet object and its content.
- clone() - Method in interface org.openscience.cdk.interfaces.IMonomer
-
- clone() - Method in interface org.openscience.cdk.interfaces.IPDBMonomer
-
- clone() - Method in interface org.openscience.cdk.interfaces.IPDBPolymer
-
- clone() - Method in interface org.openscience.cdk.interfaces.IPolymer
-
- clone() - Method in interface org.openscience.cdk.interfaces.IPseudoAtom
-
- clone() - Method in interface org.openscience.cdk.interfaces.IReactionScheme
-
Clones this IReactionScheme object and its content.
- clone() - Method in interface org.openscience.cdk.interfaces.IRing
-
- clone() - Method in interface org.openscience.cdk.interfaces.IStrand
-
- clone() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
- clone() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Clones this AtomContainer object and its content.
- clone() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Clones this query bond object, including clones of the atoms between which the
query bond is defined.
- clone() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
- clone() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolAndChargeQueryAtom
-
- clone() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolChargeIDQueryAtom
-
- clone() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom
-
- clone() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom
-
- clone() - Method in class org.openscience.cdk.Isotope
-
- clone() - Method in class org.openscience.cdk.LonePair
-
Clones this LonePair object, including a clone of the atom for which the
lone pair is defined.
- clone() - Method in class org.openscience.cdk.Mapping
-
Clones this Mapping
and the mapped IChemObject
s.
- clone() - Method in class org.openscience.cdk.Monomer
-
- clone() - Method in class org.openscience.cdk.Polymer
-
- clone() - Method in class org.openscience.cdk.protein.data.PDBMonomer
-
- clone() - Method in class org.openscience.cdk.protein.data.PDBPolymer
-
- 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 Reaction
s
too.
- clone() - Method in class org.openscience.cdk.Ring
-
- clone() - Method in class org.openscience.cdk.RingSet
-
Clones this RingSet
including the Rings.
- clone() - Method in class org.openscience.cdk.signature.Orbit
- clone() - Method in class org.openscience.cdk.silent.AdductFormula
-
Clones this AdductFormula object and its content.
- clone() - Method in class org.openscience.cdk.silent.AminoAcid
-
Clones this AminoAcid object.
- clone() - Method in class org.openscience.cdk.silent.Atom
-
Clones this atom object and its content.
- clone() - Method in class org.openscience.cdk.silent.AtomContainer
-
Clones this AtomContainer object and its content.
- clone() - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Clones this AtomContainerSet and its content.
- clone() - Method in class org.openscience.cdk.silent.AtomType
-
- clone() - Method in class org.openscience.cdk.silent.BioPolymer
-
- clone() - Method in class org.openscience.cdk.silent.Bond
-
Clones this bond object, including clones of the atoms between which the
bond is defined.
- clone() - Method in class org.openscience.cdk.silent.ChemFile
-
Allows for getting an clone of this object.
- clone() - Method in class org.openscience.cdk.silent.ChemModel
-
Clones this ChemModel
and its content.
- clone() - Method in class org.openscience.cdk.silent.ChemObject
-
Clones this IChemObject
.
- clone() - Method in class org.openscience.cdk.silent.ChemSequence
-
- clone() - Method in class org.openscience.cdk.silent.Crystal
-
Makes a clone of this crystal.
- clone() - Method in class org.openscience.cdk.silent.ElectronContainer
-
- clone() - Method in class org.openscience.cdk.silent.Element
-
- clone() - Method in class org.openscience.cdk.silent.FragmentAtom
-
- clone() - Method in class org.openscience.cdk.silent.Isotope
-
- clone() - Method in class org.openscience.cdk.silent.LonePair
-
Clones this LonePair object, including a clone of the atom for which the
lone pair is defined.
- clone() - Method in class org.openscience.cdk.silent.Mapping
-
Clones this Mapping
and the mapped IChemObject
s.
- clone() - Method in class org.openscience.cdk.silent.MolecularFormula
-
Clones this MolecularFormula object and its content.
- clone() - Method in class org.openscience.cdk.silent.MolecularFormulaSet
-
Clones this MolecularFormulaSet object and its content.
- clone() - Method in class org.openscience.cdk.silent.Monomer
-
- clone() - Method in class org.openscience.cdk.silent.PDBMonomer
-
- clone() - Method in class org.openscience.cdk.silent.PDBPolymer
-
- clone() - Method in class org.openscience.cdk.silent.Polymer
-
- clone() - Method in class org.openscience.cdk.silent.PseudoAtom
-
- clone() - Method in class org.openscience.cdk.silent.Reaction
-
Clones this Reaction
and its content.
- clone() - Method in class org.openscience.cdk.silent.ReactionScheme
-
Clones this ReactionScheme object and its content.
- clone() - Method in class org.openscience.cdk.silent.ReactionSet
-
Clones this ReactionSet
and the contained Reaction
s
too.
- clone() - Method in class org.openscience.cdk.silent.Ring
-
- clone() - Method in class org.openscience.cdk.silent.RingSet
-
Clones this RingSet
including the Rings.
- clone() - Method in class org.openscience.cdk.silent.SingleElectron
-
Clones this SingleElectron object, including a clone of the atom for which the
SingleElectron is defined.
- clone() - Method in class org.openscience.cdk.silent.Strand
-
- clone() - Method in class org.openscience.cdk.SingleElectron
-
Clones this SingleElectron object, including a clone of the atom for which the
SingleElectron is defined.
- clone() - Method in class org.openscience.cdk.Strand
-
- close() - Method in class org.openscience.cdk.io.CDKSourceCodeWriter
-
Flushes the output and closes this object.
- close() - Method in class org.openscience.cdk.io.CIFReader
-
- close() - Method in class org.openscience.cdk.io.CMLReader
-
- close() - Method in class org.openscience.cdk.io.CMLWriter
-
Flushes the output and closes this object.
- close() - Method in class org.openscience.cdk.io.CrystClustReader
-
- close() - Method in class org.openscience.cdk.io.CrystClustWriter
-
Flushes the output and closes this object.
- close() - Method in class org.openscience.cdk.io.CTXReader
-
- close() - Method in class org.openscience.cdk.io.GamessReader
-
- close() - Method in class org.openscience.cdk.io.Gaussian03Reader
-
- close() - Method in class org.openscience.cdk.io.Gaussian98Reader
-
- close() - Method in class org.openscience.cdk.io.GhemicalMMReader
-
- close() - Method in class org.openscience.cdk.io.HINReader
-
- close() - Method in class org.openscience.cdk.io.HINWriter
-
Flushes the output and closes this object.
- close() - Method in interface org.openscience.cdk.io.IChemObjectIO
-
Closes this IChemObjectIO's resources.
- close() - Method in class org.openscience.cdk.io.INChIPlainTextReader
-
- close() - Method in class org.openscience.cdk.io.INChIReader
-
- close() - Method in class org.openscience.cdk.io.iterator.event.EventCMLReader
-
- close() - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundASNReader
-
- close() - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader
-
- close() - Method in class org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader
-
- close() - Method in class org.openscience.cdk.io.iterator.IteratingSDFReader
-
- close() - Method in class org.openscience.cdk.io.iterator.IteratingSMILESReader
-
Close the reader.
- close() - Method in class org.openscience.cdk.io.MDLReader
-
- close() - Method in class org.openscience.cdk.io.MDLRXNReader
-
- close() - Method in class org.openscience.cdk.io.MDLRXNV2000Reader
-
- close() - Method in class org.openscience.cdk.io.MDLRXNV3000Reader
-
- close() - Method in class org.openscience.cdk.io.MDLRXNWriter
-
Flushes the output and closes this object.
- close() - Method in class org.openscience.cdk.io.MDLV2000Reader
-
- close() - Method in class org.openscience.cdk.io.MDLV2000Writer
-
Flushes the output and closes this object.
- close() - Method in class org.openscience.cdk.io.MDLV3000Reader
-
- close() - Method in class org.openscience.cdk.io.Mol2Reader
-
- close() - Method in class org.openscience.cdk.io.Mol2Writer
-
Flushes the output and closes this object.
- close() - Method in class org.openscience.cdk.io.Mopac7Reader
-
- close() - Method in class org.openscience.cdk.io.MoSSOutputReader
-
Closes this IChemObjectIO's resources.
- close() - Method in class org.openscience.cdk.io.PCCompoundASNReader
-
- close() - Method in class org.openscience.cdk.io.PCCompoundXMLReader
-
- close() - Method in class org.openscience.cdk.io.PCSubstanceXMLReader
-
- close() - Method in class org.openscience.cdk.io.PDBReader
-
- close() - Method in class org.openscience.cdk.io.PDBWriter
-
Flushes the output and closes this object.
- close() - Method in class org.openscience.cdk.io.PMPReader
-
- close() - Method in class org.openscience.cdk.io.program.GaussianInputWriter
-
- close() - Method in class org.openscience.cdk.io.program.Mopac7Writer
-
- close() - Method in class org.openscience.cdk.io.random.RandomAccessReader
-
- close() - Method in class org.openscience.cdk.io.rdf.CDKOWLReader
-
Closes this IChemObjectIO's resources.
- close() - Method in class org.openscience.cdk.io.rdf.CDKOWLWriter
-
Closes this IChemObjectIO's resources.
- close() - Method in class org.openscience.cdk.io.RGroupQueryReader
-
- close() - Method in class org.openscience.cdk.io.RGroupQueryWriter
-
Flushes the output and closes this object.
- close() - Method in class org.openscience.cdk.io.RssWriter
-
Flushes the output and closes this object.
- close() - Method in class org.openscience.cdk.io.SDFWriter
-
Flushes the output and closes this object.
- close() - Method in class org.openscience.cdk.io.ShelXReader
-
- close() - Method in class org.openscience.cdk.io.ShelXWriter
-
Flushes the output and closes this object.
- close() - Method in class org.openscience.cdk.io.SMILESReader
-
- close() - Method in class org.openscience.cdk.io.SMILESWriter
-
Flushes the output and closes this object.
- close() - Method in class org.openscience.cdk.io.VASPReader
-
- close() - Method in class org.openscience.cdk.io.XYZReader
-
- close() - Method in class org.openscience.cdk.io.XYZWriter
-
Flushes the output and closes this object.
- close() - Method in class org.openscience.cdk.io.ZMatrixReader
-
- Close - Class in org.openscience.cdk.renderer.elements.path
-
Indicates the closing point of the path.
- Close() - Constructor for class org.openscience.cdk.renderer.elements.path.Close
-
Make a Close PathElement.
- close() - Method in class org.openscience.cdk.renderer.elements.path.PathBuilder
-
Close the path.
- ClosedShellJob - Class in org.openscience.cdk.math.qm
-
Calculates the orbitals and orbital energies of electron systems
with closed shells
- ClosedShellJob(Orbitals) - Constructor for class org.openscience.cdk.math.qm.ClosedShellJob
-
- closeEnoughToBond(IAtom, IAtom, double) - Static method in class org.openscience.cdk.geometry.BondTools
-
Returns true if the two atoms are within the distance fudge
factor of each other.
- closeNodeScope(Node, int) - Method in class org.openscience.cdk.smiles.smarts.parser.JJTSMARTSParserState
-
- closeNodeScope(Node, boolean) - Method in class org.openscience.cdk.smiles.smarts.parser.JJTSMARTSParserState
-
- clusterPSPPocket(Point3d, List<Point3d>, int[]) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
Method performs the clustering, is called by findPockets().
- CM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- CMLCoreModule - Class in org.openscience.cdk.io.cml
-
Core CML 1.x and 2.x elements are parsed by this class.
- 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
-
- CMLFormat() - Constructor for class org.openscience.cdk.io.formats.CMLFormat
-
- CMLHandler - Class in org.openscience.cdk.io.cml
-
SAX2 implementation for CML XML fragment reading.
- CMLHandler(IChemFile) - Constructor for class org.openscience.cdk.io.cml.CMLHandler
-
Constructor for the CMLHandler.
- CMLModuleStack - Class in org.openscience.cdk.io.cml
-
Low weight alternative to Sun's Stack class.
- CMLModuleStack() - Constructor for class org.openscience.cdk.io.cml.CMLModuleStack
-
- CMLReactionModule - Class in org.openscience.cdk.io.cml
-
- CMLReactionModule(IChemFile) - Constructor for class org.openscience.cdk.io.cml.CMLReactionModule
-
- CMLReactionModule(ICMLModule) - Constructor for class org.openscience.cdk.io.cml.CMLReactionModule
-
- CMLReader - Class in org.openscience.cdk.io
-
Reads a molecule in CML 1.x and 2.0 format.
- CMLReader(InputStream) - Constructor for class org.openscience.cdk.io.CMLReader
-
Reads CML from an java.io.InputStream, for example the FileInputStream.
- CMLReader() - Constructor for class org.openscience.cdk.io.CMLReader
-
- CMLReader(String) - Constructor for class org.openscience.cdk.io.CMLReader
-
Define this CMLReader to take the input from a java.io.Reader
class.
- CMLResolver - Class in org.openscience.cdk.io.cml
-
This class resolves DOCTYPE declaration for Chemical Markup Language (CML)
files and uses a local version for validation.
- CMLResolver() - Constructor for class org.openscience.cdk.io.cml.CMLResolver
-
- CMLRSSFormat - Class in org.openscience.cdk.io.formats
-
- CMLRSSFormat() - Constructor for class org.openscience.cdk.io.formats.CMLRSSFormat
-
- CMLWriter - Class in org.openscience.cdk.io
-
- CMLWriter(Writer) - Constructor for class org.openscience.cdk.io.CMLWriter
-
Constructs a new CMLWriter class.
- CMLWriter(OutputStream) - Constructor for class org.openscience.cdk.io.CMLWriter
-
- CMLWriter() - Constructor for class org.openscience.cdk.io.CMLWriter
-
- CO - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- COBALT - Static variable in enum org.openscience.cdk.config.Elements
-
- COBALT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- color - Variable in class org.openscience.cdk.renderer.elements.ArrowElement
-
Color of the arrow.
- color - Variable in class org.openscience.cdk.renderer.elements.GeneralPath
-
The color of the path.
- color - Variable in class org.openscience.cdk.renderer.elements.LineElement
-
The color of the line.
- color - Variable in class org.openscience.cdk.renderer.elements.OvalElement
-
The color to draw the oval.
- color(Color) - Method in class org.openscience.cdk.renderer.elements.path.PathBuilder
-
Sets the color if this path.
- color - Variable in class org.openscience.cdk.renderer.elements.PathElement
-
The color of the path.
- color - Variable in class org.openscience.cdk.renderer.elements.RectangleElement
-
The color of the rectangle.
- color - Variable in class org.openscience.cdk.renderer.elements.TextElement
-
The color of the text.
- color(int) - Method in interface org.openscience.cdk.renderer.generators.HighlightGenerator.Palette
-
Obtain the color in index, id.
- column - Variable in class org.openscience.cdk.iupac.parser.SimpleCharStream
-
- column - Variable in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
- columns - Variable in class org.openscience.cdk.math.IMatrix
-
the count of columns of the matrix
- columns - Variable in class org.openscience.cdk.math.Matrix
-
the number of columns of this matrix
- COMMA - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- COMMENT - Static variable in class org.openscience.cdk.CDKConstants
-
A String comment.
- commit() - Method in class org.openscience.cdk.smiles.InvPair
-
- compare(Object) - Method in class org.openscience.cdk.Atom
-
Compares a atom with this atom.
- compare(Object) - Method in class org.openscience.cdk.AtomType
-
Compares a atom type with this atom type.
- compare(Object) - Method in class org.openscience.cdk.Bond
-
Compares a bond with this bond.
- compare(Object) - Method in class org.openscience.cdk.ChemObject
-
Compares a IChemObject with this IChemObject.
- compare(Object) - Method in class org.openscience.cdk.debug.DebugBond
-
Compares a bond with this bond.
- compare(Object) - Method in class org.openscience.cdk.Element
-
Compares an Element with this Element.
- compare(IAtom, IAtom) - Method in class org.openscience.cdk.fingerprint.SimpleAtomComparator
-
- compare(IsotopePattern, IsotopePattern) - Method in class org.openscience.cdk.formula.IsotopePatternSimilarity
-
Compare the IMolecularFormula with a isotope
abundance pattern.
- compare(ILigand, ILigand) - Method in class org.openscience.cdk.geometry.cip.rules.CIPLigandRule
-
Compares two ligands according to the particular sequence sub rule.
- compare(ILigand, ILigand) - Method in interface org.openscience.cdk.geometry.cip.rules.ISequenceSubRule
-
Compares two ligands according to the particular sequence sub rule.
- compare(Object) - Method in interface org.openscience.cdk.interfaces.IBond
-
Compares a bond with this bond.
- compare(Object) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Compares a query bond with this query bond.
- compare(Object) - Method in class org.openscience.cdk.Isotope
-
Compares a atom type with this atom type.
- compare(Object) - Method in class org.openscience.cdk.silent.Atom
-
Compares a atom with this atom.
- compare(Object) - Method in class org.openscience.cdk.silent.AtomType
-
Compares a atom type with this atom type.
- compare(Object) - Method in class org.openscience.cdk.silent.Bond
-
Compares a bond with this bond.
- compare(Object) - Method in class org.openscience.cdk.silent.ChemObject
-
Compares a IChemObject with this IChemObject.
- compare(Object) - Method in class org.openscience.cdk.silent.Element
-
Compares an Element with this Element.
- compare(Object) - Method in class org.openscience.cdk.silent.Isotope
-
Compares a atom type with this atom type.
- compare(String, String) - Method in class org.openscience.cdk.tools.ElementComparator
-
Returns a negative if o1 comes before o2 in a molecular formula,
returns zero if they are identical, and positive if o1 comes
after o2 in the formula.
- compare(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.tools.manipulator.AtomContainerComparator
-
- compare(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.tools.manipulator.AtomContainerComparatorBy2DCenter
-
Compare two AtomContainers based on their 2D position.
- compare(IMolecularFormula, IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Compare two IMolecularFormula looking at type and number of IIsotope and
charge of the formula.
- compare(IRing, IRing) - Method in class org.openscience.cdk.tools.manipulator.RingSizeComparator
-
- compareTo(DynamicFactory.ConstructorKey) - Method in class org.openscience.cdk.DynamicFactory.ConstructorKey
-
Orders constructor keys by the number of parameters and then this
name.
- compareTo(IChemFormatMatcher.MatchResult) - Method in class org.openscience.cdk.io.formats.IChemFormatMatcher.MatchResult
-
Compares the match result with another, results with lower position
are ordered before those with higher position.
- compareTo(Algorithm) - Method in enum org.openscience.cdk.smsd.interfaces.Algorithm
-
Compares algorithm types.
- compatibilityGraph() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
Generate Compatibility Graph Nodes Bond Insensitive
- compatibilityGraphCEdgeZero() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
compatibilityGraphCEdgeZero is used to
build up of the edges of the
compatibility graph BIS
- compatibilityGraphNodes() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
Generate Compatibility Graph Nodes
- compatibilityGraphNodesIfCEdgeIsZero() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
compGraphNodesCZero is used to build up of the edges of the compatibility graph
- compile() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQueryCompiler
-
Parse and build a query graph from the query moleucle.
- compile() - Method in class org.openscience.cdk.smsd.algorithm.vflib.query.QueryCompiler
-
Parse and build a query graph from the query moleucle.
- completeChemicalName() - Method in class org.openscience.cdk.iupac.parser.NomParser
-
Deprecated.
The general form all chemical names must follow.
- completed() - Method in class org.openscience.cdk.graph.AllCycles
-
Did the cycle perception complete - if not the molecule was considered
impractical and computation was aborted.
- Complex - Class in org.openscience.cdk.math
-
This class handles complex values.
- Complex(double, double) - Constructor for class org.openscience.cdk.math.Complex
-
Creates a complex number
- Complex(Complex) - Constructor for class org.openscience.cdk.math.Complex
-
Creates a copy of a complex object
- ComponentGrouping - Class in org.openscience.cdk.isomorphism
-
A predicate for verifying component level grouping in query/target structure
matching.
- ComponentGrouping(IAtomContainer, IAtomContainer) - Constructor for class org.openscience.cdk.isomorphism.ComponentGrouping
-
Create a predicate to match components for the provided query and target.
- ComponentGrouping(IAtomContainer, int[][]) - Constructor for class org.openscience.cdk.isomorphism.ComponentGrouping
-
Create a predicate to match components for the provided query and target.
- ComponentGrouping(int[], ConnectedComponents) - Constructor for class org.openscience.cdk.isomorphism.ComponentGrouping
-
Create a predicate to match components for the provided query (grouping)
and target (connected components).
- components() - Method in class org.openscience.cdk.graph.ConnectedComponents
-
Access the components each vertex belongs to.
- computeFloydAPSP(int[][]) - Static method in class org.openscience.cdk.graph.PathTools
-
All-Pairs-Shortest-Path computation based on Floyd's
algorithm [Floyd, R.W., Algorithm 97: Shortest path, Commun. ACM, 1962, 5:345].
- computeFloydAPSP(double[][]) - Static method in class org.openscience.cdk.graph.PathTools
-
All-Pairs-Shortest-Path computation based on Floyd's
algorithm [Floyd, R.W., Algorithm 97: Shortest path, Commun. ACM, 1962, 5:345].
- configure(IAtom) - Method in class org.openscience.cdk.config.AtomTypeFactory
-
Configures an atom.
- configure(IAtom) - Method in class org.openscience.cdk.config.IsotopeFactory
-
Configures an atom.
- configure(IAtom, IIsotope) - Method in class org.openscience.cdk.config.IsotopeFactory
-
Configures an atom to have all the data of the
given isotope.
- configure(IAtomContainer) - Static method in class org.openscience.cdk.smsd.tools.MoleculeSanityCheck
-
Fixes Aromaticity of the molecule
i.e.
- configure(IAtom, IAtomType) - Static method in class org.openscience.cdk.tools.manipulator.AtomTypeManipulator
-
Method that assign properties to an atom given a particular atomType.
- configureAtom(IAtom, String, boolean) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
-
- configureAtoms(IAtomContainer) - Method in class org.openscience.cdk.config.IsotopeFactory
-
Configures atoms in an AtomContainer to
carry all the correct data according to their element type.
- configureLog4j() - Static method in class org.openscience.cdk.tools.LoggingTool
-
Forces the LoggingTool
to 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
-
- connect(INode, INode, VFBondMatcher) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder
-
Construct and return an edge for a given query and target node
- ConnectedComponents - Class in org.openscience.cdk.graph
-
Compute the connected components of an adjacency list.
- ConnectedComponents(int[][]) - Constructor for class org.openscience.cdk.graph.ConnectedComponents
-
Compute the connected components of an adjacency list, g
.
- connectingFunctionalGroupsConstruct() - Method in class org.openscience.cdk.iupac.parser.NomParser
-
Deprecated.
The layout of a functional group(s) which can connect anywhere.
- connectingFunctionalGroupSuffix() - Method in class org.openscience.cdk.iupac.parser.NomParser
-
Deprecated.
Functional groups suffixs for groups which can be connected anywhere
along the main chain.
- ConnectionMatrix - Class in org.openscience.cdk.graph.matrix
-
Calculator for a connection matrix representation of this AtomContainer.
- ConnectionMatrix() - Constructor for class org.openscience.cdk.graph.matrix.ConnectionMatrix
-
- ConnectivityChecker - Class in org.openscience.cdk.graph
-
Tool class for checking whether the (sub)structure in an
AtomContainer is connected.
- ConnectivityChecker() - Constructor for class org.openscience.cdk.graph.ConnectivityChecker
-
- CONSTANT - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- construct(String, IAtomType.Hybridization, IAtomType.Hybridization) - Static method in class org.openscience.cdk.tools.diff.tree.AtomTypeHybridizationDifference
-
- 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
-
RegularExpression Id.
- contab - Variable in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
-
- container - Variable in class org.openscience.cdk.stereo.StereoElementFactory
-
Native CDK structure representation.
- containerFromPermutation(int[]) - Method in class org.openscience.cdk.graph.AtomContainerAtomPermutor
-
Generate the atom container with this permutation of the atoms.
- containerFromPermutation(int[]) - Method in class org.openscience.cdk.graph.AtomContainerBondPermutor
-
- containerFromPermutation(int[]) - Method in class org.openscience.cdk.graph.AtomContainerPermutor
-
Convert a permutation (expressed as a list of numbers) into a permuted
atom container.
- contains(IAtom) - Method in class org.openscience.cdk.Association
-
Returns true if the given atom participates in this Association.
- contains(IAtom) - Method in class org.openscience.cdk.AtomContainer
-
True, if the AtomContainer contains the given atom object.
- contains(IBond) - Method in class org.openscience.cdk.AtomContainer
-
True, if the AtomContainer contains the given bond object.
- contains(ILonePair) - Method in class org.openscience.cdk.AtomContainer
-
True, if the AtomContainer contains the given LonePair object.
- contains(ISingleElectron) - Method in class org.openscience.cdk.AtomContainer
-
True, if the AtomContainer contains the given SingleElectron object.
- contains(IElectronContainer) - Method in class org.openscience.cdk.AtomContainer
-
True, if the AtomContainer contains the given ElectronContainer object.
- contains(IAtom) - Method in class org.openscience.cdk.Bond
-
Returns true if the given atom participates in this bond.
- contains(Object) - Method in class org.openscience.cdk.ConformerContainer
-
Checks to see whether the specified conformer is currently stored.
- contains(IIsotope) - Method in class org.openscience.cdk.debug.DebugAdductFormula
-
True, if the AdductFormula contains the given IIsotope object and not
the instance.
- contains(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugAdductFormula
-
True, if the AdductFormula contains the given IMolecularFormula object.
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
True, if the AtomContainer contains the given atom object.
- contains(IBond) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
True, if the AtomContainer contains the given bond object.
- contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
True, if the AtomContainer contains the given LonePair object.
- contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
True, if the AtomContainer contains the given SingleElectron object.
- contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
True, if the AtomContainer contains the given ElectronContainer object.
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
True, if the AtomContainer contains the given atom object.
- contains(IBond) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
True, if the AtomContainer contains the given bond object.
- contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
True, if the AtomContainer contains the given LonePair object.
- contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
True, if the AtomContainer contains the given SingleElectron object.
- contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
True, if the AtomContainer contains the given ElectronContainer object.
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
True, if the AtomContainer contains the given atom object.
- contains(IBond) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
True, if the AtomContainer contains the given bond object.
- contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
True, if the AtomContainer contains the given LonePair object.
- contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
True, if the AtomContainer contains the given SingleElectron object.
- contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
True, if the AtomContainer contains the given ElectronContainer object.
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugBond
-
Returns true if the given atom participates in this bond.
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
True, if the AtomContainer contains the given atom object.
- contains(IBond) - Method in class org.openscience.cdk.debug.DebugCrystal
-
True, if the AtomContainer contains the given bond object.
- contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugCrystal
-
True, if the AtomContainer contains the given LonePair object.
- contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugCrystal
-
True, if the AtomContainer contains the given SingleElectron object.
- contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugCrystal
-
True, if the AtomContainer contains the given ElectronContainer object.
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugLonePair
-
Returns true if the given atom participates in this lone pair.
- contains(IIsotope) - Method in class org.openscience.cdk.debug.DebugMolecularFormula
-
True, if the MolecularFormula contains the given IIsotope object and not
the instance.
- contains(IMolecularFormula) - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet
-
True, if the MolecularFormulaSet contains the given IMolecularFormula object.
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
True, if the AtomContainer contains the given atom object.
- contains(IBond) - Method in class org.openscience.cdk.debug.DebugMonomer
-
True, if the AtomContainer contains the given bond object.
- contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugMonomer
-
True, if the AtomContainer contains the given LonePair object.
- contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugMonomer
-
True, if the AtomContainer contains the given SingleElectron object.
- contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugMonomer
-
True, if the AtomContainer contains the given ElectronContainer object.
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
True, if the AtomContainer contains the given atom object.
- contains(IBond) - Method in class org.openscience.cdk.debug.DebugPolymer
-
True, if the AtomContainer contains the given bond object.
- contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugPolymer
-
True, if the AtomContainer contains the given LonePair object.
- contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugPolymer
-
True, if the AtomContainer contains the given SingleElectron object.
- contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugPolymer
-
True, if the AtomContainer contains the given ElectronContainer object.
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
True, if the AtomContainer contains the given atom object.
- contains(IBond) - Method in class org.openscience.cdk.debug.DebugRing
-
True, if the AtomContainer contains the given bond object.
- contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugRing
-
True, if the AtomContainer contains the given LonePair object.
- contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugRing
-
True, if the AtomContainer contains the given SingleElectron object.
- contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugRing
-
True, if the AtomContainer contains the given ElectronContainer object.
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugRingSet
-
True, if at least one of the rings in the ringset contains
the given atom.
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
Returns true if the given atom participates in this SingleElectron.
- contains(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
True, if the AtomContainer contains the given atom object.
- contains(IBond) - Method in class org.openscience.cdk.debug.DebugStrand
-
True, if the AtomContainer contains the given bond object.
- contains(ILonePair) - Method in class org.openscience.cdk.debug.DebugStrand
-
True, if the AtomContainer contains the given LonePair object.
- contains(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugStrand
-
True, if the AtomContainer contains the given SingleElectron object.
- contains(IElectronContainer) - Method in class org.openscience.cdk.debug.DebugStrand
-
True, if the AtomContainer contains the given ElectronContainer object.
- contains(IIsotope) - Method in class org.openscience.cdk.formula.AdductFormula
-
True, if the AdductFormula contains the given IIsotope object and not
the instance.
- contains(IMolecularFormula) - Method in class org.openscience.cdk.formula.AdductFormula
-
True, if the AdductFormula contains the given IMolecularFormula object.
- contains(IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormula
-
True, if the MolecularFormula contains the given IIsotope object and not
the instance.
- contains(IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormulaRange
-
True, if the MolecularFormulaExpand contains the given IIsotope.
- contains(IMolecularFormula) - Method in class org.openscience.cdk.formula.MolecularFormulaSet
-
True, if the MolecularFormulaSet contains the given IMolecularFormula object.
- contains(IIsotope) - Method in interface org.openscience.cdk.interfaces.IAdductFormula
-
True, if the AdductFormula contains the given IIsotope object.
- contains(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
True, if the AtomContainer contains the given atom object.
- contains(IBond) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
True, if the AtomContainer contains the given bond object.
- contains(ILonePair) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
True, if the AtomContainer contains the given LonePair object.
- contains(ISingleElectron) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
True, if the AtomContainer contains the given SingleElectron object.
- contains(IElectronContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
True, if the AtomContainer contains the given ElectronContainer object.
- contains(IAtom) - Method in interface org.openscience.cdk.interfaces.IBond
-
Returns true if the given atom participates in this bond.
- contains(IAtom) - Method in interface org.openscience.cdk.interfaces.ILonePair
-
Returns true if the given atom participates in this lone pair.
- contains(IIsotope) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
-
True, if the MolecularFormula contains the given IIsotope object.
- contains(IMolecularFormula) - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet
-
True, if the IMolecularFormulaSet contains the given IMolecularFormula object.
- contains(IAtom) - Method in interface org.openscience.cdk.interfaces.IRingSet
-
True, if at least one of the rings in the ringset contains
the given atom.
- contains(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IRingSet
-
True, if this set contains the IAtomContainer.
- contains(IAtom) - Method in interface org.openscience.cdk.interfaces.ISingleElectron
-
Returns true if the given atom participates in this SingleElectron.
- contains(IAtom) - Method in interface org.openscience.cdk.interfaces.IStereoElement
-
Does the stereo element contain the provided atom.
- contains(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
True, if the AtomContainer contains the given atom object.
- contains(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
True, if the AtomContainer contains the given bond object.
- contains(ILonePair) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
True, if the AtomContainer contains the given LonePair object.
- contains(ISingleElectron) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
True, if the AtomContainer contains the given SingleElectron object.
- contains(IElectronContainer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
True, if the AtomContainer contains the given ElectronContainer object.
- contains(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Returns true if the given atom participates in this query bond.
- contains(IAtom) - Method in class org.openscience.cdk.LonePair
-
Returns true if the given atom participates in this lone pair.
- contains(IChemObject) - Method in interface org.openscience.cdk.renderer.selection.IChemObjectSelection
-
Determines if the
IChemObject
is part of the current selection.
- contains(IAtom) - Method in class org.openscience.cdk.RingSet
-
True, if at least one of the rings in the ringset contains
the given atom.
- contains(IAtomContainer) - Method in class org.openscience.cdk.RingSet
-
Checks for presence of a ring in this RingSet.
- contains(int) - Method in class org.openscience.cdk.signature.Orbit
-
Checks to see if the orbit contains this atom index.
- contains(IIsotope) - Method in class org.openscience.cdk.silent.AdductFormula
-
True, if the AdductFormula contains the given IIsotope object and not
the instance.
- contains(IMolecularFormula) - Method in class org.openscience.cdk.silent.AdductFormula
-
True, if the AdductFormula contains the given IMolecularFormula object.
- contains(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
True, if the AtomContainer contains the given atom object.
- contains(IBond) - Method in class org.openscience.cdk.silent.AtomContainer
-
True, if the AtomContainer contains the given bond object.
- contains(ILonePair) - Method in class org.openscience.cdk.silent.AtomContainer
-
True, if the AtomContainer contains the given LonePair object.
- contains(ISingleElectron) - Method in class org.openscience.cdk.silent.AtomContainer
-
True, if the AtomContainer contains the given SingleElectron object.
- contains(IElectronContainer) - Method in class org.openscience.cdk.silent.AtomContainer
-
True, if the AtomContainer contains the given ElectronContainer object.
- contains(IAtom) - Method in class org.openscience.cdk.silent.Bond
-
Returns true if the given atom participates in this bond.
- contains(IAtom) - Method in class org.openscience.cdk.silent.LonePair
-
Returns true if the given atom participates in this lone pair.
- contains(IIsotope) - Method in class org.openscience.cdk.silent.MolecularFormula
-
True, if the MolecularFormula contains the given IIsotope object and not
the instance.
- contains(IMolecularFormula) - Method in class org.openscience.cdk.silent.MolecularFormulaSet
-
True, if the MolecularFormulaSet contains the given IMolecularFormula object.
- contains(IAtom) - Method in class org.openscience.cdk.silent.RingSet
-
True, if at least one of the rings in the ringset contains
the given atom.
- contains(IAtomContainer) - Method in class org.openscience.cdk.silent.RingSet
-
Checks for presence of a ring in this RingSet.
- contains(IAtom) - Method in class org.openscience.cdk.silent.SingleElectron
-
Returns true if the given atom participates in this SingleElectron.
- contains(IAtom) - Method in class org.openscience.cdk.SingleElectron
-
Returns true if the given atom participates in this SingleElectron.
- contains(IAtom) - Method in class org.openscience.cdk.stereo.DoubleBondStereochemistry
-
- contains(IAtom) - Method in class org.openscience.cdk.stereo.ExtendedTetrahedral
-
- contains(IAtom) - Method in class org.openscience.cdk.stereo.TetrahedralChirality
-
- 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
-
- convertBondOrder(IBond) - Static method in class org.openscience.cdk.smsd.filters.ChemicalFilters
-
Get bond order value as int
value.
- convertBondStereo(IBond) - Static method in class org.openscience.cdk.smsd.filters.ChemicalFilters
-
Get stereo value as integer
- convertEdgeLabelToColor(String) - Method in class org.openscience.cdk.signature.AtomSignature
-
- convertExplicitToImplicitHydrogens(IAtomContainer) - Static method in class org.openscience.cdk.normalize.SMSDNormalizer
-
Returns IAtomContainer without Hydrogen.
- convertExplicitToImplicitHydrogens(IAtomContainer) - Static method in class org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator
-
Returns IAtomContainer without Hydrogen.
- convertImplicitToExplicitHydrogens(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Adds explicit hydrogens (without coordinates) to the IAtomContainer,
equaling the number of set implicit hydrogens.
- convertOneLetterCodeToThreeLetterCode(String) - Static method in class org.openscience.cdk.templates.AminoAcids
-
Returns the three letter code of an amino acid given a one letter code.
- Convertor - Class in org.openscience.cdk.libio.cml
-
- Convertor(boolean, String) - Constructor for class org.openscience.cdk.libio.cml.Convertor
-
Constructs a CML convertor.
- Convertor - Class in org.openscience.cdk.libio.jena
-
Helper class that converts a CDK
IChemObject
into RDF using a
Jena model and the CDK data model ontology.
- Convertor() - Constructor for class org.openscience.cdk.libio.jena.Convertor
-
- convertOrder(double) - Static method in class org.openscience.cdk.smsd.filters.ChemicalFilters
-
- convertStereo(int) - Static method in class org.openscience.cdk.smsd.filters.ChemicalFilters
-
Get stereo value as Stereo enum
- convertThreeLetterCodeToOneLetterCode(String) - Static method in class org.openscience.cdk.templates.AminoAcids
-
Returns the one letter code of an amino acid given a three letter code.
- convertToAtomContainer(IRingSet) - Static method in class org.openscience.cdk.ringsearch.RingPartitioner
-
Converts a RingSet to an AtomContainer.
- convertToDiagramBounds(Rectangle2D) - Method in class org.openscience.cdk.renderer.AbstractRenderer
-
Calculate the bounds of the diagram on screen, given the current scale,
zoom, and margin.
- coords - Variable in class org.openscience.cdk.renderer.elements.path.CubicTo
-
Coordinates of control point 1, control point 2 and end point.
- coords - Variable in class org.openscience.cdk.renderer.elements.path.LineTo
-
The point to make a line to.
- coords - Variable in class org.openscience.cdk.renderer.elements.path.MoveTo
-
The point to move to.
- coords - Variable in class org.openscience.cdk.renderer.elements.path.QuadTo
-
Coordinates of control point and end point.
- COPPER - Static variable in enum org.openscience.cdk.config.Elements
-
- COPPER - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- copyAndSuppressedHydrogens(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Copy the input container and suppress any explicit hydrogens.
- copyBlock(int) - Method in class org.openscience.cdk.group.Partition
-
Creates and returns a copy of the cell at cell index.
- COS - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- couldMatchAtomType(IAtomContainer, IAtom, IAtomType) - Method in class org.openscience.cdk.tools.SaturationChecker
-
Determines if the atom can be of type AtomType.
- couldMatchAtomType(IAtom, double, IBond.Order, IAtomType) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
-
Determines if the atom can be of type AtomType.
- couldMatchAtomType(IAtomContainer, IAtom, IAtomType) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
-
Determines if the atom can be of type AtomType.
- count() - Method in class org.openscience.cdk.isomorphism.Mappings
-
Convenience method to count the number mappings.
- count() - Method in enum org.openscience.cdk.renderer.elements.LineElement.LineType
-
Returns the count for this line type.
- countArcsLeft(List<Integer>, int, int) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
-
- countEdges() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder
-
Returns edge count.
- countEdges() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQuery
-
Returns edge count.
- countExplicitHydrogens(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Count explicit hydrogens.
- countHydrogens(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
- countMaps(IAtomContainer) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper
-
Returns solution map count.
- countMaps(TargetProperties) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper
-
Returns solution map count.
- countMaps(IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper
-
Returns solution map count.
- countMaps(TargetProperties) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper
-
Returns solution map count.
- countMaps(IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper
-
Returns solution map count.
- countMaps(TargetProperties) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper
-
Returns solution map count.
- countMatches() - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool
-
Returns the number of times the pattern was found in the target molecule.
- countNeighbors() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.NodeBuilder
-
Returns Neighbors count.
- countNeighbors(IAtom) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.TargetProperties
-
- countNeighbors() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.INode
-
Returns Neighbors count.
- countNodes() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder
-
Returns node count.
- countNodes() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQuery
-
Returns node count.
- countUnique() - Method in class org.openscience.cdk.isomorphism.Mappings
-
Convenience method to count the number of unique atom mappings.
- covalentRadius() - Method in enum org.openscience.cdk.config.Elements
-
The covalent radius, rcov, is a measure of the
size of an atom that forms part of one covalent bond.
- CovalentRadiusDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
-
This class 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
-
RegularExpression Id.
- create(Object[]) - Method in interface org.openscience.cdk.DynamicFactory.Creator
-
Create a new instance with the provided object parameters.
- create(IAtomContainer, int[][]) - Method in class org.openscience.cdk.hash.stereo.DoubleBondElementEncoderFactory
-
- create(IAtomContainer, int[][]) - Method in class org.openscience.cdk.hash.stereo.GeometricCumulativeDoubleBondFactory
-
Create a stereo encoder for cumulative double bonds.
- create(IAtomContainer, int[][]) - Method in class org.openscience.cdk.hash.stereo.GeometricDoubleBondEncoderFactory
-
Create a stereo encoder for all potential 2D and 3D double bond stereo
configurations.
- create(IAtomContainer, int[][]) - Method in class org.openscience.cdk.hash.stereo.GeometricTetrahedralEncoderFactory
-
Create a stereo encoder for all potential 2D and 3D tetrahedral
elements.
- create(IAtomContainer, int[][]) - Method in interface org.openscience.cdk.hash.stereo.StereoEncoderFactory
-
Create a stereo-encoder for possible stereo-chemical configurations.
- create(IAtomContainer, int[][]) - Method in class org.openscience.cdk.hash.stereo.TetrahedralElementEncoderFactory
-
- create(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.smiles.smarts.SmartsPattern
-
Create a
Pattern
that will match the given
smarts
query.
- create(IAtomContainer) - Method in class org.openscience.cdk.smiles.SmilesGenerator
-
Generate SMILES for the provided molecule
.
- create(IAtomContainer, int[]) - Method in class org.openscience.cdk.smiles.SmilesGenerator
-
Create a SMILES string and obtain the order which the atoms were
written.
- create(Class<?>) - Static method in class org.openscience.cdk.tools.LoggingTool
-
- create(Class<?>) - Static method in class org.openscience.cdk.tools.SystemOutLoggingTool
-
- createAAs() - Static method in class org.openscience.cdk.templates.AminoAcids
-
Creates amino acid AminoAcid objects.
- createAll() - Method in class org.openscience.cdk.stereo.StereoElementFactory
-
Creates all stereo elements found by
Stereocenters
using the or
2D/3D coordinates to specify the configuration (clockwise/anticlockwise).
- createAllCarbonAllSingleNonAromaticBondAtomContainer(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
- createAnyAtomAnyBondContainer(IAtomContainer, boolean) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
-
Creates a QueryAtomContainer with wildcard atoms and wildcard bonds.
- createAnyAtomAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.TemplateExtractor
-
- createAnyAtomContainer(IAtomContainer, boolean) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
-
Creates a QueryAtomContainer with AnyAtoms / Aromatic Atoms and OrderQueryBonds / AromaticQueryBonds.
- createAnyAtomForPseudoAtomQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
-
Creates a QueryAtomContainer with SymbolQueryAtom's and
OrderQueryBond's.
- createAutoGenPalette(float, float, boolean) - Static method in class org.openscience.cdk.renderer.generators.HighlightGenerator
-
Create an auto generating palette which will generate colors using the
provided parameters.
- createAutoGenPalette(boolean) - Static method in class org.openscience.cdk.renderer.generators.HighlightGenerator
-
Create an auto generating palette which will generate colors using the
provided parameters.
- createAutoPalette(float, float, int) - Static method in class org.openscience.cdk.renderer.generators.HighlightGenerator
-
Create an auto generating palette which will generate colors using the
provided parameters.
- createBasicQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
-
Creates a QueryAtomContainer with SymbolQueryAtom's, AromaticQueryBond's and
OrderQueryBond's.
- createBondOrder(double) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
-
Convenience method to convert a double into an IBond.Order.
- createChemObjectReader() - Method in class org.openscience.cdk.io.random.RandomAccessReader
-
- createChemObjectReader() - Method in class org.openscience.cdk.io.random.RandomAccessSDFReader
-
- createCubicGrid() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
Method creates a cubic grid with the grid generator class.
- createIDs(IChemObject) - Static method in class org.openscience.cdk.tools.IDCreator
-
Labels the Atom's and Bond's in the AtomContainer using the a1, a2, b1, b2
scheme often used in CML.
- createLoggingTool(Class<?>) - Static method in class org.openscience.cdk.tools.LoggingToolFactory
-
Dynamically create a
ILoggingTool
for the given
sourceClass
.
- createNewMolecule(IChemModel) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
-
Adds a new Molecule to the MoleculeSet inside a given ChemModel.
- createPalette(Color[]) - Static method in class org.openscience.cdk.renderer.generators.HighlightGenerator
-
Create a palette which uses the provided colors.
- createPalette(Color, Color...) - Static method in class org.openscience.cdk.renderer.generators.HighlightGenerator
-
Create a palette which uses the provided colors.
- createPath() - Method in class org.openscience.cdk.renderer.elements.path.PathBuilder
-
Create and return the final path.
- createProtein(String) - Static method in class org.openscience.cdk.tools.ProteinBuilderTool
-
Creates a BioPolymer from a sequence of amino acid as identified by a
the sequence of their one letter codes.
- createProtein(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.ProteinBuilderTool
-
Creates a BioPolymer from a sequence of amino acid as identified by a
the sequence of their one letter codes.
- createReactionScheme(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator
-
Create a IReactionScheme give a IReactionSet object.
- createReactionSMILES(IReaction) - Method in class org.openscience.cdk.smiles.SmilesGenerator
-
Generate a SMILES for the given Reaction
.
- 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(IAtomContainer) - Method in class org.openscience.cdk.smiles.SmilesGenerator
-
- createSMILES(IReaction) - Method in class org.openscience.cdk.smiles.SmilesGenerator
-
Deprecated.
use #createReactionSMILES
- createSymbolAndBondOrderQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
-
Creates a QueryAtomContainer with SymbolQueryAtom's and OrderQueryBond's.
- createSymbolAndChargeQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
-
Creates a QueryAtomContainer with SymbolAncChargeQueryAtom's and
OrderQueryBond's.
- createSymbolChargeIDQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
-
- createWriter(IChemFormat) - Method in class org.openscience.cdk.io.WriterFactory
-
Creates a new IChemObjectWriter based on the given IChemFormat.
- CRK2DFormat - Class in org.openscience.cdk.io.formats
-
- CRK2DFormat() - Constructor for class org.openscience.cdk.io.formats.CRK2DFormat
-
- CRK3DFormat - Class in org.openscience.cdk.io.formats
-
- CRK3DFormat() - Constructor for class org.openscience.cdk.io.formats.CRK3DFormat
-
- cross(Vector) - Method in class org.openscience.cdk.math.Vector
-
Cross product, only well definited in R^3
- CrossoverMachine - Class in org.openscience.cdk.structgen.stochastic.operator
-
Modified molecular structures by applying crossover operator on a pair of parent structures
and generate a pair of offspring structures.
- CrossoverMachine() - Constructor for class org.openscience.cdk.structgen.stochastic.operator.CrossoverMachine
-
Constructs a new CrossoverMachine operator.
- crystal - Variable in class org.openscience.cdk.ChemModel
-
A Crystal.
- Crystal - Class in org.openscience.cdk
-
Class representing a molecular crystal.
- Crystal() - Constructor for class org.openscience.cdk.Crystal
-
Constructs a new crystal with zero length cell axis.
- Crystal(IAtomContainer) - Constructor for class org.openscience.cdk.Crystal
-
Constructs a new crystal with zero length cell axis
and adds the atoms in the AtomContainer as cell content.
- crystal - Variable in class org.openscience.cdk.silent.ChemModel
-
A Crystal.
- Crystal - Class in org.openscience.cdk.silent
-
Class representing a molecular crystal.
- Crystal() - Constructor for class org.openscience.cdk.silent.Crystal
-
Constructs a new crystal with zero length cell axis.
- Crystal(IAtomContainer) - Constructor for class org.openscience.cdk.silent.Crystal
-
Constructs a new crystal with zero length cell axis
and adds the atoms in the AtomContainer as cell content.
- CrystalGeometryTools - Class in org.openscience.cdk.geometry
-
A set of static methods for working with crystal coordinates.
- CrystalGeometryTools() - Constructor for class org.openscience.cdk.geometry.CrystalGeometryTools
-
- crystalScalar - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- CrystClustFormat - Class in org.openscience.cdk.io.formats
-
- CrystClustFormat() - Constructor for class org.openscience.cdk.io.formats.CrystClustFormat
-
- CrystClustReader - Class in org.openscience.cdk.io
-
- CrystClustReader() - Constructor for class org.openscience.cdk.io.CrystClustReader
-
- CrystClustReader(Reader) - Constructor for class org.openscience.cdk.io.CrystClustReader
-
- CrystClustReader(InputStream) - Constructor for class org.openscience.cdk.io.CrystClustReader
-
- CrystClustWriter - Class in org.openscience.cdk.io
-
Rather stupid file format used for storing crystal information.
- CrystClustWriter(Writer) - Constructor for class org.openscience.cdk.io.CrystClustWriter
-
Constructs a new CrystClustWriter class.
- CrystClustWriter(OutputStream) - Constructor for class org.openscience.cdk.io.CrystClustWriter
-
- CrystClustWriter() - Constructor for class org.openscience.cdk.io.CrystClustWriter
-
- CS - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- CTFileQueryBond - Class in org.openscience.cdk.isomorphism.matchers
-
Captures query bond types defined in the CTFile.
- CTFileQueryBond(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.CTFileQueryBond
-
- CTFileQueryBond.Type - Enum in org.openscience.cdk.isomorphism.matchers
-
- CTXFormat - Class in org.openscience.cdk.io.formats
-
- CTXFormat() - Constructor for class org.openscience.cdk.io.formats.CTXFormat
-
- CTXReader - Class in org.openscience.cdk.io
-
Reader that extracts information from the IDENT, NAME, ATOMS and BONDS
blocks in CTX files.
- CTXReader() - Constructor for class org.openscience.cdk.io.CTXReader
-
- CTXReader(Reader) - Constructor for class org.openscience.cdk.io.CTXReader
-
- CTXReader(InputStream) - Constructor for class org.openscience.cdk.io.CTXReader
-
- CU - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- CubicTo - Class in org.openscience.cdk.renderer.elements.path
-
A cubic curve in the path.
- CubicTo(Point2d, Point2d, Point2d) - Constructor for class org.openscience.cdk.renderer.elements.path.CubicTo
-
Make a cubic curve path element.
- CubicTo(double[]) - Constructor for class org.openscience.cdk.renderer.elements.path.CubicTo
-
Make a cubic curve path element.
- CubicTo(double, double, double, double, double, double) - Constructor for class org.openscience.cdk.renderer.elements.path.CubicTo
-
Make a cubic curve path element.
- cubicTo(Point2d, Point2d, Point2d) - Method in class org.openscience.cdk.renderer.elements.path.PathBuilder
-
Make a cubic curve in the path, with two control points.
- curChar - Variable in class org.openscience.cdk.iupac.parser.NomParserTokenManager
-
- curChar - Variable in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager
-
- CURIUM - Static variable in enum org.openscience.cdk.config.Elements
-
- CURIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- curRef - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- current() - Method in class org.openscience.cdk.io.cml.CMLModuleStack
-
Returns the last added entry.
- currentAtom - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- currentBond - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- currentChars - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- currentChemFile - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- currentChemModel - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- currentChemSequence - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- CurrentElement - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- currentFontIndex - Variable in class org.openscience.cdk.renderer.font.AbstractFontManager
-
- currentMolecule - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- currentMoleculeSet - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- currentMonomer - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- currentReaction - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- currentReactionSet - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- currentRecord - Variable in class org.openscience.cdk.io.random.RandomAccessReader
-
- currentStrand - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- currentToken - Variable in exception org.openscience.cdk.iupac.parser.ParseException
-
This is the last token that has been consumed successfully.
- currentToken - Variable in exception org.openscience.cdk.smiles.smarts.parser.ParseException
-
This is the last token that has been consumed successfully.
- customize(IAtom, Object) - Method in interface org.openscience.cdk.libio.cml.ICMLCustomizer
-
Customized the nodeToAdd for the given Atom.
- customize(IBond, Object) - Method in interface org.openscience.cdk.libio.cml.ICMLCustomizer
-
Customized the nodeToAdd for the given IBond.
- customize(IAtomContainer, Object) - Method in interface org.openscience.cdk.libio.cml.ICMLCustomizer
-
Customized the nodeToAdd for the given Molecule.
- customize(IBond, Object) - Method in class org.openscience.cdk.libio.cml.MDMoleculeCustomizer
-
No customization for bonds.
- customize(IAtom, Object) - Method in class org.openscience.cdk.libio.cml.MDMoleculeCustomizer
-
Customize Atom.
- customize(IAtomContainer, Object) - Method in class org.openscience.cdk.libio.cml.MDMoleculeCustomizer
-
Customize Molecule.
- customize(IAtom, Object) - Method in class org.openscience.cdk.libio.cml.PDBAtomCustomizer
-
- customize(IAtomContainer, Object) - Method in class org.openscience.cdk.libio.cml.PDBAtomCustomizer
-
- customize(IBond, Object) - Method in class org.openscience.cdk.libio.cml.PDBAtomCustomizer
-
- customize(IBond, Object) - Method in class org.openscience.cdk.libio.cml.QSARCustomizer
-
- customize(IAtom, Object) - Method in class org.openscience.cdk.libio.cml.QSARCustomizer
-
- customize(IAtomContainer, Object) - Method in class org.openscience.cdk.libio.cml.QSARCustomizer
-
- customizeJob() - Method in class org.openscience.cdk.io.iterator.IteratingSDFReader
-
- customizeJob() - Method in class org.openscience.cdk.io.MDLReader
-
- customizeJob() - Method in class org.openscience.cdk.io.MDLV2000Reader
-
- customizeJob() - Method in class org.openscience.cdk.io.MDLV2000Writer
-
- customizeJob() - Method in class org.openscience.cdk.io.PDBReader
-
- customizeJob() - Method in class org.openscience.cdk.io.SDFWriter
-
- customizeJob() - Method in class org.openscience.cdk.io.SMILESWriter
-
- CustomSerializer - Class in org.openscience.cdk.io.cml
-
Custom Serializer
with the sole purpose and functionality to not
output the XML declaration.
- CustomSerializer(OutputStream) - Constructor for class org.openscience.cdk.io.cml.CustomSerializer
-
Instantiates a new
CustomSerializer
using the matching
Serializer.Serializer(OutputStream)
.
- CustomSerializer(OutputStream, String) - Constructor for class org.openscience.cdk.io.cml.CustomSerializer
-
Instantiates a new
CustomSerializer
using the matching
Serializer.Serializer(OutputStream, String)
.
- cycle(int[][], int[]) - Static method in class org.openscience.cdk.graph.GraphUtil
-
Arrange the vertices in a simple cyclic path.
- cycle() - Method in class org.openscience.cdk.iupac.parser.NomParser
-
Deprecated.
Deals with cyclic main chains.
- CycleBasis - Class in org.openscience.cdk.ringsearch.cyclebasis
-
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.
- CycleFinder - Interface in org.openscience.cdk.graph
-
Defines a method to find the cycles of a molecule.
- Cycles - Class in org.openscience.cdk.graph
-
A utility class for storing and computing the cycles of a chemical graph.
- cycles() - Method in class org.openscience.cdk.ringsearch.cyclebasis.CycleBasis
-
Returns the cycles that form the cycle basis.
- cycles() - Method in class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis
-
- cyclic(int) - Method in interface org.openscience.cdk.ringsearch.CyclicVertexSearch
-
Returns true if the vertex v is in a cycle.
- cyclic(int, int) - Method in interface org.openscience.cdk.ringsearch.CyclicVertexSearch
-
Is the edge between the two vertices u and v in a cycle?
- cyclic() - Method in interface org.openscience.cdk.ringsearch.CyclicVertexSearch
-
The set of cyclic vertices.
- cyclic(int, int) - Method in class org.openscience.cdk.ringsearch.RingSearch
-
Determine whether the edge between the vertices u and v is
cyclic.
- cyclic(IAtom) - Method in class org.openscience.cdk.ringsearch.RingSearch
-
Determine whether the provided atom belongs to a ring (is cyclic).
- cyclic(IBond) - Method in class org.openscience.cdk.ringsearch.RingSearch
-
Determine whether the bond is cyclic.
- cyclic(int) - Method in class org.openscience.cdk.ringsearch.RingSearch
-
Determine whether the vertex at index i is a cyclic vertex.
- cyclic() - Method in class org.openscience.cdk.ringsearch.RingSearch
-
Construct a set of vertices which belong to any cycle (ring).
- CyclicVertexSearch - Interface in org.openscience.cdk.ringsearch
-
Describes a search to identify vertices which belong to elementary cycles and
if those cycles are isolated or are part of a fused system.
- CYCLO - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- G - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- GA - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- GADOLINIUM - Static variable in enum org.openscience.cdk.config.Elements
-
- GADOLINIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- GALLIUM - Static variable in enum org.openscience.cdk.config.Elements
-
- GALLIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- GamessFormat - Class in org.openscience.cdk.io.formats
-
- GamessFormat() - Constructor for class org.openscience.cdk.io.formats.GamessFormat
-
- GamessReader - Class in org.openscience.cdk.io
-
A reader for GAMESS log file.
- GamessReader(Reader) - Constructor for class org.openscience.cdk.io.GamessReader
-
Constructs a new "GamessReader" object given a "Reader" object as input.
- GamessReader(InputStream) - Constructor for class org.openscience.cdk.io.GamessReader
-
- GamessReader() - Constructor for class org.openscience.cdk.io.GamessReader
-
- GasteigerMarsiliPartialCharges - Class in org.openscience.cdk.charges
-
The calculation of the Gasteiger Marsili (PEOE) partial charges is based on
[Gasteiger, J. and Marsili, M., Iterative partial equalization of orbital elektronegativity - a rapid access to atomic charges, Tetrahedron, 1980, 36:3219-3288].
- GasteigerMarsiliPartialCharges() - Constructor for class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
-
Constructor for the GasteigerMarsiliPartialCharges object.
- GasteigerPEPEPartialCharges - Class in org.openscience.cdk.charges
-
The calculation of the Gasteiger (PEPE) partial charges is based on
[Saller, H., Quantitative Emperische Modelle fur Elektronische Effekte in Pi-Systemen und fur die Chemische Reaktivitat, 1985, Thecn. Univ. Munchen].
- GasteigerPEPEPartialCharges() - Constructor for class org.openscience.cdk.charges.GasteigerPEPEPartialCharges
-
Constructor for the GasteigerPEPEPartialCharges object.
- Gaussian03Format - Class in org.openscience.cdk.io.formats
-
- Gaussian03Format() - Constructor for class org.openscience.cdk.io.formats.Gaussian03Format
-
- Gaussian03Reader - Class in org.openscience.cdk.io
-
A reader for Gaussian03 output.
- Gaussian03Reader(Reader) - Constructor for class org.openscience.cdk.io.Gaussian03Reader
-
- Gaussian03Reader(InputStream) - Constructor for class org.openscience.cdk.io.Gaussian03Reader
-
- Gaussian03Reader() - Constructor for class org.openscience.cdk.io.Gaussian03Reader
-
- Gaussian90Format - Class in org.openscience.cdk.io.formats
-
- Gaussian90Format() - Constructor for class org.openscience.cdk.io.formats.Gaussian90Format
-
- Gaussian92Format - Class in org.openscience.cdk.io.formats
-
- Gaussian92Format() - Constructor for class org.openscience.cdk.io.formats.Gaussian92Format
-
- Gaussian94Format - Class in org.openscience.cdk.io.formats
-
- Gaussian94Format() - Constructor for class org.openscience.cdk.io.formats.Gaussian94Format
-
- Gaussian95Format - Class in org.openscience.cdk.io.formats
-
- Gaussian95Format() - Constructor for class org.openscience.cdk.io.formats.Gaussian95Format
-
- Gaussian98Format - Class in org.openscience.cdk.io.formats
-
- Gaussian98Format() - Constructor for class org.openscience.cdk.io.formats.Gaussian98Format
-
- Gaussian98Reader - Class in org.openscience.cdk.io
-
A reader for Gaussian98 output.
- Gaussian98Reader() - Constructor for class org.openscience.cdk.io.Gaussian98Reader
-
Constructor for the Gaussian98Reader object
- Gaussian98Reader(InputStream) - Constructor for class org.openscience.cdk.io.Gaussian98Reader
-
- Gaussian98Reader(Reader) - Constructor for class org.openscience.cdk.io.Gaussian98Reader
-
Create an Gaussian98 output reader.
- gaussianDouble(double) - Static method in class org.openscience.cdk.math.RandomNumbersTool
-
Generates a random double from a Gaussian distribution with the specified
deviation.
- gaussianFloat(float) - Static method in class org.openscience.cdk.math.RandomNumbersTool
-
Generates a random float from a Gaussian distribution with the specified
deviation.
- GaussianInputFormat - Class in org.openscience.cdk.io.formats
-
- GaussianInputFormat() - Constructor for class org.openscience.cdk.io.formats.GaussianInputFormat
-
- GaussianInputWriter - Class in org.openscience.cdk.io.program
-
File writer thats generates input files for Gaussian calculation
jobs.
- GaussianInputWriter(Writer) - Constructor for class org.openscience.cdk.io.program.GaussianInputWriter
-
Constructs a new writer that produces input files to run a
Gaussian QM job.
- GaussianInputWriter(OutputStream) - Constructor for class org.openscience.cdk.io.program.GaussianInputWriter
-
- GaussianInputWriter() - Constructor for class org.openscience.cdk.io.program.GaussianInputWriter
-
- GaussiansBasis - Class in org.openscience.cdk.math.qm
-
This class contains the information to use gauss function as a base
for calculation of quantum mechanics.
- GaussiansBasis() - Constructor for class org.openscience.cdk.math.qm.GaussiansBasis
-
- GaussiansBasis(int[], int[], int[], double[], Vector[], IAtom[]) - Constructor for class org.openscience.cdk.math.qm.GaussiansBasis
-
Set up basis with gauss funktions
f(x,y,z) = (x-rx)^nx * (y-ry)^ny * (z-rz)^nz * exp(-alpha*(r-ri)^2).
- GaussJordan() - Method in class org.openscience.cdk.graph.invariant.GIMatrix
-
Gauss-Jordan algorithm.
- GD - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- GE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- GeneralPath - Class in org.openscience.cdk.renderer.elements
-
A path of rendering elements from the elements.path package.
- GeneralPath(List<PathElement>, Color) - Constructor for class org.openscience.cdk.renderer.elements.GeneralPath
-
Make a path from a list of path elements.
- generate(double) - Method in class org.openscience.cdk.formula.MassToFormulaTool
-
Deprecated.
Method that actually does the work of extracting the molecular formula.
- generate(IAtomContainer) - Method in interface org.openscience.cdk.hash.AtomHashGenerator
-
Generate invariant 64-bit hash codes for the atoms of the molecule.
- generate(Set<IAtomContainer>) - Method in interface org.openscience.cdk.hash.EnsembleHashGenerator
-
Generate invariant 64-bit hash code for an ensemble of molecules.
- generate(IAtomContainer) - Method in interface org.openscience.cdk.hash.MoleculeHashGenerator
-
Generate invariant 64-bit hash code for a molecule.
- generate(String) - Static method in class org.openscience.cdk.iupac.parser.NomParser
-
Deprecated.
Parses the chemical name and returns the built molecule.
- generate(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.iupac.parser.NomParser
-
Deprecated.
Parses the chemical name and returns the built molecule.
- generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.AtomContainerBoundsGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.AtomNumberGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IAtomContainer, IAtom, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator
-
Generate the rendering element(s) for a particular atom.
- generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IBond, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
-
Generate rendering element(s) for the current bond, including ring
elements if this bond is part of a ring.
- generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IReaction, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BoundsGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IAtomContainer, IAtom, RendererModel) - Method in class org.openscience.cdk.renderer.generators.ExtendedAtomGenerator
-
Generate the rendering element(s) for a particular atom.
- generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.HighlightGenerator
-
- generate(T, RendererModel) - Method in interface org.openscience.cdk.renderer.generators.IGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.LonePairGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IReaction, RendererModel) - Method in class org.openscience.cdk.renderer.generators.MappingGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IReaction, RendererModel) - Method in class org.openscience.cdk.renderer.generators.ProductsBoxGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.RadicalGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IReaction, RendererModel) - Method in class org.openscience.cdk.renderer.generators.ReactantsBoxGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IReaction, RendererModel) - Method in class org.openscience.cdk.renderer.generators.ReactionArrowGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IReaction, RendererModel) - Method in class org.openscience.cdk.renderer.generators.ReactionBoxGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IReaction, RendererModel) - Method in class org.openscience.cdk.renderer.generators.ReactionPlusGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IReaction, RendererModel) - Method in class org.openscience.cdk.renderer.generators.ReactionSceneGenerator
-
Converts a
IChemObject
from the chemical data model into
something that can be drawn in the chemical drawing.
- generate(IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator
-
- generate() - Method in class org.openscience.cdk.structgen.SingleStructureRandomGenerator
-
Generates a random structure based on the atoms in the given IAtomContainer.
- generate(IAtomContainerSet) - Method in class org.openscience.cdk.structgen.stochastic.PartialFilledStructureMerger
-
Randomly generates a single, connected, correctly bonded structure from
a number of fragments.
- generate3DCoordinates(IAtomContainer, boolean) - Method in class org.openscience.cdk.modeling.builder3d.ModelBuilder3D
-
Generate 3D coordinates with force field information.
- generateAtomContainerFromInchi(IChemObjectBuilder) - Method in class org.openscience.cdk.inchi.InChIToStructure
-
Gets structure from InChI, and converts InChI library data structure
into an IAtomContainer.
- generateBond(IBond, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
-
Generate stereo or bond elements for this bond.
- generateBondElement(IBond, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
-
Generate rendering elements for a bond, without ring elements but
considering the type of the bond (single, double, triple).
- generateBondElement(IBond, IBond.Order, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
-
Generate a LineElement or an ElementGroup of LineElements for this bond.
- generateCompactElement(IAtom, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator
-
Generate a compact element for an atom, such as a circle or a square,
rather than text element.
- GenerateCompatibilityGraph - Class in org.openscience.cdk.smsd.algorithm.mcsplus
-
This class generates compatibility graph between query and target molecule.
- GenerateCompatibilityGraph() - Constructor for class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
Default constructor added
- GenerateCompatibilityGraph(IAtomContainer, IAtomContainer, boolean) - Constructor for class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
Generates a compatibility graph between two molecules
- generateCoordinates(Vector2d) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
-
The main method of this StructurDiagramGenerator.
- generateCoordinates() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
-
The main method of this StructurDiagramGenerator.
- generateCSetCopy(int, List<String>) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
-
- generateCTabCopy(IAtomContainer) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
-
- generateDiagram(T) - Method in class org.openscience.cdk.renderer.AbstractRenderer
-
The main method of the renderer, that uses each of the generators
to create a different set of
IRenderingElement
s grouped
together into a tree.
- generateDiagram(T) - Method in interface org.openscience.cdk.renderer.IRenderer
-
Internal method to generate the intermediate format.
- generateDiagram(IAtomContainerSet) - Method in class org.openscience.cdk.renderer.MoleculeSetRenderer
-
The main method of the renderer, that uses each of the generators
to create a different set of
IRenderingElement
s grouped
together into a tree.
- generateDiagram(IReaction) - Method in class org.openscience.cdk.renderer.ReactionRenderer
-
The main method of the renderer, that uses each of the generators
to create a different set of
IRenderingElement
s grouped
together into a tree.
- generateElement(IAtom, int, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator
-
Generate an atom symbol element.
- generateExperimentalCoordinates() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
-
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(IAtomContainer) - Method in class org.openscience.cdk.fragment.ExhaustiveFragmenter
-
Generate fragments for the input molecule.
- generateFragments(IAtomContainer) - Method in interface org.openscience.cdk.fragment.IFragmenter
-
Generate fragments for the input molecule.
- generateFragments(IAtomContainer) - Method in class org.openscience.cdk.fragment.MurckoFragmenter
-
Perform the fragmentation procedure.
- generateGrid() - Method in class org.openscience.cdk.tools.GridGenerator
-
Main method creates a grid between given boundaries (dimensions).
- generateInnerElement(IBond, IRing, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
-
Make the inner ring bond, which is slightly shorter than the outer bond.
- generateMersenneTwisterRandomNumber(int, long) - Method in class org.openscience.cdk.fingerprint.RandomNumber
-
Mersenne Twister Random Number for a hashcode within a range between 0 to n.
- generateMoments(IAtomContainer) - Static method in class org.openscience.cdk.similarity.DistanceMoment
-
Evaluate the 12 descriptors used to characterize the 3D shape of a molecule.
- generateOrderEle() - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Returns the Elements ordered according to (approximate) probability of occurrence.
- generateParseException() - Method in class org.openscience.cdk.iupac.parser.NomParser
-
Deprecated.
Generate ParseException.
- generateParseException() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
Generate ParseException.
- generateRingElements(IBond, IRing, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
-
Generate ring elements, such as inner-ring bonds or ring stereo elements.
- generateRingElements(IBond, IRing, RendererModel) - Method in class org.openscience.cdk.renderer.generators.RingGenerator
-
Generate ring elements, such as inner-ring bonds or ring stereo elements.
- generators - Variable in class org.openscience.cdk.renderer.AbstractRenderer
-
Generators for diagram elements.
- generic() - Static method in class org.openscience.cdk.smiles.SmilesGenerator
-
Create a generator for generic SMILES.
- geometricCenterAllPlacedAtoms(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
-
Calculates the geometric center of all placed atoms in the atomcontainer.
- GeometricCumulativeDoubleBondFactory - Class in org.openscience.cdk.hash.stereo
-
Stereo encoder factory for 2D and 3D cumulative double bonds.
- GeometricCumulativeDoubleBondFactory() - Constructor for class org.openscience.cdk.hash.stereo.GeometricCumulativeDoubleBondFactory
-
- GeometricDoubleBondEncoderFactory - Class in org.openscience.cdk.hash.stereo
-
A stereo encoder factory encoding double bond configurations by 2D and 3D
coordinates.
- GeometricDoubleBondEncoderFactory() - Constructor for class org.openscience.cdk.hash.stereo.GeometricDoubleBondEncoderFactory
-
- GeometricTetrahedralEncoderFactory - Class in org.openscience.cdk.hash.stereo
-
A stereo encoder factory for tetrahedral centres.
- GeometricTetrahedralEncoderFactory() - Constructor for class org.openscience.cdk.hash.stereo.GeometricTetrahedralEncoderFactory
-
- Geometry3DValidator - Class in org.openscience.cdk.validate
-
Validates the 3D geometry of the model.
- Geometry3DValidator() - Constructor for class org.openscience.cdk.validate.Geometry3DValidator
-
- GeometryTools - Class in org.openscience.cdk.geometry
-
A set of static utility classes for geometric calculations and operations.
- GeometryTools() - Constructor for class org.openscience.cdk.geometry.GeometryTools
-
- GeometryTools.CoordinateCoverage - Enum in org.openscience.cdk.geometry
-
Provides the coverage of coordinates for this molecule.
- GeometryUtil - Class in org.openscience.cdk.geometry
-
A set of static utility classes for geometric calculations and operations.
- GeometryUtil.CoordinateCoverage - Enum in org.openscience.cdk.geometry
-
Provides the coverage of coordinates for this molecule.
- GERMAINIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- GERMANIUM - Static variable in enum org.openscience.cdk.config.Elements
-
- get(int) - Method in class org.openscience.cdk.ConformerContainer
-
Get the conformer at a specified position.
- get(int) - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
-
- get(int) - Method in interface org.openscience.cdk.fingerprint.IBitFingerprint
-
Returns the value of the bit with the specified index.
- get(int) - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
-
- get(int, int) - Method in class org.openscience.cdk.graph.GraphUtil.EdgeToBondMap
-
Access the bond store at the end points v and w.
- get(int) - Method in class org.openscience.cdk.group.DisjointSetForest
-
Get the value of the forest at this index - note that this will
not
necessarily give the set for that element : use
DisjointSetForest.getSets()
after
union-ing elements.
- get(int) - Method in class org.openscience.cdk.group.Permutation
-
Get the value at this index.
- get(int, int) - Method in class org.openscience.cdk.group.PermutationGroup
-
Get one of the permutations that make up the compact representation.
- get(String) - Method in class org.openscience.cdk.io.setting.SettingManager
-
Access the setting stored for given name.
- get(String, Class<S>) - Method in class org.openscience.cdk.io.setting.SettingManager
-
Convenience method that allows specification of return ISetting type so that you can nest the call to
access the setting value.
- get(int) - Method in class org.openscience.cdk.qsar.result.DoubleArrayResult
-
The first double is at index = 0;
- get(int) - Method in class org.openscience.cdk.qsar.result.IntegerArrayResult
-
The first int is at index = 0.
- get(Class<T>) - Method in class org.openscience.cdk.renderer.RendererModel
-
- get2DCenter() - Method in class org.openscience.cdk.Bond
-
Returns the geometric 2D center of the bond.
- get2DCenter() - Method in class org.openscience.cdk.debug.DebugBond
-
Returns the geometric 2D center of the bond.
- get2DCenter(Iterable<IAtom>) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Calculates the center of the given atoms and returns it as a Point2d.
- get2DCenter(Iterator<IAtom>) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Calculates the center of the given atoms and returns it as a Point2d.
- get2DCenter(IRingSet) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Returns the geometric center of all the rings in this ringset.
- get2DCenter(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Returns the geometric center of all the atoms in the atomContainer.
- get2DCenter(Iterable<IAtom>) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Calculates the center of the given atoms and returns it as a Point2d.
- get2DCenter(Iterator<IAtom>) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Calculates the center of the given atoms and returns it as a Point2d.
- get2DCenter(IRingSet) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Returns the geometric center of all the rings in this ringset.
- get2DCenter(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Returns the geometric center of all the atoms in the atomContainer.
- get2DCenter() - Method in interface org.openscience.cdk.interfaces.IBond
-
Returns the geometric 2D center of the bond.
- get2DCenter() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Returns the geometric 2D center of the query bond.
- get2DCenter() - Method in class org.openscience.cdk.silent.Bond
-
Returns the geometric 2D center of the bond.
- get2DCentreOfMass(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Calculates the center of mass for the Atom
s in the
AtomContainer for the 2D coordinates.
- get2DCentreOfMass(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Calculates the center of mass for the Atom
s in the AtomContainer for the 2D
coordinates.
- get2DCoordinateCoverage(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
- get2DCoordinateCoverage(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
- get2DDimension(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Returns the java.awt.Dimension of a molecule.
- get2DDimension(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Returns the dimension of a molecule (width/height).
- get3DCenter() - Method in class org.openscience.cdk.Bond
-
Returns the geometric 3D center of the bond.
- get3DCenter() - Method in class org.openscience.cdk.debug.DebugBond
-
Returns the geometric 3D center of the bond.
- get3DCenter(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Returns the geometric center of all the atoms in this atomContainer.
- get3DCenter(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Returns the geometric center of all the atoms in this atomContainer.
- get3DCenter() - Method in interface org.openscience.cdk.interfaces.IBond
-
Returns the geometric 3D center of the bond.
- get3DCenter() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Returns the geometric 3D center of the query bond.
- get3DCenter() - Method in class org.openscience.cdk.silent.Bond
-
Returns the geometric 3D center of the bond.
- get3DCentreOfMass(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Calculates the center of mass for the Atom
s in the
AtomContainer for the 2D coordinates.
- get3DCentreOfMass(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Calculates the center of mass for the Atom
s in the AtomContainer for the 2D
coordinates.
- get3DCoordinateCoverage(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
- get3DCoordinateCoverage(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
- get3DCoordinatesForLigands(IAtom, IAtomContainer, IAtomContainer, IAtom, int, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Adds 3D coordinates for singly-bonded ligands of a reference atom (A).
- get3DCoordinatesForSP2Ligands(IAtom, IAtomContainer, IAtomContainer, IAtom, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Main method for the calculation of the ligand coordinates for sp2 atoms.
- get3DCoordinatesForSP3Ligands(IAtom, IAtomContainer, IAtomContainer, IAtom, int, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Main method for the calculation of the ligand coordinates for sp3 atoms.
- get3DCoordinatesForSPLigands(IAtom, IAtomContainer, double, double) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
- getA() - Method in class org.openscience.cdk.Crystal
-
Gets the A unit cell axes in Cartesian coordinates
as a three element double array.
- getA() - Method in class org.openscience.cdk.debug.DebugCrystal
-
Gets the A unit cell axes in Cartesian coordinates
as a three element double array.
- getA() - Method in interface org.openscience.cdk.interfaces.ICrystal
-
Gets the A unit cell axes in carthesian coordinates
as a three element double array.
- getA() - Method in class org.openscience.cdk.silent.Crystal
-
Gets the A unit cell axes in Cartesian coordinates
as a three element double array.
- getAgents() - Method in class org.openscience.cdk.debug.DebugReaction
-
Returns a MoleculeSet containing the agents in this reaction.
- getAgents() - Method in interface org.openscience.cdk.interfaces.IReaction
-
Returns a IAtomContaineSet containing the agents in this reaction.
- getAgents() - Method in class org.openscience.cdk.Reaction
-
Returns a MoleculeSet containing the agents in this reaction.
- getAgents() - Method in class org.openscience.cdk.silent.Reaction
-
Returns a MoleculeSet containing the agents in this reaction.
- getAllAtomContainers(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
-
Returns all the AtomContainer's of a MoleculeSet.
- getAllAtomContainers(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator
-
Returns all the AtomContainer's of a ChemFile.
- getAllAtomContainers(IChemModel) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
-
Returns all the AtomContainer's of a ChemModel.
- getAllAtomContainers(IChemSequence) - Static method in class org.openscience.cdk.tools.manipulator.ChemSequenceManipulator
-
Returns all the AtomContainer's of a ChemSequence.
- getAllAtomContainers(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
-
Returns all the AtomContainer's of a MoleculeSet.
- getAllAtomContainers(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
-
Returns all the AtomContainer's of a Reaction.
- getAllAtomContainers(IReactionScheme, IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator
-
- getAllAtomContainers(IReactionScheme) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator
-
get all AtomContainers object from a set of Reactions.
- getAllAtomContainers(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
-
Returns all the AtomContainer's of a Reaction.
- getAllAtomContainers(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator
-
Returns all the AtomContainer's in a RingSet.
- getAllAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler
-
Returns all plausible mappings between query and target molecules.
- getAllAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler
-
Returns all plausible mappings between query and target molecules.
- getAllAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler
-
Returns all plausible mappings between query and target molecules.
- getAllAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler
-
Returns all plausible mappings between query and target molecules.
- getAllAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler
-
Returns all plausible mappings between query and target molecules.
- getAllAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler
-
Returns all plausible mappings between query and target molecules.
- getAllAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler
-
Returns all plausible mappings between query and target molecules.
- getAllAtomMapping() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
Returns all plausible mappings between query and target molecules
Each map in the list has atom-atom equivalence of the mappings
between query and target molecule i.e.
- getAllAtomMapping() - Method in interface org.openscience.cdk.smsd.interfaces.IMCSBase
-
Returns all plausible mappings between query and target molecules.
- getAllAtomMapping() - Method in class org.openscience.cdk.smsd.Isomorphism
-
Returns all plausible mappings between query and target molecules
Each map in the list has atom-atom equivalence of the mappings
between query and target molecule i.e.
- getAllAtomRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>, boolean) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Return the RMSD between the 2 aligned molecules.
- getAllAtomRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>, boolean) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Return the RMSD between the 2 aligned molecules.
- getAllAtomTypes() - Method in class org.openscience.cdk.config.AtomTypeFactory
-
Gets the allAtomTypes attribute of the AtomTypeFactory object.
- getAllBondMaps() - Method in class org.openscience.cdk.smsd.Isomorphism
-
- getAllChemModels(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator
-
Get a list of all ChemModels inside an IChemFile.
- getAllChemObjects(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
-
Does not recursively return the contents of the AtomContainer.
- getAllChemObjects(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator
-
Returns a List of all IChemObject inside a ChemFile.
- getAllChemObjects(IChemModel) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
-
Retrieve a List of all ChemObject objects within an IChemModel.
- getAllChemObjects(IChemSequence) - Static method in class org.openscience.cdk.tools.manipulator.ChemSequenceManipulator
-
Returns a List of all IChemObject inside a ChemSequence.
- getAllChemObjects(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
-
- getAllChemObjects(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
-
- getAllChemObjects(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
-
- getAllConfigurations() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
-
Produces all combinations of the root structure (scaffold) with the R-groups
substituted in valid ways, using each R-group's definitions and conditions.
- getAllConfigurations() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
- getAllFormulas() - Method in class org.openscience.cdk.formula.MolecularFormulaGenerator
-
- getAllIDs(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
- getAllIDs(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
-
- getAllIDs(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator
-
- getAllIDs(IChemModel) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
-
- getAllIDs(IChemSequence) - Static method in class org.openscience.cdk.tools.manipulator.ChemSequenceManipulator
-
- getAllIDs(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
-
- getAllIDs(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
-
- getAllIDs(IReactionScheme) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator
-
Get all ID of this IReactionSet.
- getAllIDs(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
-
- getAllInOneContainer(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator
-
Puts all rings of a ringSet in a single atomContainer
- getAllMapping() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler
-
Returns all plausible mappings between query and target molecules.
- getAllMapping() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler
-
Returns all plausible mappings between query and target molecules.
- getAllMapping() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler
-
Returns all plausible mappings between query and target molecules.
- getAllMapping() - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler
-
Returns all plausible mappings between query and target molecules.
- getAllMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler
-
Returns all plausible mappings between query and target molecules.
- getAllMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler
-
Returns all plausible mappings between query and target molecules.
- getAllMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler
-
Returns all plausible mappings between query and target molecules.
- getAllMapping() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
Returns all plausible mappings between query and target molecules
Each map in the list has atom-atom equivalence index of the mappings
between query and target molecule i.e.
- getAllMapping() - Method in interface org.openscience.cdk.smsd.interfaces.IMCSBase
-
Returns all plausible mappings between query and target molecules.
- getAllMapping() - Method in class org.openscience.cdk.smsd.Isomorphism
-
Returns all plausible mappings between query and target molecules
Each map in the list has atom-atom equivalence index of the mappings
between query and target molecule i.e.
- getAllMaximum(List<List<CDKRMap>>) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
-
- getAllMolecules(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
-
Get all molecule of a
IReaction
: reactants + products.
- getAllMolecules(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
-
get all Molecules object from a set of Reactions.
- getAllPaths(IAtomContainer, IAtom, IAtom) - Static method in class org.openscience.cdk.graph.PathTools
-
Get a list of all the paths between two atoms.
- getAllProducts(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
-
get all products of a IReaction
- getAllReactants(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
-
get all reactants of a IReaction
- getAllReactions(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator
-
Get a list of all IReaction inside an IChemFile.
- getAllReactions(IReactionScheme) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator
-
Get all IReaction's object from a given IReactionScheme.
- getAllRgroupQueryAtoms() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
Returns all R# type atoms (pseudo atoms) found in the root structure.
- getAllRings() - Method in class org.openscience.cdk.graph.SpanningTree
-
All basic rings and the all pairs of basic rings share at least one edge
combined.
- getAllSurfaceAreas() - Method in class org.openscience.cdk.geometry.surface.NumericalSurface
-
Get an array containing the accessible surface area for each atom.
- getAllSurfacePoints() - Method in class org.openscience.cdk.geometry.surface.NumericalSurface
-
Get an array of all the points on the molecular surface.
- getAltLoc() - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
get the Alternate location indicator of this atom.
- getAltLoc() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
get the Alternate location indicator of this atom.
- getAltLoc() - Method in class org.openscience.cdk.protein.data.PDBAtom
-
get the Alternate location indicator of this atom.
- getAltLoc() - Method in class org.openscience.cdk.silent.PDBAtom
-
get the Alternate location indicator of this atom.
- getAngle(double, double) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Gets the angle attribute of the GeometryTools class.
- getAngle(double, double) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Gets the angle attribute of the GeometryTools class.
- getAngleData(String, String, String, String) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94ParametersCall
-
Gets the angle parameter set.
- getAngleRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Return the variation of each angle value between the 2 aligned molecules.
- getAngleRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Return the variation of each angle value between the 2 aligned molecules.
- getAngleValue(String, String, String) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
-
Gets the angleKey attribute of the AtomPlacer3D object.
- getAngleValue(String, String, String) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Gets the angleKey attribute of the AtomPlacer3D object.
- getArrayValue() - Method in class org.openscience.cdk.graph.invariant.GIMatrix
-
Returns the internal representation of the matrix, that is an array of double objects.
- getAtom(int) - Method in class org.openscience.cdk.AtomContainer
-
Get the atom at position number
in [0,..].
- getAtom(int) - Method in class org.openscience.cdk.Bond
-
Returns an Atom from this bond.
- getAtom(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Get the atom at position number
in [0,..].
- getAtom(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Get the atom at position number
in [0,..].
- getAtom(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Get the atom at position number
in [0,..].
- getAtom(int) - Method in class org.openscience.cdk.debug.DebugBond
-
Returns an Atom from this bond.
- getAtom(int) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Get the atom at position number
in [0,..].
- getAtom() - Method in class org.openscience.cdk.debug.DebugLonePair
-
Returns the associated Atom.
- getAtom(int) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Get the atom at position number
in [0,..].
- getAtom(int) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Get the atom at position number
in [0,..].
- getAtom(int) - Method in class org.openscience.cdk.debug.DebugRing
-
Get the atom at position number
in [0,..].
- getAtom() - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
Returns the associated Atom.
- getAtom(int) - Method in class org.openscience.cdk.debug.DebugStrand
-
Get the atom at position number
in [0,..].
- getAtom(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Get the atom at position number
in [0,..].
- getAtom(int) - Method in interface org.openscience.cdk.interfaces.IBond
-
Returns an Atom from this bond.
- getAtom() - Method in interface org.openscience.cdk.interfaces.ILonePair
-
Returns the associated Atom.
- getAtom() - Method in interface org.openscience.cdk.interfaces.ISingleElectron
-
Returns the associated Atom.
- getAtom(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Get the atom at position number
in [0,..].
- getAtom(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Returns an Atom from this query bond.
- getAtom() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RingIdentifierAtom
-
- getAtom() - Method in class org.openscience.cdk.LonePair
-
Returns the associated Atom.
- getAtom(int) - Method in class org.openscience.cdk.silent.AtomContainer
-
Get the atom at position number
in [0,..].
- getAtom(int) - Method in class org.openscience.cdk.silent.Bond
-
Returns an Atom from this bond.
- getAtom() - Method in class org.openscience.cdk.silent.LonePair
-
Returns the associated Atom.
- getAtom() - Method in class org.openscience.cdk.silent.SingleElectron
-
Returns the associated Atom.
- getAtom() - Method in class org.openscience.cdk.SingleElectron
-
Returns the associated Atom.
- getAtom() - Method in class org.openscience.cdk.smiles.InvPair
-
- getAtom(int) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.TargetProperties
-
- getAtom(INode) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder
-
Returns an atom associated with this node.
- getAtom(INode) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQuery
-
Returns an atom associated with this node.
- getAtomArray(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Constructs an array of Atom objects from an AtomContainer.
- getAtomArray(List<IAtom>) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Constructs an array of Atom objects from a List of Atom objects.
- getAtomArray(IBond) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
-
Constructs an array of Atom objects from Bond.
- getAtomAt(int) - Method in class org.openscience.cdk.Association
-
Returns an Atom from this Association.
- getAtomById(IAtomContainer, String) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Returns an atom in an atomcontainer identified by id
- getAtomColor(IAtom) - Method in class org.openscience.cdk.renderer.color.CDK2DAtomColors
-
Returns the CDK 2D color for the given atom's element.
- getAtomColor(IAtom, Color) - Method in class org.openscience.cdk.renderer.color.CDK2DAtomColors
-
Returns the CDK 2D color for the given atom's element, or defaults to the given color if no
color is defined.
- getAtomColor(IAtom) - Method in class org.openscience.cdk.renderer.color.CDKAtomColors
-
Returns the CDK scheme color for the given atom's element.
- getAtomColor(IAtom, Color) - Method in class org.openscience.cdk.renderer.color.CDKAtomColors
-
Returns the CDK scheme color for the given atom's element, or
defaults to the given color if no color is defined.
- getAtomColor(IAtom) - Method in class org.openscience.cdk.renderer.color.CPKAtomColors
-
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
-
Returns the a color reflecting the given atom's partial charge.
- getAtomColor(IAtom, Color) - Method in class org.openscience.cdk.renderer.color.PartialAtomicChargeColors
-
Returns the a color reflecting the given atom's partial charge, or
defaults to the given color if no color is defined.
- getAtomColor(IAtom) - Method in class org.openscience.cdk.renderer.color.RasmolColors
-
Returns the Rasmol color for the given atom's element.
- getAtomColor(IAtom, Color) - Method in class org.openscience.cdk.renderer.color.RasmolColors
-
Returns the Rasmol color for the given atom's element, or
defaults to the given color if no color is defined.
- getAtomColor(IAtom) - Method in class org.openscience.cdk.renderer.color.UniColor
-
- getAtomColor(IAtom, Color) - Method in class org.openscience.cdk.renderer.color.UniColor
-
- getAtomColor(IAtom, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator
-
Returns the drawing color of the given atom.
- getAtomContainer(int) - Method in class org.openscience.cdk.AtomContainerSet
-
Returns the AtomContainer at position number
in the
container.
- getAtomContainer(int) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
Returns the AtomContainer at position number
in the
container.
- getAtomContainer(int) - Method in class org.openscience.cdk.debug.DebugSubstance
-
Returns the AtomContainer at position number
in the
container.
- getAtomContainer() - Method in interface org.openscience.cdk.geometry.cip.ILigand
-
- getAtomContainer() - Method in class org.openscience.cdk.geometry.cip.Ligand
-
- getAtomContainer() - Method in class org.openscience.cdk.inchi.InChIToStructure
-
Returns generated molecule.
- getAtomContainer(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
-
Returns the AtomContainer at position number
in the
container.
- getAtomContainer() - Method in class org.openscience.cdk.io.iterator.event.EventCMLHandler
-
- getAtomContainer() - Method in class org.openscience.cdk.io.iterator.event.EventCMLReader
-
- getAtomContainer() - Method in interface org.openscience.cdk.io.iterator.event.IEventChemObjectReader
-
- getAtomContainer() - Method in class org.openscience.cdk.signature.MoleculeFromSignatureBuilder
-
Gets the atom container.
- getAtomContainer(int) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Returns the AtomContainer at position number
in the
container.
- getAtomContainer(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Method that actually does the work of convert the IMolecularFormula
to IAtomContainer.
- getAtomContainer(IMolecularFormula, IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Method that actually does the work of convert the IMolecularFormula
to IAtomContainer given a IAtomContainer.
- getAtomContainer(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Converts a formula string (like "C2H4") into an atom container with atoms
but no bonds.
- getAtomContainerCount() - Method in class org.openscience.cdk.AtomContainerSet
-
Returns the number of AtomContainers in this Container.
- getAtomContainerCount() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
Returns the number of AtomContainers in this Container.
- getAtomContainerCount() - Method in class org.openscience.cdk.debug.DebugSubstance
-
Returns the number of AtomContainers in this Container.
- getAtomContainerCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
-
Returns the number of AtomContainers in this Container.
- getAtomContainerCount() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
-
Return the total number of atom containers (count the root plus all substituents).
- getAtomContainerCount() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
- getAtomContainerCount() - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Returns the number of AtomContainers in this Container.
- getAtomContainerSet(IAtomContainer, IAtomContainer, IReactionScheme) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator
-
Extract the list of AtomContainers taking part in the IReactionScheme to originate a
product given a reactant.
- getAtomCount() - Method in class org.openscience.cdk.Association
-
Returns the number of Atoms in this Association.
- getAtomCount() - Method in class org.openscience.cdk.AtomContainer
-
Returns the number of Atoms in this Container.
- getAtomCount() - Method in class org.openscience.cdk.Bond
-
Returns the number of Atoms in this Bond.
- getAtomCount() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns the number of Atoms in this Container.
- getAtomCount() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns the number of Atoms in this Container.
- getAtomCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns the number of Atoms in this Container.
- getAtomCount() - Method in class org.openscience.cdk.debug.DebugBond
-
Returns the number of Atoms in this Bond.
- getAtomCount() - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns the number of Atoms in this Container.
- getAtomCount() - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns the number of Atoms in this Container.
- getAtomCount() - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns the number of Atoms in this Container.
- getAtomCount() - Method in class org.openscience.cdk.debug.DebugRing
-
Returns the number of Atoms in this Container.
- getAtomCount() - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns the number of Atoms in this Container.
- getAtomCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the number of Atoms in this Container.
- getAtomCount() - Method in interface org.openscience.cdk.interfaces.IBond
-
Returns the number of Atoms in this Bond.
- getAtomCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the number of Atoms in this Container.
- getAtomCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Returns the number of Atoms in this Bond.
- getAtomCount() - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the number of Atoms in this Container.
- getAtomCount() - Method in class org.openscience.cdk.silent.Bond
-
Returns the number of Atoms in this Bond.
- getAtomCount() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.TargetProperties
-
- getAtomCount(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
-
- getAtomCount(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator
-
Get the total number of atoms inside an IChemFile.
- getAtomCount(IChemModel) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
-
Get the total number of atoms inside an IChemModel.
- getAtomCount(IChemSequence) - Static method in class org.openscience.cdk.tools.manipulator.ChemSequenceManipulator
-
Get the total number of atoms inside an IChemSequence.
- getAtomCount(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Checks a set of Nodes for the occurrence of each isotopes
instance in the molecular formula.
- getAtomCount(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
-
- getAtomCount(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
-
- getAtomCount(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
-
- getAtomCount(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator
-
Return the total number of atoms over all the rings in the colllection.
- getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugAtom
-
Returns the atomic number of this element.
- getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugAtomType
-
Returns the atomic number of this element.
- getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugElement
-
Returns the atomic number of this element.
- getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Returns the atomic number of this element.
- getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugIsotope
-
Returns the atomic number of this element.
- getAtomicNumber() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Returns the atomic number of this element.
- getAtomicNumber() - Method in class org.openscience.cdk.Element
-
Returns the atomic number of this element.
- getAtomicNumber() - Method in interface org.openscience.cdk.interfaces.IElement
-
Returns the atomic number of this element.
- getAtomicNumber() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Returns the atomic number of this element.
- getAtomicNumber() - Method in class org.openscience.cdk.silent.Element
-
Returns the atomic number of this element.
- getAtomicNumber(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
-
Get the atomic number of the element.
- getAtomicSoftnessCore(IAtomContainer, int) - Method in class org.openscience.cdk.charges.InductivePartialCharges
-
Gets the atomicSoftnessCore attribute of the InductivePartialCharges object.
- getAtomIndices() - Method in class org.openscience.cdk.signature.Orbit
-
Gets all the atom indices as a list.
- getAtomLayers(int[][]) - Static method in class org.openscience.cdk.graph.invariant.HuLuIndexTool
-
- getAtomMatcher() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.NodeBuilder
-
Returns Query Atom.
- getAtomMatcher() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.INode
-
Returns Query Atom.
- getAtomNumber(IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Returns the position of a given atom in the atoms array.
- getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns the position of a given atom in the atoms array.
- getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns the position of a given atom in the atoms array.
- getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns the position of a given atom in the atoms array.
- getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns the position of a given atom in the atoms array.
- getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns the position of a given atom in the atoms array.
- getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns the position of a given atom in the atoms array.
- getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
Returns the position of a given atom in the atoms array.
- getAtomNumber(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns the position of a given atom in the atoms array.
- getAtomNumber(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the position of a given atom in the atoms array.
- getAtomNumber(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the position of a given atom in the atoms array.
- getAtomNumber(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the position of a given atom in the atoms array.
- getAtomOverlapScore(IAtomContainer, Vector) - Method in class org.openscience.cdk.layout.OverlapResolver
-
Deprecated.
Calculates a score based on the overlap of atoms.
- getAtomPlacer() - Method in class org.openscience.cdk.layout.RingPlacer
-
- getAtoms() - Method in class org.openscience.cdk.Association
-
Returns the array of atoms making up this Association.
- getAtoms() - Method in class org.openscience.cdk.smsd.ring.PathEdge
-
- getAtomType(String) - Method in class org.openscience.cdk.config.AtomTypeFactory
-
Get an AtomType with the given ID.
- getAtomTypeFactory(IChemObjectBuilder) - Method in class org.openscience.cdk.tools.SaturationChecker
-
- getAtomTypeFactory(IChemObjectBuilder) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
-
- getAtomTypeMappings() - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingHandler
-
Returns a
Map
with atom type mappings.
- getAtomTypeName() - Method in class org.openscience.cdk.AtomType
-
Gets the id attribute of the AtomType object.
- getAtomTypeName() - Method in class org.openscience.cdk.debug.DebugAtom
-
Gets the id attribute of the AtomType object.
- getAtomTypeName() - Method in class org.openscience.cdk.debug.DebugAtomType
-
Gets the id attribute of the AtomType object.
- getAtomTypeName() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Gets the id attribute of the AtomType object.
- getAtomTypeName() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Gets the id attribute of the AtomType object.
- getAtomTypeName() - Method in interface org.openscience.cdk.interfaces.IAtomType
-
Gets the id attribute of the AtomType object.
- getAtomTypeName() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Gets the id attribute of the AtomType object.
- getAtomTypeName() - Method in class org.openscience.cdk.silent.AtomType
-
Gets the id attribute of the AtomType object.
- getAtomTypePatterns() - Method in class org.openscience.cdk.modeling.builder3d.MM2BasedAtomTypePattern
-
Gets the atomTypePatterns attribute of the MM2BasedAtomTypePattern object
- getAtomTypePatterns() - Method in class org.openscience.cdk.modeling.builder3d.MMFF94BasedAtomTypePattern
-
Gets the atomTypePatterns attribute of the MM2BasedAtomTypePattern object
- getAtomTypes(String) - Method in class org.openscience.cdk.config.AtomTypeFactory
-
Get an array of all atomTypes known to the AtomTypeFactory for the given
element symbol and atomtype class.
- getAtomTypes() - Method in class org.openscience.cdk.config.atomtypes.AtomTypeHandler
-
Returns a List with read IAtomType's.
- getAtomTypes() - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeHandler
-
Returns a List with read IAtomType's.
- getAtomTypes() - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
-
Gets the atomTypes attribute of the ForceFieldConfigurator object
- getAtomTypes() - Method in class org.openscience.cdk.modeling.builder3d.MM2BasedParameterSetReader
-
- getAtomTypes() - Method in class org.openscience.cdk.modeling.builder3d.MMFF94BasedParameterSetReader
-
- getAtomVector(int) - Method in class org.openscience.cdk.Vibration
-
Gets a atom vector at index given.
- getAtomVectorCount() - Method in class org.openscience.cdk.Vibration
-
Gets the number of atom vectors in the vibration.
- getAtomVectors() - Method in class org.openscience.cdk.Vibration
-
Returns an Enumeration of the atom vectors of this vibration.
- getAtomWeights(AtomContainer) - Static method in class org.openscience.cdk.graph.invariant.HuLuIndexTool
-
- getAutomorphismGroup() - Method in class org.openscience.cdk.group.AbstractDiscretePartitionRefiner
-
Get the automorphism group used to prune the search.
- getAutomorphismGroup(IAtomContainer) - Method in class org.openscience.cdk.group.AtomDiscretePartitionRefiner
-
Gets the automorphism group of the atom container.
- getAutomorphismGroup(IAtomContainer, PermutationGroup) - Method in class org.openscience.cdk.group.AtomDiscretePartitionRefiner
-
Speed up the search for the automorphism group using the automorphisms in
the supplied group.
- getAutomorphismGroup(IAtomContainer, Partition) - Method in class org.openscience.cdk.group.AtomDiscretePartitionRefiner
-
Get the automorphism group of the molecule given an initial partition.
- getAutomorphismGroup(IAtomContainer) - Method in class org.openscience.cdk.group.BondDiscretePartitionRefiner
-
Gets the automorphism group of the atom container.
- getAutomorphismGroup(IAtomContainer, PermutationGroup) - Method in class org.openscience.cdk.group.BondDiscretePartitionRefiner
-
Speed up the search for the automorphism group using the automorphisms in
the supplied group.
- getAutomorphismGroup(IAtomContainer, Partition) - Method in class org.openscience.cdk.group.BondDiscretePartitionRefiner
-
Get the automorphism group of the molecule given an initial partition.
- getAutomorphismPartition() - Method in class org.openscience.cdk.group.AbstractDiscretePartitionRefiner
-
The automorphism partition is a partition of the elements of the group.
- getAutomorphismPartition(IAtomContainer) - Method in class org.openscience.cdk.group.AtomDiscretePartitionRefiner
-
Get the automorphism partition (equivalence classes) of the atoms.
- getAutomorphismPartition(IAtomContainer) - Method in class org.openscience.cdk.group.BondDiscretePartitionRefiner
-
Get the automorphism partition (equivalence classes) of the bonds.
- getAuxInfo() - Method in class org.openscience.cdk.inchi.InChIGenerator
-
Gets auxillary information.
- getAvailableDictionaryClasses() - Method in class org.openscience.cdk.qsar.DescriptorEngine
-
Get the all the unique dictionary classes that the descriptors belong to.
- getB() - Method in class org.openscience.cdk.Crystal
-
Gets the B unit cell axes in Cartesian coordinates
as a three element double array.
- getB() - Method in class org.openscience.cdk.debug.DebugCrystal
-
Gets the B unit cell axes in Cartesian coordinates
as a three element double array.
- getB() - Method in interface org.openscience.cdk.interfaces.ICrystal
-
Gets the B unit cell axes in carthesian coordinates
as a three element double array.
- getB() - Method in class org.openscience.cdk.silent.Crystal
-
Gets the B unit cell axes in Cartesian coordinates
as a three element double array.
- getBasicRings() - Method in class org.openscience.cdk.graph.SpanningTree
-
The basic rings of the spanning tree.
- getBasis() - Method in class org.openscience.cdk.math.qm.Orbitals
-
Returns the basis set of this orbitals
- getBeginColumn() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Get token beginning column number.
- getBeginColumn() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Get token beginning column number.
- getBeginLine() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Get token beginning line number.
- getBeginLine() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Get token beginning line number.
- getBest() - Method in class org.openscience.cdk.group.AbstractDiscretePartitionRefiner
-
Get the best permutation found.
- getBestAlignmentForLabel(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Determines the best alignment for the label of an atom in 2D space.
- getBestAlignmentForLabel(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Determines the best alignment for the label of an atom in 2D space.
- getBestAlignmentForLabelXY(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Determines the best alignment for the label of an atom in 2D space.
- getBestAlignmentForLabelXY(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Determines the best alignment for the label of an atom in 2D space.
- getBestCliqueSize() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.BKKCKCF
-
- getBestHalfMatrixString() - Method in class org.openscience.cdk.group.AbstractDiscretePartitionRefiner
-
Get the half-matrix string under the best permutation.
- getBibData() - Method in class org.openscience.cdk.tools.BremserOneSphereHOSECodePredictor
-
- getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter
-
Calculates the circular fingerprint for the given
IAtomContainer
, and
folds the result into a single bitset
(see getSize()).
- getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.EStateFingerprinter
-
- getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter
-
Generates a fingerprint of the default size for the given
AtomContainer, using path and ring metrics.
- getBitFingerprint(IAtomContainer, IRingSet, List<IRingSet>) - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter
-
Generates a fingerprint of the default size for the given
AtomContainer, using path and ring metrics.
- getBitFingerprint(IAtomContainer, AllRingsFinder) - Method in class org.openscience.cdk.fingerprint.Fingerprinter
-
Generates a fingerprint of the default size for the given AtomContainer.
- getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.Fingerprinter
-
Generates a fingerprint of the default size for the given AtomContainer.
- getBitFingerprint(IAtomContainer, int) - Method in class org.openscience.cdk.fingerprint.GraphOnlyFingerprinter
-
- getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.HybridizationFingerprinter
-
Generates a fingerprint of the default size for the given AtomContainer.
- getBitFingerprint(IAtomContainer) - Method in interface org.openscience.cdk.fingerprint.IFingerprinter
-
- getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.LingoFingerprinter
-
- getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.MACCSFingerprinter
-
- getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.PubchemFingerprinter
-
Calculate 881 bit Pubchem fingerprint for a molecule.
- getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.ShortestPathFingerprinter
-
Generates a shortest path based BitSet fingerprint for the given AtomContainer.
- getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.SignatureFingerprinter
-
- getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.SubstructureFingerprinter
-
- getBitSet(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
-
Transforms an AtomContainer into a
BitSet
(which's size = number of bond
in the atomContainer, all the bit are set to true).
- getBitSet(IAtomContainer) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
-
Transforms an AtomContainer into atom BitSet (which's size = number of bondA1
in the atomContainer, all the bit are set to true).
- getBitSetFromFile(StringTokenizer) - Static method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D
-
- getBond(int) - Method in class org.openscience.cdk.AtomContainer
-
Get the bond at position number
in [0,..].
- getBond(IAtom, IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Returns the bond that connects the two given atoms.
- getBond(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Get the bond at position number
in [0,..].
- getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns the bond that connects the two given atoms.
- getBond(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Get the bond at position number
in [0,..].
- getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns the bond that connects the two given atoms.
- getBond(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Get the bond at position number
in [0,..].
- getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns the bond that connects the two given atoms.
- getBond(int) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Get the bond at position number
in [0,..].
- getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns the bond that connects the two given atoms.
- getBond(int) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Get the bond at position number
in [0,..].
- getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns the bond that connects the two given atoms.
- getBond(int) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Get the bond at position number
in [0,..].
- getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns the bond that connects the two given atoms.
- getBond(int) - Method in class org.openscience.cdk.debug.DebugRing
-
Get the bond at position number
in [0,..].
- getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
Returns the bond that connects the two given atoms.
- getBond(int) - Method in class org.openscience.cdk.debug.DebugStrand
-
Get the bond at position number
in [0,..].
- getBond(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns the bond that connects the two given atoms.
- getBond(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Get the bond at position number
in [0,..].
- getBond(IAtom, IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the bond that connectes the two given atoms.
- getBond(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Get the bond at position number
in [0,..].
- getBond(IAtom, IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the bond that connects the two given atoms.
- getBond(int) - Method in class org.openscience.cdk.silent.AtomContainer
-
Get the bond at position number
in [0,..].
- getBond(IAtom, IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the bond that connects the two given atoms.
- getBond(IAtom, IAtom) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.TargetProperties
-
- getBondAngleInteractionData(String, String, String, String) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94ParametersCall
-
Gets the bond-angle interaction parameter set.
- getBondArray(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Constructs an array of Bond objects from an AtomContainer.
- getBondArray(List<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Constructs an array of Atom objects from a List of Atom objects.
- getBondCoordinates(IBond) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Writes the coordinates of the atoms participating the given bond into an
array.
- getBondCoordinates(IBond) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Writes the coordinates of the atoms participating the given bond into an array.
- getBondCount() - Method in class org.openscience.cdk.AtomContainer
-
Returns the number of Bonds in this Container.
- getBondCount() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns the number of Bonds in this Container.
- getBondCount() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns the number of Bonds in this Container.
- getBondCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns the number of Bonds in this Container.
- getBondCount() - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns the number of Bonds in this Container.
- getBondCount() - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns the number of Bonds in this Container.
- getBondCount() - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns the number of Bonds in this Container.
- getBondCount() - Method in class org.openscience.cdk.debug.DebugRing
-
Returns the number of Bonds in this Container.
- getBondCount() - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns the number of Bonds in this Container.
- getBondCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the number of Bonds in this Container.
- getBondCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the number of Bonds in this Container.
- getBondCount() - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the number of Bonds in this Container.
- getBondCount(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
-
- getBondCount(IChemFile) - Static method in class org.openscience.cdk.tools.manipulator.ChemFileManipulator
-
Get the total number of bonds inside an IChemFile.
- getBondCount(IChemModel) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
-
Get the total number of bonds inside an IChemModel.
- getBondCount(IChemSequence) - Static method in class org.openscience.cdk.tools.manipulator.ChemSequenceManipulator
-
Get the total number of bonds inside an IChemSequence.
- getBondCount(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
-
- getBondCount(IReaction) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
-
- getBondCount(IReactionSet) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
-
- getBondCount(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator
-
Return the total number of bonds over all the rings in the colllection.
- getBondData(String, String, String) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94ParametersCall
-
Gets the bond parameter set.
- getBondInSensitiveTimeOut() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
get timeout in mins for bond insensitive searches
- getBondInSensitiveTimeOut() - Method in class org.openscience.cdk.smsd.Isomorphism
-
get timeout in mins for bond insensitive searches
- getBondLength() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
-
Returns the bond length used for laying out the molecule.
- getBondLength() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAngleBond
-
Get the angle between the three pharmacophore groups that make up the constraint.
- getBondLength() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreBond
-
Get the distance between the two pharmacophore groups that make up the constraint.
- getBondLengthAverage(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
An average of all 2D bond length values is produced.
- getBondLengthAverage(IReaction) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
- getBondLengthAverage(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
An average of all 2D bond length values is produced.
- getBondLengthAverage(IReaction) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
- getBondLengthAverage3D(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
An average of all 3D bond length values is produced, using point3ds in atoms.
- getBondLengthAverage3D(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
An average of all 3D bond length values is produced, using point3ds in atoms.
- getBondLengthMedian(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Calculate the median bond length of an atom container.
- getBondLengthMedian(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Calculate the median bond length of an atom container.
- getBondLengthRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>, boolean) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Return the RMSD of bonds length between the 2 aligned molecules.
- getBondLengthRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>, boolean) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Return the RMSD of bonds length between the 2 aligned molecules.
- getBondLengthValue(String, String) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
-
Gets the distanceValue attribute of the parameter set.
- getBondMatcher() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.EdgeBuilder
-
Returns bond matcher.
- getBondMatcher() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IEdge
-
Returns bond matcher.
- getBondNumA() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.QueryProcessor
-
- getBondNumB() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.TargetProcessor
-
- getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Returns the position of the bond between two given atoms in the
electronContainers array.
- getBondNumber(IBond) - Method in class org.openscience.cdk.AtomContainer
-
Returns the position of a given bond in the electronContainers array.
- getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns the position of the bond between two given atoms in the
electronContainers array.
- getBondNumber(IBond) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns the position of a given bond in the electronContainers array.
- getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns the position of the bond between two given atoms in the
electronContainers array.
- getBondNumber(IBond) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns the position of a given bond in the electronContainers array.
- getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns the position of the bond between two given atoms in the
electronContainers array.
- getBondNumber(IBond) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns the position of a given bond in the electronContainers array.
- getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns the position of the bond between two given atoms in the
electronContainers array.
- getBondNumber(IBond) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns the position of a given bond in the electronContainers array.
- getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns the position of the bond between two given atoms in the
electronContainers array.
- getBondNumber(IBond) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns the position of a given bond in the electronContainers array.
- getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns the position of the bond between two given atoms in the
electronContainers array.
- getBondNumber(IBond) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns the position of a given bond in the electronContainers array.
- getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
Returns the position of the bond between two given atoms in the
electronContainers array.
- getBondNumber(IBond) - Method in class org.openscience.cdk.debug.DebugRing
-
Returns the position of a given bond in the electronContainers array.
- getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns the position of the bond between two given atoms in the
electronContainers array.
- getBondNumber(IBond) - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns the position of a given bond in the electronContainers array.
- getBondNumber(IAtom, IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
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.
- getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the position of the bond between two given atoms in the
electronContainers array.
- getBondNumber(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the position of a given bond in the electronContainers array.
- getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the position of the bond between two given atoms in the
electronContainers array.
- getBondNumber(IBond) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the position of a given bond in the electronContainers array.
- getBondOrder() - Method in class org.openscience.cdk.smsd.helper.BondEnergy
-
Returns the bond order for this bond type energy.
- getBondOrderSum(IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Deprecated.
Replaced by AtomContainerManipulator#getBondOrderSum(IAtomContainer, IAtom)
- getBondOrderSum() - Method in class org.openscience.cdk.AtomType
-
Gets the bondOrderSum attribute of the AtomType object.
- getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns the sum of the bond orders for a given Atom.
- getBondOrderSum() - Method in class org.openscience.cdk.debug.DebugAtom
-
Gets the bondOrderSum attribute of the AtomType object.
- getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns the sum of the bond orders for a given Atom.
- getBondOrderSum() - Method in class org.openscience.cdk.debug.DebugAtomType
-
Gets the bondOrderSum attribute of the AtomType object.
- getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns the sum of the bond orders for a given Atom.
- getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns the sum of the bond orders for a given Atom.
- getBondOrderSum() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Gets the bondOrderSum attribute of the AtomType object.
- getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns the sum of the bond orders for a given Atom.
- getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns the sum of the bond orders for a given Atom.
- getBondOrderSum() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Gets the bondOrderSum attribute of the AtomType object.
- getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
Returns the sum of the bond orders for a given Atom.
- getBondOrderSum() - Method in class org.openscience.cdk.debug.DebugRing
-
Returns the sum of all bond orders in the ring.
- getBondOrderSum(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns the sum of the bond orders for a given Atom.
- getBondOrderSum(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the sum of the bond orders for a given Atom.
- getBondOrderSum() - Method in interface org.openscience.cdk.interfaces.IAtomType
-
Gets the bondOrderSum attribute of the AtomType object.
- getBondOrderSum() - Method in interface org.openscience.cdk.interfaces.IRing
-
Returns the sum of all bond orders in the ring.
- getBondOrderSum() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Gets the bondOrderSum attribute of the AtomType object.
- getBondOrderSum(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Deprecated.
Replaced by AtomContainerManipulator#getBondOrderSum(IAtomContainer, IAtom)
- getBondOrderSum() - Method in class org.openscience.cdk.Ring
-
Returns the sum of all bond orders in the ring.
- getBondOrderSum(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Deprecated.
Replaced by AtomContainerManipulator#getBondOrderSum(IAtomContainer, IAtom)
- getBondOrderSum() - Method in class org.openscience.cdk.silent.AtomType
-
Gets the bondOrderSum attribute of the AtomType object.
- getBondOrderSum() - Method in class org.openscience.cdk.silent.Ring
-
Returns the sum of all bond orders in the ring.
- getBondOrderSum(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Returns the sum of the bond order equivalents for a given IAtom.
- getBondOverlapScore(IAtomContainer, Vector) - Method in class org.openscience.cdk.layout.OverlapResolver
-
Deprecated.
Calculates a score based on the intersection of bonds.
- getBondPartition(IAtomContainer) - Method in class org.openscience.cdk.group.BondDiscretePartitionRefiner
-
Get the bond partition, based on the element types of the atoms at either end
of the bond, and the bond order.
- getBonds() - Method in interface org.openscience.cdk.interfaces.IDoubleBondStereochemistry
-
Returns an array of ligand bonds around the double bond.
- getBonds() - Method in class org.openscience.cdk.stereo.DoubleBondStereochemistry
-
Returns an array of ligand bonds around the double bond.
- getBondsAcyclicCount() - Method in class org.openscience.cdk.graph.SpanningTree
-
Number of acyclic bonds.
- getBondsCyclicCount() - Method in class org.openscience.cdk.graph.SpanningTree
-
Number of cyclic bonds.
- getBondSensitiveTimeOut() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
get timeout in mins for bond sensitive searches
- getBondSensitiveTimeOut() - Method in class org.openscience.cdk.smsd.Isomorphism
-
get timeout in mins for bond sensitive searches
- getBondSymbol(IBond) - Method in class org.openscience.cdk.fingerprint.Fingerprinter
-
Gets the bondSymbol attribute of the Fingerprinter class
- getBondSymbol(IBond) - Method in class org.openscience.cdk.fingerprint.GraphOnlyFingerprinter
-
Gets the bondSymbol attribute of the Fingerprinter class.
- getBondSymbol(IBond) - Method in class org.openscience.cdk.fingerprint.HybridizationFingerprinter
-
Gets the bond Symbol attribute of the Fingerprinter class.
- getBounds(IRenderingElement) - Method in class org.openscience.cdk.renderer.AbstractRenderer
-
Given a rendering element, traverse the elements compute required bounds
to full display all elements.
- getBuilder() - Method in class org.openscience.cdk.ChemObject
-
- getBuilder() - Method in class org.openscience.cdk.debug.DebugAdductFormula
-
- 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.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.debug.DebugSubstance
-
- getBuilder() - Method in class org.openscience.cdk.formula.AdductFormula
-
- getBuilder() - Method in class org.openscience.cdk.formula.MolecularFormula
-
- getBuilder() - Method in class org.openscience.cdk.formula.MolecularFormulaSet
-
- getBuilder() - Method in interface org.openscience.cdk.interfaces.ICDKObject
-
- getBuilder() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
- getBuilder() - Method in class org.openscience.cdk.silent.AdductFormula
-
- getBuilder() - Method in class org.openscience.cdk.silent.ChemObject
-
- getBuilder() - Method in class org.openscience.cdk.silent.MolecularFormula
-
- getBuilder() - Method in class org.openscience.cdk.silent.MolecularFormulaSet
-
- getBuilder() - Method in class org.openscience.cdk.stereo.DoubleBondStereochemistry
-
- getBuilder() - Method in class org.openscience.cdk.stereo.ExtendedTetrahedral
-
- getBuilder() - Method in class org.openscience.cdk.stereo.TetrahedralChirality
-
- getC() - Method in class org.openscience.cdk.Crystal
-
Gets the C unit cell axes in Cartesian coordinates
as a three element double array.
- getC() - Method in class org.openscience.cdk.debug.DebugCrystal
-
Gets the C unit cell axes in Cartesian coordinates
as a three element double array.
- getC() - Method in interface org.openscience.cdk.interfaces.ICrystal
-
Gets the C unit cell axes in carthesian coordinates
as a three element double array.
- getC() - Method in class org.openscience.cdk.silent.Crystal
-
Gets the C unit cell axes in Cartesian coordinates
as a three element double array.
- getCachedDescriptorValue(IAtom) - Method in class org.openscience.cdk.qsar.AbstractAtomicDescriptor
-
Returns the cached DescriptorValue for the given IAtom.
- getCachedDescriptorValue(IBond) - Method in class org.openscience.cdk.qsar.AbstractBondDescriptor
-
Returns the cached DescriptorValue for the given IBond.
- getCanonicalMolecule(IAtomContainer) - Method in class org.openscience.cdk.smsd.labelling.CanonicalLabellingAdaptor
- getCanonicalMolecule(IAtomContainer) - Method in interface org.openscience.cdk.smsd.labelling.ICanonicalMoleculeLabeller
-
- getCanonicalMolecule(IAtomContainer) - Method in class org.openscience.cdk.smsd.labelling.MoleculeSignatureLabellingAdaptor
- getCanonicalPermutation(IAtomContainer) - Method in class org.openscience.cdk.smsd.labelling.CanonicalLabellingAdaptor
- getCanonicalPermutation(IAtomContainer) - Method in interface org.openscience.cdk.smsd.labelling.ICanonicalMoleculeLabeller
-
- getCanonicalPermutation(IAtomContainer) - Method in class org.openscience.cdk.smsd.labelling.MoleculeSignatureLabellingAdaptor
- getCanonicalReaction(IReaction) - Method in interface org.openscience.cdk.smsd.labelling.ICanonicalReactionLabeller
-
Convert a reaction into a canonical form by canonizing each of the
structures in the reaction in turn.
- getCanonicalReaction(IReaction) - Method in class org.openscience.cdk.smsd.labelling.SignatureReactionCanoniser
-
Convert a reaction into a canonical form by canonizing each of the
structures in the reaction in turn.
- getCanonicalReaction(IReaction) - Method in class org.openscience.cdk.smsd.labelling.SmilesReactionCanoniser
-
Convert a reaction into a canonical form by canonizing each of the
structures in the reaction in turn.
- getCASId(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
-
Get the CAS ID for an element.
- getcBondNeighborsA() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper
-
- getcBondNeighborsB() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper
-
- getCBondSetA() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper
-
- getCBondSetB() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper
-
- getCDKErrorCount() - Method in class org.openscience.cdk.validate.ValidationReport
-
Returns the number of CDK errors.
- getCDKErrors() - Method in class org.openscience.cdk.validate.ValidationReport
-
Returns an array of ValidationTest indicating CDK problems.
- getCEdgesSize() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
- getCEgdes() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
- getCell(int) - Method in class org.openscience.cdk.group.Partition
-
Gets the cell at this index.
- getCenterOfMass() - Method in class org.openscience.cdk.geometry.alignment.KabschAlignment
-
Returns the center of mass for the first molecule or fragment used in the calculation.
- getCentralAtom() - Method in interface org.openscience.cdk.geometry.cip.ILigand
-
The central
IAtom
to which this ligand is connected via one
IBond
.
- getCentralAtom() - Method in class org.openscience.cdk.geometry.cip.Ligand
-
The central
IAtom
to which this ligand is connected via one
IBond
.
- getChainID() - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
get the Chain identifier of this atom.
- getChainID() - Method in class org.openscience.cdk.debug.DebugPDBMonomer
-
Gets the Chain ID of this monomer.
- getChainID() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
get the Chain identifier of this atom.
- getChainID() - Method in interface org.openscience.cdk.interfaces.IPDBMonomer
-
Gets the Chain ID of this monomer.
- getChainID() - Method in class org.openscience.cdk.protein.data.PDBAtom
-
get the Chain identifier of this atom.
- getChainID() - Method in class org.openscience.cdk.protein.data.PDBMonomer
-
- getChainID() - Method in class org.openscience.cdk.silent.PDBAtom
-
get the Chain identifier of this atom.
- getChainID() - Method in class org.openscience.cdk.silent.PDBMonomer
-
- getCharge() - Method in class org.openscience.cdk.Atom
-
Returns the partial charge of this atom.
- getCharge() - Method in class org.openscience.cdk.debug.DebugAdductFormula
-
Returns the partial charge of this Adduct.
- getCharge() - Method in class org.openscience.cdk.debug.DebugAtom
-
Returns the partial charge of this atom.
- getCharge() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Returns the partial charge of this atom.
- getCharge() - Method in class org.openscience.cdk.debug.DebugMolecularFormula
-
Returns the partial charge of this IMolecularFormula.
- getCharge() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Returns the partial charge of this atom.
- getCharge() - Method in class org.openscience.cdk.formula.AdductFormula
-
Returns the partial charge of this Adduct.
- getCharge() - Method in class org.openscience.cdk.formula.IsotopePattern
-
Get the charge in this pattern.
- getCharge() - Method in class org.openscience.cdk.formula.MolecularFormula
-
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.isomorphism.matchers.QueryAtom
-
Returns the partial charge of this atom.
- getCharge() - Method in class org.openscience.cdk.silent.AdductFormula
-
Returns the partial charge of this Adduct.
- getCharge() - Method in class org.openscience.cdk.silent.Atom
-
Returns the partial charge of this atom.
- getCharge() - Method in class org.openscience.cdk.silent.MolecularFormula
-
Returns the partial charge of this IMolecularFormula.
- getChargeGroups() - Method in class org.openscience.cdk.libio.md.MDMolecule
-
- getChemFile() - Method in class org.openscience.cdk.io.inchi.INChIHandler
-
- getChemicalSeries(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
-
Get the chemical series for an element.
- getChemModel(int) - Method in class org.openscience.cdk.ChemSequence
-
Returns the ChemModel at position number
in the
container.
- getChemModel(int) - Method in class org.openscience.cdk.debug.DebugChemSequence
-
Returns the ChemModel at position number
in the
container.
- getChemModel(int) - Method in interface org.openscience.cdk.interfaces.IChemSequence
-
Returns the ChemModel at position number
in the
container.
- getChemModel(int) - Method in class org.openscience.cdk.silent.ChemSequence
-
Returns the ChemModel at position number
in the
container.
- getChemModelCount() - Method in class org.openscience.cdk.ChemSequence
-
Returns the number of ChemModels in this Container.
- getChemModelCount() - Method in class org.openscience.cdk.debug.DebugChemSequence
-
Returns the number of ChemModels in this Container.
- getChemModelCount() - Method in interface org.openscience.cdk.interfaces.IChemSequence
-
Returns the number of ChemModels in this Container.
- getChemModelCount() - Method in class org.openscience.cdk.silent.ChemSequence
-
Returns the number of ChemModels in this Container.
- getChemObject(int) - Method in class org.openscience.cdk.debug.DebugMapping
-
Retrieves the first or second of the related IChemObjects.
- getChemObject(int) - Method in interface org.openscience.cdk.interfaces.IMapping
-
Retrieve the first or second of the related IChemObjects.
- getChemObject(int) - Method in class org.openscience.cdk.Mapping
-
Retrieves the first or second of the related IChemObjects.
- getChemObject(int) - Method in class org.openscience.cdk.silent.Mapping
-
Retrieves the first or second of the related IChemObjects.
- getChemObject() - Method in class org.openscience.cdk.validate.ValidationTest
-
- getChemObjectReader() - Method in class org.openscience.cdk.io.random.RandomAccessReader
-
- getChemSequence(int) - Method in class org.openscience.cdk.ChemFile
-
Returns the ChemSequence at position number
in the container.
- getChemSequence(int) - Method in class org.openscience.cdk.debug.DebugChemFile
-
Returns the ChemSequence at position number
in the container.
- getChemSequence(int) - Method in interface org.openscience.cdk.interfaces.IChemFile
-
Returns the ChemSequence at position number
in the container.
- getChemSequence(int) - Method in class org.openscience.cdk.silent.ChemFile
-
Returns the ChemSequence at position number
in the container.
- getChemSequenceCount() - Method in class org.openscience.cdk.ChemFile
-
Returns the number of ChemSequences in this Container.
- getChemSequenceCount() - Method in class org.openscience.cdk.debug.DebugChemFile
-
Returns the number of ChemSequences in this Container.
- getChemSequenceCount() - Method in interface org.openscience.cdk.interfaces.IChemFile
-
Returns the number of ChemSequences in this Container.
- getChemSequenceCount() - Method in class org.openscience.cdk.silent.ChemFile
-
Returns the number of ChemSequences in this Container.
- getChiCatHydrogen() - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
-
Gets chi_cat value for hydrogen, because H poses a special problem due to lack of possible second ionisation.
- getChildren() - Method in class org.openscience.cdk.tools.diff.tree.AbstractDifferenceList
-
- getChildren() - Method in interface org.openscience.cdk.tools.diff.tree.IDifferenceList
-
- getChiralAtom() - Method in interface org.openscience.cdk.interfaces.ITetrahedralChirality
-
Atom that is the chirality center.
- getChiralAtom() - Method in class org.openscience.cdk.stereo.TetrahedralChirality
-
Atom that is the chirality center.
- getCID(XmlPullParser) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
-
- getCIPChirality(LigancyFourChirality) - Static method in class org.openscience.cdk.geometry.cip.CIPTool
-
Returns the R or S chirality according to the CIP rules, based on the given
chirality information.
- getCIPChirality(IAtomContainer, ITetrahedralChirality) - Static method in class org.openscience.cdk.geometry.cip.CIPTool
-
Returns the R or S chirality according to the CIP rules, based on the given
chirality information.
- getCIPChirality(IAtomContainer, IDoubleBondStereochemistry) - Static method in class org.openscience.cdk.geometry.cip.CIPTool
-
- getClassName() - Method in class org.openscience.cdk.dict.Entry
-
- getClipboardContent() - Method in class org.openscience.cdk.renderer.RendererModel
-
Returns the atoms and bonds on the Renderer2D clipboard.
- getClosestAtom(int, int, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Returns the atom of the given molecule that is closest to the given
coordinates.
- getClosestAtom(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Returns the atom of the given molecule that is closest to the given atom
(excluding itself).
- getClosestAtom(double, double, IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Returns the atom of the given molecule that is closest to the given
coordinates and is not the atom.
- getClosestAtom(double, double, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Returns the atom of the given molecule that is closest to the given
coordinates.
- getClosestAtom(int, int, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Returns the atom of the given molecule that is closest to the given coordinates.
- getClosestAtom(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Returns the atom of the given molecule that is closest to the given atom (excluding itself).
- getClosestAtom(double, double, IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Returns the atom of the given molecule that is closest to the given coordinates and is not
the atom.
- getClosestAtom(double, double, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Returns the atom of the given molecule that is closest to the given coordinates.
- getClosestBond(int, int, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Returns the bond of the given molecule that is closest to the given
coordinates.
- getClosestBond(double, double, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Returns the bond of the given molecule that is closest to the given
coordinates.
- getClosestBond(int, int, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Returns the bond of the given molecule that is closest to the given coordinates.
- getClosestBond(double, double, IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Returns the bond of the given molecule that is closest to the given coordinates.
- getCoefficients() - Method in class org.openscience.cdk.math.qm.Orbitals
-
Get the coefficient matrix
- getColorForBond(IBond, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
-
Determine the color of a bond, returning either the default color,
the override color or whatever is in the color hash for that bond.
- getColumn(int) - Method in class org.openscience.cdk.graph.invariant.GIMatrix
-
Returns the column-matrix at the given line index.
- getColumn() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Deprecated.
- getColumn() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Deprecated.
- getColumns() - Method in class org.openscience.cdk.math.IMatrix
-
Returns the count of columns
- getColumns() - Method in class org.openscience.cdk.math.Matrix
-
Returns the number of columns.
- getCompGraphNodes() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
- getCompGraphNodesCZero() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
- getConfidenceLimit(String) - Method in class org.openscience.cdk.tools.BremserOneSphereHOSECodePredictor
-
- getConnected(int) - Method in class org.openscience.cdk.signature.AtomSignature
-
- getConnectedAtom(IAtom) - Method in class org.openscience.cdk.Bond
-
Returns the atom connected to the given atom.
- getConnectedAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugBond
-
Returns the atom connected to the given atom.
- getConnectedAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.IBond
-
Returns the atom connected to the given atom.
- getConnectedAtom(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Returns the atom connected to the given atom.
- getConnectedAtom(IAtom) - Method in class org.openscience.cdk.silent.Bond
-
Returns the atom connected to the given atom.
- getConnectedAtomContainer() - Method in interface org.openscience.cdk.renderer.selection.IChemObjectSelection
-
Make an IAtomContainer where all the bonds
only have atoms that are in the selection.
- getConnectedAtoms(IAtom) - Method in class org.openscience.cdk.Bond
-
Returns all the atoms in the bond connected to the specified atom.
- getConnectedAtoms(IAtom) - Method in interface org.openscience.cdk.interfaces.IBond
-
Returns all the atoms in the bond connected to the given atom.
- getConnectedAtoms(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Returns all the atoms in the query bond connected to the specified atom.
- getConnectedAtoms(IAtom) - Method in class org.openscience.cdk.silent.Bond
-
Returns all the atoms in the bond connected to the specified atom.
- getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Returns the number of atoms connected to the given atom.
- getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns the number of atoms connected to the given atom.
- getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns the number of atoms connected to the given atom.
- getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns the number of atoms connected to the given atom.
- getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns the number of atoms connected to the given atom.
- getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns the number of atoms connected to the given atom.
- getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns the number of atoms connected to the given atom.
- getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
Returns the number of atoms connected to the given atom.
- getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns the number of atoms connected to the given atom.
- getConnectedAtomsCount(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the number of atoms connected to the given atom.
- getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the number of atoms connected to the given atom.
- getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the number of atoms connected to the given atom.
- getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Returns an ArrayList of all atoms connected to the given atom.
- getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns an ArrayList of all atoms connected to the given atom.
- getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns an ArrayList of all atoms connected to the given atom.
- getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns an ArrayList of all atoms connected to the given atom.
- getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns an ArrayList of all atoms connected to the given atom.
- getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns an ArrayList of all atoms connected to the given atom.
- getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns an ArrayList of all atoms connected to the given atom.
- getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
Returns an ArrayList of all atoms connected to the given atom.
- getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns an ArrayList of all atoms connected to the given atom.
- getConnectedAtomsList(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns an ArrayList of all atoms connected to the given atom.
- getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns an ArrayList of all atoms connected to the given atom.
- getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns an ArrayList of all atoms connected to the given atom.
- getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Returns the number of Bonds for a given Atom.
- getConnectedBondsCount(int) - Method in class org.openscience.cdk.AtomContainer
-
Returns the number of connected atoms (degree) to the given atom.
- getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns the number of Bonds for a given Atom.
- getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns the number of Bonds for a given Atom.
- getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns the number of Bonds for a given Atom.
- getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns the number of Bonds for a given Atom.
- getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns the number of Bonds for a given Atom.
- getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns the number of Bonds for a given Atom.
- getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
Returns the number of Bonds for a given Atom.
- getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns the number of Bonds for a given Atom.
- getConnectedBondsCount(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the number of Bonds for a given Atom.
- getConnectedBondsCount(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the number of connected atoms (degree) to the given atom.
- getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the number of Bonds for a given Atom.
- getConnectedBondsCount(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the number of connected atoms (degree) to the given atom.
- getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the number of Bonds for a given Atom.
- getConnectedBondsCount(int) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the number of connected atoms (degree) to the given atom.
- getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Returns an ArrayList of all Bonds connected to the given atom.
- getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns an ArrayList of all Bonds connected to the given atom.
- getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns an ArrayList of all Bonds connected to the given atom.
- getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns an ArrayList of all Bonds connected to the given atom.
- getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns an ArrayList of all Bonds connected to the given atom.
- getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns an ArrayList of all Bonds connected to the given atom.
- getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns an ArrayList of all Bonds connected to the given atom.
- getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
Returns an ArrayList of all Bonds connected to the given atom.
- getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns an ArrayList of all Bonds connected to the given atom.
- getConnectedBondsList(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns an ArrayList of all Bonds connected to the given atom.
- getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns an ArrayList of all Bonds connected to the given atom.
- getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns an ArrayList of all Bonds connected to the given atom.
- getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Returns an ArrayList of all electronContainers connected to the given atom.
- getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns an ArrayList of all electronContainers connected to the given atom.
- getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns an ArrayList of all electronContainers connected to the given atom.
- getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns an ArrayList of all electronContainers connected to the given atom.
- getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns an ArrayList of all electronContainers connected to the given atom.
- getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns an ArrayList of all electronContainers connected to the given atom.
- getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns an ArrayList of all electronContainers connected to the given atom.
- getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
Returns an ArrayList of all electronContainers connected to the given atom.
- getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns an ArrayList of all electronContainers connected to the given atom.
- getConnectedElectronContainersList(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns an ArrayList of all electronContainers connected to the given atom.
- getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns an ArrayList of all electronContainers connected to the given atom.
- getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns an ArrayList of all electronContainers connected to the given atom.
- getConnectedIndices(int) - Method in class org.openscience.cdk.group.AtomDiscretePartitionRefiner
-
Used by the equitable refiner to get the indices of atoms connected to
the atom at atomIndex
.
- getConnectedIndices(int) - Method in class org.openscience.cdk.group.BondDiscretePartitionRefiner
-
Used by the equitable refiner to get the indices of bonds connected to
the bond at bondIndex
.
- getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Returns the number of LonePairs for a given Atom.
- getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns the number of LonePairs for a given Atom.
- getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns the number of LonePairs for a given Atom.
- getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns the number of LonePairs for a given Atom.
- getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns the number of LonePairs for a given Atom.
- getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns the number of LonePairs for a given Atom.
- getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns the number of LonePairs for a given Atom.
- getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
Returns the number of LonePairs for a given Atom.
- getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns the number of LonePairs for a given Atom.
- getConnectedLonePairsCount(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the number of LonePairs for a given Atom.
- getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the number of LonePairs for a given Atom.
- getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the number of LonePairs for a given Atom.
- getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Returns the array of lone pairs connected to an atom.
- getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns the array of lone pairs connected to an atom.
- getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns the array of lone pairs connected to an atom.
- getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns the array of lone pairs connected to an atom.
- getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns the array of lone pairs connected to an atom.
- getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns the array of lone pairs connected to an atom.
- getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns the array of lone pairs connected to an atom.
- getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
Returns the array of lone pairs connected to an atom.
- getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns the array of lone pairs connected to an atom.
- getConnectedLonePairsList(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the array of lone pairs connected to an atom.
- getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the array of lone pairs connected to an atom.
- getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the array of lone pairs connected to an atom.
- getConnectedRings(IRing) - Method in class org.openscience.cdk.debug.DebugRingSet
-
Returns all the rings in the RingSet that share
one or more atoms with a given ring.
- getConnectedRings(IRing) - Method in interface org.openscience.cdk.interfaces.IRingSet
-
Returns all the rings in the RingSet that share
one or more atoms with a given ring.
- getConnectedRings(IRing) - Method in class org.openscience.cdk.RingSet
-
Returns all the rings in the RingSet that share
one or more atoms with a given ring.
- getConnectedRings(IRing) - Method in class org.openscience.cdk.silent.RingSet
-
Returns all the rings in the RingSet that share
one or more atoms with a given ring.
- getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Returns the sum of the SingleElectron for a given Atom.
- getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns the sum of the SingleElectron for a given Atom.
- getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns the sum of the SingleElectron for a given Atom.
- getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns the sum of the SingleElectron for a given Atom.
- getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns the sum of the SingleElectron for a given Atom.
- getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns the sum of the SingleElectron for a given Atom.
- getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns the sum of the SingleElectron for a given Atom.
- getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
Returns the sum of the SingleElectron for a given Atom.
- getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns the sum of the SingleElectron for a given Atom.
- getConnectedSingleElectronsCount(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the sum of the SingleElectron for a given Atom.
- getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the sum of the SingleElectron for a given Atom.
- getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the sum of the SingleElectron for a given Atom.
- getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Returns an array of all SingleElectron connected to the given atom.
- getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns an array of all SingleElectron connected to the given atom.
- getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns an array of all SingleElectron connected to the given atom.
- getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns an array of all SingleElectron connected to the given atom.
- getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns an array of all SingleElectron connected to the given atom.
- getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns an array of all SingleElectron connected to the given atom.
- getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns an array of all SingleElectron connected to the given atom.
- getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
Returns an array of all SingleElectron connected to the given atom.
- getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns an array of all SingleElectron connected to the given atom.
- getConnectedSingleElectronsList(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns an array of all SingleElectron connected to the given atom.
- getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns an array of all SingleElectron connected to the given atom.
- getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns an array of all SingleElectron connected to the given atom.
- getConnectivity(int, int) - Method in class org.openscience.cdk.group.AbstractDiscretePartitionRefiner
-
Get the connectivity between two vertices as an integer, to allow
for multigraphs : so a single edge is 1, a double edge 2, etc.
- getConnectivity(int, int) - Method in class org.openscience.cdk.group.AtomDiscretePartitionRefiner
-
- getConnectivity(int, int) - Method in class org.openscience.cdk.group.BondDiscretePartitionRefiner
-
- getContainer(IAtomContainer, IAtom) - Method in class org.openscience.cdk.tools.StructureResonanceGenerator
-
Get the container which the atom is found on resonance from a
IAtomContainer
.
- getContainer(IAtomContainer, IBond) - Method in class org.openscience.cdk.tools.StructureResonanceGenerator
-
Get the container which the bond is found on resonance from a
IAtomContainer
.
- getContainers(IAtomContainer) - Method in class org.openscience.cdk.tools.StructureResonanceGenerator
-
- getCoordinatesFromGridPoint(Point3d) - Method in class org.openscience.cdk.tools.GridGenerator
-
Method calculates coordinates from a given grid point.
- getCoordinatesFromGridPoint(int) - Method in class org.openscience.cdk.tools.GridGenerator
-
Method calculates coordinates from a given grid array position.
- getCount(int) - Method in interface org.openscience.cdk.fingerprint.ICountFingerprint
-
Returns the count value for the bin with the given index.
- getCount(int) - Method in class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
-
- getCount() - Method in class org.openscience.cdk.validate.ValidationReport
-
Returns the number of CDK errors.
- getCountBasis() - Method in class org.openscience.cdk.math.qm.Orbitals
-
Set the count of bases
- getCountElectrons() - Method in class org.openscience.cdk.math.qm.Orbitals
-
Gets the count of electrons, which occupies the orbitals
- getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter
-
Calculates the circular fingerprint for the given
IAtomContainer
, and returns a datastructure that enumerates all
of the fingerprints, and their counts (i.e.
- getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.EStateFingerprinter
-
- getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter
-
- getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.Fingerprinter
-
- getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.HybridizationFingerprinter
-
- getCountFingerprint(IAtomContainer) - Method in interface org.openscience.cdk.fingerprint.IFingerprinter
-
- getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.LingoFingerprinter
-
- getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.MACCSFingerprinter
-
- getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.PubchemFingerprinter
-
- getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.ShortestPathFingerprinter
-
- getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.SignatureFingerprinter
-
- getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.SubstructureFingerprinter
-
- getCountForHash(int) - Method in interface org.openscience.cdk.fingerprint.ICountFingerprint
-
Get the number of times a certain hash exists in the fingerprint.
- getCountForHash(int) - Method in class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
-
- getCountOrbitals() - Method in class org.openscience.cdk.math.qm.Orbitals
-
Returns the count of orbitals
- getCovalentRadius() - Method in class org.openscience.cdk.AtomType
-
Returns the covalent radius for this AtomType.
- getCovalentRadius() - Method in class org.openscience.cdk.debug.DebugAtom
-
Returns the covalent radius for this AtomType.
- getCovalentRadius() - Method in class org.openscience.cdk.debug.DebugAtomType
-
Returns the covalent radius for this AtomType.
- getCovalentRadius() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Returns the covalent radius for this AtomType.
- getCovalentRadius() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Returns the covalent radius for this AtomType.
- getCovalentRadius() - Method in interface org.openscience.cdk.interfaces.IAtomType
-
Returns the covalent radius for this AtomType.
- getCovalentRadius() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Returns the covalent radius for this AtomType.
- getCovalentRadius() - Method in class org.openscience.cdk.silent.AtomType
-
Returns the covalent radius for this AtomType.
- getCovalentRadius(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
-
Get the covalent radius for an element.
- getCreatormap() - Method in class org.openscience.cdk.io.RssWriter
-
- getCrystal() - Method in class org.openscience.cdk.ChemModel
-
Gets the Crystal contained in this ChemModel.
- getCrystal() - Method in class org.openscience.cdk.debug.DebugChemModel
-
Gets the Crystal contained in this ChemModel.
- getCrystal() - Method in interface org.openscience.cdk.interfaces.IChemModel
-
Gets the Crystal contained in this ChemModel.
- getCrystal() - Method in class org.openscience.cdk.silent.ChemModel
-
Gets the Crystal contained in this ChemModel.
- getCTab1() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.QueryProcessor
-
- getCTab1() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.TargetProcessor
-
- getCTab2() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.QueryProcessor
-
- getCTab2() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.TargetProcessor
-
- getCTerminus() - Method in class org.openscience.cdk.AminoAcid
-
Retrieves the C-terminus atom.
- getCTerminus() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Retrieves the C-terminus atom.
- getCTerminus() - Method in interface org.openscience.cdk.interfaces.IAminoAcid
-
Retrieves the C-terminus atom.
- getCTerminus() - Method in class org.openscience.cdk.silent.AminoAcid
-
Retrieves the C-terminus atom.
- getCurr() - Method in class org.openscience.cdk.smiles.InvPair
-
Get the current seed.
- getCurrentMaxBondOrder(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker
-
Returns the currently maximum formable bond order for this atom.
- getCurrentPermutation() - Method in class org.openscience.cdk.graph.Permutor
-
Get the permutation that is currently being used.
- getCurrentPermutation() - Method in class org.openscience.cdk.smsd.labelling.Permutor
-
Get the permutation that is currently being used.
- getCurrentRecord() - Method in class org.openscience.cdk.io.random.RandomAccessReader
-
- getCyclicFragmentsContainer() - Method in class org.openscience.cdk.graph.SpanningTree
-
Returns an IAtomContainer which contains all the atoms and bonds which
are involved in ring systems.
- getDatemap() - Method in class org.openscience.cdk.io.RssWriter
-
- getDBE(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Returns the number of double bond equivalents in this molecule.
- getDeclaringClass() - Method in class org.openscience.cdk.DynamicFactory.BasicCreator
-
- getDeclaringClass() - Method in interface org.openscience.cdk.DynamicFactory.Creator
-
Access the implementation of this class.
- getDEdgesSize() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
- getDefault() - Method in class org.openscience.cdk.renderer.generators.AtomNumberGenerator.AtomColorer
-
Gets the default value for this parameter.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.AtomNumberGenerator.AtomNumberTextColor
-
Gets the default value for this parameter.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.AtomNumberGenerator.ColorByType
-
Gets the default value for this parameter.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.AtomNumberGenerator.Offset
-
Gets the default value for this parameter.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.AtomNumberGenerator.WillDrawAtomNumbers
-
Gets the default value for this parameter.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.AtomColor
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.AtomColorer
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.AtomRadius
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.ColorByType
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.CompactAtom
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.CompactShape
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.KekuleStructure
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.ShowEndCarbons
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator.ShowExplicitHydrogens
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator.BondDistance
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator.BondWidth
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator.DefaultBondColor
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator.TowardsRingCenterProportion
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator.WedgeWidth
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ArrowHeadWidth
-
Returns the default arrow head width.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.BackgroundColor
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.BondLength
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.FitToScreen
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.FontName
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ForegroundColor
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.Margin
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.Scale
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ShowMoleculeTitle
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ShowTooltip
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.UseAntiAliasing
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.UsedFontStyle
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator.ZoomFactor
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.BoundsGenerator.BoundsColor
-
Gets the default value for this parameter.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.ExtendedAtomGenerator.ShowAtomTypeNames
-
Gets the default value for this parameter.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.ExtendedAtomGenerator.ShowImplicitHydrogens
-
Gets the default value for this parameter.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.HighlightGenerator.HighlightPalette
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.HighlightGenerator.HighlightRadius
-
Returns the default value.
- getDefault() - Method in interface org.openscience.cdk.renderer.generators.IGeneratorParameter
-
Gets the default value for this parameter.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.MappingGenerator.AtomAtomMappingLineColor
-
Gets the default value for this parameter.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.MappingGenerator.MappingLineWidth
-
Gets the default value for this parameter.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.MappingGenerator.ShowAtomAtomMapping
-
Gets the default value for this parameter.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.ReactionSceneGenerator.ArrowHeadWidth
-
Gets the default value for this parameter.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.ReactionSceneGenerator.ShowReactionBoxes
-
Gets the default value for this parameter.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.RingGenerator.CDKStyleAromaticity
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.RingGenerator.MaxDrawableAromaticRing
-
The maximum default ring size for which an aromatic ring should be drawn.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.RingGenerator.RingProportion
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.RingGenerator.ShowAromaticity
-
Returns the default value.
- getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.AnnotationColor
-
- getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.AnnotationDistance
-
- getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.AnnotationFontScale
-
- getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.AtomColor
-
- getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.BondSeparation
-
- getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.DashSection
-
- getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.FancyBoldWedges
-
- getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.FancyHashedWedges
-
- getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.HashSpacing
-
- getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.Highlighting
-
- getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.OuterGlowWidth
-
- getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.StrokeRatio
-
- getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.SymbolMarginRatio
-
- getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.Visibility
-
- getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.WaveSpacing
-
- getDefault() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator.WedgeRatio
-
- getDefault() - Method in class org.openscience.cdk.renderer.RendererModel.ColorHash
-
Gets the default value for this parameter.
- getDefault() - Method in class org.openscience.cdk.renderer.RendererModel.ExternalHighlightColor
-
Gets the default value for this parameter.
- getDefault(Class<T>) - Method in class org.openscience.cdk.renderer.RendererModel
-
- getDefault() - Method in class org.openscience.cdk.renderer.RendererModel.SelectionColor
-
Gets the default value for this parameter.
- getDefaultSetting() - Method in class org.openscience.cdk.io.setting.IOSetting
-
- getDefaultStretchBendData(int, int, int) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94ParametersCall
-
Gets the bond-angle interaction parameter set.
- getDefinition() - Method in class org.openscience.cdk.dict.Entry
-
- getDEgdes() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
- getDegree() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom
-
- getDescription() - Method in class org.openscience.cdk.dict.Entry
-
- getDescriptorClassNameByInterface(String, String[]) - Static method in class org.openscience.cdk.qsar.DescriptorEngine
-
Returns a list containing the classes that implement a specific interface.
- getDescriptorClassNameByPackage(String, String[]) - Static method in class org.openscience.cdk.qsar.DescriptorEngine
-
Returns a list containing the classes found in the specified descriptor package.
- getDescriptorClassNames() - Method in class org.openscience.cdk.qsar.DescriptorEngine
-
Returns a list containing the names of the classes implementing the descriptors.
- getDescriptorInstances() - Method in class org.openscience.cdk.qsar.DescriptorEngine
-
Returns a List containing the instantiated descriptor classes.
- getDescriptorMetadata() - Method in class org.openscience.cdk.dict.Entry
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor
-
- 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.AcidicGroupCountDescriptor
-
Returns an array of names for each descriptor value calculated.
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor
-
Returns an array of names for each descriptor value calculated.
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor
-
Returns an array of names for each descriptor value calculated.
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor
-
Returns the names of the descriptors made available by this class.
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor
-
- getDescriptorNames() - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor
-
- getDescriptorNames() - Method in interface org.openscience.cdk.qsar.IDescriptor
-
Returns an array of names for each descriptor value calculated.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
-
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
-
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
-
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor
-
Returns the specific type of the FMF descriptor value.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor
-
Returns a type of return value calculated by this descriptor.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor
-
Returns a placeholder with the descriptor size and type.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorResultType() - Method in interface org.openscience.cdk.qsar.IMolecularDescriptor
-
Returns the specific type of the DescriptorResult object.
- getDescriptorSpecifications() - Method in class org.openscience.cdk.qsar.DescriptorEngine
-
Returns the DescriptorSpecification objects for all available descriptors.
- getDetails() - Method in class org.openscience.cdk.validate.ValidationTest
-
- getDictionary(String) - Method in class org.openscience.cdk.dict.DictionaryDatabase
-
- getDictionary() - Method in class org.openscience.cdk.dict.DictionaryHandler
-
- getDictionaryClass(String) - Method in class org.openscience.cdk.qsar.DescriptorEngine
-
Returns the class(es) of the decsriptor as defined in the descriptor dictionary.
- getDictionaryClass(IImplementationSpecification) - Method in class org.openscience.cdk.qsar.DescriptorEngine
-
Returns the class(es) of the descriptor as defined in the descriptor dictionary.
- getDictionaryDefinition(String) - Method in class org.openscience.cdk.qsar.DescriptorEngine
-
Gets the definition of the descriptor.
- getDictionaryDefinition(DescriptorSpecification) - Method in class org.openscience.cdk.qsar.DescriptorEngine
-
Gets the definition of the descriptor.
- getDictionaryEntries(String) - Method in class org.openscience.cdk.dict.DictionaryDatabase
-
Returns a String[] with the id's of all entries in the specified database.
- getDictionaryEntry(String) - Method in class org.openscience.cdk.dict.DictionaryDatabase
-
- getDictionaryNames() - Method in class org.openscience.cdk.dict.DictionaryDatabase
-
Returns a String[] with the names of the known dictionaries.
- getDictionaryTitle(String) - Method in class org.openscience.cdk.qsar.DescriptorEngine
-
Gets the label (title) of the descriptor.
- getDictionaryTitle(DescriptorSpecification) - Method in class org.openscience.cdk.qsar.DescriptorEngine
-
Gets the label (title) of the descriptor.
- getDictionaryType(String) - Method in class org.openscience.cdk.qsar.DescriptorEngine
-
Returns the type of the descriptor as defined in the descriptor dictionary.
- getDictionaryType(IImplementationSpecification) - Method in class org.openscience.cdk.qsar.DescriptorEngine
-
Returns the type of the descriptor as defined in the descriptor dictionary.
- getDim() - Method in class org.openscience.cdk.tools.GridGenerator
-
- getDimValue(int) - Method in interface org.openscience.cdk.graph.rebond.Bspt.Tuple
-
- getDimValue(int) - Method in class org.openscience.cdk.graph.rebond.Point
-
- getDirection() - Method in class org.openscience.cdk.debug.DebugReaction
-
Returns the direction of the reaction.
- getDirection() - Method in interface org.openscience.cdk.interfaces.IReaction
-
- getDirection() - Method in class org.openscience.cdk.Reaction
-
Returns the direction of the reaction.
- getDirection() - Method in class org.openscience.cdk.silent.Reaction
-
Returns the direction of the reaction.
- getDisplayMode() - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Get the display mode
- getDrawCenter() - Method in class org.openscience.cdk.renderer.AbstractRenderer
-
Get the position on screen that the diagram will be drawn.
- getDuration(long, long) - Static method in class org.openscience.cdk.tools.SwissArmyKnife
-
Deprecated.
Returns a string reporting the time passed between startTime and endTime,
both given in milliseconds, in hours, minutes, seconds and milliseconds.
- getDuration(long) - Static method in class org.openscience.cdk.tools.SwissArmyKnife
-
Deprecated.
Returns a String reporting the time passed during a given number of milliseconds.
- getEAIDNumber(AtomContainer) - Static method in class org.openscience.cdk.graph.invariant.HuLuIndexTool
-
Calculates the extended adjacency matrix index.
- getEdge(int) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder
-
Returns an edge of the query mol at a given position.
- getEdge(INode, INode) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder
-
Returns an edge associated between two nodes.
- getEdge(int) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQuery
-
Returns an edge of the query mol at a given position.
- getEdge(INode, INode) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQuery
-
Returns an edge associated between two nodes.
- getEdgeLabel(int, int) - Method in class org.openscience.cdk.signature.AtomSignature
-
- getEdges() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.NodeBuilder
-
Returns List of Edges.
- getEdges() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.INode
-
Returns List of Edges.
- getElapsedTimeInHours() - Method in class org.openscience.cdk.smsd.tools.TimeManager
-
Returns Elapsed Time In Hours
- getElapsedTimeInMilliSeconds() - Method in class org.openscience.cdk.smsd.tools.TimeManager
-
Returns Elapsed Time In Mill Seconds
- getElapsedTimeInMinutes() - Method in class org.openscience.cdk.smsd.tools.TimeManager
-
Returns Elapsed Time In Minutes
- getElapsedTimeInSeconds() - Method in class org.openscience.cdk.smsd.tools.TimeManager
-
Return Elapsed Time In Seconds
- getElectronContainer(int) - Method in class org.openscience.cdk.AtomContainer
-
Returns the ElectronContainer at position number
in the
container.
- getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns the ElectronContainer at position number
in the
container.
- getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns the ElectronContainer at position number
in the
container.
- getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns the ElectronContainer at position number
in the
container.
- getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns the ElectronContainer at position number
in the
container.
- getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns the ElectronContainer at position number
in the
container.
- getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns the ElectronContainer at position number
in the
container.
- getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugRing
-
Returns the ElectronContainer at position number
in the
container.
- getElectronContainer(int) - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns the ElectronContainer at position number
in the
container.
- getElectronContainer(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the ElectronContainer at position number
in the
container.
- getElectronContainer(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the ElectronContainer at position number
in the
container.
- getElectronContainer(int) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the ElectronContainer at position number
in the
container.
- getElectronContainerArray(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Constructs an array of Bond objects from an AtomContainer.
- getElectronContainerArray(List<IElectronContainer>) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Constructs an array of Atom objects from a List of Atom objects.
- getElectronContainerCount() - Method in class org.openscience.cdk.AtomContainer
-
Returns the number of ElectronContainers in this Container.
- getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns the number of ElectronContainers in this Container.
- getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns the number of ElectronContainers in this Container.
- getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns the number of ElectronContainers in this Container.
- getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns the number of ElectronContainers in this Container.
- getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns the number of ElectronContainers in this Container.
- getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns the number of ElectronContainers in this Container.
- getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugRing
-
Returns the number of ElectronContainers in this Container.
- getElectronContainerCount() - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns the number of ElectronContainers in this Container.
- getElectronContainerCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the number of ElectronContainers in this Container.
- getElectronContainerCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the number of ElectronContainers in this Container.
- getElectronContainerCount() - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the number of ElectronContainers in this Container.
- getElectronCount() - Method in class org.openscience.cdk.Association
-
Returns the number of electrons in a Association.
- getElectronCount() - Method in class org.openscience.cdk.debug.DebugBond
-
Returns the number of electrons in this electron container.
- getElectronCount() - Method in class org.openscience.cdk.debug.DebugElectronContainer
-
Returns the number of electrons in this electron container.
- getElectronCount() - Method in class org.openscience.cdk.debug.DebugLonePair
-
Returns the number of electrons in a LonePair.
- getElectronCount() - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
Returns the number of electrons in this SingleElectron.
- getElectronCount() - Method in class org.openscience.cdk.ElectronContainer
-
Returns the number of electrons in this electron container.
- getElectronCount() - Method in interface org.openscience.cdk.interfaces.IElectronContainer
-
Returns the number of electrons in this electron container.
- getElectronCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Returns the number of electrons in this bond
- getElectronCount() - Method in class org.openscience.cdk.LonePair
-
Returns the number of electrons in a LonePair.
- getElectronCount() - Method in class org.openscience.cdk.silent.ElectronContainer
-
Returns the number of electrons in this electron container.
- getElectronCount() - Method in class org.openscience.cdk.silent.LonePair
-
Returns the number of electrons in a LonePair.
- getElectronCount() - Method in class org.openscience.cdk.silent.SingleElectron
-
Returns the number of electrons in this SingleElectron.
- getElectronCount() - Method in class org.openscience.cdk.SingleElectron
-
Returns the number of electrons in this SingleElectron.
- getElectronegativity(String) - Method in class org.openscience.cdk.tools.AtomicProperties
-
- getElement(String) - Method in class org.openscience.cdk.config.IsotopeFactory
-
Returns an Element with a given element symbol.
- getElement(int) - Method in class org.openscience.cdk.config.IsotopeFactory
-
Returns an element according to a given atomic number.
- getElementCount(IMolecularFormula, IElement) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Checks a set of Nodes for the occurrence of the isotopes in the
molecular formula from a particular IElement.
- getElementCount(IMolecularFormula, IIsotope) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Occurrences of a given element from an isotope in a molecular formula.
- getElementCount(IMolecularFormula, String) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Occurrences of a given element in a molecular formula.
- getElementCount() - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
-
Return the number of elements currently considered in the periodic
table.
- getElementPartition(IAtomContainer) - Method in class org.openscience.cdk.group.AtomDiscretePartitionRefiner
-
Get the element partition from an atom container, which is simply a list
of sets of atom indices where all atoms in one set have the same element
symbol.
- 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
-
get the ending Chain identifier of this structure.
- getEndChainID() - Method in interface org.openscience.cdk.interfaces.IPDBStructure
-
get the ending Chain identifier of this structure.
- getEndChainID() - Method in class org.openscience.cdk.protein.data.PDBStructure
-
get the ending Chain identifier of this structure.
- getEndChainID() - Method in class org.openscience.cdk.silent.PDBStructure
-
get the ending Chain identifier of this structure.
- getEndColumn() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Get token end column number.
- getEndColumn() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Get token end column number.
- getEndInsertionCode() - Method in class org.openscience.cdk.debug.DebugPDBStructure
-
get the ending Code for insertion of residues of this structure.
- getEndInsertionCode() - Method in interface org.openscience.cdk.interfaces.IPDBStructure
-
get the ending Code for insertion of residues of this structure.
- getEndInsertionCode() - Method in class org.openscience.cdk.protein.data.PDBStructure
-
get the ending Code for insertion of residues of this structure.
- getEndInsertionCode() - Method in class org.openscience.cdk.silent.PDBStructure
-
get the ending Code for insertion of residues of this structure.
- getEndLine() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Get token end line number.
- getEndLine() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Get token end line number.
- getEndSequenceNumber() - Method in class org.openscience.cdk.debug.DebugPDBStructure
-
get the ending sequence number of this structure.
- getEndSequenceNumber() - Method in interface org.openscience.cdk.interfaces.IPDBStructure
-
get the ending sequence number of this structure.
- getEndSequenceNumber() - Method in class org.openscience.cdk.protein.data.PDBStructure
-
get the ending sequence number of this structure.
- getEndSequenceNumber() - Method in class org.openscience.cdk.silent.PDBStructure
-
get the ending sequence number of this structure.
- getEnergies() - Method in class org.openscience.cdk.math.qm.ClosedShellJob
-
- getEnergies() - Method in class org.openscience.cdk.math.qm.OneElectronJob
-
Returns the energies of the orbitals
- getEnergies(IAtom, IAtom, IBond.Order) - Method in class org.openscience.cdk.smsd.tools.BondEnergies
-
Returns bond energy for a bond type, given atoms and bond type
- getEnergies(String, String, IBond.Order) - Method in class org.openscience.cdk.smsd.tools.BondEnergies
-
Returns bond energy for a bond type, given atoms and bond type
- getEnergies(IBond) - Method in class org.openscience.cdk.smsd.tools.BondEnergies
-
Returns bond energy for a bond type, given atoms and bond type
- getEnergy() - Method in class org.openscience.cdk.smsd.helper.BondEnergy
-
Returns the energy for this bond type.
- getEnergyScore(int) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
Returns summation energy score of the disorder if the MCS is removed
from the target and query graph.
- getEnergyScore(int) - Method in class org.openscience.cdk.smsd.Isomorphism
-
Returns summation energy score of the disorder if the MCS is removed
from the target and query graph.
- getEntries() - Method in class org.openscience.cdk.dict.Dictionary
-
- getEntry(String) - Method in class org.openscience.cdk.dict.Dictionary
-
- getEqual() - Method in class org.openscience.cdk.smsd.helper.BinaryTree
-
Returns equal node
- 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.
- getEuclideanDistance() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
Returns Euclidean Distance between query and target molecule.
- getEuclideanDistance() - Method in class org.openscience.cdk.smsd.Isomorphism
-
Returns Euclidean Distance between query and target molecule.
- getExactMass() - Method in class org.openscience.cdk.debug.DebugAtom
-
Gets the ExactMass attribute of the Isotope object.
- getExactMass() - Method in class org.openscience.cdk.debug.DebugAtomType
-
Gets the ExactMass attribute of the Isotope object.
- getExactMass() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
The exact mass of an FragmentAtom is defined as the sum of exact masses
of the IAtom's in the fragment.
- getExactMass() - Method in class org.openscience.cdk.debug.DebugIsotope
-
Gets the ExactMass attribute of the Isotope object.
- getExactMass() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Gets the ExactMass attribute of the Isotope object.
- getExactMass() - Method in class org.openscience.cdk.FragmentAtom
-
The exact mass of an FragmentAtom is defined as the sum of exact masses
of the IAtom's in the fragment.
- getExactMass() - Method in interface org.openscience.cdk.interfaces.IIsotope
-
Gets the ExactMass attribute of the Isotope object.
- getExactMass() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Gets the ExactMass attribute of the Isotope object.
- getExactMass() - Method in class org.openscience.cdk.Isotope
-
Gets the ExactMass attribute of the Isotope object.
- getExactMass() - Method in class org.openscience.cdk.silent.FragmentAtom
-
The exact mass of an FragmentAtom is defined as the sum of exact masses
of the IAtom's in the fragment.
- getExactMass() - Method in class org.openscience.cdk.silent.Isotope
-
Gets the ExactMass attribute of the Isotope object.
- getExampleReactions() - Method in class org.openscience.cdk.dict.EntryReact
-
- getException() - Method in class org.openscience.cdk.qsar.DescriptorValue
-
- getExplicitHydrogenCount(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.normalize.SMSDNormalizer
-
Returns The number of explicit hydrogens for a given IAtom.
- getExplicitHydrogenCount(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator
-
Returns The number of explicit hydrogens for a given IAtom.
- getExtendedAdjacenyMatrix(AtomContainer) - Static method in class org.openscience.cdk.graph.invariant.HuLuIndexTool
-
- getExtendGrid() - Method in class org.openscience.cdk.tools.GridGenerator
-
- getExtension() - Method in class org.openscience.cdk.isomorphism.mcss.RNode
-
Gets the extension attribute of the RNode object.
- getExtension() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode
-
Gets the extension attribute of the RNode object
- getExternalSelectedPart() - Method in class org.openscience.cdk.renderer.RendererModel
-
Get externally selected atoms.
- getExternalSubset(String, String) - Method in class org.openscience.cdk.io.cml.CMLResolver
-
Not implemented: always returns null.
- getFarthestAtom(Point3d, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
-
Gets the farthestAtom attribute of the AtomPlacer3D object.
- getFfTypes() - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
-
gives a list of possible force field types
- getFfTypes() - Method in class org.openscience.cdk.modeling.builder3d.ModelBuilder3D
-
Gives a list of possible force field types.
- getFinalMapping() - Method in class org.openscience.cdk.smsd.helper.FinalMappings
-
Returns the stored mappings
- getFinalMapping() - Method in interface org.openscience.cdk.smsd.interfaces.IFinalMapping
-
Returns the stored mappings
- getFingerprintAsBytes() - Method in class org.openscience.cdk.fingerprint.PubchemFingerprinter
-
Returns the fingerprint generated for a molecule as a byte[].
- getFinishedPercentage() - Method in class org.openscience.cdk.formula.MolecularFormulaGenerator
-
Returns a value between 0.0 and 1.0 indicating what portion of the search
space has been examined so far by this MolecularFormulaGenerator.
- getFirst() - Method in class org.openscience.cdk.group.AbstractDiscretePartitionRefiner
-
Get the first permutation reached by the search.
- getFirstAtom() - Method in class org.openscience.cdk.AtomContainer
-
Returns the atom at position 0 in the container.
- getFirstAtom() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns the atom at position 0 in the container.
- getFirstAtom() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns the atom at position 0 in the container.
- getFirstAtom() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns the atom at position 0 in the container.
- getFirstAtom() - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns the atom at position 0 in the container.
- getFirstAtom() - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns the atom at position 0 in the container.
- getFirstAtom() - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns the atom at position 0 in the container.
- getFirstAtom() - Method in class org.openscience.cdk.debug.DebugRing
-
Returns the atom at position 0 in the container.
- getFirstAtom() - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns the atom at position 0 in the container.
- getFirstAtom() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the atom at position 0 in the container.
- getFirstAtom() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the atom at position 0 in the container.
- getFirstAtom() - Method in class org.openscience.cdk.signature.Orbit
-
Gets the first atom index of the orbit.
- getFirstAtom() - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the atom at position 0 in the container.
- getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler
-
Returns one of the best matches with atoms mapped.
- getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler
-
Returns one of the best matches with atoms mapped.
- getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler
-
Returns one of the best matches with atoms mapped.
- getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler
-
Returns one of the best matches with atoms mapped.
- getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler
-
Returns one of the best matches with atoms mapped.
- getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler
-
Returns one of the best matches with atoms mapped.
- getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler
-
Returns one of the best matches with atoms mapped.
- getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
Returns one of the best matches with atoms mapped.
- getFirstAtomMapping() - Method in interface org.openscience.cdk.smsd.interfaces.IMCSBase
-
Returns one of the best matches with atoms mapped.
- getFirstAtomMapping() - Method in class org.openscience.cdk.smsd.Isomorphism
-
Returns one of the best matches with atoms mapped.
- getFirstAttachmentPoint() - Method in class org.openscience.cdk.isomorphism.matchers.RGroup
-
- getFirstBondMap() - Method in class org.openscience.cdk.smsd.Isomorphism
-
- getFirstGraphSize() - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
-
Returns the size of the first of the two
compared graphs.
- getFirstGraphSize() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
-
Returns the size of the first of the two
compared graphs.
- getFirstHalfMatrixString() - Method in class org.openscience.cdk.group.AbstractDiscretePartitionRefiner
-
Get the half-matrix string under the first permutation.
- getFirstInCell(int) - Method in class org.openscience.cdk.group.Partition
-
Gets the first element in the specified cell.
- getFirstMap(IAtomContainer) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper
-
Returns first solution map.
- getFirstMap(TargetProperties) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper
-
Returns first solution map.
- getFirstMap(IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper
-
Returns first solution map.
- getFirstMap(TargetProperties) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper
-
Returns first solution map.
- getFirstMap(IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper
-
Returns first solution map.
- getFirstMap(TargetProperties) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper
-
Returns first solution map.
- getFirstMapping() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler
-
Returns one of the best matches with atom indexes mapped.
- getFirstMapping() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler
-
Returns one of the best matches with atom indexes mapped.
- getFirstMapping() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler
-
Returns one of the best matches with atom indexes mapped.
- getFirstMapping() - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler
-
Returns one of the best matches with atom indexes mapped.
- getFirstMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler
-
Returns one of the best matches with atom indexes mapped.
- getFirstMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler
-
Returns one of the best matches with atom indexes mapped.
- getFirstMapping() - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler
-
Returns one of the best matches with atom indexes mapped.
- getFirstMapping() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
Returns one of the best matches with atom indexes mapped.
- getFirstMapping() - Method in interface org.openscience.cdk.smsd.interfaces.IMCSBase
-
Returns one of the best matches with atom indexes mapped.
- getFirstMapping() - Method in class org.openscience.cdk.smsd.Isomorphism
-
Returns one of the best matches with atom indexes mapped.
- getFlag(int) - Method in class org.openscience.cdk.ChemObject
-
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns the value of a given flag.
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugAtom
-
Returns the value of a given flag.
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns the value of a given flag.
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
Returns the value of a given flag.
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugAtomType
-
Returns the value of a given flag.
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns the value of a given flag.
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugBond
-
Returns the value of a given flag.
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugChemFile
-
Returns the value of a given flag.
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugChemModel
-
Returns the value of a given flag.
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugChemObject
-
Returns the value of a given flag.
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugChemSequence
-
Returns the value of a given flag.
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns the value of a given flag.
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugElectronContainer
-
Returns the value of a given flag.
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugElement
-
Returns the value of a given flag.
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Returns the value of a given flag.
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugIsotope
-
Returns the value of a given flag.
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugLonePair
-
Returns the value of a given flag.
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugMapping
-
Returns the value of a given flag.
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns the value of a given flag.
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns the value of a given flag.
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Returns the value of a given flag.
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugReaction
-
Returns the value of a given flag.
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugReactionScheme
-
Returns the value of a given flag.
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugReactionSet
-
Returns the value of a given flag.
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugRing
-
Returns the value of a given flag.
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
Returns the value of a given flag.
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns the value of a given flag.
- getFlag(int) - Method in class org.openscience.cdk.debug.DebugSubstance
-
Returns the value of a given flag.
- getFlag(int) - Method in interface org.openscience.cdk.interfaces.IChemObject
-
Returns the value of a given flag.
- getFlag(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
- getFlag(int) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom
-
Deprecated.
- getFlag(int) - Method in class org.openscience.cdk.silent.ChemObject
-
- getFlags() - Method in class org.openscience.cdk.ChemObject
-
Returns the whole set of flags.
- getFlags() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns the whole set of flags.
- getFlags() - Method in class org.openscience.cdk.debug.DebugAtom
-
Returns the whole set of flags.
- getFlags() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns the whole set of flags.
- getFlags() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
Returns the whole set of flags.
- getFlags() - Method in class org.openscience.cdk.debug.DebugAtomType
-
Returns the whole set of flags.
- getFlags() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns the whole set of flags.
- getFlags() - Method in class org.openscience.cdk.debug.DebugBond
-
Returns the whole set of flags.
- getFlags() - Method in class org.openscience.cdk.debug.DebugChemFile
-
Returns the whole set of flags.
- getFlags() - Method in class org.openscience.cdk.debug.DebugChemModel
-
Returns the whole set of flags.
- getFlags() - Method in class org.openscience.cdk.debug.DebugChemObject
-
Returns the whole set of flags.
- getFlags() - Method in class org.openscience.cdk.debug.DebugChemSequence
-
Returns the whole set of flags.
- getFlags() - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns the whole set of flags.
- getFlags() - Method in class org.openscience.cdk.debug.DebugElectronContainer
-
Returns the whole set of flags.
- getFlags() - Method in class org.openscience.cdk.debug.DebugElement
-
Returns the whole set of flags.
- getFlags() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Returns the whole set of flags.
- getFlags() - Method in class org.openscience.cdk.debug.DebugIsotope
-
Returns the whole set of flags.
- getFlags() - Method in class org.openscience.cdk.debug.DebugLonePair
-
Returns the whole set of flags.
- getFlags() - Method in class org.openscience.cdk.debug.DebugMapping
-
Returns the whole set of flags.
- getFlags() - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns the whole set of flags.
- getFlags() - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns the whole set of flags.
- getFlags() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Returns the whole set of flags.
- getFlags() - Method in class org.openscience.cdk.debug.DebugReaction
-
Returns the whole set of flags.
- getFlags() - Method in class org.openscience.cdk.debug.DebugReactionScheme
-
Returns the whole set of flags.
- getFlags() - Method in class org.openscience.cdk.debug.DebugReactionSet
-
Returns the whole set of flags.
- getFlags() - Method in class org.openscience.cdk.debug.DebugRing
-
Returns the whole set of flags.
- getFlags() - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
Returns the whole set of flags.
- getFlags() - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns the whole set of flags.
- getFlags() - Method in class org.openscience.cdk.debug.DebugSubstance
-
Returns the whole set of flags.
- getFlags() - Method in interface org.openscience.cdk.interfaces.IChemObject
-
Returns the whole set of flags.
- getFlags() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
- getFlags() - Method in class org.openscience.cdk.silent.ChemObject
-
- getFlagValue() - Method in class org.openscience.cdk.ChemObject
-
- getFlagValue() - Method in interface org.openscience.cdk.interfaces.IChemObject
-
Access the internal value used to store the flags.
- getFlagValue() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
- getFlagValue() - Method in class org.openscience.cdk.silent.ChemObject
-
- getFont() - Method in class org.openscience.cdk.renderer.font.AWTFontManager
-
Get the current font.
- getFontName() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
-
Get the font family name used in this font manager.
- getFontSizeForZoom(double) - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
-
For a particular zoom, get the appropriate font size.
- getFontStyle() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
-
- getForbidden() - Method in class org.openscience.cdk.isomorphism.mcss.RNode
-
Gets the forbidden attribute of the RNode object.
- getForbidden() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode
-
Gets the forbidden attribute of the RNode object
- getFormalCharge() - Method in class org.openscience.cdk.AtomType
-
Returns the formal charge of this atom.
- getFormalCharge() - Method in class org.openscience.cdk.debug.DebugAtom
-
Returns the formal charge of this atom.
- getFormalCharge() - Method in class org.openscience.cdk.debug.DebugAtomType
-
Returns the formal charge of this atom.
- getFormalCharge() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Returns the formal charge of this atom.
- getFormalCharge() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Returns the formal charge of this atom.
- getFormalCharge() - Method in interface org.openscience.cdk.interfaces.IAtomType
-
Returns the formal charge of this atom.
- getFormalCharge() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Returns the formal charge of this atom.
- getFormalCharge() - Method in class org.openscience.cdk.silent.AtomType
-
Returns the formal charge of this atom.
- getFormalNeighbourCount() - Method in class org.openscience.cdk.AtomType
-
Returns the formal neighbour count of this atom.
- getFormalNeighbourCount() - Method in class org.openscience.cdk.debug.DebugAtom
-
Returns the formal neighbour count of this atom.
- getFormalNeighbourCount() - Method in class org.openscience.cdk.debug.DebugAtomType
-
Returns the formal neighbour count of this atom.
- getFormalNeighbourCount() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Returns the formal neighbour count of this atom.
- getFormalNeighbourCount() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Returns the formal neighbour count of this atom.
- getFormalNeighbourCount() - Method in interface org.openscience.cdk.interfaces.IAtomType
-
Returns the formal neighbour count of this atom.
- getFormalNeighbourCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Returns the formal neighbour count of this atom.
- getFormalNeighbourCount() - Method in class org.openscience.cdk.silent.AtomType
-
Returns the formal neighbour count of this atom.
- getFormat() - Method in class org.openscience.cdk.io.CDKSourceCodeWriter
-
- getFormat() - Method in class org.openscience.cdk.io.CIFReader
-
- getFormat() - Method in class org.openscience.cdk.io.CMLReader
-
- getFormat() - Method in class org.openscience.cdk.io.CMLWriter
-
- getFormat() - Method in class org.openscience.cdk.io.CrystClustReader
-
- getFormat() - Method in class org.openscience.cdk.io.CrystClustWriter
-
- getFormat() - Method in class org.openscience.cdk.io.CTXReader
-
- getFormat() - Method in class org.openscience.cdk.io.GamessReader
-
- getFormat() - Method in class org.openscience.cdk.io.Gaussian03Reader
-
- getFormat() - Method in class org.openscience.cdk.io.Gaussian98Reader
-
- getFormat() - Method in class org.openscience.cdk.io.GhemicalMMReader
-
- getFormat() - Method in class org.openscience.cdk.io.HINReader
-
- getFormat() - Method in class org.openscience.cdk.io.HINWriter
-
- getFormat() - Method in interface org.openscience.cdk.io.IChemObjectIO
-
- getFormat() - Method in class org.openscience.cdk.io.INChIPlainTextReader
-
- getFormat() - Method in class org.openscience.cdk.io.INChIReader
-
- getFormat() - Method in class org.openscience.cdk.io.iterator.event.EventCMLReader
-
- getFormat() - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundASNReader
-
- getFormat() - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader
-
- getFormat() - Method in class org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader
-
- getFormat() - Method in class org.openscience.cdk.io.iterator.IteratingSDFReader
-
- getFormat() - Method in class org.openscience.cdk.io.iterator.IteratingSMILESReader
-
Get the format for this reader.
- getFormat() - Method in class org.openscience.cdk.io.MDLReader
-
- getFormat() - Method in class org.openscience.cdk.io.MDLRXNReader
-
- getFormat() - Method in class org.openscience.cdk.io.MDLRXNV2000Reader
-
- getFormat() - Method in class org.openscience.cdk.io.MDLRXNV3000Reader
-
- getFormat() - Method in class org.openscience.cdk.io.MDLRXNWriter
-
- getFormat() - Method in class org.openscience.cdk.io.MDLV2000Reader
-
- getFormat() - Method in class org.openscience.cdk.io.MDLV2000Writer
-
- getFormat() - Method in class org.openscience.cdk.io.MDLV3000Reader
-
- getFormat() - Method in class org.openscience.cdk.io.Mol2Reader
-
- getFormat() - Method in class org.openscience.cdk.io.Mol2Writer
-
- getFormat() - Method in class org.openscience.cdk.io.Mopac7Reader
-
- getFormat() - Method in class org.openscience.cdk.io.MoSSOutputReader
-
- getFormat() - Method in class org.openscience.cdk.io.PCCompoundASNReader
-
- getFormat() - Method in class org.openscience.cdk.io.PCCompoundXMLReader
-
- getFormat() - Method in class org.openscience.cdk.io.PCSubstanceXMLReader
-
- getFormat() - Method in class org.openscience.cdk.io.PDBReader
-
- getFormat() - Method in class org.openscience.cdk.io.PDBWriter
-
- getFormat() - Method in class org.openscience.cdk.io.PMPReader
-
- getFormat() - Method in class org.openscience.cdk.io.program.GaussianInputWriter
-
- getFormat() - Method in class org.openscience.cdk.io.program.Mopac7Writer
-
- getFormat() - Method in class org.openscience.cdk.io.random.RandomAccessSDFReader
-
- getFormat() - Method in class org.openscience.cdk.io.rdf.CDKOWLReader
-
- getFormat() - Method in class org.openscience.cdk.io.rdf.CDKOWLWriter
-
- getFormat() - Method in class org.openscience.cdk.io.RGroupQueryReader
-
- getFormat() - Method in class org.openscience.cdk.io.RGroupQueryWriter
-
Returns output format.
- getFormat() - Method in class org.openscience.cdk.io.RssWriter
-
- getFormat() - Method in class org.openscience.cdk.io.SDFWriter
-
- getFormat() - Method in class org.openscience.cdk.io.ShelXReader
-
- getFormat() - Method in class org.openscience.cdk.io.ShelXWriter
-
- getFormat() - Method in class org.openscience.cdk.io.SMILESReader
-
- getFormat() - Method in class org.openscience.cdk.io.SMILESWriter
-
- getFormat() - Method in class org.openscience.cdk.io.VASPReader
-
- getFormat() - Method in class org.openscience.cdk.io.XYZReader
-
- getFormat() - Method in class org.openscience.cdk.io.XYZWriter
-
- getFormat() - Method in class org.openscience.cdk.io.ZMatrixReader
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.ABINITFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.Aces2Format
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.ADFFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.AlchemyFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.BGFFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.BSFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.CACheFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.CIFFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.CMLFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.CRK2DFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.CRK3DFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.CrystClustFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.CTXFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.DaltonFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.DMol3Format
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.DOCK5Format
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.FingerprintFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.GamessFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian03Format
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian90Format
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian92Format
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian94Format
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian95Format
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.Gaussian98Format
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat
-
- getFormatName() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.GROMOS96Format
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.HINFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.INChIFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in interface org.openscience.cdk.io.formats.IResourceFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.JaguarFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.JMEFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.MacroModelFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.MDLFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.MDLV2000Format
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.MDLV3000Format
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.MMODFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.Mol2Format
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC7Format
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC93Format
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.MOPAC97Format
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.MPQCFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.NWChemFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.PCModelFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.PDBFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.PDBMLFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.PMPFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.POVRayFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.PQSChemFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.QChemFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.RawCopyFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.SDFFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.ShelXFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.SMARTSFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.SMILESFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.SpartanFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.SVGFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.VASPFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.ViewmolFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.XEDFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.XYZFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.YasaraFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.ZindoFormat
-
Returns a one-lined format name of the format.
- getFormatName() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat
-
Returns a one-lined format name of the format.
- getFormats() - Method in class org.openscience.cdk.io.FormatFactory
-
Returns the list of recognizable formats.
- getFormats() - Method in class org.openscience.cdk.io.ReaderFactory
-
- getFormula() - Method in class org.openscience.cdk.formula.IsotopeContainer
-
Get the IMolecularFormula object of this container.
- getFP(int) - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter
-
Returns the requested fingerprint.
- getFPCount() - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter
-
Returns the number of fingerprints generated.
- getFractionalPoint3d() - Method in class org.openscience.cdk.Atom
-
Returns a point specifying the location of this
atom in a Crystal unit cell.
- getFractionalPoint3d() - Method in class org.openscience.cdk.debug.DebugAtom
-
Returns a point specifying the location of this
atom in a Crystal unit cell.
- getFractionalPoint3d() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Returns a point specifying the location of this
atom in a Crystal unit cell.
- getFractionalPoint3d() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Returns a point specifying the location of this
atom in a Crystal unit cell.
- getFractionalPoint3d() - Method in interface org.openscience.cdk.interfaces.IAtom
-
Returns a point specifying the location of this
atom in a Crystal unit cell.
- getFractionalPoint3d() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Returns a point specifying the location of this
atom in a Crystal unit cell.
- getFractionalPoint3d() - Method in class org.openscience.cdk.silent.Atom
-
Returns a point specifying the location of this
atom in a Crystal unit cell.
- getFragment() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Returns the fully expended form of the IFragmentAtom.
- getFragment() - Method in class org.openscience.cdk.FragmentAtom
-
- getFragment() - Method in interface org.openscience.cdk.interfaces.IFragmentAtom
-
Returns the fully expended form of the IFragmentAtom.
- getFragment() - Method in class org.openscience.cdk.silent.FragmentAtom
-
- getFragments() - Method in class org.openscience.cdk.fragment.ExhaustiveFragmenter
-
Get the fragments generated as SMILES strings.
- getFragments() - Method in interface org.openscience.cdk.fragment.IFragmenter
-
Get the fragments generated as SMILES strings.
- getFragments() - Method in class org.openscience.cdk.fragment.MurckoFragmenter
-
This returns the frameworks and ring systems from a Murcko fragmentation.
- getFragmentsAsContainers() - Method in class org.openscience.cdk.fragment.ExhaustiveFragmenter
-
- getFragmentsAsContainers() - Method in interface org.openscience.cdk.fragment.IFragmenter
-
- getFragmentsAsContainers() - Method in class org.openscience.cdk.fragment.MurckoFragmenter
-
- getFragmentSize(int) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
Returns number of fragment generated in the solution space,
if the MCS is removed from the target and query graph.
- getFragmentSize(int) - Method in class org.openscience.cdk.smsd.Isomorphism
-
Returns number of fragment generated in the solution space,
if the MCS is removed from the target and query graph.
- getFrameworks() - Method in class org.openscience.cdk.fragment.MurckoFragmenter
-
Get frameworks as SMILES strings.
- getFrameworksAsContainers() - Method in class org.openscience.cdk.fragment.MurckoFragmenter
-
- getFunction(int) - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Get a function from this set
- getFunctionalGroupSMARTS() - Static method in class org.openscience.cdk.fingerprint.StandardSubstructureSets
-
The functional groups.
- getFunctionColor(int) - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Get a color from a function in this set
- getFunctionsSize() - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Get the count of functions in this set
- getGenerators() - Method in class org.openscience.cdk.renderer.AtomContainerRenderer
-
- getGenerators() - Method in class org.openscience.cdk.renderer.ChemModelRenderer
-
- getGenerators() - Method in interface org.openscience.cdk.renderer.IRenderer
-
- getGenerators() - Method in class org.openscience.cdk.renderer.MoleculeSetRenderer
-
- getGenerators() - Method in class org.openscience.cdk.renderer.ReactionRenderer
-
- getGenerators() - Method in class org.openscience.cdk.renderer.ReactionSetRenderer
-
- getGraph() - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
-
Returns the graph object of this RGraph.
- getGraph() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
-
Returns the graph object of this CDKRGraph.
- getGraphics() - Method in class org.openscience.cdk.renderer.visitor.AWTDrawVisitor
-
- getGrid() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- getGrid() - Method in class org.openscience.cdk.tools.GridGenerator
-
- getGridArray() - Method in class org.openscience.cdk.tools.GridGenerator
-
- getGridPointFrom3dCoordinates(Point3d) - Method in class org.openscience.cdk.tools.GridGenerator
-
Method calculates the nearest grid point from given coordinates.
- getGroup() - Method in class org.openscience.cdk.isomorphism.matchers.RGroup
-
- getGroup(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
-
Get the group of the element.
- getHalfMatrixString(Permutation) - Method in class org.openscience.cdk.group.AbstractDiscretePartitionRefiner
-
Get the upper-half of the adjacency matrix under the permutation.
- getHalfMatrixString() - Method in class org.openscience.cdk.group.AbstractDiscretePartitionRefiner
-
Get the initial (unpermuted) half-matrix string.
- getHandedness(IAtom, IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.stereo.StereoTool
-
Gets the tetrahedral handedness of four atoms - three of which form the
'base' of the tetrahedron, and the other the apex.
- getHash(int) - Method in interface org.openscience.cdk.fingerprint.ICountFingerprint
-
Returns the hash corresponding to the given index in the fingerprint.
- getHash(int) - Method in class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
-
- getHashMapBySingleCharCode() - Static method in class org.openscience.cdk.templates.AminoAcids
-
Returns a HashMap where the key is one of G, A, V, L, I, S, T, C, M, D,
N, E, Q, R, K, H, F, Y, W and P.
- getHashMapByThreeLetterCode() - Static method in class org.openscience.cdk.templates.AminoAcids
-
Returns a HashMap where the key is one of GLY, ALA, VAL, LEU, ILE, SER,
THR, CYS, MET, ASP, ASN, GLU, GLN, ARG, LYS, HIS, PHE, TYR, TRP AND PRO.
- getHeaviestRing(IRingSet, IBond) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator
-
We define the heaviest ring as the one with the highest number of double bonds.
- getHeavyAtomRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>, boolean, boolean) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Return the RMSD of the heavy atoms between the 2 aligned molecules.
- getHeavyAtomRMSD(IAtomContainer, IAtomContainer, Map<Integer, Integer>, boolean, boolean) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Return the RMSD of the heavy atoms between the 2 aligned molecules.
- getHeavyAtoms(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Returns a set of nodes excluding all the hydrogens.
- getHeavyElements(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Returns a set of nodes excluding all the hydrogens.
- getHeight() - Method in class org.openscience.cdk.signature.Orbit
-
Gets the height of the signature label.
- getHetAtom() - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
Determine whether this is a heteroatom or not.
- getHetAtom() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
Determine whether this is a heteroatom or not.
- getHetAtom() - Method in class org.openscience.cdk.protein.data.PDBAtom
-
- getHetAtom() - Method in class org.openscience.cdk.silent.PDBAtom
-
- getHighlightedAtom() - Method in class org.openscience.cdk.renderer.RendererModel
-
Returns the atom currently highlighted.
- getHighlightedBond() - Method in class org.openscience.cdk.renderer.RendererModel
-
Returns the Bond currently highlighted.
- getHillString(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
- getHOSECode(IAtomContainer, IAtom, int) - Method in class org.openscience.cdk.tools.HOSECodeGenerator
-
- getHOSECode(IAtomContainer, IAtom, int, boolean) - Method in class org.openscience.cdk.tools.HOSECodeGenerator
-
- getHTML(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Returns the string representation of the molecule formula based on Hill
System with numbers wrapped in <sub></sub> tags.
- getHTML(IMolecularFormula, boolean, boolean) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Returns the string representation of the molecule formula based on Hill
System with numbers wrapped in <sub></sub> tags and the
isotope of each Element in <sup></sup> tags and the total
charge of IMolecularFormula in <sup></sup> tags.
- getHTML(IMolecularFormula, String[], boolean, boolean) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Returns the string representation of the molecule formula with numbers
wrapped in <sub></sub> tags and the isotope of each Element
in <sup></sup> tags and the total charge of IMolecularFormula
in <sup></sup> tags.
- getHybridization() - Method in class org.openscience.cdk.AtomType
-
Returns the hybridization of this atom.
- getHybridization() - Method in class org.openscience.cdk.debug.DebugAtom
-
Returns the hybridization of this atom.
- getHybridization() - Method in class org.openscience.cdk.debug.DebugAtomType
-
Returns the hybridization of this atom.
- getHybridization() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Returns the hybridization of this atom.
- getHybridization() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Returns the hybridization of this atom.
- getHybridization() - Method in interface org.openscience.cdk.interfaces.IAtomType
-
Returns the hybridization of this atom.
- getHybridization() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Returns the hybridization of this atom.
- getHybridization() - Method in class org.openscience.cdk.silent.AtomType
-
Returns the hybridization of this atom.
- getHydrogenCount(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.normalize.SMSDNormalizer
-
The summed implicit + explicit hydrogens of the given IAtom.
- getHydrogenCount(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator
-
The summed implicit + explicit hydrogens of the given IAtom.
- getiBondNeighborAtomsA() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper
-
- getiBondNeighborAtomsB() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper
-
- getIBondSetA() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper
-
- getIBondSetB() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper
-
- getICode() - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
get Code for insertion of residues of this atom.
- getICode() - Method in class org.openscience.cdk.debug.DebugPDBMonomer
-
Gets the ICode of this monomer.
- getICode() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
get Code for insertion of residues of this atom.
- getICode() - Method in interface org.openscience.cdk.interfaces.IPDBMonomer
-
Gets the ICode of this monomer.
- getICode() - Method in class org.openscience.cdk.protein.data.PDBAtom
-
get Code for insertion of residues of this atom.
- getICode() - Method in class org.openscience.cdk.protein.data.PDBMonomer
-
- getICode() - Method in class org.openscience.cdk.silent.PDBAtom
-
get Code for insertion of residues of this atom.
- getICode() - Method in class org.openscience.cdk.silent.PDBMonomer
-
- getID() - Method in class org.openscience.cdk.ChemObject
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.debug.DebugAtom
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.debug.DebugAtomType
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.debug.DebugBond
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.debug.DebugChemFile
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.debug.DebugChemModel
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.debug.DebugChemObject
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.debug.DebugChemSequence
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.debug.DebugElectronContainer
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.debug.DebugElement
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.debug.DebugIsotope
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.debug.DebugLonePair
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.debug.DebugMapping
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.debug.DebugReaction
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.debug.DebugReactionScheme
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.debug.DebugReactionSet
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.debug.DebugRing
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.debug.DebugSubstance
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.dict.Entry
-
- getID() - Method in interface org.openscience.cdk.interfaces.IChemObject
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
Returns the identifier (ID) of this object.
- getID() - Method in class org.openscience.cdk.silent.ChemObject
-
Returns the identifier (ID) of this object.
- getId1() - Method in class org.openscience.cdk.isomorphism.mcss.RMap
-
Gets the id1 attribute of the RMap object.
- getId1() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMap
-
Gets the id1 attribute of the CDKRMap object
- getId2() - Method in class org.openscience.cdk.isomorphism.mcss.RMap
-
Gets the id2 attribute of the RMap object.
- getId2() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMap
-
Gets the id2 attribute of the CDKRMap object
- getIgnoreAromaticBonds() - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory
-
Deprecated.
- GetImage() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Get token literal value.
- GetImage() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Get token literal value.
- getImaginaryPart() - Method in class org.openscience.cdk.math.Complex
-
Gets the imaginary part of this value
- getIminus() - Method in class org.openscience.cdk.math.qm.AngularMomentum
-
Calculates the I- operator
- getImplementationIdentifier() - Method in interface org.openscience.cdk.IImplementationSpecification
-
Identifier for this implementation which must include
version information.
- getImplementationIdentifier() - Method in class org.openscience.cdk.qsar.DescriptorSpecification
-
- getImplementationIdentifier() - Method in class org.openscience.cdk.reaction.ReactionSpecification
-
- getImplementationTitle() - Method in interface org.openscience.cdk.IImplementationSpecification
-
Human-readable name for the implementation for the algorithm
specified by the reference.
- getImplementationTitle() - Method in class org.openscience.cdk.qsar.DescriptorSpecification
-
- getImplementationTitle() - Method in class org.openscience.cdk.reaction.ReactionSpecification
-
- getImplementationVendor() - Method in interface org.openscience.cdk.IImplementationSpecification
-
Human-readable name for the vendor that holds copyright for this
implementation.
- getImplementationVendor() - Method in class org.openscience.cdk.qsar.DescriptorSpecification
-
- getImplementationVendor() - Method in class org.openscience.cdk.reaction.ReactionSpecification
-
- getImplicitHydrogenCount() - Method in class org.openscience.cdk.Atom
-
Returns the hydrogen count of this atom.
- getImplicitHydrogenCount() - Method in class org.openscience.cdk.debug.DebugAtom
-
Returns the hydrogen count of this atom.
- getImplicitHydrogenCount() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Returns the hydrogen count of this atom.
- getImplicitHydrogenCount() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Returns the hydrogen count of this atom.
- getImplicitHydrogenCount() - Method in interface org.openscience.cdk.interfaces.IAtom
-
Returns the implicit hydrogen count of this atom.
- getImplicitHydrogenCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Returns the hydrogen count of this atom.
- getImplicitHydrogenCount(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.normalize.SMSDNormalizer
-
Returns The number of Implicit Hydrogen Count for a given IAtom.
- getImplicitHydrogenCount() - Method in class org.openscience.cdk.silent.Atom
-
Returns the hydrogen count of this atom.
- getImplicitHydrogenCount(IAtom) - Static method in class org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator
-
Returns The number of Implicit Hydrogen Count for a given IAtom.
- getImplicitHydrogenCount(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Counts the number of implicit hydrogens on the provided IAtomContainer.
- getInchi() - Method in class org.openscience.cdk.inchi.InChIGenerator
-
Gets generated InChI string.
- getInChIGenerator(IAtomContainer) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory
-
- getInChIGenerator(IAtomContainer, String) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory
-
Gets InChI generator for CDK IAtomContainer.
- getInChIGenerator(IAtomContainer, List<INCHI_OPTION>) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory
-
Gets InChI generator for CDK IAtomContainer.
- getInchiKey() - Method in class org.openscience.cdk.inchi.InChIGenerator
-
Gets generated InChIKey string.
- getInchimap() - Method in class org.openscience.cdk.io.RssWriter
-
- getInChIToStructure(String, IChemObjectBuilder) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory
-
Gets structure generator for an InChI string.
- getInChIToStructure(String, IChemObjectBuilder, String) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory
-
Gets structure generator for an InChI string.
- getInChIToStructure(String, IChemObjectBuilder, List<String>) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory
-
Gets structure generator for an InChI string.
- getIndexFile(String) - Static method in class org.openscience.cdk.io.random.RandomAccessReader
-
Opens the file index _cdk.index in a temporary folder, as specified by "java.io.tmpdir" property.
- getIndexOfFirstNonDiscreteCell() - Method in class org.openscience.cdk.group.Partition
-
Gets the index of the first cell in the partition that is discrete.
- getInitialLongestChain(IAtomContainer) - Static method in class org.openscience.cdk.layout.AtomPlacer
-
Search an aliphatic molecule for the longest chain.
- getInstance(IChemObjectBuilder) - Static method in class org.openscience.cdk.atomtype.CDKAtomTypeMatcher
-
- getInstance(IChemObjectBuilder, int) - Static method in class org.openscience.cdk.atomtype.CDKAtomTypeMatcher
-
- getInstance(String) - Static method in class org.openscience.cdk.atomtype.mapper.AtomTypeMapper
-
Instantiates an atom type to atom type mapping, based on the given mapping file.
- getInstance(String, InputStream) - Static method in class org.openscience.cdk.atomtype.mapper.AtomTypeMapper
-
Instantiates an atom type to atom type mapping, based on the given
InputStream
.
- getInstance(IChemObjectBuilder) - Static method in class org.openscience.cdk.atomtype.SybylAtomTypeMatcher
-
Returns an instance of this atom typer.
- getInstance(InputStream, String, IChemObjectBuilder) - Static method in class org.openscience.cdk.config.AtomTypeFactory
-
Method to create a default AtomTypeFactory, using the given InputStream.
- getInstance(IChemObjectBuilder) - Static method in class org.openscience.cdk.config.AtomTypeFactory
-
Method to create a default AtomTypeFactory, using the structgen atom type list.
- getInstance(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.config.AtomTypeFactory
-
Method to create a specialized AtomTypeFactory.
- getInstance() - Static method in class org.openscience.cdk.config.Isotopes
-
Returns a singleton instance of this class.
- getInstance(IChemObjectBuilder) - Static method in class org.openscience.cdk.config.XMLIsotopeFactory
-
Returns an IsotopeFactory instance.
- getInstance() - Static method in class org.openscience.cdk.debug.DebugChemObjectBuilder
-
Access the singleton instance of this DebugChemObjectBuilder.
- getInstance() - Static method in class org.openscience.cdk.DefaultChemObjectBuilder
-
Access the singleton instance of this DefaultChemObjectBuilder.
- getInstance() - Static method in class org.openscience.cdk.inchi.InChIGeneratorFactory
-
Gives the one InChIGeneratorFactory
instance,
if needed also creates it.
- getInstance() - Static method in class org.openscience.cdk.io.formats.ABINITFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.Aces2Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.ADFFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.AlchemyFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.BGFFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.BSFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.CacaoInternalFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.CACheFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.CDKOWLFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.ChemDrawFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.ChemtoolFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.CIFFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.CMLFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.CMLRSSFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.CRK2DFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.CRK3DFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.CrystClustFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.CTXFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.DaltonFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.DMol3Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.DOCK5Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.FingerprintFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.GamessFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.Gaussian03Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.Gaussian90Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.Gaussian92Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.Gaussian94Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.Gaussian95Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.Gaussian98Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.GaussianInputFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.GhemicalMMFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.GhemicalSPMFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.GROMOS96Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.HINFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.INChIFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.INChIPlainTextFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.JaguarFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.JMEFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.MacroModelFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.MDLFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.MDLRXNFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.MDLRXNV3000Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.MDLV2000Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.MDLV3000Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.MMODFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.Mol2Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC2002Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC2007Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC2009Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC2012Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC7Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC7InputFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC93Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.MOPAC97Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.MoSSOutputFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.MPQCFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.NWChemFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.PCModelFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.PDBFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.PDBMLFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.PMPFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.POVRayFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.PQSChemFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemASNFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.QChemFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.RawCopyFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.RGroupQueryFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.SDFFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.ShelXFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.SMARTSFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.SMILESFIXFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.SMILESFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.SpartanFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.SVGFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.SybylDescriptorFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.TinkerMM2Format
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.TinkerXYZFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.TurboMoleFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.UniChemXYZFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.VASPFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.ViewmolFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.XEDFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.XYZFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.YasaraFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.ZindoFormat
-
- getInstance() - Static method in class org.openscience.cdk.io.formats.ZMatrixFormat
-
- getInstance(TemplateHandler3D, String, IChemObjectBuilder) - Static method in class org.openscience.cdk.modeling.builder3d.ModelBuilder3D
-
- getInstance(IChemObjectBuilder) - Static method in class org.openscience.cdk.modeling.builder3d.ModelBuilder3D
-
- getInstance() - Static method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D
-
- getInstance() - Static method in class org.openscience.cdk.silent.SilentChemObjectBuilder
-
Access the singleton instance of this SilentChemObjectBuilder.
- getInstance() - Static method in class org.openscience.cdk.smsd.global.TimeOut
-
Get Instance of the timeout.
- getInstance() - Static method in class org.openscience.cdk.smsd.helper.FinalMappings
-
Stores mapping solutions
- getInstance() - Static method in class org.openscience.cdk.smsd.helper.LabelContainer
-
Create ids from atom labels
- getInstance() - Static method in class org.openscience.cdk.smsd.tools.BondEnergies
-
Returns Singleton pattern instance for the Bond Energy class
- getInstance() - Static method in class org.openscience.cdk.tools.AtomicProperties
-
- getInstance(IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.CDKHydrogenAdder
-
- getInstance(IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.CDKValencyChecker
-
- getInt2DColumnSum(int[][]) - Static method in class org.openscience.cdk.graph.PathTools
-
Sums up the columns in a 2D int matrix.
- getIntensity() - Method in class org.openscience.cdk.formula.IsotopeContainer
-
Get the intensity value of this container.
- getInterfaces(Class<?>) - Method in class org.openscience.cdk.DynamicFactory.DefaultInterfaceProvider
-
- getInterfaces(Class<?>) - Method in interface org.openscience.cdk.DynamicFactory.InterfaceProvider
-
Access the interfaces for a given class.
- getIntersection(IAtomContainer, IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Compares this AtomContainer with another given AtomContainer and returns
the Intersection between them.
- getIntLabel(int) - Method in class org.openscience.cdk.signature.AtomSignature
-
- getIOSettings() - Method in class org.openscience.cdk.io.ChemObjectIO
-
- getIOSettings() - Method in interface org.openscience.cdk.io.IChemObjectIO
-
Returns an array of
IOSetting
s defined by this IChemObjectIO class.
- getIOSettings() - Method in class org.openscience.cdk.io.random.DefaultRandomAccessChemObjectReader
-
- getIplus() - Method in class org.openscience.cdk.math.qm.AngularMomentum
-
Calculates the I+ operator
- getIsobutane(IChemObjectBuilder) - Static method in class org.openscience.cdk.templates.saturatedhydrocarbons.IsoAlkanes
-
- getIsohexane(IChemObjectBuilder) - Static method in class org.openscience.cdk.templates.saturatedhydrocarbons.IsoAlkanes
-
- getIsomorphAtomsMap(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
-
Returns the first isomorph 'atom mapping' found for g2 in g1.
- getIsomorphAtomsMap(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
-
Returns the first isomorph 'atom mapping' found for targetGraph in sourceGraph.
- getIsomorphMap(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
-
Returns the first isomorph mapping found or null.
- getIsomorphMap(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
-
Returns the first isomorph mapping found or null.
- getIsomorphMaps(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
-
Returns all the isomorph 'mappings' found between two
atom containers.
- getIsomorphMaps(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
-
Returns all the isomorph 'mappings' found between two
atom containers.
- getIsopentane(IChemObjectBuilder) - Static method in class org.openscience.cdk.templates.saturatedhydrocarbons.IsoAlkanes
-
- getIsotope(String, int) - Method in class org.openscience.cdk.config.IsotopeFactory
-
Get isotope based on element symbol and mass number.
- getIsotope(String, double, double) - Method in class org.openscience.cdk.config.IsotopeFactory
-
Get an isotope based on the element symbol and exact mass.
- getIsotope(String, int) - Method in class org.openscience.cdk.config.Isotopes
-
Get isotope based on element symbol and mass number.
- getIsotope(String, double, double) - Method in class org.openscience.cdk.config.Isotopes
-
Get an isotope based on the element symbol and exact mass.
- getIsotope(int) - Method in class org.openscience.cdk.formula.IsotopePattern
-
Returns the a isotopes given a specific position.
- getIsotopeCount(IIsotope) - Method in class org.openscience.cdk.debug.DebugAdductFormula
-
Checks a set of Nodes for the occurrence of the isotope in the
adduct formula from a particular isotope.
- getIsotopeCount() - Method in class org.openscience.cdk.debug.DebugAdductFormula
-
Checks a set of Nodes for the number of different isotopes in the
adduct formula.
- getIsotopeCount(IIsotope) - Method in class org.openscience.cdk.debug.DebugMolecularFormula
-
Checks a set of Nodes for the occurrence of the isotope in the
IMolecularFormula from a particular isotope.
- getIsotopeCount() - Method in class org.openscience.cdk.debug.DebugMolecularFormula
-
Checks a set of Nodes for the number of different isotopes in the
IMolecularFormula.
- getIsotopeCount(IIsotope) - Method in class org.openscience.cdk.formula.AdductFormula
-
Checks a set of Nodes for the occurrence of the isotope in the
adduct formula from a particular isotope.
- getIsotopeCount() - Method in class org.openscience.cdk.formula.AdductFormula
-
Checks a set of Nodes for the number of different isotopes in the
adduct formula.
- getIsotopeCount(IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormula
-
Checks a set of Nodes for the occurrence of the isotope in the
IMolecularFormula from a particular isotope.
- getIsotopeCount() - Method in class org.openscience.cdk.formula.MolecularFormula
-
Checks a set of Nodes for the number of different isotopes in the
IMolecularFormula.
- getIsotopeCount() - Method in class org.openscience.cdk.formula.MolecularFormulaRange
-
Checks a set of Nodes for the number of different isotopes in the
MolecularFormulaExpand.
- getIsotopeCount(IIsotope) - Method in interface org.openscience.cdk.interfaces.IAdductFormula
-
Checks a set of Nodes for the occurrence of the isotope in the
adduct formula from a particular isotope.
- getIsotopeCount() - Method in interface org.openscience.cdk.interfaces.IAdductFormula
-
Checks a set of Nodes for the number of different isotopes in the
adduct formula.
- getIsotopeCount(IIsotope) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
-
Checks a set of Nodes for the occurrence of the isotope in the
IMolecularFormula from a particular isotope.
- getIsotopeCount() - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
-
Checks a set of Nodes for the number of different isotopes in the
IMolecularFormula.
- getIsotopeCount(IIsotope) - Method in class org.openscience.cdk.silent.AdductFormula
-
Checks a set of Nodes for the occurrence of the isotope in the
adduct formula from a particular isotope.
- getIsotopeCount() - Method in class org.openscience.cdk.silent.AdductFormula
-
Checks a set of Nodes for the number of different isotopes in the
adduct formula.
- getIsotopeCount(IIsotope) - Method in class org.openscience.cdk.silent.MolecularFormula
-
Checks a set of Nodes for the occurrence of the isotope in the
IMolecularFormula from a particular isotope.
- getIsotopeCount() - Method in class org.openscience.cdk.silent.MolecularFormula
-
Checks a set of Nodes for the number of different isotopes in the
IMolecularFormula.
- getIsotopeCountMax(IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormulaRange
-
Checks a set of Nodes for the maximal occurrence of the isotope in the
MolecularFormulaExpand from a particular isotope.
- getIsotopeCountMin(IIsotope) - Method in class org.openscience.cdk.formula.MolecularFormulaRange
-
Checks a set of Nodes for the minimal occurrence of the isotope in the
MolecularFormulaExpand from a particular isotope.
- getIsotopes(String) - Method in class org.openscience.cdk.config.IsotopeFactory
-
Gets an array of all isotopes known to the IsotopeFactory for the given
element symbol.
- getIsotopes() - Method in class org.openscience.cdk.config.IsotopeFactory
-
Gets a array of all isotopes known to the IsotopeFactory.
- getIsotopes(double, double) - Method in class org.openscience.cdk.config.IsotopeFactory
-
Gets an array of all isotopes matching the searched exact mass within
a certain difference.
- getIsotopes(String) - Method in class org.openscience.cdk.config.Isotopes
-
Gets an array of all isotopes known to the IsotopeFactory for the given
element symbol.
- getIsotopes() - Method in class org.openscience.cdk.config.Isotopes
-
Gets a array of all isotopes known to the IsotopeFactory.
- getIsotopes(double, double) - Method in class org.openscience.cdk.config.Isotopes
-
Gets an array of all isotopes matching the searched exact mass within
a certain difference.
- getIsotopes() - Method in class org.openscience.cdk.config.isotopes.IsotopeHandler
-
Returns the isotopes read from the XML file.
- getIsotopes() - Method in class org.openscience.cdk.formula.IsotopePattern
-
Returns the all isotopes that form this isotope pattern.
- getIsotopes(IMolecularFormula) - Method in class org.openscience.cdk.formula.IsotopePatternGenerator
-
Get all combinatorial chemical isotopes given a structure.
- getIsotopes(IMolecularFormula, IElement) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Get a list of IIsotope from a given IElement which is contained
molecular.
- getIterator() - Method in class org.openscience.cdk.smsd.helper.FinalMappings
-
Returns a mapping Iterator
- getIterator() - Method in interface org.openscience.cdk.smsd.interfaces.IFinalMapping
-
Returns a mapping Iterator
- getIx() - Method in class org.openscience.cdk.math.qm.AngularMomentum
-
Calculates the Ix operator
- getIy() - Method in class org.openscience.cdk.math.qm.AngularMomentum
-
Calculates the Iy operator
- getIz() - Method in class org.openscience.cdk.math.qm.AngularMomentum
-
Calculates the Iz operator
- getLabel() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Returns the label of this PseudoAtom.
- getLabel() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Returns the label of this PseudoAtom.
- getLabel() - Method in class org.openscience.cdk.dict.Entry
-
- getLabel() - Method in interface org.openscience.cdk.interfaces.IPseudoAtom
-
Returns the label of this PseudoAtom.
- getLabel() - Method in class org.openscience.cdk.PseudoAtom
-
Returns the label of this PseudoAtom.
- getLabel() - Method in class org.openscience.cdk.signature.Orbit
-
Gets the label of the orbit.
- getLabel() - Method in class org.openscience.cdk.silent.PseudoAtom
-
Returns the label of this PseudoAtom.
- getLabel(Integer) - Method in class org.openscience.cdk.smsd.helper.LabelContainer
-
Returns Label of a given ID
- getLabel() - Method in class org.openscience.cdk.Vibration
-
Gets the label identifying this vibration.
- getLabelID(String) - Method in class org.openscience.cdk.smsd.helper.LabelContainer
-
Returns label ID
- getLargestRingSet(List<IRingSet>) - Method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D
-
Returns the largest (number of atoms) ring set in a molecule.
- getLargestRingSet(List<IRingSet>) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator
-
Returns the largest (number of atoms) ring set in a molecule
- getLast() - Method in class org.openscience.cdk.smiles.InvPair
-
- getLastAtom() - Method in class org.openscience.cdk.AtomContainer
-
Returns the atom at the last position in the container.
- getLastAtom() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns the atom at the last position in the container.
- getLastAtom() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns the atom at the last position in the container.
- getLastAtom() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns the atom at the last position in the container.
- getLastAtom() - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns the atom at the last position in the container.
- getLastAtom() - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns the atom at the last position in the container.
- getLastAtom() - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns the atom at the last position in the container.
- getLastAtom() - Method in class org.openscience.cdk.debug.DebugRing
-
Returns the atom at the last position in the container.
- getLastAtom() - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns the atom at the last position in the container.
- getLastAtom() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the atom at the last position in the container.
- getLastAtom() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the atom at the last position in the container.
- getLastAtom() - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the atom at the last position in the container.
- getLatticeConstant() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- getLatticeConstant() - Method in class org.openscience.cdk.tools.GridGenerator
-
- getLeft() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom
-
Deprecated.
- getLeft() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond
-
- getLeftTransversal(int) - Method in class org.openscience.cdk.group.PermutationGroup
-
Get the traversal Ui from the list of transversals.
- getLength() - Method in class org.openscience.cdk.iupac.parser.AttachedGroup
-
Getter for property length.
- getLength2D(IBond) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Returns the geometric length of this bond in 2D space.
- getLength2D(IBond) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Returns the geometric length of this bond in 2D space.
- getLevel() - Method in class org.openscience.cdk.io.setting.IOSetting
-
- getLigandAtom() - Method in interface org.openscience.cdk.geometry.cip.ILigand
-
- getLigandAtom() - Method in class org.openscience.cdk.geometry.cip.Ligand
-
- getLigandLigands(ILigand) - Static method in class org.openscience.cdk.geometry.cip.CIPTool
-
Returns a CIP-expanded array of side chains of a ligand.
- getLigands() - Method in interface org.openscience.cdk.interfaces.ITetrahedralChirality
-
Returns an array of ligand atoms around the chiral atom.
- getLigands() - Method in class org.openscience.cdk.stereo.TetrahedralChirality
-
Returns an array of ligand atoms around the chiral atom.
- getLimitedPathsOfLengthUpto(IAtomContainer, IAtom, int, int) - Static method in class org.openscience.cdk.graph.PathTools
-
Get all the paths starting from an atom of length 0 up to the specified
length.
- getLine(int) - Method in class org.openscience.cdk.graph.invariant.GIMatrix
-
Returns the line-matrix at the given line index.
- getLine() - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Deprecated.
- getLine() - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Deprecated.
- getLinkageRadius() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- getLinkmap() - Method in class org.openscience.cdk.io.RssWriter
-
- getListenerCount() - Method in class org.openscience.cdk.ChemObject
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugAtom
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugAtomType
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugBond
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugChemFile
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugChemModel
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugChemObject
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugChemSequence
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugElectronContainer
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugElement
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugIsotope
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugLonePair
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugMapping
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugReaction
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugReactionScheme
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugReactionSet
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugRing
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in class org.openscience.cdk.debug.DebugSubstance
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in interface org.openscience.cdk.interfaces.IChemObject
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
Returns the number of ChemObjectListeners registered with this object.
- getListenerCount() - Method in class org.openscience.cdk.silent.ChemObject
-
Returns the number of ChemObjectListeners registered with this object.
- getListeners() - Method in class org.openscience.cdk.io.ChemObjectIO
-
- getListeners() - Method in interface org.openscience.cdk.io.IChemObjectIO
-
Access all the listeners for this ChemObject Reader or Writer.
- getLocations() - Method in class org.openscience.cdk.iupac.parser.AttachedGroup
-
Getter for property locations.
- getLog() - Method in class org.openscience.cdk.inchi.InChIGenerator
-
Gets generated log.
- getLog() - Method in class org.openscience.cdk.inchi.InChIToStructure
-
Gets generated log.
- getLoggingToolClass() - Static method in class org.openscience.cdk.tools.LoggingToolFactory
-
- getLonePair(int) - Method in class org.openscience.cdk.AtomContainer
-
Get the lone pair at position number
in [0,..].
- getLonePair(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Get the lone pair at position number
in [0,..].
- getLonePair(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Get the lone pair at position number
in [0,..].
- getLonePair(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Get the lone pair at position number
in [0,..].
- getLonePair(int) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Get the lone pair at position number
in [0,..].
- getLonePair(int) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Get the lone pair at position number
in [0,..].
- getLonePair(int) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Get the lone pair at position number
in [0,..].
- getLonePair(int) - Method in class org.openscience.cdk.debug.DebugRing
-
Get the lone pair at position number
in [0,..].
- getLonePair(int) - Method in class org.openscience.cdk.debug.DebugStrand
-
Get the lone pair at position number
in [0,..].
- getLonePair(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Get the lone pair at position number
in [0,..].
- getLonePair(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Get the lone pair at position number
in [0,..].
- getLonePair(int) - Method in class org.openscience.cdk.silent.AtomContainer
-
Get the lone pair at position number
in [0,..].
- getLonePairCount() - Method in class org.openscience.cdk.AtomContainer
-
Returns the number of LonePairs in this Container.
- getLonePairCount() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns the number of LonePairs in this Container.
- getLonePairCount() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns the number of LonePairs in this Container.
- getLonePairCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns the number of LonePairs in this Container.
- getLonePairCount() - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns the number of LonePairs in this Container.
- getLonePairCount() - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns the number of LonePairs in this Container.
- getLonePairCount() - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns the number of LonePairs in this Container.
- getLonePairCount() - Method in class org.openscience.cdk.debug.DebugRing
-
Returns the number of LonePairs in this Container.
- getLonePairCount() - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns the number of LonePairs in this Container.
- getLonePairCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the number of LonePairs in this Container.
- getLonePairCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the number of LonePairs in this Container.
- getLonePairCount() - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the number of LonePairs in this Container.
- getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.AtomContainer
-
Returns the position of a given lone pair in the lone pair array.
- getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns the position of a given lone pair in the lone pair array.
- getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns the position of a given lone pair in the lone pair array.
- getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns the position of a given lone pair in the lone pair array.
- getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns the position of a given lone pair in the lone pair array.
- getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns the position of a given lone pair in the lone pair array.
- getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns the position of a given lone pair in the lone pair array.
- getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugRing
-
Returns the position of a given lone pair in the lone pair array.
- getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns the position of a given lone pair in the lone pair array.
- getLonePairNumber(ILonePair) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the position of a given lone pair in the lone pair array.
- getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the position of a given lone pair in the lone pair array.
- getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the position of a given lone pair in the lone pair array.
- getLongestUnplacedChain(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.layout.AtomPlacer
-
Search a molecule for the longest unplaced, aliphatic chain in it.
- getLower() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryAngleBond
-
- getLower() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryBond
-
- getMajorIsotope(int) - Method in class org.openscience.cdk.config.IsotopeFactory
-
Returns the most abundant (major) isotope with a given atomic number.
- getMajorIsotope(String) - Method in class org.openscience.cdk.config.IsotopeFactory
-
Returns the most abundant (major) isotope whose symbol equals element.
- getMajorIsotope(int) - Method in class org.openscience.cdk.config.Isotopes
-
Returns the most abundant (major) isotope with a given atomic number.
- getMajorIsotope(String) - Method in class org.openscience.cdk.config.Isotopes
-
Returns the most abundant (major) isotope whose symbol equals element.
- getMajorIsotopeMass(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Get the summed major isotopic mass of all elements from an MolecularFormula.
- getMajorIsotopeMolecularFormula(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Construct an instance of IMolecularFormula, initialized with a molecular
formula string.
- getMap() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IState
-
Returns the current mapping of query atoms onto target atoms.
- getMap() - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFState
-
Returns the current mapping of query atoms onto target atoms.
- getMappedAtomCount() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper
-
- getMappedAtomsOrg() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper
-
- getMappedChemObject(IReaction, IChemObject) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
-
get the IAtom which is mapped
- getMappedSubstructures(IAtomContainer) - Method in class org.openscience.cdk.layout.TemplateHandler
-
Checks if one of the loaded templates is a substructure in the given
Molecule and returns all matched substructures in a IAtomContainerSet.
- getMapping() - Method in class org.openscience.cdk.atomtype.mapper.AtomTypeMapper
-
Returns the name of this mapping.
- getMapping(int) - Method in interface org.openscience.cdk.interfaces.IReaction
-
Retrieves a mapping between the reactant and product side to this
Reaction.
- getMapping(int) - Method in class org.openscience.cdk.Reaction
-
Retrieves a mapping between the reactant and product side to this
Reaction.
- getMapping(int) - Method in class org.openscience.cdk.silent.Reaction
-
Retrieves a mapping between the reactant and product side to this
Reaction.
- getMappingCount() - Method in interface org.openscience.cdk.interfaces.IReaction
-
Get the number of mappings between the reactant and product side to this
Reaction.
- getMappingCount() - Method in class org.openscience.cdk.Reaction
-
Get the number of mappings between the reactant and product side to this
Reaction.
- getMappingCount() - Method in class org.openscience.cdk.silent.Reaction
-
Get the number of mappings between the reactant and product side to this
Reaction.
- getMappings() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregor
-
Returns computed mappings.
- getMappings() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
-
Returns mapping solutions
- getMaps(IAtomContainer) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper
-
Returns all solution map.
- getMaps(TargetProperties) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper
-
Returns all solution map.
- getMaps(IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper
-
Returns all solution map.
- getMaps(TargetProperties) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper
-
Returns all solution map.
- getMaps(IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper
-
Returns all solution map.
- getMaps(TargetProperties) - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper
-
Returns all solution map.
- getMass() - Method in class org.openscience.cdk.formula.IsotopeContainer
-
Get the mass value of this container.
- getMass(String) - Method in class org.openscience.cdk.tools.AtomicProperties
-
- getMassNumber() - Method in class org.openscience.cdk.debug.DebugAtom
-
Returns the atomic mass of this element.
- getMassNumber() - Method in class org.openscience.cdk.debug.DebugAtomType
-
Returns the atomic mass of this element.
- getMassNumber() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Returns the atomic mass of this element.
- getMassNumber() - Method in class org.openscience.cdk.debug.DebugIsotope
-
Returns the atomic mass of this element.
- getMassNumber() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Returns the atomic mass of this element.
- getMassNumber() - Method in interface org.openscience.cdk.interfaces.IIsotope
-
Returns the atomic mass of this element.
- getMassNumber() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Returns the atomic mass of this element.
- getMassNumber() - Method in class org.openscience.cdk.Isotope
-
Returns the atomic mass of this element.
- getMassNumber() - Method in class org.openscience.cdk.silent.Isotope
-
Returns the atomic mass of this element.
- getMatchingAtoms() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom
-
Get the atoms of a target molecule that correspond to this group.
- getMatchingAtoms() - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool
-
Get the atoms in the target molecule that match the query pattern.
- getMatchingPharmacophoreAtoms() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher
-
Get the matching pharmacophore groups.
- getMatchingPharmacophoreBonds() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher
-
Get the matching pharmacophore constraints.
- getMatrix(IAtomContainer) - Static method in class org.openscience.cdk.graph.matrix.AdjacencyMatrix
-
Returns the adjacency matrix for the given AtomContainer.
- getMatrix(IAtomContainer) - Static method in class org.openscience.cdk.graph.matrix.ConnectionMatrix
-
Returns the connection matrix representation of this AtomContainer.
- getMatrix(IAtomContainer) - Static method in class org.openscience.cdk.graph.matrix.TopologicalMatrix
-
Returns the topological matrix for the given AtomContainer.
- getMaxBondOrder() - Method in class org.openscience.cdk.AtomType
-
Gets the MaxBondOrder attribute of the AtomType object.
- getMaxBondOrder() - Method in class org.openscience.cdk.debug.DebugAtom
-
Gets the MaxBondOrder attribute of the AtomType object.
- getMaxBondOrder() - Method in class org.openscience.cdk.debug.DebugAtomType
-
Gets the MaxBondOrder attribute of the AtomType object.
- getMaxBondOrder() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Gets the MaxBondOrder attribute of the AtomType object.
- getMaxBondOrder() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Gets the MaxBondOrder attribute of the AtomType object.
- getMaxBondOrder() - Method in interface org.openscience.cdk.interfaces.IAtomType
-
Gets the MaxBondOrder attribute of the AtomType object.
- getMaxBondOrder() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Gets the MaxBondOrder attribute of the AtomType object.
- getMaxBondOrder() - Method in class org.openscience.cdk.silent.AtomType
-
Gets the MaxBondOrder attribute of the AtomType object.
- getMaxCliqueSet() - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.BKKCKCF
-
- getMaxGasteigerDamp() - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
-
Gets the maxGasteigerDamp attribute of the GasteigerMarsiliPartialCharges
object.
- getMaxGasteigerIters() - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
-
Gets the maxGasteigerIters attribute of the GasteigerMarsiliPartialCharges
object.
- getMaxGasteigerIters() - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges
-
Gets the maxGasteigerIters attribute of the GasteigerPEPEPartialCharges
object.
- getMaximalFormula(MolecularFormulaRange, IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaRangeManipulator
-
Returns the maximal occurrence of the IIsotope into IMolecularFormula
from this MolelecularFormulaRange.
- getMaximalStructures() - Method in class org.openscience.cdk.tools.StructureResonanceGenerator
-
Get the number maximal of resonance structures to be found.
- getMaximum(List) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
-
- getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Returns the maximum bond order that this atom currently has in the context
of this AtomContainer.
- getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns the maximum bond order that this atom currently has in the context
of this AtomContainer.
- getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns the maximum bond order that this atom currently has in the context
of this AtomContainer.
- getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns the maximum bond order that this atom currently has in the context
of this AtomContainer.
- getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns the maximum bond order that this atom currently has in the context
of this AtomContainer.
- getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns the maximum bond order that this atom currently has in the context
of this AtomContainer.
- getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns the maximum bond order that this atom currently has in the context
of this AtomContainer.
- getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
Returns the maximum bond order that this atom currently has in the context
of this AtomContainer.
- getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns the maximum bond order that this atom currently has in the context
of this AtomContainer.
- getMaximumBondOrder(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the maximum bond order that this atom currently has in the context
of this AtomContainer.
- getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the maximum bond order that this atom currently has in the context
of this AtomContainer.
- getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the maximum bond order that this atom currently has in the context
of this AtomContainer.
- getMaximumBondOrder(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
- getMaximumBondOrder(List<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
-
Returns the maximum bond order for a List of bonds.
- getMaximumBondOrder(Iterator<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
-
Returns the maximum bond order for a List of bonds, given an iterator to the list.
- getMaximumBondOrder(IBond, IBond) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
-
Returns the maximum bond order for the two bonds.
- getMaximumBondOrder(IBond.Order, IBond.Order) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
-
Returns the maximum bond order for the two bond orders.
- getMaxIterations() - Method in class org.openscience.cdk.charges.Electronegativity
-
get the maximum number of Iterations.
- getMaxIterations() - Method in class org.openscience.cdk.charges.PiElectronegativity
-
get the maximum number of Iterations.
- getMaxNoOfBonds(IAtom) - Method in class org.openscience.cdk.tools.AtomTypeAwareSaturationChecker
-
This method calculates the number of bonds that an IAtom
can have.
- getMaxOccurrenceElements(IMolecularFormulaSet) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaSetManipulator
-
Extract from a set of MolecularFormula the maximum occurrence of each element found and
put the element and occurrence in a new IMolecularFormula.
- getMaxResonStruc() - Method in class org.openscience.cdk.charges.Electronegativity
-
get the maximum number of resonance structures.
- getMaxResonStruc() - Method in class org.openscience.cdk.charges.PiElectronegativity
-
get the maximum number of resonance structures.
- getMaxResoStruc() - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges
-
Gets the maximum resonance structures to be searched.
- getMaxX() - Method in class org.openscience.cdk.math.qm.FourierGridBasis
-
- getMaxX() - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Gets the dimension of the volume, which describes the base.
- getMaxX() - Method in interface org.openscience.cdk.math.qm.IBasis
-
Gets the dimension of the volume, which describes the base.
- getMaxx() - Method in class org.openscience.cdk.tools.GridGenerator
-
- getMaxY() - Method in class org.openscience.cdk.math.qm.FourierGridBasis
-
- getMaxY() - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Gets the dimension of the volume, which describes the base.
- getMaxY() - Method in interface org.openscience.cdk.math.qm.IBasis
-
Gets the dimension of the volume, which describes the base.
- getMaxy() - Method in class org.openscience.cdk.tools.GridGenerator
-
- getMaxZ() - Method in class org.openscience.cdk.math.qm.FourierGridBasis
-
- getMaxZ() - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Gets the dimension of the volume, which describes the base.
- getMaxZ() - Method in interface org.openscience.cdk.math.qm.IBasis
-
Gets the dimension of the volume, which describes the base.
- getMaxz() - Method in class org.openscience.cdk.tools.GridGenerator
-
- getMCSSize() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregor
-
Returns MCS size.
- getMechanism() - Method in class org.openscience.cdk.dict.EntryReact
-
Get the mechanism of this reaction.
- getMerge() - Method in class org.openscience.cdk.renderer.RendererModel
-
This is the central facility for handling "merges" of atoms.
- getMessage() - Method in class org.openscience.cdk.inchi.InChIGenerator
-
Gets generated (error/warning) messages.
- getMessage() - Method in class org.openscience.cdk.inchi.InChIToStructure
-
Gets generated (error/warning) messages.
- getMessage() - Method in error org.openscience.cdk.iupac.parser.TokenMgrError
-
You can also modify the body of this method to customize your error messages.
- getMessage() - Method in error org.openscience.cdk.smiles.smarts.parser.TokenMgrError
-
You can also modify the body of this method to customize your error messages.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.ABINITFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.Aces2Format
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.ADFFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.AlchemyFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.BGFFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.BSFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.CACheFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.CIFFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.CMLFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.CRK2DFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.CRK3DFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.CrystClustFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.CTXFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.DaltonFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.DMol3Format
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.DOCK5Format
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.FingerprintFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.GamessFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian03Format
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian90Format
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian92Format
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian94Format
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian95Format
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.Gaussian98Format
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat
-
- getMIMEType() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.GROMOS96Format
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.HINFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.INChIFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in interface org.openscience.cdk.io.formats.IResourceFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.JaguarFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.JMEFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.MacroModelFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.MDLFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.MDLV2000Format
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.MDLV3000Format
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.MMODFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.Mol2Format
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC7Format
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC93Format
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.MOPAC97Format
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.MPQCFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.NWChemFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.PCModelFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.PDBFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.PDBMLFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.PMPFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.POVRayFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.PQSChemFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.QChemFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.RawCopyFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.SDFFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.ShelXFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.SMARTSFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.SMILESFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.SpartanFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.SVGFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.VASPFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.ViewmolFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.XEDFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.XYZFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.YasaraFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.ZindoFormat
-
Returns the accepted MIME type for this format.
- getMIMEType() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat
-
Returns the accepted MIME type for this format.
- getMinimalFormula(MolecularFormulaRange, IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaRangeManipulator
-
Returns the minimal occurrence of the IIsotope into IMolecularFormula
from this MolelecularFormulaRange.
- getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Returns the minimum bond order that this atom currently has in the context
of this AtomContainer.
- getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns the minimum bond order that this atom currently has in the context
of this AtomContainer.
- getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns the minimum bond order that this atom currently has in the context
of this AtomContainer.
- getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns the minimum bond order that this atom currently has in the context
of this AtomContainer.
- getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns the minimum bond order that this atom currently has in the context
of this AtomContainer.
- getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns the minimum bond order that this atom currently has in the context
of this AtomContainer.
- getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns the minimum bond order that this atom currently has in the context
of this AtomContainer.
- getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
Returns the minimum bond order that this atom currently has in the context
of this AtomContainer.
- getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns the minimum bond order that this atom currently has in the context
of this AtomContainer.
- getMinimumBondOrder(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the minimum bond order that this atom currently has in the context
of this AtomContainer.
- getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the minimum bond order that this atom currently has in the context
of this AtomContainer.
- getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the minimum bond order that this atom currently has in the context
of this AtomContainer.
- getMinimumBondOrder(List<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
-
Returns the minimum bond order for a List of bonds.
- getMinimumBondOrder(Iterator<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
-
Returns the minimum bond order for a List of bonds, given an iterator
to the list.
- getMinMax(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Returns the minimum and maximum X and Y coordinates of the atoms in the
AtomContainer.
- getMinMax(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Returns the minimum and maximum X and Y coordinates of the atoms in the
AtomContainer.
- getMinOccurrenceElements(IMolecularFormulaSet) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaSetManipulator
-
Extract from a set of MolecularFormula the minimal occurrence of each element found and
put the element and occurrence in a new IMolecularFormula.
- getMinPSCluster() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- getMinPSPocket() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- getMinX() - Method in class org.openscience.cdk.math.qm.FourierGridBasis
-
- getMinX() - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Gets the dimension of the volume, which describes the base.
- getMinX() - Method in interface org.openscience.cdk.math.qm.IBasis
-
Gets the dimension of the volume, which describes the base.
- getMinx() - Method in class org.openscience.cdk.tools.GridGenerator
-
- getMinY() - Method in class org.openscience.cdk.math.qm.FourierGridBasis
-
- getMinY() - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Gets the dimension of the volume, which describes the base.
- getMinY() - Method in interface org.openscience.cdk.math.qm.IBasis
-
Gets the dimension of the volume, which describes the base.
- getMiny() - Method in class org.openscience.cdk.tools.GridGenerator
-
- getMinZ() - Method in class org.openscience.cdk.math.qm.FourierGridBasis
-
- getMinZ() - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Gets the dimension of the volume, which describes the base.
- getMinZ() - Method in interface org.openscience.cdk.math.qm.IBasis
-
Gets the dimension of the volume, which describes the base.
- getMinz() - Method in class org.openscience.cdk.tools.GridGenerator
-
- getModelCenter() - Method in class org.openscience.cdk.renderer.AbstractRenderer
-
Get the center of the model.
- getMolecularFormula(int) - Method in class org.openscience.cdk.debug.DebugAdductFormula
-
Returns the MolecularFormula at position number
in the
chemObject.
- getMolecularFormula(int) - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet
-
Returns the MolecularFormula at position number
in the
chemObject.
- getMolecularFormula(int) - Method in class org.openscience.cdk.formula.AdductFormula
-
Returns the MolecularFormula at position number
in the
chemObject.
- getMolecularFormula(int) - Method in class org.openscience.cdk.formula.MolecularFormulaSet
-
Returns the MolecularFormula at position number
in the
chemObject.
- getMolecularFormula(int) - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet
-
Returns the IMolecularFormula at position number
in the
chemObject.
- getMolecularFormula(int) - Method in class org.openscience.cdk.silent.AdductFormula
-
Returns the MolecularFormula at position number
in the
chemObject.
- getMolecularFormula(int) - Method in class org.openscience.cdk.silent.MolecularFormulaSet
-
Returns the MolecularFormula at position number
in the
chemObject.
- getMolecularFormula(String, IChemObjectBuilder) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Construct an instance of IMolecularFormula, initialized with a molecular
formula string.
- getMolecularFormula(String, IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
add in a instance of IMolecularFormula the elements extracts form
molecular formula string.
- getMolecularFormula(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Method that actually does the work of convert the atomContainer
to IMolecularFormula.
- getMolecularFormula(IAtomContainer, IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Method that actually does the work of convert the atomContainer
to IMolecularFormula given a IMolecularFormula.
- getMolecularGraphDiameter(IAtomContainer) - Static method in class org.openscience.cdk.graph.PathTools
-
Returns the diameter of the molecular graph.
- getMolecularGraphRadius(IAtomContainer) - Static method in class org.openscience.cdk.graph.PathTools
-
Returns the radius of the molecular graph.
- getMolecule() - Method in class org.openscience.cdk.layout.AtomPlacer
-
Return the molecule the AtomPlacer currently works with
- getMolecule() - Method in class org.openscience.cdk.layout.RingPlacer
-
- getMolecule() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
-
Returns the molecule, usually used after a call of generateCoordinates()
- getMolecule() - Method in class org.openscience.cdk.smsd.tools.MolHandler
-
Returns the modified container
- getMolecule() - Method in class org.openscience.cdk.structgen.RandomGenerator
-
Returns the molecule which reflects the current state of this
stochastic structure generator.
- getMoleculeGraph(IAtomContainer) - Static method in class org.openscience.cdk.graph.MoleculeGraphs
-
Creates a molecule graph for use with jgrapht.
- getMoleculeSet() - Method in class org.openscience.cdk.ChemModel
-
Returns the MoleculeSet of this ChemModel.
- getMoleculeSet() - Method in class org.openscience.cdk.debug.DebugChemModel
-
Returns the MoleculeSet of this ChemModel.
- getMoleculeSet() - Method in interface org.openscience.cdk.interfaces.IChemModel
-
Returns the IAtomContainerSet of this ChemModel.
- getMoleculeSet() - Method in class org.openscience.cdk.silent.ChemModel
-
Returns the MoleculeSet of this ChemModel.
- getMonoIsotope() - Method in class org.openscience.cdk.formula.IsotopePattern
-
Returns the mono-isotope peak that form this isotope pattern.
- getMonomer(String, String) - Method in class org.openscience.cdk.BioPolymer
-
Retrieves a Monomer object by specifying its name.
- getMonomer(String) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Retrieves a Monomer object by specifying its name.
- getMonomer(String, String) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Retrieves a Monomer object by specifying its name.
- getMonomer(String) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Retrieves a Monomer object by specifying its name.
- getMonomer(String) - Method in class org.openscience.cdk.debug.DebugStrand
-
Retrieves a Monomer object by specifying its name.
- getMonomer(String, String) - Method in interface org.openscience.cdk.interfaces.IBioPolymer
-
Retrieve a Monomer
object by specifying its name.
- getMonomer(String) - Method in interface org.openscience.cdk.interfaces.IPolymer
-
Retrieve a Monomer object by specifying its name.
- getMonomer(String) - Method in interface org.openscience.cdk.interfaces.IStrand
-
Retrieve a Monomer object by specifying its name.
- getMonomer(String) - Method in class org.openscience.cdk.Polymer
-
Retrieves a Monomer object by specifying its name.
- getMonomer(String, String) - Method in class org.openscience.cdk.silent.BioPolymer
-
Retrieves a Monomer object by specifying its name.
- getMonomer(String) - Method in class org.openscience.cdk.silent.Polymer
-
Retrieves a Monomer object by specifying its name.
- getMonomer(String) - Method in class org.openscience.cdk.silent.Strand
-
Retrieves a Monomer object by specifying its name.
- getMonomer(String) - Method in class org.openscience.cdk.Strand
-
Retrieves a Monomer object by specifying its name.
- getMonomerCount() - Method in class org.openscience.cdk.BioPolymer
-
Returns the number of monomers present in BioPolymer.
- getMonomerCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns the number of monomers present in BioPolymer.
- getMonomerCount() - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns the number of monomers present in the Polymer.
- getMonomerCount() - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns the number of monomers present in the Strand.
- getMonomerCount() - Method in interface org.openscience.cdk.interfaces.IBioPolymer
-
Return the number of monomers present in BioPolymer.
- getMonomerCount() - Method in interface org.openscience.cdk.interfaces.IPolymer
-
Return the number of monomers present in the Polymer.
- getMonomerCount() - Method in interface org.openscience.cdk.interfaces.IStrand
-
Return the number of monomers present in the Strand.
- getMonomerCount() - Method in class org.openscience.cdk.Polymer
-
Returns the number of monomers present in the Polymer.
- getMonomerCount() - Method in class org.openscience.cdk.silent.BioPolymer
-
Returns the number of monomers present in BioPolymer.
- getMonomerCount() - Method in class org.openscience.cdk.silent.Polymer
-
Returns the number of monomers present in the Polymer.
- getMonomerCount() - Method in class org.openscience.cdk.silent.Strand
-
Returns the number of monomers present in the Strand.
- getMonomerCount() - Method in class org.openscience.cdk.Strand
-
Returns the number of monomers present in the Strand.
- getMonomerName() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Retrieves the monomer name.
- getMonomerName() - Method in class org.openscience.cdk.debug.DebugMonomer
-
Retrieves the monomer name.
- getMonomerName() - Method in interface org.openscience.cdk.interfaces.IMonomer
-
Retrieve the monomer name.
- getMonomerName() - Method in class org.openscience.cdk.Monomer
-
Retrieves the monomer name.
- getMonomerName() - Method in class org.openscience.cdk.silent.Monomer
-
Retrieves the monomer name.
- getMonomerNames() - Method in class org.openscience.cdk.BioPolymer
-
Returns a collection of the names of all Monomer
s in this
BioPolymer.
- getMonomerNames() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns a collection of the names of all Monomer
s in this
BioPolymer.
- getMonomerNames() - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns a collection of the names of all Monomer
s in this
polymer.
- getMonomerNames() - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns a collection of the names of all Monomer
s in this
polymer.
- getMonomerNames() - Method in interface org.openscience.cdk.interfaces.IBioPolymer
-
Returns a collection of the names of all Monomer
s in this
BioPolymer.
- getMonomerNames() - Method in interface org.openscience.cdk.interfaces.IPolymer
-
Returns a collection of the names of all Monomer
s in this
polymer.
- getMonomerNames() - Method in interface org.openscience.cdk.interfaces.IStrand
-
Returns a collection of the names of all Monomer
s in this
polymer.
- getMonomerNames() - Method in class org.openscience.cdk.Polymer
-
Returns a collection of the names of all Monomer
s in this
polymer.
- getMonomerNames() - Method in class org.openscience.cdk.silent.BioPolymer
-
Returns a collection of the names of all Monomer
s in this
BioPolymer.
- getMonomerNames() - Method in class org.openscience.cdk.silent.Polymer
-
Returns a collection of the names of all Monomer
s in this
polymer.
- getMonomerNames() - Method in class org.openscience.cdk.silent.Strand
-
Returns a collection of the names of all Monomer
s in this
polymer.
- getMonomerNames() - Method in class org.openscience.cdk.Strand
-
Returns a collection of the names of all Monomer
s in this
polymer.
- getMonomerNamesInSequentialOrder() - Method in class org.openscience.cdk.protein.data.PDBPolymer
-
Returns the monomer names in the order in which they were added.
- getMonomerNamesInSequentialOrder() - Method in class org.openscience.cdk.protein.data.PDBStrand
-
Returns the monomer names in the order in which they were added.
- getMonomerNamesInSequentialOrder() - Method in class org.openscience.cdk.silent.PDBPolymer
-
Returns the monomer names in the order in which they were added.
- getMonomers() - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns a hashtable containing the monomers in the strand.
- getMonomers() - Method in interface org.openscience.cdk.interfaces.IStrand
-
Returns the monomers in this strand.
- getMonomers() - Method in class org.openscience.cdk.silent.Strand
-
Returns a hashtable containing the monomers in the strand.
- getMonomers() - Method in class org.openscience.cdk.Strand
-
Returns a hashtable containing the monomers in the strand.
- getMonomerType() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Retrieves the monomer type.
- getMonomerType() - Method in class org.openscience.cdk.debug.DebugMonomer
-
Retrieves the monomer type.
- getMonomerType() - Method in interface org.openscience.cdk.interfaces.IMonomer
-
Retrieve the monomer type.
- getMonomerType() - Method in class org.openscience.cdk.Monomer
-
Retrieves the monomer type.
- getMonomerType() - Method in class org.openscience.cdk.silent.Monomer
-
Retrieves the monomer type.
- getMorganNumbers(IAtomContainer) - Static method in class org.openscience.cdk.graph.invariant.MorganNumbersTools
-
Makes an array containing the morgan numbers of the atoms of
atomContainer.
- getMorganNumbersWithElementSymbol(IAtomContainer) - Static method in class org.openscience.cdk.graph.invariant.MorganNumbersTools
-
Makes an array containing the morgan numbers+element symbol of the atoms
of atomContainer
.
- getMostComplexRing(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator
-
Returns the ring with the highest numbers of other rings attached to it.
- getMultiMap() - Method in class org.openscience.cdk.io.RssWriter
-
- getMultiplier(int) - Method in class org.openscience.cdk.AtomContainerSet
-
Returns the multiplier for the AtomContainer at position number
in the
container.
- getMultiplier(IAtomContainer) - Method in class org.openscience.cdk.AtomContainerSet
-
Returns the multiplier of the given AtomContainer.
- getMultiplier(int) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
Returns the multiplier for the AtomContainer at position number
in the
container.
- getMultiplier(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
Returns the multiplier of the given AtomContainer.
- getMultiplier(int) - Method in class org.openscience.cdk.debug.DebugSubstance
-
Returns the multiplier for the AtomContainer at position number
in the
container.
- getMultiplier(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugSubstance
-
Returns the multiplier of the given AtomContainer.
- getMultiplier(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
-
Returns the multiplier for the AtomContainer at position number
in the
container.
- getMultiplier(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
-
Returns the multiplier of the given AtomContainer.
- getMultiplier(int) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Returns the multiplier for the AtomContainer at position number
in the
container.
- getMultiplier(IAtomContainer) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Returns the multiplier of the given AtomContainer.
- getMultipliers() - Method in class org.openscience.cdk.AtomContainerSet
-
Returns an array of double with the stoichiometric coefficients
of the products.
- getMultipliers() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
Returns an array of double with the stoichiometric coefficients
of the products.
- getMultipliers() - Method in class org.openscience.cdk.debug.DebugSubstance
-
Returns an array of double with the stoichiometric coefficients
of the products.
- getMultipliers() - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
-
Returns an array of double with the stoichiometric coefficients
of the products.
- getMultipliers() - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Returns an array of double with the stoichiometric coefficients
of the products.
- getName() - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
get the Atom name of this atom.
- getName() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
get the Atom name of this atom.
- getName() - Method in interface org.openscience.cdk.interfaces.ISetting
-
Access the name of the setting.
- getName() - Method in class org.openscience.cdk.io.setting.IOSetting
-
- getName() - Method in class org.openscience.cdk.iupac.parser.AttachedGroup
-
Getter for property name.
- getName() - Method in class org.openscience.cdk.libio.md.Residue
-
- getName() - Method in class org.openscience.cdk.protein.data.PDBAtom
-
get the Atom name of this atom.
- getName() - Method in class org.openscience.cdk.silent.PDBAtom
-
get the Atom name of this atom.
- getName(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
-
Get the name of the element.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.ABINITFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.Aces2Format
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.ADFFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.AlchemyFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.BGFFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.BSFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.CACheFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.CIFFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.CMLFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.CRK2DFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.CRK3DFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.CrystClustFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.CTXFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.DaltonFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.DMol3Format
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.DOCK5Format
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.FingerprintFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.GamessFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian03Format
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian90Format
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian92Format
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian94Format
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian95Format
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.Gaussian98Format
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat
-
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.GROMOS96Format
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.HINFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.INChIFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in interface org.openscience.cdk.io.formats.IResourceFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.JaguarFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.JMEFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.MacroModelFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.MDLFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.MDLV2000Format
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.MDLV3000Format
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.MMODFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.Mol2Format
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC7Format
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC93Format
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.MOPAC97Format
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.MPQCFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.NWChemFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.PCModelFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.PDBFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.PDBMLFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.PMPFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.POVRayFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.PQSChemFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.QChemFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.RawCopyFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.SDFFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.ShelXFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.SMARTSFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.SMILESFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.SpartanFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.SVGFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.VASPFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.ViewmolFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.XEDFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.XYZFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.YasaraFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.ZindoFormat
-
Returns an array of common resource name extensions.
- getNameExtensions() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat
-
Returns an array of common resource name extensions.
- getNames() - Static method in class org.openscience.cdk.config.fragments.EStateFragments
-
Get the fragment names.
- getNames() - Method in class org.openscience.cdk.qsar.DescriptorValue
-
Returns an array of names for each descriptor value calculated.
- getNativeRingRadius(IRing, double) - Method in class org.openscience.cdk.layout.RingPlacer
-
Returns the ring radius of a perfect polygons of size ring.getAtomCount()
The ring radius is the distance of each atom to the ringcenter.
- getNaturalAbundance() - Method in class org.openscience.cdk.debug.DebugAtom
-
Gets the NaturalAbundance attribute of the Isotope object.
- getNaturalAbundance() - Method in class org.openscience.cdk.debug.DebugAtomType
-
Gets the NaturalAbundance attribute of the Isotope object.
- getNaturalAbundance() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Gets the NaturalAbundance attribute of the Isotope object.
- getNaturalAbundance() - Method in class org.openscience.cdk.debug.DebugIsotope
-
Gets the NaturalAbundance attribute of the Isotope object.
- getNaturalAbundance() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Gets the NaturalAbundance attribute of the Isotope object.
- getNaturalAbundance() - Method in interface org.openscience.cdk.interfaces.IIsotope
-
Gets the NaturalAbundance attribute of the Isotope object.
- getNaturalAbundance() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Gets the NaturalAbundance attribute of the Isotope object.
- getNaturalAbundance() - Method in class org.openscience.cdk.Isotope
-
Gets the NaturalAbundance attribute of the Isotope object.
- getNaturalAbundance() - Method in class org.openscience.cdk.silent.Isotope
-
Gets the NaturalAbundance attribute of the Isotope object.
- getNaturalExactMass(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Returns the molecular mass of the IAtomContainer.
- getNaturalExactMass(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Get the summed natural mass of all elements from an MolecularFormula.
- getNaturalMass(IElement) - Method in class org.openscience.cdk.config.IsotopeFactory
-
Gets the natural mass of this element, defined as average of masses of isotopes,
weighted by abundance.
- getNeighborBondNumA() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper
-
- getNeighborBondNumA() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.QueryProcessor
-
- getNeighborBondNumB() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper
-
- getNeighborBondNumB() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.TargetProcessor
-
- getNeighbors(int) - Method in class org.openscience.cdk.geometry.surface.NeighborList
-
- getNeighbors(IAtom) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.TargetProperties
-
- getNextBond(IBond, IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
Returns the next bond in order, relative to a given bond and atom.
- getNextBond(IBond, IAtom) - Method in interface org.openscience.cdk.interfaces.IRing
-
Returns the next bond in order, relative to a given bond and atom.
- getNextBond(IBond, IAtom) - Method in class org.openscience.cdk.Ring
-
Returns the next bond in order, relative to a given bond and atom.
- getNextBond(IBond, IAtom) - Method in class org.openscience.cdk.silent.Ring
-
Returns the next bond in order, relative to a given bond and atom.
- getNextBondVector(IAtom, IAtom, Point2d, boolean) - Method in class org.openscience.cdk.layout.AtomPlacer
-
Returns the next bond vector needed for drawing an extended linear chain of
atoms.
- getNextFormula() - Method in class org.openscience.cdk.formula.MolecularFormulaGenerator
-
Returns next generated formula or null in case no new formula was found
(search is finished).
- getNextPermutation() - Method in class org.openscience.cdk.graph.Permutor
-
Get the next permutation in the list.
- getNextPermutation() - Method in class org.openscience.cdk.smsd.labelling.Permutor
-
Get the next permutation in the list.
- getNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
-
Gets the nextPlacedHeavyAtomWithAliphaticPlacedNeigbor from an atom container or molecule.
- getNextPlacedHeavyAtomWithUnplacedRingNeighbour(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
-
Gets the nextPlacedHeavyAtomWithUnplacedRingNeighbour attribute of the AtomPlacer3D object.
- getNextToken() - Method in class org.openscience.cdk.iupac.parser.NomParser
-
Deprecated.
Get the next Token.
- getNextToken() - Method in class org.openscience.cdk.iupac.parser.NomParserTokenManager
-
Get the next Token.
- getNextToken() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
Get the next Token.
- getNextToken() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager
-
Get the next Token.
- getNextUnplacedHeavyAtomWithAliphaticPlacedNeighbour(IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
-
Gets the nextUnplacedHeavyAtomWithAliphaticPlacedNeighbour from an atom container or molecule.
- getNode(int) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder
-
Returns a node of the query mol at a given position.
- getNode(IAtom) - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder
-
Return a node for a given atom else return null
- getNode(int) - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQuery
-
Returns a node of the query mol at a given position.
- getNodesInSphere(int) - Method in class org.openscience.cdk.tools.HOSECodeGenerator
-
- getNormal(Point3d, Point3d, Point3d) - Static method in class org.openscience.cdk.stereo.StereoTool
-
Given three points (A, B, C), makes the vectors A-B and A-C, and makes
the cross product of these two vectors; this has the effect of making a
third vector at right angles to AB and AC.
- getNormalizationFactor(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Calculates the normalization factor in order to get an average bond length
of 1.5.
- getNormalizationFactor(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Calculates the normalization factor in order to get an average bond length of 1.5.
- getNormalizedElectronegativity(String) - Method in class org.openscience.cdk.tools.AtomicProperties
-
- getNormalizedMass(String) - Method in class org.openscience.cdk.tools.AtomicProperties
-
- getNormalizedPolarizability(String) - Method in class org.openscience.cdk.tools.AtomicProperties
-
- getNormalizedVdWVolume(String) - Method in class org.openscience.cdk.tools.AtomicProperties
-
- getNotEqual() - Method in class org.openscience.cdk.smsd.helper.BinaryTree
-
Returns not equal node
- getNotification() - Method in class org.openscience.cdk.ChemObject
-
- getNotification() - Method in class org.openscience.cdk.debug.DebugChemObject
-
Returns the flag that indicates whether notification messages are sent around.
- getNotification() - Method in interface org.openscience.cdk.interfaces.IChemObject
-
Returns the flag that indicates whether notification messages are sent around.
- getNotification() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
- getNotification() - Method in class org.openscience.cdk.renderer.RendererModel
-
Determines if the model sends around change notifications.
- getNotification() - Method in class org.openscience.cdk.silent.ChemObject
-
- getNS() - Method in class org.openscience.cdk.dict.Dictionary
-
- getNTerminus() - Method in class org.openscience.cdk.AminoAcid
-
Retrieves the N-terminus atom.
- getNTerminus() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Retrieves the N-terminus atom.
- getNTerminus() - Method in interface org.openscience.cdk.interfaces.IAminoAcid
-
Retrieves the N-terminus atom.
- getNTerminus() - Method in class org.openscience.cdk.silent.AminoAcid
-
Retrieves the N-terminus atom.
- getNumAtoms() - Method in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
-
- getNumber() - Method in class org.openscience.cdk.libio.md.ChargeGroup
-
- getNumber() - Method in class org.openscience.cdk.libio.md.Residue
-
- getNumberOfFontSizes() - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
-
Get the number of font sizes used.
- getNumberOfIsotopes() - Method in class org.openscience.cdk.formula.IsotopePattern
-
Returns the number of isotopes in this pattern.
- getNumberOfNeighbors(int) - Method in class org.openscience.cdk.geometry.surface.NeighborList
-
- getNumberOfTriangles() - Method in class org.openscience.cdk.geometry.surface.Tessellate
-
- getNumbers(IAtomContainer) - Static method in class org.openscience.cdk.graph.invariant.InChINumbersTools
-
Makes an array containing the InChI atom numbers of the non-hydrogen
atoms in the atomContainer.
- getOccupancy() - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
get the Occupancy of this atom.
- getOccupancy() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
get the Occupancy of this atom.
- getOccupancy() - Method in class org.openscience.cdk.protein.data.PDBAtom
-
get the Occupancy of this atom.
- getOccupancy() - Method in class org.openscience.cdk.silent.PDBAtom
-
get the Occupancy of this atom.
- getOccurrence() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
-
Returns the occurrence value.
- getOKCount() - Method in class org.openscience.cdk.validate.ValidationReport
-
Returns the number of tests without errors.
- getOKs() - Method in class org.openscience.cdk.validate.ValidationReport
-
Returns an array of ValidationTest which did not find problems.
- getOperator() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom
-
Deprecated.
- getOperator() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond
-
- getOptions() - Method in class org.openscience.cdk.io.setting.OptionIOSetting
-
Returns a Vector of Strings containing all possible options.
- getOrbit(int) - Method in class org.openscience.cdk.group.Permutation
-
Get all the elements in the same orbit in the permutation (unsorted).
- getOrder() - Method in class org.openscience.cdk.Bond
-
Returns the bond order of this bond.
- getOrder() - Method in class org.openscience.cdk.debug.DebugBond
-
Returns the bond order of this bond.
- getOrder() - Method in interface org.openscience.cdk.interfaces.IBond
-
Returns the bond order of this bond.
- getOrder() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Returns the query bond order of this query bond.
- getOrder() - Method in class org.openscience.cdk.silent.Bond
-
Returns the bond order of this bond.
- getOtherBondAtom(IAtom, IBond) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
-
Returns the other atom of the bond.
- getOverlaps(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
-
Returns all the maximal common substructure between two atom containers.
- getOverlaps(IAtomContainer, IAtomContainer, boolean) - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlus
-
- getOverlaps(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
-
Returns all the maximal common substructure between 2 atom containers.
- getOverLaps(IAtomContainer, IAtomContainer, boolean) - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMapping
-
Returns single mapping solutions.
- getOverLaps(IQueryAtomContainer, IAtomContainer, boolean) - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMapping
-
Returns single mapping solutions.
- getOverlapScore(IAtomContainer, Vector, Vector) - Method in class org.openscience.cdk.layout.OverlapResolver
-
Deprecated.
Calculates a score based on the overlap of atoms and intersection of bonds.
- getOxt() - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
Returns true of this atom is a PDB OXT atom.
- getOxt() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
Returns true of this atom is a PDB OXT atom.
- getOxt() - Method in class org.openscience.cdk.protein.data.PDBAtom
-
- getOxt() - Method in class org.openscience.cdk.silent.PDBAtom
-
- getParameter(Class<T>) - Method in class org.openscience.cdk.renderer.RendererModel
-
- 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.AcidicGroupCountDescriptor
-
Returns the names of the parameters for this descriptor.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
-
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor
-
Gets the parameterNames attribute of the AromaticAtomsCountDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor
-
Gets the parameterNames attribute of the APolDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor
-
Gets the parameterNames attribute of the AromaticAtomsCountDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor
-
Gets the parameterNames attribute of the AromaticBondsCountDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor
-
Gets the parameterNames attribute of the AtomCountDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
-
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
-
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
-
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor
-
Returns the names of the parameters for this descriptor.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor
-
Gets the parameterNames attribute of the BCUTDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor
-
Gets the parameterNames attribute of the BondCountDescriptor object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor
-
Gets the parameterNames attribute of the BPolDescriptor object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor
-
Gets the parameterNames attribute of the GravitationalIndexDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
-
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
-
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
-
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
-
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor
-
Gets the parameterNames attribute of the CPSADescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor
-
Gets the parameterNames attribute of the EccentricConnectivityIndexDescriptor object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor
-
Returns the names of the parameters for this descriptor.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor
-
Returns the names of the parameters for this descriptor.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor
-
Gets the parameterNames attribute of the FragmentComplexityDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor
-
Gets the parameterNames attribute of the GravitationalIndexDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor
-
Gets the parameterNames attribute of the HBondAcceptorCountDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor
-
Gets the parameterNames of the HBondDonorCountDescriptor.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor
-
Gets the parameterNames attribute of the HybridizationRatioDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor
-
Gets the parameterNames attribute of the IPMolecularLearningDescriptor object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor
-
Gets the parameterNames attribute of the
KappaShapeIndicesDescriptor object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor
-
Gets the parameterNames attribute of the descriptor.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor
-
Gets the parameterNames attribute of the LargestPiSystemDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor
-
Gets the parameterNames attribute of the LargestPiSystemDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor
-
Gets the parameterNames attribute of the PetitjeanNumberDescriptor object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor
-
Gets the parameterNames attribute of the LongestAliphaticChainDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor
-
Gets the parameterNames attribute for this descriptor.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
-
Gets the parameterNames attribute of the WeightDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor
-
Gets the parameterNames attribute of the MomentOfInertiaDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor
-
Gets the parameterNames attribute of the PetitjeanNumberDescriptor object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor
-
Gets the parameterNames attribute of the PetitjeanShapeIndexDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor
-
Gets the parameterNames attribute of the RotatableBondsCountDescriptor
object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor
-
Gets the parameterNames attribute of the RuleOfFiveDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor
-
Get parameters: empty, there are none.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor
-
Gets the parameterNames attribute of the TPSADescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor
-
Returns the names of the parameters for this descriptor.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor
-
Gets the parameterNames attribute of the VAdjMaDescriptor object
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor
-
Gets the parameterNames attribute of the WeightDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor
-
Gets the parameterNames attribute of the WeightedPathDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor
-
Gets the parameterNames attribute of the WHIMDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor
-
Gets the parameterNames attribute of the WienerNumbersDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor
-
Gets the parameterNames attribute of the XLogPDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor
-
Gets the parameterNames attribute of the ZagrebIndexDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor
-
Gets the parameterNames attribute of the TaeAminOAcidDescriptor object.
- getParameterNames() - Method in class org.openscience.cdk.qsar.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.AcidicGroupCountDescriptor
-
Returns the current parameter values.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
-
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor
-
Gets the parameters attribute of the AminoAcidsCountDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor
-
Gets the parameters attribute of the APolDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor
-
Gets the parameters attribute of the AromaticAtomsCountDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor
-
Gets the parameters attribute of the AromaticBondsCountDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor
-
Gets the parameters attribute of the AtomCountDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
-
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
-
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
-
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor
-
Returns the current parameter values.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor
-
Gets the parameters attribute of the BCUTDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor
-
Gets the parameters attribute of the BondCountDescriptor object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor
-
Gets the parameters attribute of the BPolDescriptor object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor
-
Gets the parameters attribute of the GravitationalIndexDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
-
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
-
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
-
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
-
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor
-
Gets the parameters attribute of the CPSADescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor
-
Gets the parameters attribute of the EccentricConnectivityIndexDescriptor object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor
-
Returns the current parameter values.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor
-
Returns the current parameter values.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor
-
Gets the parameters attribute of the FragmentComplexityDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor
-
Gets the parameters attribute of the GravitationalIndexDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor
-
Gets the parameters attribute of the HBondAcceptorCountDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor
-
Gets the parameters of the HBondDonorCountDescriptor instance.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor
-
Gets the parameters attribute of the HybridizationRatioDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor
-
Gets the parameters attribute of the IPMolecularLearningDescriptor object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor
-
Gets the parameters attribute of the
KappaShapeIndicesDescriptor object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor
-
Gets the parameters attribute of the descriptor.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor
-
Gets the parameters attribute of the LargestChainDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor
-
Gets the parameters attribute of the LargestPiSystemDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor
-
Gets the parameters attribute of the PetitjeanNumberDescriptor object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor
-
Gets the parameters attribute of the LongestAliphaticChainDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor
-
Gets the parameters attribute of the MannholdLogPDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
-
Gets the parameters attribute of the WeightDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor
-
Gets the parameters attribute of the MomentOfInertiaDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor
-
Gets the parameters attribute of the PetitjeanNumberDescriptor object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor
-
Gets the parameters attribute of the PetitjeanShapeIndexDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor
-
Gets the parameters attribute of the RotatableBondsCountDescriptor object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor
-
Gets the parameters attribute of the RuleOfFiveDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor
-
Get parameters: returns empty array, there are none.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor
-
Gets the parameters attribute of the TPSADescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor
-
Returns the current parameter values.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor
-
Gets the parameters attribute of the VAdjMaDescriptor object
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor
-
Gets the parameters attribute of the WeightDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor
-
Gets the parameters attribute of the WeightedPathDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor
-
Gets the parameters attribute of the WHIMDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor
-
Gets the parameters attribute of the WienerNumbersDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor
-
Gets the parameters attribute of the XLogPDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor
-
Gets the parameters attribute of the ZagrebIndexDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor
-
Gets the parameters attribute of the TaeAminoAcidDescriptor object.
- getParameters() - Method in class org.openscience.cdk.qsar.DescriptorValue
-
- getParameters() - Method in interface org.openscience.cdk.qsar.IDescriptor
-
Returns the current parameter values.
- getParameters() - Method in class org.openscience.cdk.renderer.generators.AtomContainerBoundsGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.AtomNumberGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.BasicGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.BasicSceneGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.BoundsGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.ExtendedAtomGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.HighlightGenerator
-
- getParameters() - Method in interface org.openscience.cdk.renderer.generators.IGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.LonePairGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.MappingGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.ProductsBoxGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.RadicalGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.ReactantsBoxGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.ReactionArrowGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.ReactionBoxGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.ReactionPlusGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.ReactionSceneGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.RingGenerator
-
- getParameters() - Method in class org.openscience.cdk.renderer.generators.standard.StandardGenerator
-
- 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.AcidicGroupCountDescriptor
-
Returns a class matching that of the parameter with the given name.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
-
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor
-
Gets the parameterType attribute of the AromaticAtomsCountDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor
-
Gets the parameterType attribute of the APolDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor
-
Gets the parameterType attribute of the AromaticAtomsCountDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor
-
Gets the parameterType attribute of the AromaticBondsCountDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor
-
Gets the parameterType attribute of the AtomCountDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
-
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
-
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
-
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor
-
Returns a class matching that of the parameter with the given name.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor
-
Gets the parameterType attribute of the BCUTDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor
-
Gets the parameterType attribute of the BondCountDescriptor object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor
-
Gets the parameterType attribute of the BPolDescriptor object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor
-
Gets the parameterType attribute of the GravitationalIndexDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
-
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
-
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
-
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
-
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor
-
Gets the parameterType attribute of the CPSADescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor
-
Gets the parameterType attribute of the EccentricConnectivityIndexDescriptor object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor
-
Returns a class matching that of the parameter with the given name.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor
-
Returns a class matching that of the parameter with the given name.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor
-
Gets the parameterType attribute of the FragmentComplexityDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor
-
Gets the parameterType attribute of the GravitationalIndexDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor
-
Gets the parameterType attribute of the HBondAcceptorCountDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor
-
Gets the parameterType of the HBondDonorCountDescriptor.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor
-
Gets the parameterType attribute of the HybridizationRatioDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor
-
Gets the parameterType attribute of the IPMolecularLearningDescriptor object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor
-
Gets the parameterType attribute of the
KappaShapeIndicesDescriptor object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor
-
Gets the parameterType attribute of the descriptor.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor
-
Gets the parameterType attribute of the LargestChainDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor
-
Gets the parameterType attribute of the LargestPiSystemDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor
-
Gets the parameterType attribute of the PetitjeanNumberDescriptor object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor
-
Gets the parameterType attribute of the LongestAliphaticChainDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor
-
Gets the parameterType attribute for a given parameter name.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
-
Gets the parameterType attribute of the WeightDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor
-
Gets the parameterType attribute of the MomentOfInertiaDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor
-
Gets the parameterType attribute of the PetitjeanNumberDescriptor object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor
-
Gets the parameterType attribute of the PetitjeanShapeIndexDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor
-
Gets the parameterType attribute of the RotatableBondsCountDescriptor
object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor
-
Gets the parameterType attribute of the RuleOfFiveDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor
-
Parameter types: there aren't any.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor
-
Gets the parameterType attribute of the TPSADescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor
-
Returns a class matching that of the parameter with the given name.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor
-
Gets the parameterType attribute of the VAdjMaDescriptor object
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor
-
Gets the parameterType attribute of the WeightDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor
-
Gets the parameterType attribute of the WeightedPathDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor
-
Gets the parameterType attribute of the WHIMDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor
-
Gets the parameterType attribute of the WienerNumbersDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor
-
Gets the parameterType attribute of the XLogPDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor
-
Gets the parameterType attribute of the ZagrebIndexDescriptor object.
- getParameterType(String) - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor
-
Gets the parameterType attribute of the TaeAminoAcidDescriptor object.
- getParameterType(String) - Method in 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
-
- getPath(IAtomContainer, IAtom, IAtom) - Method in class org.openscience.cdk.graph.SpanningTree
-
Find a path connected a1 and a2 in the tree.
- getPathsOfLength(IAtomContainer, IAtom, int) - Static method in class org.openscience.cdk.graph.PathTools
-
Get the paths starting from an atom of specified length.
- getPathsOfLengthUpto(IAtomContainer, IAtom, int) - Static method in class org.openscience.cdk.graph.PathTools
-
Get all the paths starting from an atom of length 0 upto the specified length.
- getPaulingElectronegativities(IAtomContainer, boolean) - Method in class org.openscience.cdk.charges.InductivePartialCharges
-
Gets the paulingElectronegativities attribute of the
InductivePartialCharges object.
- getPaulingElectronegativity(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
-
Get the Pauling electronegativity of an element.
- getPeriod(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
-
Get the period of the element.
- getPharmacophoreQuery() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher
-
Get the query pharmacophore.
- getPhase(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
-
Get the phase of the element.
- getPlacedAtoms(IAtomContainer) - Static method in class org.openscience.cdk.layout.AtomPlacer
-
Get all the placed atoms in an AtomContainer
- getPlacedAtomsInAtomContainer(IAtom, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Gets all placed neighbouring atoms of a atom.
- getPlacedHeavyAtom(IAtomContainer, IAtom) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
-
Returns a placed atom connected to a given atom.
- getPlacedHeavyAtom(IAtomContainer, IAtom, IAtom) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
-
Gets the first placed Heavy Atom around atomA which is not atomB.
- getPlacedHeavyAtomInAtomContainer(IAtom, IAtom, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Returns a placed neighbouring atom of a central atom atomA, which is not
atomB.
- getPlacedHeavyAtoms(IAtomContainer, IAtom) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
-
Gets the placed Heavy Atoms connected to an atom.
- getPockets() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- getPocketSize() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- getPoint2d() - Method in class org.openscience.cdk.Atom
-
Returns a point specifying the location of this
atom in a 2D space.
- getPoint2d() - Method in class org.openscience.cdk.debug.DebugAtom
-
Returns a point specifying the location of this
atom in a 2D space.
- getPoint2d() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Returns a point specifying the location of this
atom in a 2D space.
- getPoint2d() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Returns a point specifying the location of this
atom in a 2D space.
- getPoint2d() - Method in interface org.openscience.cdk.interfaces.IAtom
-
Returns a point specifying the location of this
atom in a 2D space.
- getPoint2d() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Returns a point specifying the location of this
atom in a 2D space.
- getPoint2d() - Method in class org.openscience.cdk.silent.Atom
-
Returns a point specifying the location of this
atom in a 2D space.
- getPoint3d() - Method in class org.openscience.cdk.Atom
-
Returns a point specifying the location of this
atom in a 3D space.
- getPoint3d() - Method in class org.openscience.cdk.debug.DebugAtom
-
Returns a point specifying the location of this
atom in a 3D space.
- getPoint3d() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Returns a point specifying the location of this
atom in a 3D space.
- getPoint3d() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Returns a point specifying the location of this
atom in a 3D space.
- getPoint3d() - Method in interface org.openscience.cdk.interfaces.IAtom
-
Returns a point specifying the location of this
atom in a 3D space.
- getPoint3d() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Returns a point specifying the location of this
atom in a 3D space.
- getPoint3d() - Method in class org.openscience.cdk.silent.Atom
-
Returns a point specifying the location of this
atom in a 3D space.
- getPolarizabilitiyFactorForAtom(IAtomContainer, IAtom) - Method in class org.openscience.cdk.charges.Polarizability
-
Gets the polarizabilitiyFactorForAtom.
- getPolarizability(String) - Method in class org.openscience.cdk.tools.AtomicProperties
-
- getPosition(int) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Gets the position of a base.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ABINITFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Aces2Format
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ADFFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.AlchemyFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.BGFFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.BSFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CACheFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CIFFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CMLFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CRK2DFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CRK3DFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CrystClustFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.CTXFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.DaltonFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.DMol3Format
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.DOCK5Format
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.FingerprintFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.GamessFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian03Format
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian90Format
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian92Format
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian94Format
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian95Format
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Gaussian98Format
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat
-
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.GROMOS96Format
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.HINFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.INChIFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in interface org.openscience.cdk.io.formats.IResourceFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.JaguarFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.JMEFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MacroModelFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MDLFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MDLV2000Format
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MDLV3000Format
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MMODFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.Mol2Format
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC7Format
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC93Format
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MOPAC97Format
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.MPQCFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.NWChemFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PCModelFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PDBFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PDBMLFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PMPFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.POVRayFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PQSChemFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.QChemFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.RawCopyFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SDFFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ShelXFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SMARTSFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SMILESFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SpartanFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SVGFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.VASPFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ViewmolFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.XEDFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.XYZFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.YasaraFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ZindoFormat
-
Returns the preferred resource name extension.
- getPreferredNameExtension() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat
-
Returns the preferred resource name extension.
- getPrime() - Method in class org.openscience.cdk.smiles.InvPair
-
Get the current prime number.
- getPrimeAt(int) - Static method in class org.openscience.cdk.math.Primes
-
Deprecated.
Returns the i-th prime number in the sequence of
all prime numbers below 19700.
- getProductCoefficient(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugReaction
-
Returns the stoichiometry coefficient of the given product.
- getProductCoefficient(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IReaction
-
Returns the stoichiometry coefficient of the given product.
- getProductCoefficient(IAtomContainer) - Method in class org.openscience.cdk.Reaction
-
Returns the stoichiometry coefficient of the given product.
- getProductCoefficient(IAtomContainer) - Method in class org.openscience.cdk.silent.Reaction
-
Returns the stoichiometry coefficient of the given product.
- getProductCoefficients() - Method in class org.openscience.cdk.debug.DebugReaction
-
Returns an array of double with the stoichiometric coefficients
of the products.
- getProductCoefficients() - Method in interface org.openscience.cdk.interfaces.IReaction
-
Returns an array of double with the stoichiometric coefficients
of the products.
- getProductCoefficients() - Method in class org.openscience.cdk.Reaction
-
Returns an array of double with the stoichiometric coefficients
of the products.
- getProductCoefficients() - Method in class org.openscience.cdk.silent.Reaction
-
Returns an array of double with the stoichiometric coefficients
of the products.
- getProductCount() - Method in class org.openscience.cdk.debug.DebugReaction
-
Returns the number of products in this reaction.
- getProductCount() - Method in interface org.openscience.cdk.interfaces.IReaction
-
Returns the number of products in this reaction.
- getProductCount() - Method in class org.openscience.cdk.Reaction
-
Returns the number of products in this reaction.
- getProductCount() - Method in class org.openscience.cdk.silent.Reaction
-
Returns the number of products in this reaction.
- getProductMolecule() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
Returns modified target molecule on which mapping was
performed.
- getProductMolecule() - Method in class org.openscience.cdk.smsd.Isomorphism
-
Returns modified target molecule on which mapping was
performed.
- getProducts() - Method in class org.openscience.cdk.debug.DebugReaction
-
Returns a MoleculeSet containing the products of this reaction.
- getProducts() - Method in interface org.openscience.cdk.interfaces.IReaction
-
Returns a IAtomContaineSet containing the products of this reaction.
- getProducts() - Method in class org.openscience.cdk.Reaction
-
Returns a MoleculeSet containing the products of this reaction.
- getProducts() - Method in class org.openscience.cdk.silent.Reaction
-
Returns a MoleculeSet containing the products of this reaction.
- getProperties() - Method in class org.openscience.cdk.ChemObject
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.debug.DebugAtom
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.debug.DebugAtomType
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.debug.DebugBond
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.debug.DebugChemFile
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.debug.DebugChemModel
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.debug.DebugChemObject
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.debug.DebugChemSequence
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.debug.DebugElectronContainer
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.debug.DebugElement
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.debug.DebugIsotope
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.debug.DebugLonePair
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.debug.DebugMapping
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.debug.DebugMolecularFormula
-
Returns a Map with the IChemObject's properties.I should
integrate into ChemObject.
- getProperties() - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.debug.DebugReaction
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.debug.DebugReactionScheme
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.debug.DebugReactionSet
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.debug.DebugRing
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.debug.DebugSubstance
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.formula.MolecularFormula
-
Returns a Map with the IChemObject's properties.I should
integrate into ChemObject.
- getProperties() - Method in interface org.openscience.cdk.interfaces.IChemObject
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
-
Returns a Map with the IChemObject's properties.I should
integrate into ChemObject.
- getProperties() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.silent.ChemObject
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.silent.MolecularFormula
-
Returns a Map with the IChemObject's properties.I should
integrate into ChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.ChemObject
-
Returns a property for the IChemObject.
- getProperty(Object, Class<T>) - Method in class org.openscience.cdk.ChemObject
-
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns a property for the IChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugAtom
-
Returns a property for the IChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns a property for the IChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
Returns a property for the IChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugAtomType
-
Returns a property for the IChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns a property for the IChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugBond
-
Returns a property for the IChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugChemFile
-
Returns a property for the IChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugChemModel
-
Returns a property for the IChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugChemObject
-
Returns a property for the IChemObject.
- getProperty(Object, Class<T>) - Method in class org.openscience.cdk.debug.DebugChemObject
-
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugChemSequence
-
Returns a property for the IChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns a property for the IChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugElectronContainer
-
Returns a property for the IChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugElement
-
Returns a property for the IChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Returns a property for the IChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugIsotope
-
Returns a property for the IChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugLonePair
-
Returns a property for the IChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugMapping
-
Returns a property for the IChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugMolecularFormula
-
Returns a property for the IChemObject - the object is automatically
cast to the required type.
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns a property for the IChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns a property for the IChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Returns a property for the IChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugReaction
-
Returns a property for the IChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugReactionScheme
-
Returns a property for the IChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugReactionSet
-
Returns a property for the IChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugRing
-
Returns a property for the IChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
Returns a property for the IChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns a property for the IChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.debug.DebugSubstance
-
Returns a property for the IChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.formula.MolecularFormula
-
- getProperty(Object, Class<T>) - Method in class org.openscience.cdk.formula.MolecularFormula
-
- getProperty(Object) - Method in interface org.openscience.cdk.interfaces.IChemObject
-
Returns a property for the IChemObject - the object is automatically
cast to the required type.
- getProperty(Object, Class<T>) - Method in interface org.openscience.cdk.interfaces.IChemObject
-
Access a property of the given description and cast the specified class.
- getProperty(Object) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
-
Returns a property for the IChemObject - the object is automatically
cast to the required type.
- getProperty(Object, Class<T>) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
-
Access a property of the given description and cast the specified class.
- getProperty(Object) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
Returns a property for the IChemObject.
- getProperty(Object, Class<T>) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
- getProperty(Object) - Method in class org.openscience.cdk.silent.ChemObject
-
Returns a property for the IChemObject.
- getProperty(Object, Class<T>) - Method in class org.openscience.cdk.silent.ChemObject
-
- getProperty(Object) - Method in class org.openscience.cdk.silent.MolecularFormula
-
- getProperty(Object, Class<T>) - Method in class org.openscience.cdk.silent.MolecularFormula
-
- getProtein() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- getProteinInterior() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- getQSARs(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.tools.IonizationPotentialTool
-
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.
- getQueryNode() - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.Match
-
Return query node
- getQuestion() - Method in class org.openscience.cdk.io.setting.IOSetting
-
- getRandom() - Static method in class org.openscience.cdk.math.RandomNumbersTool
-
Returns the instance of Random used by this class.
- getRandomNextPermutation() - Method in class org.openscience.cdk.graph.Permutor
-
Randomly skip ahead in the list of permutations.
- getRandomNextPermutation() - Method in class org.openscience.cdk.smsd.labelling.Permutor
-
Randomly skip ahead in the list of permutations.
- getRandomSeed() - Static method in class org.openscience.cdk.math.RandomNumbersTool
-
Returns the seed being used by this random number generator.
- getRange(IMolecularFormulaSet) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaRangeManipulator
-
Extract from a set of MolecularFormula the range of each each element found and
put the element and occurrence in a new MolecularFormulaRange.
- getRank() - Method in class org.openscience.cdk.graph.Permutor
-
Get the current rank.
- getRank() - Method in class org.openscience.cdk.smsd.labelling.Permutor
-
- getRAtom() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- getRawContent() - Method in class org.openscience.cdk.dict.Entry
-
- getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter
-
Invalid: it is not appropriate to convert the integer hash codes into strings.
- getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.EStateFingerprinter
-
Returns the raw representation of the fingerprint for the given IAtomContainer.
- getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter
-
Returns the raw representation of the fingerprint for the given IAtomContainer.
- getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.Fingerprinter
-
Returns the raw representation of the fingerprint for the given IAtomContainer.
- getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.HybridizationFingerprinter
-
Returns the raw representation of the fingerprint for the given IAtomContainer.
- getRawFingerprint(IAtomContainer) - Method in interface org.openscience.cdk.fingerprint.IFingerprinter
-
Returns the raw representation of the fingerprint for the given IAtomContainer.
- getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.LingoFingerprinter
-
- getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.MACCSFingerprinter
-
Returns the raw representation of the fingerprint for the given IAtomContainer.
- getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.PubchemFingerprinter
-
Returns the raw representation of the fingerprint for the given IAtomContainer.
- getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.ShortestPathFingerprinter
-
Returns the raw representation of the fingerprint for the given IAtomContainer.
- getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.SignatureFingerprinter
-
- getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.SubstructureFingerprinter
-
Returns the raw representation of the fingerprint for the given IAtomContainer.
- getRDBEValue(IMolecularFormula) - Method in class org.openscience.cdk.formula.rules.RDBERule
-
Method to extract the Ring Double Bond Equivalents (RDB) value.
- getReactantCoefficient(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugReaction
-
Returns the stoichiometry coefficient of the given reactant.
- getReactantCoefficient(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IReaction
-
Returns the stoichiometry coefficient of the given reactant.
- getReactantCoefficient(IAtomContainer) - Method in class org.openscience.cdk.Reaction
-
Returns the stoichiometry coefficient of the given reactant.
- getReactantCoefficient(IAtomContainer) - Method in class org.openscience.cdk.silent.Reaction
-
Returns the stoichiometry coefficient of the given reactant.
- getReactantCoefficients() - Method in class org.openscience.cdk.debug.DebugReaction
-
Returns an array of double with the stoichiometric coefficients
of the reactants.
- getReactantCoefficients() - Method in interface org.openscience.cdk.interfaces.IReaction
-
Returns an array of double with the stoichiometric coefficients
of the reactants.
- getReactantCoefficients() - Method in class org.openscience.cdk.Reaction
-
Returns an array of double with the stoichiometric coefficients
of the reactants.
- getReactantCoefficients() - Method in class org.openscience.cdk.silent.Reaction
-
Returns an array of double with the stoichiometric coefficients
of the reactants.
- getReactantCount() - Method in class org.openscience.cdk.debug.DebugReaction
-
Returns the number of reactants in this reaction.
- getReactantCount() - Method in interface org.openscience.cdk.interfaces.IReaction
-
Returns the number of reactants in this reaction.
- getReactantCount() - Method in class org.openscience.cdk.Reaction
-
Returns the number of reactants in this reaction.
- getReactantCount() - Method in class org.openscience.cdk.silent.Reaction
-
Returns the number of reactants in this reaction.
- getReactantMolecule() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
Returns modified query molecule on which mapping was
performed.
- getReactantMolecule() - Method in class org.openscience.cdk.smsd.Isomorphism
-
Returns modified query molecule on which mapping was
performed.
- getReactants() - Method in class org.openscience.cdk.debug.DebugReaction
-
Returns a MoleculeSet containing the reactants in this reaction.
- getReactants() - Method in interface org.openscience.cdk.interfaces.IReaction
-
Returns a IAtomContaineSet containing the reactants in this reaction.
- getReactants() - Method in class org.openscience.cdk.Reaction
-
Returns a MoleculeSet containing the reactants in this reaction.
- getReactants() - Method in class org.openscience.cdk.silent.Reaction
-
Returns a MoleculeSet containing the reactants in this reaction.
- getReaction(int) - Method in class org.openscience.cdk.debug.DebugReactionSet
-
Returns the Reaction at position number
in the
container.
- getReaction(int) - Method in interface org.openscience.cdk.interfaces.IReactionSet
-
Returns the Reaction at position number
in the
container.
- getReaction(int) - Method in class org.openscience.cdk.reaction.ReactionChain
-
Get the reaction of this chain reaction object at the position.
- getReaction(int) - Method in class org.openscience.cdk.ReactionSet
-
Returns the Reaction at position number
in the
container.
- getReaction(int) - Method in class org.openscience.cdk.silent.ReactionSet
-
Returns the Reaction at position number
in the
container.
- getReactionByAtomContainerID(IReactionSet, String) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
-
Gets a reaction from a ReactionSet by ID of any product or reactant.
- getReactionByReactionID(IReactionSet, String) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
-
Gets a reaction from a ReactionSet by ID.
- getReactionCount() - Method in class org.openscience.cdk.debug.DebugReactionSet
-
Returns the number of Reactions in this Container.
- getReactionCount() - Method in interface org.openscience.cdk.interfaces.IReactionSet
-
Returns the number of Reactions in this Container.
- getReactionCount() - Method in class org.openscience.cdk.ReactionSet
-
Returns the number of Reactions in this Container.
- getReactionCount() - Method in class org.openscience.cdk.silent.ReactionSet
-
Returns the number of Reactions in this Container.
- getReactionMetadata() - Method in class org.openscience.cdk.dict.EntryReact
-
- getReactions() - Method in class org.openscience.cdk.tools.StructureResonanceGenerator
-
Get the reactions that must be presents in the generation of the resonance.
- getReactionSchemeCount() - Method in class org.openscience.cdk.debug.DebugReactionScheme
-
Returns the number of ReactionScheme in this Scheme.
- getReactionSchemeCount() - Method in interface org.openscience.cdk.interfaces.IReactionScheme
-
Returns the number of ReactionScheme in this Scheme.
- getReactionSchemeCount() - Method in class org.openscience.cdk.ReactionScheme
-
Returns the number of ReactionScheme in this Scheme.
- getReactionSchemeCount() - Method in class org.openscience.cdk.silent.ReactionScheme
-
Returns the number of ReactionScheme in this Scheme.
- getReactionSet() - Method in class org.openscience.cdk.ChemModel
-
Gets the ReactionSet contained in this ChemModel.
- getReactionSet() - Method in class org.openscience.cdk.debug.DebugChemModel
-
Gets the ReactionSet contained in this ChemModel.
- getReactionSet() - Method in interface org.openscience.cdk.interfaces.IChemModel
-
Gets the ReactionSet contained in this ChemModel.
- getReactionSet() - Method in class org.openscience.cdk.silent.ChemModel
-
Gets the ReactionSet contained in this ChemModel.
- getReactionStep(IReaction) - Method in class org.openscience.cdk.reaction.ReactionChain
-
Get the position of the reaction into this chain reaction object.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.ABINITFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.Aces2Format
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.ADFFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.AlchemyFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.BGFFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.BSFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.CACheFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.CIFFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.CMLFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.CRK2DFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.CRK3DFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.CrystClustFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.CTXFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.DaltonFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.DMol3Format
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.DOCK5Format
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.FingerprintFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.GamessFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian03Format
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian90Format
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian92Format
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian94Format
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian95Format
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.Gaussian98Format
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat
-
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.GROMOS96Format
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.HINFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in interface org.openscience.cdk.io.formats.IChemFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.INChIFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.JaguarFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.JMEFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.MacroModelFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.MDLFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.MDLV2000Format
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.MDLV3000Format
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.MMODFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.Mol2Format
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC7Format
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC93Format
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.MOPAC97Format
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.MPQCFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.NWChemFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.PCModelFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.PDBFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.PDBMLFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.PMPFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.PQSChemFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.QChemFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.RawCopyFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.SDFFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.ShelXFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.SMARTSFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.SMILESFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.SpartanFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.VASPFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.ViewmolFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.XEDFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.XYZFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.YasaraFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.ZindoFormat
-
Returns the class name of the CDK Reader for this format.
- getReaderClassName() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat
-
Returns the class name of the CDK Reader for this format.
- getRealPart() - Method in class org.openscience.cdk.math.Complex
-
Gets the real part of this complex value
- getRecord() - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
get one entire line from the PDB entry file which describe the IPDBAtom.
- getRecord() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
Get one entire line from the PDB entry file which describe the IPDBAtom.
- getRecord() - Method in class org.openscience.cdk.protein.data.PDBAtom
-
get one entire line from the PDB entry file which describe the IPDBAtom.
- getRecord() - Method in class org.openscience.cdk.silent.PDBAtom
-
get one entire line from the PDB entry file which describe the IPDBAtom.
- getRectangle2D(IAtomContainer) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Returns the 2D rectangle spanning the space occupied by the atom
container.
- getReference() - Method in class org.openscience.cdk.dict.DictRef
-
- getRelevantAtomContainer(IAtomContainerSet, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
-
- getRelevantAtomContainer(IAtomContainerSet, IBond) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
-
- getRelevantAtomContainer(IChemModel, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
-
This badly named methods tries to determine which AtomContainer in the
ChemModel is best suited to contain added Atom's and Bond's.
- getRelevantAtomContainer(IChemModel, IBond) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
-
Retrieves the first IAtomContainer containing a given IBond from an
IChemModel.
- getRelevantAtomContainer(IAtomContainerSet, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
-
- getRelevantAtomContainer(IAtomContainerSet, IBond) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
-
- getRelevantAtomContainer(IReaction, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
-
- getRelevantAtomContainer(IReaction, IBond) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
-
- getRelevantAtomContainer(IReactionSet, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
-
- getRelevantAtomContainer(IReactionSet, IBond) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
-
- getRelevantReaction(IChemModel, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
-
Retrieves the first IReaction containing a given IAtom from an
IChemModel.
- getRelevantReaction(IReactionSet, IAtom) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
-
- getRelevantReaction(IReactionSet, IBond) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
-
- getRelevantReactions(IReactionSet, IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
-
Get all Reactions object containing a Molecule from a set of Reactions.
- getRelevantReactionsAsProduct(IReactionSet, IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
-
Get all Reactions object containing a Molecule as a Product from a set of
Reactions.
- getRelevantReactionsAsReactant(IReactionSet, IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
-
Get all Reactions object containing a Molecule as a Reactant from a set
of Reactions.
- getRemoveHydrogenFlag() - Method in class org.openscience.cdk.smsd.tools.MolHandler
-
Returns true if hydrogens were made implicit else return false
- getRenderer2DModel() - Method in class org.openscience.cdk.renderer.AbstractRenderer
-
Get the
RendererModel
used by this renderer, which provides
access to the various parameters used to generate and draw the diagram.
- getRenderer2DModel() - Method in interface org.openscience.cdk.renderer.IRenderer
-
Returns the drawing model, giving access to drawing parameters.
- getRendererModel() - Method in class org.openscience.cdk.renderer.visitor.AWTDrawVisitor
-
- getRenderingParameters() - Method in class org.openscience.cdk.renderer.RendererModel
-
- getRepresentations() - Method in class org.openscience.cdk.dict.EntryReact
-
Get the Representation of the reaction.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.CDKSourceCodeWriter
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ABINITFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Aces2Format
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ADFFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.AlchemyFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.BGFFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.BSFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CACheFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
-
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CIFFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CMLFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CRK2DFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CRK3DFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CrystClustFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.CTXFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.DaltonFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.DMol3Format
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.DOCK5Format
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.FingerprintFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.GamessFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian03Format
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian90Format
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian92Format
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian94Format
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian95Format
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian98Format
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.GROMOS96Format
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.HINFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in interface org.openscience.cdk.io.formats.IChemFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.INChIFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.JaguarFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.JMEFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MacroModelFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLV2000Format
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLV3000Format
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MMODFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.Mol2Format
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC7Format
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC93Format
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC97Format
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.MPQCFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.NWChemFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PCModelFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PDBFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PDBMLFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PMPFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PQSChemFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.QChemFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.RawCopyFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SDFFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ShelXFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SMARTSFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SMILESFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SpartanFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.VASPFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ViewmolFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.XEDFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.XYZFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.YasaraFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ZindoFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredDataFeatures() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat
-
Returns an integer indicating the data features that this
format requires.
- getRequiredRGroupNumber() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
-
- getResidues() - Method in class org.openscience.cdk.libio.md.MDMolecule
-
- getResName() - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
get the Residue name of this atom.
- getResName() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
get the Residue name of this atom.
- getResName() - Method in class org.openscience.cdk.protein.data.PDBAtom
-
get the Residue name of this atom.
- getResName() - Method in class org.openscience.cdk.silent.PDBAtom
-
get the Residue name of this atom.
- getResSeq() - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
get the Residue sequence number of this atom.
- getResSeq() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
get the Residue sequence number of this atom.
- getResSeq() - Method in interface org.openscience.cdk.interfaces.IPDBMonomer
-
Gets the sequence identifier of this monomer.
- getResSeq() - Method in class org.openscience.cdk.protein.data.PDBAtom
-
get the Residue sequence number of this atom.
- getResSeq() - Method in class org.openscience.cdk.protein.data.PDBMonomer
-
- getResSeq() - Method in class org.openscience.cdk.silent.PDBAtom
-
get the Residue sequence number of this atom.
- getResSeq() - Method in class org.openscience.cdk.silent.PDBMonomer
-
- getRestrictions() - Method in class org.openscience.cdk.formula.MassToFormulaTool
-
Deprecated.
Get the restrictions that must be presents in the molecular formula.
- getReturnStatus() - Method in class org.openscience.cdk.inchi.InChIGenerator
-
Gets return status from InChI process.
- getReturnStatus() - Method in class org.openscience.cdk.inchi.InChIToStructure
-
Gets return status from InChI process.
- getRGroupDefinitions() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
-
Getter for the R-group definitions (substituents).
- getRGroupDefinitions() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
- getRGroupNumber() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
-
- getRgroupQueryAtoms(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
Returns all R# type atoms (pseudo atoms) found in the root structure
for a certain provided RGgroup number.
- getRGroups() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
-
- getRight() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom
-
Deprecated.
- getRight() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond
-
- getRingBond() - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RingIdentifierAtom
-
- getRings(IBond) - Method in class org.openscience.cdk.debug.DebugRingSet
-
Returns a vector of all rings that this bond is part of.
- getRings(IAtom) - Method in class org.openscience.cdk.debug.DebugRingSet
-
Returns a vector of all rings that this atom is part of.
- getRings(IBond) - Method in interface org.openscience.cdk.interfaces.IRingSet
-
Returns a vector of all rings that this bond is part of.
- getRings(IAtom) - Method in interface org.openscience.cdk.interfaces.IRingSet
-
Returns a vector of all rings that this atom is part of.
- getRings(IBond) - Method in class org.openscience.cdk.RingSet
-
Returns a vector of all rings that this bond is part of.
- getRings(IAtom) - Method in class org.openscience.cdk.RingSet
-
Returns a vector of all rings that this atom is part of.
- getRings(IBond) - Method in class org.openscience.cdk.silent.RingSet
-
Returns a vector of all rings that this bond is part of.
- getRings(IAtom) - Method in class org.openscience.cdk.silent.RingSet
-
Returns a vector of all rings that this atom is part of.
- getRingSet() - Method in class org.openscience.cdk.ChemModel
-
Returns the RingSet of this ChemModel.
- getRingSet() - Method in class org.openscience.cdk.debug.DebugChemModel
-
Returns the RingSet of this ChemModel.
- getRingSet() - Method in interface org.openscience.cdk.interfaces.IChemModel
-
Returns the RingSet of this ChemModel.
- getRingSet(IAtomContainer) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
-
Determine the ring set for this atom container.
- getRingSet() - Method in class org.openscience.cdk.silent.ChemModel
-
Returns the RingSet of this ChemModel.
- getRingSet(IAtomContainer) - Method in class org.openscience.cdk.smsd.ring.HanserRingFinder
-
Returns Ring set based on Hanser Ring Finding method
- getRingSet(IAtomContainer) - Method in interface org.openscience.cdk.smsd.ring.RingFinder
-
Returns CDK object Ring set based on Hanser Ring Finding method
- getRingSize() - Method in class org.openscience.cdk.debug.DebugRing
-
Returns the number of atoms\edges in this ring.
- getRingSize() - Method in interface org.openscience.cdk.interfaces.IRing
-
Returns the number of atoms/bonds in this ring.
- getRingSize() - Method in class org.openscience.cdk.Ring
-
Returns the number of atoms\edges in this ring.
- getRingSize() - Method in class org.openscience.cdk.silent.Ring
-
Returns the number of atoms\edges in this ring.
- getRingSystems() - Method in class org.openscience.cdk.fragment.MurckoFragmenter
-
Get the ring system fragments as SMILES strings.
- getRingSystemsAsContainers() - Method in class org.openscience.cdk.fragment.MurckoFragmenter
-
- getRMap() - Method in class org.openscience.cdk.isomorphism.mcss.RNode
-
Gets the rMap attribute of the RNode object.
- getRMap() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode
-
Gets the rMap attribute of the RNode object
- getrMap() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode
-
Returns resolution Map
- getRMSD() - Method in class org.openscience.cdk.geometry.alignment.KabschAlignment
-
Returns the RMSD from the alignment.
- getRoot(int) - Method in class org.openscience.cdk.group.DisjointSetForest
-
Travel up the tree that this element is in, until the root of the set
is found, and return that root.
- getRoot(Node) - Method in class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
-
- getRootAttachmentPoints() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
-
Getter for root attachment points = bonds that connect R pseudo-atoms to the scaffold.
- getRootAttachmentPoints() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
- getRootStructure() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
-
Getter for the root structure of this R-Group.
- getRootStructure() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
- getRotationMatrix() - Method in class org.openscience.cdk.geometry.alignment.KabschAlignment
-
Returns the rotation matrix (u).
- getRows() - Method in class org.openscience.cdk.math.IMatrix
-
Returns the count of rows
- getRows() - Method in class org.openscience.cdk.math.Matrix
-
Returns the number of rows.
- getRSolvent() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- getRules() - Method in class org.openscience.cdk.formula.MolecularFormulaChecker
-
Get the IRules to be applied to validate the IMolecularFormula.
- getScaleFactor(IAtomContainer, double) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Determines the scale factor for displaying a structure loaded from disk in
a frame.
- getScaleFactor(IAtomContainer, double) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Determines the scale factor for displaying a structure loaded from disk in a frame.
- getSearchDepth() - Method in class org.openscience.cdk.fingerprint.Fingerprinter
-
- getSearchDepth() - Method in class org.openscience.cdk.fingerprint.HybridizationFingerprinter
-
- getSecondAttachmentPoint() - Method in class org.openscience.cdk.isomorphism.matchers.RGroup
-
- getSecondGraphSize() - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
-
Returns the size of the second of the two
compared graphs.
- getSecondGraphSize() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
-
Returns the size of the second of the two
compared graphs.
- getSegID() - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
get the Segment identifier, left-justified of this atom.
- getSegID() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
get the Segment identifier, left-justified of this atom.
- getSegID() - Method in class org.openscience.cdk.protein.data.PDBAtom
-
get the Segment identifier, left-justified of this atom.
- getSegID() - Method in class org.openscience.cdk.silent.PDBAtom
-
get the Segment identifier, left-justified of this atom.
- getSelection() - Method in class org.openscience.cdk.renderer.RendererModel
-
- getSerial() - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
get the Atom serial number of this atom.
- getSerial() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
get the Atom serial number of this atom.
- getSerial() - Method in class org.openscience.cdk.protein.data.PDBAtom
-
get the Atom serial number of this atom.
- getSerial() - Method in class org.openscience.cdk.silent.PDBAtom
-
get the Atom serial number of this atom.
- getSetbits() - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
-
- getSetbits() - Method in interface org.openscience.cdk.fingerprint.IBitFingerprint
-
Returns a listing of the bits in the fingerprint that are set to true.
- getSetbits() - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
-
- getSetNumA() - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper
-
- getSets() - Method in class org.openscience.cdk.group.DisjointSetForest
-
Retrieve the sets as 2D-array of ints.
- getSetting(String) - Method in class org.openscience.cdk.io.ChemObjectIO
-
- getSetting(String, Class<S>) - Method in class org.openscience.cdk.io.ChemObjectIO
-
- getSetting(String) - Method in interface org.openscience.cdk.io.IChemObjectIO
-
Access a named setting managed by this reader/writer.
- getSetting(String, Class<S>) - Method in interface org.openscience.cdk.io.IChemObjectIO
-
Access a named setting managed by this reader/writer.
- getSetting() - Method in class org.openscience.cdk.io.setting.IOSetting
-
Sets the setting for a certain question.
- getSettings() - Method in class org.openscience.cdk.io.ChemObjectIO
-
- getSettings() - Method in interface org.openscience.cdk.io.IChemObjectIO
-
Access a collection of
IOSetting
s for this reader/writer.
- getSettings() - Method in class org.openscience.cdk.io.setting.SettingManager
-
Access a collection of all settings in the manager.
- getSettingValue() - Method in class org.openscience.cdk.io.setting.IntegerIOSetting
-
- getShortestPath(IAtomContainer, IAtom, IAtom) - Static method in class org.openscience.cdk.graph.PathTools
-
Deprecated.
This implementation recalculates all shortest paths from the start atom
for each method call and does not indicate if there are equally short paths
from the start to the end. Replaced by ShortestPaths.atomsTo(IAtom)
- getSID(XmlPullParser) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
-
- getSingleBondEquivalentSum(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Returns the sum of bond orders, where a single bond counts as one
single bond equivalent, a double as two, etc.
- getSingleBondEquivalentSum(List<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
-
Get the single bond equivalent (SBE) of a list of bonds.
- getSingleBondEquivalentSum(Iterator<IBond>) - Static method in class org.openscience.cdk.tools.manipulator.BondManipulator
-
Get the single bond equivalent (SBE) of a list of bonds, given an iterator to the list.
- getSingleElectron(int) - Method in class org.openscience.cdk.AtomContainer
-
Get the single electron at position number
in [0,..].
- getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Get the single electron at position number
in [0,..].
- getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Get the single electron at position number
in [0,..].
- getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Get the single electron at position number
in [0,..].
- getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Get the single electron at position number
in [0,..].
- getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Get the single electron at position number
in [0,..].
- getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Get the single electron at position number
in [0,..].
- getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugRing
-
Get the single electron at position number
in [0,..].
- getSingleElectron(int) - Method in class org.openscience.cdk.debug.DebugStrand
-
Get the single electron at position number
in [0,..].
- getSingleElectron(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Get the single electron at position number
in [0,..].
- getSingleElectron(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Get the single electron at position number
in [0,..].
- getSingleElectron(int) - Method in class org.openscience.cdk.silent.AtomContainer
-
Get the single electron at position number
in [0,..].
- getSingleElectronCount() - Method in class org.openscience.cdk.AtomContainer
-
Returns the number of the single electrons in this container.
- getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns the number of the single electrons in this container.
- getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns the number of the single electrons in this container.
- getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns the number of the single electrons in this container.
- getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns the number of the single electrons in this container.
- getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns the number of the single electrons in this container.
- getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns the number of the single electrons in this container.
- getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugRing
-
Returns the number of the single electrons in this container.
- getSingleElectronCount() - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns the number of the single electrons in this container.
- getSingleElectronCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the number of the single electrons in this container.
- getSingleElectronCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the number of the single electrons in this container,
- getSingleElectronCount() - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the number of the single electrons in this container,
- getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.AtomContainer
-
Returns the position of a given single electron in the single electron array.
- getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns the position of a given single electron in the single electron array.
- getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns the position of a given single electron in the single electron array.
- getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns the position of a given single electron in the single electron array.
- getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns the position of a given single electron in the single electron array.
- getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns the position of a given single electron in the single electron array.
- getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns the position of a given single electron in the single electron array.
- getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugRing
-
Returns the position of a given single electron in the single electron array.
- getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns the position of a given single electron in the single electron array.
- getSingleElectronNumber(ISingleElectron) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the position of a given single electron in the single electron array.
- getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the position of a given single electron in the single electron array.
- getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the position of a given single electron in the single electron array.
- getSingleElectrons() - Method in enum org.openscience.cdk.io.MDLV2000Writer.SPIN_MULTIPLICITY
-
The number of single electrons that correspond to the spin multiplicity.
- getSize() - Method in class org.openscience.cdk.config.AtomTypeFactory
-
Returns the number of atom types in this list.
- getSize() - Method in class org.openscience.cdk.config.IsotopeFactory
-
Returns the number of isotopes defined by this class.
- getSize() - Method in class org.openscience.cdk.fingerprint.CircularFingerprinter
-
Returns the extent of the folded fingerprints.
- getSize() - Method in class org.openscience.cdk.fingerprint.EStateFingerprinter
-
Returns the size of the fingerprints calculated.
- getSize() - Method in class org.openscience.cdk.fingerprint.ExtendedFingerprinter
-
Returns the size of the fingerprints calculated.
- getSize() - Method in class org.openscience.cdk.fingerprint.Fingerprinter
-
- getSize() - Method in class org.openscience.cdk.fingerprint.HybridizationFingerprinter
-
- getSize() - Method in interface org.openscience.cdk.fingerprint.IFingerprinter
-
Returns the size of the fingerprints calculated.
- getSize() - Method in class org.openscience.cdk.fingerprint.LingoFingerprinter
-
- getSize() - Method in class org.openscience.cdk.fingerprint.MACCSFingerprinter
-
Returns the size of the fingerprints calculated.
- getSize() - Method in class org.openscience.cdk.fingerprint.PubchemFingerprinter
-
Get the size of the fingerprint.
- getSize() - Method in class org.openscience.cdk.fingerprint.ShortestPathFingerprinter
-
- getSize() - Method in class org.openscience.cdk.fingerprint.SignatureFingerprinter
-
- getSize() - Method in class org.openscience.cdk.fingerprint.SubstructureFingerprinter
-
Returns the size of the fingerprints calculated.
- getSize() - Method in class org.openscience.cdk.group.PermutationGroup
-
Get the number of elements in each permutation in the group.
- getSize() - Method in class org.openscience.cdk.math.IVector
-
Return the size from this vector
- getSize() - Method in class org.openscience.cdk.math.qm.FourierGridBasis
-
- getSize() - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Gets the number of base vectors.
- getSize() - Method in interface org.openscience.cdk.math.qm.IBasis
-
Gets the number of base vectors
- getSize() - Method in class org.openscience.cdk.math.Vector
-
Returns the size of this vector
- getSize() - Method in class org.openscience.cdk.smsd.helper.FinalMappings
-
Returns number of stored mappings
- getSize() - Method in class org.openscience.cdk.smsd.helper.LabelContainer
-
Returns label count
- getSize() - Method in interface org.openscience.cdk.smsd.interfaces.IFinalMapping
-
Returns number of stored mappings
- getSmarts() - Static method in class org.openscience.cdk.config.fragments.EStateFragments
-
Get the SMARTS patterns.
- getSmarts() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom
-
Get the SMARTS for the group.
- getSmarts() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryAtom
-
Get the SMARTS pattern for this pharmacophore group.
- getSmarts() - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool
-
Returns the current SMARTS pattern being used.
- getSolutions() - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
-
Returns the list of solutions.
- getSolutions() - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
-
Returns the list of solutions.
- getSolvantValue() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- getSortedEnergy() - Method in class org.openscience.cdk.smsd.filters.ChemicalFilters
-
Return sorted energy in ascending order.
- getSortedFragment() - Method in class org.openscience.cdk.smsd.filters.ChemicalFilters
-
Return sorted fragment in ascending order of the size.
- getSource() - Method in interface org.openscience.cdk.interfaces.IChemObjectChangeEvent
-
IChemObject that fired the event.
- getSource() - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
-
Returns source molecule
- getSource() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.EdgeBuilder
-
Returns source Node.
- getSource() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IEdge
-
Returns source Node.
- getSource() - Method in class org.openscience.cdk.smsd.ring.PathEdge
-
- getSpaceGroup() - Method in class org.openscience.cdk.Crystal
-
Gets the space group of this crystal.
- getSpaceGroup() - Method in class org.openscience.cdk.debug.DebugCrystal
-
Gets the space group of this crystal.
- getSpaceGroup() - Method in interface org.openscience.cdk.interfaces.ICrystal
-
Gets the space group of this crystal.
- getSpaceGroup() - Method in class org.openscience.cdk.silent.Crystal
-
Gets the space group of this crystal.
- getSpanningTree() - Method in class org.openscience.cdk.graph.SpanningTree
-
Access the computed spanning tree of the input molecule.
- getSpanningTreeSize() - Method in class org.openscience.cdk.graph.SpanningTree
-
Size of the spanning tree specified as the number of edges in the tree.
- getSpatproduct(Vector3d, Vector3d, Vector3d) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Gets the spatproduct of three vectors.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor
-
Gets the specification attribute of the AtomHybridizationDescriptor object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor
-
Gets the specification attribute of the AtomHybridizationVSEPRDescriptor object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor
-
Gets the specification attribute of the AtomValenceDescriptor object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor
-
Gets the specification attribute of the BondsToAtomDescriptor object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor
-
Returns a Map
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor
-
Gets the specification attribute of the DistanceToAtomDescriptor object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor
-
Gets the specification attribute of the EffectiveAtomPolarizabilityDescriptor
object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor
-
Gets the specification attribute of the InductiveAtomicHardnessDescriptor
object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor
-
Gets the specification attribute of the InductiveAtomicSoftnessDescriptor
object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor
-
Gets the specification attribute of the IPAtomicHOSEDescriptor object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor
-
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.AcidicGroupCountDescriptor
-
Returns a IImplementationSpecification
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor
-
Returns a Map
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor
-
Returns a Map
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor
-
Returns a Map
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor
-
Returns a Map
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor
-
Returns a Map
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor
-
Returns a IImplementationSpecification
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor
-
Gets the specification attribute of the BondCountDescriptor object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor
-
Returns a Map
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor
-
Returns a IImplementationSpecification
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor
-
Returns a Map
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor
-
Gets the specification attribute of the HBondAcceptorCountDescriptor object.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor
-
Gets the specification attribute of the HBondDonorCountDescriptor
object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor
-
- 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.MannholdLogPDescriptor
-
Gets the specification attribute of the MannholdLogPDescriptor object.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
-
Returns a Map
which specifies which descriptor is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor
-
Gets the specification attribute of the PetitjeanNumberDescriptor object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor
-
Gets the specification attribute of the RotatableBondsCountDescriptor
object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor
-
Returns a Map
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor
-
Fetch descriptor specification.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor
-
Gets the specification attribute of the TPSADescriptor object.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor
-
Returns a IImplementationSpecification
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor
-
Gets the specification attribute of the VAdjMaDescriptor object
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor
-
Returns a Map
which specifies which descriptor is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor
-
Returns a Map
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor
-
Gets the specification attribute of the XLogPDescriptor object.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor
-
Gets the specification attribute of the ZagrebIndexDescriptor object.
- getSpecification() - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor
-
- getSpecification() - Method in class org.openscience.cdk.qsar.DescriptorValue
-
- getSpecification() - Method in interface org.openscience.cdk.qsar.IDescriptor
-
Returns a IImplementationSpecification
which specifies which descriptor
is implemented by this class.
- getSpecification() - Method in interface org.openscience.cdk.reaction.IReactionProcess
-
Returns a Map
which specifies which reaction
is implemented by this class.
- getSpecification() - Method in class org.openscience.cdk.reaction.type.AdductionProtonLPReaction
-
Gets the specification attribute of the AdductionProtonLPReaction object.
- getSpecification() - Method in class org.openscience.cdk.reaction.type.AdductionProtonPBReaction
-
Gets the specification attribute of the AdductionProtonPBReaction object.
- getSpecification() - Method in class org.openscience.cdk.reaction.type.AdductionSodiumLPReaction
-
Gets the specification attribute of the AdductionSodiumLPReaction object.
- getSpecification() - Method in class org.openscience.cdk.reaction.type.CarbonylEliminationReaction
-
Gets the specification attribute of the CarbonylEliminationReaction object.
- getSpecification() - Method in class org.openscience.cdk.reaction.type.ElectronImpactNBEReaction
-
Gets the specification attribute of the ElectronImpactNBEReaction object.
- getSpecification() - Method in class org.openscience.cdk.reaction.type.ElectronImpactPDBReaction
-
Gets the specification attribute of the ElectronImpactPDBReaction object.
- getSpecification() - Method in class org.openscience.cdk.reaction.type.ElectronImpactSDBReaction
-
Gets the specification attribute of the ElectronImpactSDBReaction object.
- getSpecification() - Method in class org.openscience.cdk.reaction.type.HeterolyticCleavagePBReaction
-
Gets the specification attribute of the HeterolyticCleavagePBReaction object.
- getSpecification() - Method in class org.openscience.cdk.reaction.type.HeterolyticCleavageSBReaction
-
Gets the specification attribute of the HeterolyticCleavageSBReaction object.
- getSpecification() - Method in class org.openscience.cdk.reaction.type.HomolyticCleavageReaction
-
Gets the specification attribute of the HomolyticCleavageReaction object.
- getSpecification() - Method in class org.openscience.cdk.reaction.type.HyperconjugationReaction
-
Gets the specification attribute of the HyperconjugationReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.PiBondingMovementReaction
-
Gets the specification attribute of the PiBondingMovementReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalChargeSiteInitiationHReaction
-
Gets the specification attribute of the RadicalChargeSiteInitiationHReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalChargeSiteInitiationReaction
-
Gets the specification attribute of the RadicalChargeSiteInitiationReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrAlphaReaction
-
Gets the specification attribute of the RadicalSiteHrAlphaReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrBetaReaction
-
Gets the specification attribute of the RadicalSiteHrBetaReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrDeltaReaction
-
Gets the specification attribute of the RadicalSiteHrDeltaReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteHrGammaReaction
-
Gets the specification attribute of the RadicalSiteHrGammaReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteInitiationHReaction
-
Gets the specification attribute of the RadicalSiteInitiationHReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteInitiationReaction
-
Gets the specification attribute of the RadicalSiteInitiationReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrAlphaReaction
-
Gets the specification attribute of the RadicalSiteRrAlphaReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrBetaReaction
-
Gets the specification attribute of the RadicalSiteRrBetaReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrDeltaReaction
-
Gets the specification attribute of the RadicalSiteRrDeltaReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.RadicalSiteRrGammaReaction
-
Gets the specification attribute of the RadicalSiteRrGammaReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.RearrangementAnionReaction
-
Gets the specification attribute of the RearrangementAnionReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.RearrangementCationReaction
-
Gets the specification attribute of the RearrangementCationReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.RearrangementLonePairReaction
-
Gets the specification attribute of the RearrangementLonePairReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.RearrangementRadicalReaction
-
Gets the specification attribute of the RearrangementRadicalReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.SharingAnionReaction
-
Gets the specification attribute of the SharingAnionReaction object.
- getSpecification() - Method in class org.openscience.cdk.reaction.type.SharingChargeDBReaction
-
Gets the specification attribute of the SharingChargeDBReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.SharingChargeSBReaction
-
Gets the specification attribute of the SharingChargeSBReaction object
- getSpecification() - Method in class org.openscience.cdk.reaction.type.SharingLonePairReaction
-
Gets the specification attribute of the SharingLonePairReaction object.
- getSpecification() - Method in class org.openscience.cdk.reaction.type.TautomerizationReaction
-
Gets the specification attribute of the TautomerizationReaction object.
- getSpecificationReference() - Method in interface org.openscience.cdk.IImplementationSpecification
-
Pointer to a dictionary or ontology describing a unique
algorithm.
- getSpecificationReference() - Method in class org.openscience.cdk.qsar.DescriptorSpecification
-
- getSpecificationReference() - Method in class org.openscience.cdk.reaction.ReactionSpecification
-
- getSpheres(IAtomContainer, IAtom, int, boolean) - Method in class org.openscience.cdk.tools.HOSECodeGenerator
-
This method is intended to be used to get the atoms around an atom in spheres.
- getSpinVector(double, double) - Method in class org.openscience.cdk.math.qm.AngularMomentum
-
Calculates a spin vector by a direction specified by theta and phi
- getSquarePlanarShape(IAtom, IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.stereo.StereoTool
-
Given four atoms (assumed to be in the same plane), returns the
arrangement of those atoms in that plane.
- getSSSRWeightVector() - Method in class org.openscience.cdk.ringsearch.SSSRFinder
-
Returns a vector containing the lengths of the rings in a SSSR.
- getStartChainID() - Method in class org.openscience.cdk.debug.DebugPDBStructure
-
get start Chain identifier of this structure.
- getStartChainID() - Method in interface org.openscience.cdk.interfaces.IPDBStructure
-
get start Chain identifier of this structure.
- getStartChainID() - Method in class org.openscience.cdk.protein.data.PDBStructure
-
get start Chain identifier of this structure.
- getStartChainID() - Method in class org.openscience.cdk.silent.PDBStructure
-
get start Chain identifier of this structure.
- getStartInsertionCode() - Method in class org.openscience.cdk.debug.DebugPDBStructure
-
get start Code for insertion of residues of this structure.
- getStartInsertionCode() - Method in interface org.openscience.cdk.interfaces.IPDBStructure
-
get start Code for insertion of residues of this structure.
- getStartInsertionCode() - Method in class org.openscience.cdk.protein.data.PDBStructure
-
get start Code for insertion of residues of this structure.
- getStartInsertionCode() - Method in class org.openscience.cdk.silent.PDBStructure
-
get start Code for insertion of residues of this structure.
- getStartSequenceNumber() - Method in class org.openscience.cdk.debug.DebugPDBStructure
-
get the start sequence number of this structure.
- getStartSequenceNumber() - Method in interface org.openscience.cdk.interfaces.IPDBStructure
-
get the start sequence number of this structure.
- getStartSequenceNumber() - Method in class org.openscience.cdk.protein.data.PDBStructure
-
get the start sequence number of this structure.
- getStartSequenceNumber() - Method in class org.openscience.cdk.silent.PDBStructure
-
get the start sequence number of this structure.
- getStepSize() - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
-
Get the StepSize attribute of the GasteigerMarsiliPartialCharges
object.
- getStepSize() - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges
-
Get the StepSize attribute of the GasteigerMarsiliPartialCharges
object.
- getStereo() - Method in class org.openscience.cdk.Bond
-
Returns the stereo descriptor for this bond.
- getStereo() - Method in class org.openscience.cdk.debug.DebugBond
-
Returns the stereo descriptor for this bond.
- getStereo() - Method in interface org.openscience.cdk.interfaces.IBond
-
Returns the stereo descriptor for this bond.
- getStereo() - Method in interface org.openscience.cdk.interfaces.IDoubleBondStereochemistry
-
Defines the stereochemistry around the double bond.
- getStereo() - Method in interface org.openscience.cdk.interfaces.ITetrahedralChirality
-
Defines the stereochemistry around the chiral atom.
- getStereo() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Returns the stereo descriptor for this query bond.
- getStereo() - Method in class org.openscience.cdk.silent.Bond
-
Returns the stereo descriptor for this bond.
- getStereo() - Method in class org.openscience.cdk.stereo.DoubleBondStereochemistry
-
Defines the stereochemistry around the double bond.
- getStereo(IAtom, IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.stereo.StereoTool
-
Take four atoms, and return Stereo.CLOCKWISE or Stereo.ANTI_CLOCKWISE.
- getStereo() - Method in class org.openscience.cdk.stereo.TetrahedralChirality
-
Defines the stereochemistry around the chiral atom.
- getStereoBond() - Method in interface org.openscience.cdk.interfaces.IDoubleBondStereochemistry
-
IBond
that is the stereo center.
- getStereoBond() - Method in class org.openscience.cdk.stereo.DoubleBondStereochemistry
-
IBond
that is the stereo center.
- getStereoMatches() - Method in class org.openscience.cdk.smsd.filters.ChemicalFilters
-
Return Stereo matches in descending order.
- getStereoParity() - Method in class org.openscience.cdk.Atom
-
Returns the stereo parity of this atom.
- getStereoParity() - Method in class org.openscience.cdk.debug.DebugAtom
-
Returns the stereo parity of this atom.
- getStereoParity() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Returns the stereo parity of this atom.
- getStereoParity() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Returns the stereo parity of this atom.
- getStereoParity() - Method in interface org.openscience.cdk.interfaces.IAtom
-
Returns the stereo parity of this atom.
- getStereoParity() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Returns the stereo parity of this atom.
- getStereoParity() - Method in class org.openscience.cdk.silent.Atom
-
Returns the stereo parity of this atom.
- getStereoScore(int) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
Returns a number which denotes the quality of the mcs.
- getStereoScore(int) - Method in class org.openscience.cdk.smsd.Isomorphism
-
Returns a number which denotes the quality of the mcs.
- getStrand(String) - Method in class org.openscience.cdk.BioPolymer
-
Retrieves a Monomer object by specifying its name.
- getStrand(String) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Retrieves a Monomer object by specifying its name.
- getStrand(String) - Method in interface org.openscience.cdk.interfaces.IBioPolymer
-
Retrieve a Monomer object by specifying its name.
- getStrand(String) - Method in class org.openscience.cdk.silent.BioPolymer
-
Retrieves a Monomer object by specifying its name.
- getStrandCount() - Method in class org.openscience.cdk.BioPolymer
-
Returns the number of strands present in the BioPolymer.
- getStrandCount() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns the number of strands present in the BioPolymer.
- getStrandCount() - Method in interface org.openscience.cdk.interfaces.IBioPolymer
-
Return the number of strands present in the BioPolymer.
- getStrandCount() - Method in class org.openscience.cdk.silent.BioPolymer
-
Returns the number of strands present in the BioPolymer.
- getStrandName() - Method in class org.openscience.cdk.debug.DebugStrand
-
Retrieves the strand name.
- getStrandName() - Method in interface org.openscience.cdk.interfaces.IStrand
-
Retrieve the strand name.
- getStrandName() - Method in class org.openscience.cdk.silent.Strand
-
Retrieves the strand name.
- getStrandName() - Method in class org.openscience.cdk.Strand
-
Retrieves the strand name.
- getStrandNames() - Method in class org.openscience.cdk.BioPolymer
-
Returns a collection of the names of all Strand
s in this
BioPolymer.
- getStrandNames() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns a collection of the names of all Strand
s in this
BioPolymer.
- getStrandNames() - Method in interface org.openscience.cdk.interfaces.IBioPolymer
-
Returns a collection of the names of all Strand
s in this
BioPolymer.
- getStrandNames() - Method in class org.openscience.cdk.silent.BioPolymer
-
Returns a collection of the names of all Strand
s in this
BioPolymer.
- getStrands() - Method in class org.openscience.cdk.BioPolymer
-
- getStrands() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns a Map containing the strands in the Polymer.
- getStrands() - Method in interface org.openscience.cdk.interfaces.IBioPolymer
-
Returns a Map containing the strands in the Polymer.
- getStrands() - Method in class org.openscience.cdk.silent.BioPolymer
-
- getStrandType() - Method in class org.openscience.cdk.debug.DebugStrand
-
Retrieves the strand type.
- getStrandType() - Method in interface org.openscience.cdk.interfaces.IStrand
-
Retrieve the strand type.
- getStrandType() - Method in class org.openscience.cdk.silent.Strand
-
Retrieves the strand type.
- getStrandType() - Method in class org.openscience.cdk.Strand
-
Retrieves the strand type.
- getString(IMolecularFormula, String[], boolean) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Returns the string representation of the molecule formula.
- getString(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Returns the string representation of the molecule formula.
- getString(IMolecularFormula, boolean) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Returns the string representation of the molecule formula.
- getStrokeMap() - Method in class org.openscience.cdk.renderer.visitor.AWTDrawVisitor
-
Returns the current stroke map.
- getStructures() - Method in class org.openscience.cdk.debug.DebugPDBPolymer
-
Returns a Collection containing the PDBStructure in the PDBPolymer.
- getStructures() - Method in interface org.openscience.cdk.interfaces.IPDBPolymer
-
Returns a Collection containing the PDBStructure in the PDBPolymer.
- getStructures() - Method in class org.openscience.cdk.protein.data.PDBPolymer
-
- getStructures() - Method in class org.openscience.cdk.silent.PDBPolymer
-
- getStructures(IAtomContainer) - Method in class org.openscience.cdk.tools.StructureResonanceGenerator
-
- getStructureType() - Method in class org.openscience.cdk.debug.DebugPDBStructure
-
get Structure Type of this structure.
- getStructureType() - Method in interface org.openscience.cdk.interfaces.IPDBStructure
-
get Structure Type of this structure.
- getStructureType() - Method in class org.openscience.cdk.protein.data.PDBStructure
-
get Structure Type of this structure.
- getStructureType() - Method in class org.openscience.cdk.silent.PDBStructure
-
get Structure Type of this structure.
- getSubgraph() - Method in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
-
- getSubgraphAtomsMap(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
-
Returns the first subgraph 'atom mapping' found for g2 in g1, where g2 must be a substructure
of g1.
- getSubgraphAtomsMap(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
-
Returns the first subgraph 'atom mapping' found for targetGraph in sourceGraph.
- getSubgraphAtomsMaps(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
-
Returns all subgraph 'atom mappings' found for g2 in g1, where g2 must be a substructure
of g1.
- getSubgraphAtomsMaps(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
-
Returns all subgraph 'atom mappings' found for targetGraph in sourceGraph.
- getSubgraphMap(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
-
Returns the first subgraph 'bond mapping' found for g2 in g1.
- getSubgraphMap(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
-
Returns the first subgraph 'bondA1 mapping' found for targetGraph in sourceGraph.
- getSubgraphMaps(IAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
-
Returns all the subgraph 'bond mappings' found for g2 in g1.
- getSubgraphMaps(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
-
Returns all the subgraph 'bondA1 mappings' found for targetGraph in sourceGraph.
- getSubstituents() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
-
Return all the substituent atom containers, in other words the atom containers
defined in this RGroupQuery except for the root structure.
- getSubstituents() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
- getSubstructure(int) - Method in class org.openscience.cdk.fingerprint.SubstructureFingerprinter
-
Retrieves the SMARTS representation of a substructure for a given
bit in the fingerprint.
- GetSuffix(int) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Get the suffix.
- GetSuffix(int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Get the suffix.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.CDKSourceCodeWriter
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ABINITFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Aces2Format
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ADFFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.AlchemyFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.BGFFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.BSFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CACheFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
-
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CIFFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CMLFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CRK2DFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CRK3DFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CrystClustFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.CTXFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.DaltonFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.DMol3Format
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.DOCK5Format
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.FingerprintFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.GamessFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian03Format
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian90Format
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian92Format
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian94Format
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian95Format
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Gaussian98Format
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.GROMOS96Format
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.HINFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in interface org.openscience.cdk.io.formats.IChemFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.INChIFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.JaguarFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.JMEFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MacroModelFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLV2000Format
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MDLV3000Format
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MMODFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.Mol2Format
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC7Format
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC93Format
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MOPAC97Format
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.MPQCFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.NWChemFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PCModelFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PDBFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PDBMLFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PMPFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PQSChemFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.QChemFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.RawCopyFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SDFFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ShelXFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SMARTSFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SMILESFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SpartanFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.VASPFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ViewmolFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.XEDFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.XYZFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.YasaraFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ZindoFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat
-
Returns an integer indicating the data features that this
format supports.
- getSupportedDataFeatures(IAtomContainer) - Static method in class org.openscience.cdk.tools.DataFeaturesTool
-
- getSurfaceArea(int) - Method in class org.openscience.cdk.geometry.surface.NumericalSurface
-
Get the surface area for the specified atom.
- getSurfacePoints(int) - Method in class org.openscience.cdk.geometry.surface.NumericalSurface
-
Get an array of the points on the accessible surface of a specific atom.
- getSwitchingAtom() - Method in class org.openscience.cdk.libio.md.ChargeGroup
-
- getSymbol() - Method in class org.openscience.cdk.debug.DebugAtom
-
Returns the element symbol of this element.
- getSymbol() - Method in class org.openscience.cdk.debug.DebugAtomType
-
Returns the element symbol of this element.
- getSymbol() - Method in class org.openscience.cdk.debug.DebugElement
-
Returns the element symbol of this element.
- getSymbol() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Returns the element symbol of this element.
- getSymbol() - Method in class org.openscience.cdk.debug.DebugIsotope
-
Returns the element symbol of this element.
- getSymbol() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Returns the element symbol of this element.
- getSymbol() - Method in class org.openscience.cdk.Element
-
Returns the element symbol of this element.
- getSymbol() - Method in interface org.openscience.cdk.interfaces.IElement
-
Returns the element symbol of this element.
- getSymbol() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Returns the element symbol of this element.
- getSymbol() - Method in class org.openscience.cdk.silent.Element
-
Returns the element symbol of this element.
- getSymbol(int) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
-
Get the symbol for the specified atomic number.
- getSymbolFirstAtom() - Method in class org.openscience.cdk.smsd.helper.BondEnergy
-
Returns the element symbol of the first atom.
- getSymbolSecondAtom() - Method in class org.openscience.cdk.smsd.helper.BondEnergy
-
Returns the element symbol of the second atom.
- getSymbolSet() - Method in class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom
-
Retrieve the Set of symbols
- getSymbolSet() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom
-
Retrieve the Set of symbols
- getTabSize(int) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
-
- getTabSize(int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
- getTanimotoAtomSimilarity() - Method in class org.openscience.cdk.smsd.Isomorphism
-
- getTanimotoBondSimilarity() - Method in class org.openscience.cdk.smsd.Isomorphism
-
- getTanimotoSimilarity() - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
Returns Tanimoto similarity between query and target molecules
(Score is between 0-min and 1-max).
- getTanimotoSimilarity() - Method in class org.openscience.cdk.smsd.Isomorphism
-
Returns Tanimoto similarity between query and target molecules
(Score is between 0-min and 1-max).
- getTarget() - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
-
Returns target molecule
- getTarget() - Method in class org.openscience.cdk.smsd.algorithm.vflib.builder.EdgeBuilder
-
Returns target Node.
- getTarget() - Method in interface org.openscience.cdk.smsd.algorithm.vflib.interfaces.IEdge
-
Returns target Node.
- getTarget() - Method in class org.openscience.cdk.smsd.ring.PathEdge
-
- getTargetAtom() - Method in class org.openscience.cdk.smsd.algorithm.vflib.map.Match
-
Return Target Atom
- getTargetQueryBondMappings() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher
-
Return a list of HashMap's that allows one to get the query constraint for a given pharmacophore bond.
- getTautomers(IAtomContainer) - Method in class org.openscience.cdk.tautomers.InChITautomerGenerator
-
Public method to get tautomers for an input molecule, based on the InChI which will be calculated by jniinchi.
- getTautomers(IAtomContainer, String) - Method in class org.openscience.cdk.tautomers.InChITautomerGenerator
-
- getTempFactor() - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
get the Temperature factor of this atom.
- getTempFactor() - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
get the Temperature factor of this atom.
- getTempFactor() - Method in class org.openscience.cdk.protein.data.PDBAtom
-
get the Temperature factor of this atom.
- getTempFactor() - Method in class org.openscience.cdk.silent.PDBAtom
-
get the Temperature factor of this atom.
- getTemplateAt(int) - Method in class org.openscience.cdk.layout.TemplateHandler
-
Gets the templateAt attribute of the TemplateHandler object
- getTemplateAt(int) - Method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D
-
Gets the templateAt attribute of the TemplateHandler object.
- getTemplateCount() - Method in class org.openscience.cdk.layout.TemplateHandler
-
Gets the templateCount attribute of the TemplateHandler object
- getTemplateCount() - Method in class org.openscience.cdk.modeling.builder3d.ModelBuilder3D
-
Returns the number of loaded templates.
- getTemplateCount() - Method in class org.openscience.cdk.modeling.builder3d.TemplateHandler3D
-
Gets the templateCount attribute of the TemplateHandler object.
- getTemplateHandler() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
-
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
-
- getTextBasePoint(String, double, double, Graphics2D) - Method in class org.openscience.cdk.renderer.visitor.AbstractAWTDrawVisitor
-
Calculates the base point where text should be rendered, as text in Java
is typically placed using the left-lower corner point in screen coordinates.
- getTextBounds(String, double, double, Graphics2D) - Method in class org.openscience.cdk.renderer.visitor.AbstractAWTDrawVisitor
-
Calculates the boundaries of a text string in screen coordinates.
- getTextBounds(String, Graphics2D) - Method in class org.openscience.cdk.renderer.visitor.AbstractAWTDrawVisitor
-
Obtain the exact bounding box of the text
in the provided
graphics environment.
- getTimeManager() - Static method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlus
-
- getTimeManager() - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
-
- getTimeManager() - Static method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper
-
- getTimeManager() - Static method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper
-
- getTimeout() - Method in class org.openscience.cdk.ringsearch.AllRingsFinder
-
Deprecated.
timeout not used
- getTimeout() - Static method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlus
-
- getTimeout() - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
-
- getTimeout() - Static method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper
-
- getTimeout() - Static method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper
-
- getTimeOut() - Method in class org.openscience.cdk.smsd.global.TimeOut
-
Return cutoff value for time out.
- getTitle() - Method in class org.openscience.cdk.ConformerContainer
-
Get the title of the conformers.
- getTitle() - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Get the main title
- getTitlemap() - Method in class org.openscience.cdk.io.RssWriter
-
- getToken(int) - Method in class org.openscience.cdk.iupac.parser.NomParser
-
Deprecated.
Get the specific Token.
- getToken(int) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
Get the specific Token.
- getTolerance() - Method in class org.openscience.cdk.formula.IsotopePatternSimilarity
-
Get the tolerance of the mass accuracy.
- getToolTipText(IAtom) - Method in class org.openscience.cdk.renderer.RendererModel
-
Gets the toolTipText for atom certain atom.
- getToolTipTextMap() - Method in class org.openscience.cdk.renderer.RendererModel
-
Gets the toolTipTextMap.
- getTopoEquivClassbyHuXu(IAtomContainer) - Method in class org.openscience.cdk.graph.invariant.EquivalentClassPartitioner
-
Get the topological equivalent class of the molecule.
- getTorsionAngle(Point3d, Point3d, Point3d, Point3d) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Calculates the torsionAngle of a-b-c-d.
- getTorsionData(String, String, String, String, String) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94ParametersCall
-
Gets the bond parameter set.
- getTotalCharge(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Get the summed charge of all atoms in an AtomContainer
- getTotalCharge(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
-
- getTotalCharge(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
-
- getTotalExactMass(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Get the summed exact mass of all atoms in an AtomContainer.
- getTotalExactMass(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Get the summed exact mass of all isotopes from an MolecularFormula.
- getTotalFormalCharge(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Get the total formal charge on a molecule.
- getTotalFormalCharge(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
-
- getTotalFormalCharge(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
-
- getTotalHydrogenCount(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Counts the number of hydrogens on the provided IAtomContainer.
- getTotalHydrogenCount(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
-
- getTotalHydrogenCount(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
-
- getTotalMassNumber(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Get the summed mass number of all isotopes from an MolecularFormula.
- getTotalNaturalAbundance(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Get the summed natural abundance of all atoms in an AtomContainer
- getTotalNaturalAbundance(IMolecularFormula) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Get the summed natural abundance of all isotopes from an MolecularFormula.
- getTotalNegativeFormalCharge(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Get the total formal negative charge on a molecule.
- getTotalPositiveFormalCharge(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Get the total positive formal charge on a molecule.
- getTotalSurfaceArea() - Method in class org.openscience.cdk.geometry.surface.NumericalSurface
-
Get the total surface area for the AtomContainer.
- getType() - Method in class org.openscience.cdk.dict.DictRef
-
- getType() - Method in class org.openscience.cdk.isomorphism.matchers.CTFileQueryBond
-
Getter for type
- getUncommon(IAtomContainer, IAtomContainer, boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler
-
- getUncommon(IAtomContainer, IAtomContainer, boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler
-
- getUniqueMatchingAtoms() - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool
-
Get the atoms in the target molecule that match the query pattern.
- getUniqueMatchingPharmacophoreAtoms() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher
-
Get the uniue matching pharmacophore groups.
- getUnplacedRingHeavyAtom(IAtomContainer, IAtom) - Method in class org.openscience.cdk.modeling.builder3d.AtomPlacer3D
-
Gets the unplacedRingHeavyAtom attribute of the AtomPlacer3D object.
- getUnsetAtomsInAtomContainer(IAtom, IAtomContainer) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Gets the unsetAtomsInAtomContainer attribute of the
AtomTetrahedralLigandPlacer3D object.
- getUpper() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryAngleBond
-
- getUpper() - Method in class org.openscience.cdk.pharmacophore.PharmacophoreQueryBond
-
- getUseTemplates() - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
-
Returns whether the use of templates is enabled or disabled.
- getUSmilesNumbers(IAtomContainer) - Static method in class org.openscience.cdk.graph.invariant.InChINumbersTools
-
Obtain the InChI numbers for the input container to be used to order
atoms in Universal SMILES [O’Boyle, Noel, Towards a Universal SMILES representation - A standard method to generate canonical SMILES based on the InChI, Journal of Cheminformatics, 2012, 4:?-?].
- getValence(IAtom) - Static method in class org.openscience.cdk.qsar.AtomValenceTool
-
- getValency() - Method in class org.openscience.cdk.AtomType
-
Gets the the exact electron valency of the AtomType object.
- getValency() - Method in class org.openscience.cdk.debug.DebugAtom
-
Gets the the exact electron valency of the AtomType object.
- getValency() - Method in class org.openscience.cdk.debug.DebugAtomType
-
Gets the the exact electron valency of the AtomType object.
- getValency() - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Gets the the exact electron valency of the AtomType object.
- getValency() - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Gets the the exact electron valency of the AtomType object.
- getValency() - Method in interface org.openscience.cdk.interfaces.IAtomType
-
Gets the the exact electron valency of the AtomType object.
- getValency() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Gets the the exact electron valency of the AtomType object.
- getValency() - Method in class org.openscience.cdk.silent.AtomType
-
Gets the the exact electron valency of the AtomType object.
- getValue() - Method in enum org.openscience.cdk.io.MDLV2000Writer.SPIN_MULTIPLICITY
-
Radical value for the spin multiplicity in the properties block.
- getValue() - Method in class org.openscience.cdk.iupac.parser.Token
-
An optional attribute value of the Token.
- getValue(double, double, double) - Method in interface org.openscience.cdk.math.IFunction
-
Return the function value at (x,y,z)
- getValue(int, double, double, double) - Method in class org.openscience.cdk.math.qm.FourierGridBasis
-
- getValue(int, double, double, double) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Calculates the function value an (x,y,z).
- getValue(int, double, double, double) - Method in interface org.openscience.cdk.math.qm.IBasis
-
Calculates the function value an (x,y,z).
- getValue(int, double, double, double) - Method in class org.openscience.cdk.math.qm.Orbitals
-
Get the function value of a orbital at the position (x,y,z)
- getValue() - Method in class org.openscience.cdk.qsar.DescriptorValue
-
- getValue() - Method in interface org.openscience.cdk.reaction.type.parameters.IParameterReact
-
Get the value of the parameter.
- getValue() - Method in class org.openscience.cdk.reaction.type.parameters.ParameterReact
-
Get the value of the parameter.
- getValue() - Method in interface org.openscience.cdk.renderer.generators.IGeneratorParameter
-
Gets the value for this parameter.
- getValue() - Method in class org.openscience.cdk.renderer.generators.parameter.AbstractGeneratorParameter
-
Gets the value for this parameter.
- getValue() - Method in class org.openscience.cdk.smiles.smarts.parser.Token
-
An optional attribute value of the Token.
- getValue() - Method in class org.openscience.cdk.smsd.helper.BinaryTree
-
Return value of the node
- getValueAt(int, int) - Method in class org.openscience.cdk.graph.invariant.GIMatrix
-
Returns the value of the given element.
- getValues() - Method in class org.openscience.cdk.group.Permutation
-
Get all the values as an array.
- getValues(Matrix) - Method in interface org.openscience.cdk.math.IFunction
-
Return the function value
The rows of the matrix x are the Parameters like x,y,z
and the columns are the values which must calculated.
- getValues(int, Matrix) - Method in class org.openscience.cdk.math.qm.FourierGridBasis
-
- getValues(int, Matrix) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Calculates the function values.
- getValues(int, Matrix) - Method in interface org.openscience.cdk.math.qm.IBasis
-
Calculates the function values.
- getValues(int, Matrix) - Method in class org.openscience.cdk.math.qm.Orbitals
-
Get the function value of a orbital
- getVanDerWaalsFile() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- getVdwRadius(String) - Static method in class org.openscience.cdk.tools.periodictable.PeriodicTable
-
Get the Van der Waals radius for the element in question.
- getVdWVolume(String) - Method in class org.openscience.cdk.tools.AtomicProperties
-
- getVectorFromColumn(int) - Method in class org.openscience.cdk.math.IMatrix
-
Creates a vector with the content of a column from this matrix
- getVectorFromColumn(int) - Method in class org.openscience.cdk.math.Matrix
-
Creates a Vector with the content of a column from this Matrix.
- getVectorFromDiagonal() - Method in class org.openscience.cdk.math.IMatrix
-
Creates a vector with the content of the diagonal elements from this matrix
- getVectorFromDiagonal() - Method in class org.openscience.cdk.math.Matrix
-
Creates a Vector with the content of the diagonal elements from this Matrix.
- getVectorFromRow(int) - Method in class org.openscience.cdk.math.IMatrix
-
Creates a vector with the content of a row from this matrix
- getVectorFromRow(int) - Method in class org.openscience.cdk.math.Matrix
-
Creates a Vector with the content of a row from this Matrix.
- getVersion() - Static method in class org.openscience.cdk.CDK
-
Returns the version of this CDK library.
- getVertexCount() - Method in class org.openscience.cdk.group.AbstractDiscretePartitionRefiner
-
Get the number of vertices in the graph to be refined.
- getVertexCount() - Method in class org.openscience.cdk.group.AbstractEquitablePartitionRefiner
-
Gets from the graph the number of vertices.
- getVertexCount() - Method in class org.openscience.cdk.group.AtomDiscretePartitionRefiner
-
- getVertexCount() - Method in class org.openscience.cdk.group.AtomEquitablePartitionRefiner
-
- getVertexCount() - Method in class org.openscience.cdk.group.BondDiscretePartitionRefiner
-
- getVertexCount() - Method in class org.openscience.cdk.group.BondEquitablePartitionRefiner
-
- getVertexCount() - Method in class org.openscience.cdk.signature.MoleculeSignature
-
- getVertexCountAtDistance(IAtomContainer, int) - Static method in class org.openscience.cdk.graph.PathTools
-
Returns the number of vertices that are a distance 'd' apart.
- getVertexSymbol(int) - Method in class org.openscience.cdk.signature.AtomSignature
-
- getVisitedAtoms() - Method in interface org.openscience.cdk.geometry.cip.ILigand
-
Returns a list of visitedAtoms.
- getVisitedAtoms() - Method in class org.openscience.cdk.geometry.cip.Ligand
-
Returns a list of visitedAtoms.
- getWarningCount() - Method in class org.openscience.cdk.validate.ValidationReport
-
Returns the number of tests which gave warnings.
- getWarningFlags() - Method in class org.openscience.cdk.inchi.InChIToStructure
-
Returns warning flags, see INCHIDIFF in inchicmp.h.
- getWarnings() - Method in class org.openscience.cdk.validate.ValidationReport
-
Returns an array of ValidationTest warnings.
- getWidthForBond(IBond, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
-
Determine the width of a bond, returning either the width defined
in the model, or the override width.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.ABINITFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.Aces2Format
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.ADFFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.AlchemyFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.BGFFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.BSFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.CacaoCartesianFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.CacaoInternalFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.CACheFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.CDKOWLFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.CDKSourceCodeFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.ChemDrawFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.ChemtoolFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.CIFFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.CMLFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.CMLRSSFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.CRK2DFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.CRK3DFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.CrystClustFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.CTXFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.DaltonFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.DMol3Format
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.DOCK5Format
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.FingerprintFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.GamessFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.Gaussian03Format
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.Gaussian90Format
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.Gaussian92Format
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.Gaussian94Format
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.Gaussian95Format
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.Gaussian98Format
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.GaussianInputFormat
-
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.GhemicalMMFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.GhemicalSPMFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.GROMOS96Format
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.HINFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in interface org.openscience.cdk.io.formats.IChemFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.INChIFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.INChIPlainTextFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.JaguarFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.JMEFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.MacroModelFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.MDLFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.MDLRXNFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.MDLRXNV3000Format
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.MDLV2000Format
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.MDLV3000Format
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.MMODFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.Mol2Format
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2002Format
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2007Format
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2009Format
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC2012Format
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC7Format
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC7InputFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC93Format
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.MOPAC97Format
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.MoSSOutputFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.MPQCFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.NWChemFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.PCModelFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.PDBFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.PDBMLFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.PMPFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.PQSChemFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemASNFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemCompoundXMLFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesASNFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.QChemFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.RawCopyFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.RGroupQueryFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.SDFFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.ShelXFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.SMARTSFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.SMILESFIXFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.SMILESFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.SpartanFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.SybylDescriptorFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.TinkerMM2Format
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.TinkerXYZFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.TurboMoleFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.UniChemXYZFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.VASPFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.ViewmolFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.XEDFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.XYZFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.YasaraFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.ZindoFormat
-
Returns the class name of the CDK Writer for this format.
- getWriterClassName() - Method in class org.openscience.cdk.io.formats.ZMatrixFormat
-
Returns the class name of the CDK Writer for this format.
- getXMax() - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Sets the function area, which will painted
- getXMin() - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Gets the function area, which will painted
- getXTitle() - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Get the title of the x axis
- getYMax() - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Sets the function area, which will painted
- getYMin() - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Sets the function area, which will painted
- getYTitle() - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Get the title of the y axis
- getZ() - Method in class org.openscience.cdk.Crystal
-
Gets the number of asymmetric parts in the unit cell.
- getZ() - Method in class org.openscience.cdk.debug.DebugCrystal
-
Gets the number of asymmetric parts in the unit cell.
- getZ() - Method in interface org.openscience.cdk.interfaces.ICrystal
-
Gets the number of asymmetric parts in the unit cell.
- getZ() - Method in class org.openscience.cdk.silent.Crystal
-
Gets the number of asymmetric parts in the unit cell.
- GhemicalMMFormat - Class in org.openscience.cdk.io.formats
-
- GhemicalMMFormat() - Constructor for class org.openscience.cdk.io.formats.GhemicalMMFormat
-
- GhemicalMMReader - Class in org.openscience.cdk.io
-
- GhemicalMMReader(Reader) - Constructor for class org.openscience.cdk.io.GhemicalMMReader
-
- GhemicalMMReader(InputStream) - Constructor for class org.openscience.cdk.io.GhemicalMMReader
-
- GhemicalMMReader() - Constructor for class org.openscience.cdk.io.GhemicalMMReader
-
- GhemicalSPMFormat - Class in org.openscience.cdk.io.formats
-
- GhemicalSPMFormat() - Constructor for class org.openscience.cdk.io.formats.GhemicalSPMFormat
-
- GIMatrix - Class in org.openscience.cdk.graph.invariant
-
This class is intended to provide the user an efficient way of implementing matrix of double number and
using normal operations (linear operations, addition, subtraction, multiplication, inversion, concatenation)
on them.
- GIMatrix(int[][]) - Constructor for class org.openscience.cdk.graph.invariant.GIMatrix
-
Class constructor.
- GIMatrix(double[][]) - Constructor for class org.openscience.cdk.graph.invariant.GIMatrix
-
Class constructor.
- GIMatrix(int, int) - Constructor for class org.openscience.cdk.graph.invariant.GIMatrix
-
Class constructor.
- GIMatrix(GIMatrix) - Constructor for class org.openscience.cdk.graph.invariant.GIMatrix
-
Class constructor.
- GIMatrix(GIMatrix[][]) - Constructor for class org.openscience.cdk.graph.invariant.GIMatrix
-
Class constructor.
- giveAngle(IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.geometry.BondTools
-
Calls giveAngleBothMethods with bool = true.
- giveAngleBothMethods(IAtom, IAtom, IAtom, boolean) - Static method in class org.openscience.cdk.geometry.BondTools
-
Gives the angle between two lines starting at atom from and going to to1
and to2.
- giveAngleBothMethods(Point2d, Point2d, Point2d, boolean) - Static method in class org.openscience.cdk.geometry.BondTools
-
- giveAngleFromMiddle(IAtom, IAtom, IAtom) - Static method in class org.openscience.cdk.geometry.BondTools
-
Calls giveAngleBothMethods with bool = false.
- GOLD - Static variable in enum org.openscience.cdk.config.Elements
-
- GOLD - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- graph - Variable in class org.openscience.cdk.stereo.StereoElementFactory
-
Adjacency list graph representation.
- GraphOnlyFingerprinter - Class in org.openscience.cdk.fingerprint
-
Specialized version of the
Fingerprinter
which does not take bond orders
into account.
- GraphOnlyFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.GraphOnlyFingerprinter
-
Creates a fingerprint generator of length defaultSize
and with a search depth of defaultSearchDepth
.
- GraphOnlyFingerprinter(int) - Constructor for class org.openscience.cdk.fingerprint.GraphOnlyFingerprinter
-
- GraphOnlyFingerprinter(int, int) - Constructor for class org.openscience.cdk.fingerprint.GraphOnlyFingerprinter
-
- GraphRendererModel - Class in org.openscience.cdk.renderer
-
This class handles a set of function for the GraphRenderer
- GraphRendererModel() - Constructor for class org.openscience.cdk.renderer.GraphRendererModel
-
- GraphUtil - Class in org.openscience.cdk.graph
-
Collection of static utilities for manipulating adjacency list
representations stored as a int[][].
- GraphUtil.EdgeToBondMap - Class in org.openscience.cdk.graph
-
Utility for storing
IBond
s indexed by vertex end points.
- GravitationalIndexDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
-
IDescriptor characterizing the mass distribution of the molecule.
- GravitationalIndexDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor
-
- GridGenerator - Class in org.openscience.cdk.tools
-
Generates a grid of points in 3D space within given boundaries.
- GridGenerator() - Constructor for class org.openscience.cdk.tools.GridGenerator
-
- GridGenerator(double, double) - Constructor for class org.openscience.cdk.tools.GridGenerator
-
- GridGenerator(double, double, double) - Constructor for class org.openscience.cdk.tools.GridGenerator
-
- GridGenerator(double[], double, boolean) - Constructor for class org.openscience.cdk.tools.GridGenerator
-
- gridToGridArray(double[][][]) - Method in class org.openscience.cdk.tools.GridGenerator
-
Method transforms the grid to an array.
- gridToPmesh(String) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
Method writes the grid to pmesh format.
- GROMOS96Format - Class in org.openscience.cdk.io.formats
-
- GROMOS96Format() - Constructor for class org.openscience.cdk.io.formats.GROMOS96Format
-
- group() - Method in enum org.openscience.cdk.config.Elements
-
Return the group in the periodic table this element belongs to.
- GroupExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
- groupOneMetals() - Method in class org.openscience.cdk.iupac.parser.NomParser
-
Deprecated.
- groupTwoMetals() - Method in class org.openscience.cdk.iupac.parser.NomParser
-
Deprecated.
- growArraySize - Variable in class org.openscience.cdk.AtomContainer
-
Amount by which the bond and atom arrays grow when elements are added and
the arrays are not large enough for that.
- growArraySize - Variable in class org.openscience.cdk.AtomContainerSet
-
Amount by which the AtomContainers array grows when elements are added and
the array is not large enough for that.
- growArraySize - Variable in class org.openscience.cdk.ChemFile
-
Amount by which the chemsequence array grows when elements are added and
the array is not large enough for that.
- growArraySize - Variable in class org.openscience.cdk.ChemSequence
-
Amount by which the chemModels array grows when elements are added and
the array is not large enough for that.
- growArraySize - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Amount by which the bond and atom arrays grow when elements are added and
the arrays are not large enough for that.
- growArraySize - Variable in class org.openscience.cdk.Reaction
-
- growArraySize - Variable in class org.openscience.cdk.silent.AtomContainer
-
Amount by which the bond and atom arrays grow when elements are added and
the arrays are not large enough for that.
- growArraySize - Variable in class org.openscience.cdk.silent.AtomContainerSet
-
Amount by which the AtomContainers array grows when elements are added and
the array is not large enough for that.
- growArraySize - Variable in class org.openscience.cdk.silent.ChemFile
-
Amount by which the chemsequence array grows when elements are added and
the array is not large enough for that.
- growArraySize - Variable in class org.openscience.cdk.silent.ChemSequence
-
Amount by which the chemModels array grows when elements are added and
the array is not large enough for that.
- growArraySize - Variable in class org.openscience.cdk.silent.Reaction
-
- growAtomContainerArray() - Method in class org.openscience.cdk.AtomContainerSet
-
Grows the atomContainer array by a given size.
- growAtomContainerArray() - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Grows the atomContainer array by a given size.
- growChemModelArray() - Method in class org.openscience.cdk.ChemSequence
-
Grows the chemModel array by a given size.
- growChemModelArray() - Method in class org.openscience.cdk.silent.ChemSequence
-
Grows the chemModel array by a given size.
- growChemSequenceArray() - Method in class org.openscience.cdk.ChemFile
-
Grows the ChemSequence array by a given size.
- growChemSequenceArray() - Method in class org.openscience.cdk.silent.ChemFile
-
Grows the ChemSequence array by a given size.
- guessFormat(Reader) - Method in class org.openscience.cdk.io.FormatFactory
-
Creates a String of the Class name of the IChemObject
reader
for this file format.
- guessFormat(InputStream) - Method in class org.openscience.cdk.io.FormatFactory
-
- s - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- S - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- S_BOND - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- SAMARIUM - Static variable in enum org.openscience.cdk.config.Elements
-
- sample(IAtomContainer) - Static method in class org.openscience.cdk.structgen.VicinitySampler
-
Choose any possible quadruple of the set of atoms
in ac and establish all of the possible bonding schemes according to
Faulon's equations.
- SANARIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- saturate(IAtomContainer) - Method in class org.openscience.cdk.tools.AtomTypeAwareSaturationChecker
- saturate(IAtomContainer) - Method in interface org.openscience.cdk.tools.IDeduceBondOrderTool
-
- saturate(IAtomContainer) - Method in class org.openscience.cdk.tools.LonePairElectronChecker
-
Saturates a molecule by setting appropriate number lone pair electrons.
- saturate(IAtom, IAtomContainer) - Method in class org.openscience.cdk.tools.LonePairElectronChecker
-
Saturates an IAtom by adding the appropriate number lone pairs.
- saturate(IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker
-
The method is known to fail for certain compounds.
- saturate(IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
-
Saturates a molecule by setting appropriate bond orders.
- saturate(IBond[], IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
-
Saturates a set of Bonds in an AtomContainer.
- saturateByIncreasingBondOrder(IBond, IAtomContainer) - Method in class org.openscience.cdk.tools.SmilesValencyChecker
-
Tries to saturate a bond by increasing its bond orders by 1.0.
- saturateRingSystems(IAtomContainer) - Method in class org.openscience.cdk.tools.SaturationChecker
-
- SaturationChecker - Class in org.openscience.cdk.tools
-
Provides methods for checking whether an atoms valences are saturated with
respect to a particular atom type.
- SaturationChecker() - Constructor for class org.openscience.cdk.tools.SaturationChecker
-
- saveIndex(File) - Method in class org.openscience.cdk.io.random.RandomAccessReader
-
- SB - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- SC - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- scaleMolecule(IAtomContainer, Dimension, double) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Scales a molecule such that it fills a given percentage of a given
dimension.
- scaleMolecule(IAtomContainer, double) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Multiplies all the coordinates of the atoms of the given molecule with the
scalefactor.
- scaleMolecule(IAtomContainer, double[], double) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Scales a molecule such that it fills a given percentage of a given dimension.
- scaleMolecule(IAtomContainer, double) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Multiplies all the coordinates of the atoms of the given molecule with the scalefactor.
- SCANDIUM - Static variable in enum org.openscience.cdk.config.Elements
-
- SCANDIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- SDFFormat - Class in org.openscience.cdk.io.formats
-
- SDFFormat() - Constructor for class org.openscience.cdk.io.formats.SDFFormat
-
- SDFWriter - Class in org.openscience.cdk.io
-
Writes MDL SD files ([Dalby, A. and Nourse, J. G. and Hounshell, W. D. and
Gushurst, A. K. and Grier, D. L. and Leland, B. A. and
Laufer, J., Description of Several Chemical Structure File Formats Used by
Computer Programs Developed at Molecular Design Limited, Journal of Chemical Information and Computer Sciences, 1992, 32:244-255]).
- SDFWriter(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
-
- SDFWriter(Writer, Set<String>) - Constructor for class org.openscience.cdk.io.SDFWriter
-
Constructs a new SDFWriter that writes to the given
Writer
.
- SDFWriter(OutputStream, Set<String>) - Constructor for class org.openscience.cdk.io.SDFWriter
-
Constructs a new SdfWriter that can write to a given
OutputStream
.
- SDFWriter(Set<String>) - Constructor for class org.openscience.cdk.io.SDFWriter
-
Writes SD-File to a String including the given properties
- se - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- SE - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- SEABORGIUM - Static variable in enum org.openscience.cdk.config.Elements
-
- SEABORGIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- search(IAtomContainer, IAtomContainer, BitSet, BitSet, boolean, boolean) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
-
General
RGraph
parsing method (usually not used directly)
This method is the entry point for the recursive search
adapted to the atom container input.
- search(IAtomContainer, IAtomContainer, BitSet, BitSet, boolean, boolean, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
-
General Rgraph parsing method (usually not used directly)
This method is the entry point for the recursive search
adapted to the atom container input.
- searchCorrespondingAtom(int, int, int, List<Integer>) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
-
- searchMCS(boolean) - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler
-
Initialise the MCS search algorithm.
- searchMCS(boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler
-
Initialise the MCS search algorithm.
- searchMCS(boolean) - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler
-
Initialise the MCS search algorithm.
- searchMCS(boolean) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler
-
Initialise the MCS search algorithm.
- searchMCS(boolean) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCSAlgorithm
-
Initialise the MCS search algorithm.
- secondPointX - Variable in class org.openscience.cdk.renderer.elements.LineElement
-
The x-coordinate of the second point.
- secondPointY - Variable in class org.openscience.cdk.renderer.elements.LineElement
-
The y-coordinate of the second point.
- select(IChemModel) - Method in class org.openscience.cdk.renderer.selection.AbstractSelection
-
Perform a selection by some method.
- select(IChemModel) - Method in interface org.openscience.cdk.renderer.selection.IChemObjectSelection
-
Perform a selection by some method.
- SelectionVisibility - Class in org.openscience.cdk.renderer.generators.standard
-
Extended existing symbol visibility options to account for selection of atoms in the standard
generator.
- SELENIUM - Static variable in enum org.openscience.cdk.config.Elements
-
- SELENIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- SERIAL_FORMAT - Variable in class org.openscience.cdk.io.PDBWriter
-
- set(int, IAtomContainer) - Method in class org.openscience.cdk.ConformerContainer
-
- set(int, boolean) - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
-
- set(int) - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
-
- set(int, boolean) - Method in interface org.openscience.cdk.fingerprint.IBitFingerprint
-
Sets the bit at the specified index to the specified value.
- set(int) - Method in interface org.openscience.cdk.fingerprint.IBitFingerprint
-
Sets the bit at the specified index to true.
- set(int, boolean) - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
-
- set(int) - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
-
- set(int, int) - Method in class org.openscience.cdk.group.Permutation
-
Set the value at the specified index.
- set(IChemObject) - Method in class org.openscience.cdk.io.random.RandomAccessReader
-
- set(Class<T>, U) - Method in class org.openscience.cdk.renderer.RendererModel
-
- set(MolHandler, MolHandler) - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler
-
Initialise the query and target molecule.
- set(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler
-
Initialise the query and target molecule.
- set(MolHandler, MolHandler) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler
-
Initialise the query and target molecule.
- set(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler
-
Initialise the query and target molecule.
- set(MolHandler, MolHandler) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler
-
Initialise the query and target molecule.
- set(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler
-
Initialise the query and target molecule.
- set(MolHandler, MolHandler) - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler
-
Initialise the query and target molecule.
- set(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler
-
Initialise the query and target molecule.
- set(MolHandler, MolHandler) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler
-
Initialise the query and target molecule.
- set(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler
-
Initialise the query and target molecule.
- set(MolHandler, MolHandler) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler
-
Initialise the query and target molecule.
- set(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler
-
Initialise the query and target molecule.
- set(MolHandler, MolHandler) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler
-
Initialise the query and target molecule.
- set(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler
-
Initialise the query and target molecule.
- set(List<Map<Integer, Integer>>) - Method in class org.openscience.cdk.smsd.helper.FinalMappings
-
Sets mapping list
- set(List<Map<Integer, Integer>>) - Method in interface org.openscience.cdk.smsd.interfaces.IFinalMapping
-
Sets mapping list
- set(MolHandler, MolHandler) - Method in interface org.openscience.cdk.smsd.interfaces.IMCSBase
-
Initialise the query and target molecule.
- set(IQueryAtomContainer, IAtomContainer) - Method in interface org.openscience.cdk.smsd.interfaces.IMCSBase
-
Initialise the query and target molecule.
- SET_UNIQUE_POLICY - Static variable in class org.openscience.cdk.tools.IDCreator
-
Old ID generation policy - to generate IDs unique over the entire set
- setA(Vector3d) - Method in class org.openscience.cdk.Crystal
-
Sets the A unit cell axes in Cartesian coordinates in a
Euclidean space.
- setA(Vector3d) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Sets the A unit cell axes in Cartesian coordinates in a
Euclidean space.
- setA(Vector3d) - Method in interface org.openscience.cdk.interfaces.ICrystal
-
Sets the A unit cell axes in carthesian coordinates in a
eucledian space.
- setA(Vector3d) - Method in class org.openscience.cdk.silent.Crystal
-
Sets the A unit cell axes in Cartesian coordinates in a
Euclidean space.
- setAbout(String) - Method in class org.openscience.cdk.io.RssWriter
-
- setAllMap(boolean) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
-
Sets the 'finAllMap' option.
- setAllMap(boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
-
Sets the 'finAllMap' option.
- setAllStructure(boolean) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
-
Sets the 'AllStructres' option.
- setAllStructure(boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
-
Sets the 'AllStructres' option.
- setAltLoc(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
set the Alternate location indicator of this atom.
- setAltLoc(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
set the Alternate location indicator of this atom.
- setAltLoc(String) - Method in class org.openscience.cdk.protein.data.PDBAtom
-
set the Alternate location indicator of this atom.
- setAltLoc(String) - Method in class org.openscience.cdk.silent.PDBAtom
-
set the Alternate location indicator of this atom.
- setArcs(IAtomContainer, IAtomContainer, int, int, List<Integer>, List<Integer>, List<String>, List<String>, List<Integer>, boolean) - Static method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
-
- setAromaticity(Aromaticity) - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool
-
Set the aromaticity perception to use.
- setArrayValue(double[][]) - Method in class org.openscience.cdk.graph.invariant.GIMatrix
-
Resets the value of the matrix to the given array of double numbers.
- setAsPermutation(int) - Method in class org.openscience.cdk.group.Partition
-
Fill the elements of a permutation from the first element of each
cell, up to the point upTo
.
- setAtom(int, IAtom) - Method in class org.openscience.cdk.AtomContainer
-
Sets the atom at position number
in [0,..].
- setAtom(IAtom, int) - Method in class org.openscience.cdk.Bond
-
Sets an Atom in this bond.
- setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Sets the atom at position number
in [0,..].
- setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Sets the atom at position number
in [0,..].
- setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Sets the atom at position number
in [0,..].
- setAtom(IAtom, int) - Method in class org.openscience.cdk.debug.DebugBond
-
Sets an Atom in this bond.
- setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Sets the atom at position number
in [0,..].
- setAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugLonePair
-
Sets the associated Atom.
- setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Sets the atom at position number
in [0,..].
- setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Sets the atom at position number
in [0,..].
- setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugRing
-
Sets the atom at position number
in [0,..].
- setAtom(IAtom) - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
Sets the associated Atom.
- setAtom(int, IAtom) - Method in class org.openscience.cdk.debug.DebugStrand
-
Sets the atom at position number
in [0,..].
- setAtom(int, IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Set the atom at position number
in [0,..].
- setAtom(IAtom, int) - Method in interface org.openscience.cdk.interfaces.IBond
-
Sets an Atom in this bond.
- setAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.ILonePair
-
Sets the associated Atom.
- setAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.ISingleElectron
-
Sets the associated Atom.
- setAtom(int, IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Sets the atom at position number
in [0,..].
- setAtom(IAtom, int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Sets an atom in this query bond.
- setAtom(IQueryAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RingIdentifierAtom
-
- setAtom(IAtom) - Method in class org.openscience.cdk.LonePair
-
Sets the associated Atom.
- setAtom(int, IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Sets the atom at position number
in [0,..].
- setAtom(IAtom, int) - Method in class org.openscience.cdk.silent.Bond
-
Sets an Atom in this bond.
- setAtom(IAtom) - Method in class org.openscience.cdk.silent.LonePair
-
Sets the associated Atom.
- setAtom(IAtom) - Method in class org.openscience.cdk.silent.SingleElectron
-
Sets the associated Atom.
- setAtom(IAtom) - Method in class org.openscience.cdk.SingleElectron
-
Sets the associated Atom.
- setAtom(IAtom) - Method in class org.openscience.cdk.smiles.InvPair
-
- setAtomAt(IAtom, int) - Method in class org.openscience.cdk.Association
-
Sets an Atom in this Association.
- setAtomAt(IAtom, int) - Method in class org.openscience.cdk.isomorphism.matchers.OrderQueryBond
-
- setAtomAt(IAtom, int) - Method in class org.openscience.cdk.isomorphism.matchers.OrderQueryBondOrderOnly
-
- setAtomCheckRadius(double) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- setAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.structgen.SingleStructureRandomGenerator
-
Sets the AtomContainer attribute of the SingleStructureRandomGenerator object.
- setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugAtom
-
Sets the atomic number of this element.
- setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugAtomType
-
Sets the atomic number of this element.
- setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugElement
-
Sets the atomic number of this element.
- setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Sets the atomic number of this element.
- setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugIsotope
-
Sets the atomic number of this element.
- setAtomicNumber(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Sets the atomic number of this element.
- setAtomicNumber(Integer) - Method in class org.openscience.cdk.Element
-
Sets the atomic number of this element.
- setAtomicNumber(Integer) - Method in interface org.openscience.cdk.interfaces.IElement
-
Sets the atomic number of this element.
- setAtomicNumber(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets the atomic number of this element.
- setAtomicNumber(Integer) - Method in class org.openscience.cdk.silent.Element
-
Sets the atomic number of this element.
- setAtomPlacer(AtomPlacer) - Method in class org.openscience.cdk.layout.RingPlacer
-
- setAtomProperties(IAtomContainer, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Sets a property on all Atom
s in the given container.
- setAtomProperties(IAtomContainerSet, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
-
- setAtomProperties(IChemModel, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.ChemModelManipulator
-
Sets the AtomProperties of all Atoms inside an IChemModel.
- setAtomProperties(IAtomContainerSet, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
-
- setAtomProperties(IReaction, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.ReactionManipulator
-
- setAtomProperties(IReactionSet, Object, Object) - Static method in class org.openscience.cdk.tools.manipulator.ReactionSetManipulator
-
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.Association
-
Sets the array of atoms making up this Association.
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.AtomContainer
-
Sets the array of atoms of this AtomContainer.
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.Bond
-
Sets the array of atoms making up this bond.
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Sets the array of atoms of this AtomContainer.
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Sets the array of atoms of this AtomContainer.
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Sets the array of atoms of this AtomContainer.
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugBond
-
Sets the array of atoms making up this bond.
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Sets the array of atoms of this AtomContainer.
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Sets the array of atoms of this AtomContainer.
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Sets the array of atoms of this AtomContainer.
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugRing
-
Sets the array of atoms of this AtomContainer.
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.debug.DebugStrand
-
Sets the array of atoms of this AtomContainer.
- setAtoms(IAtom[]) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Sets the array of atoms of this AtomContainer.
- setAtoms(IAtom[]) - Method in interface org.openscience.cdk.interfaces.IBond
-
Sets the array of atoms making up this bond.
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.isomorphism.matchers.OrderQueryBond
-
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.isomorphism.matchers.OrderQueryBondOrderOnly
-
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Sets the array of atoms of this AtomContainer.
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Sets the array of atoms making up this query bond.
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond
-
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.silent.AtomContainer
-
Sets the array of atoms of this AtomContainer.
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.silent.Bond
-
Sets the array of atoms making up this bond.
- setAtomTypeName(String) - Method in class org.openscience.cdk.AtomType
-
Sets the if attribute of the AtomType object.
- setAtomTypeName(String) - Method in class org.openscience.cdk.debug.DebugAtom
-
Sets the if attribute of the AtomType object.
- setAtomTypeName(String) - Method in class org.openscience.cdk.debug.DebugAtomType
-
Sets the if attribute of the AtomType object.
- setAtomTypeName(String) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Sets the if attribute of the AtomType object.
- setAtomTypeName(String) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Sets the if attribute of the AtomType object.
- setAtomTypeName(String) - Method in interface org.openscience.cdk.interfaces.IAtomType
-
Sets the if attribute of the AtomType object.
- setAtomTypeName(String) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets the if attribute of the AtomType object.
- setAtomTypeName(String) - Method in class org.openscience.cdk.silent.AtomType
-
Sets the if attribute of the AtomType object.
- setAtomTypes(List<IAtomType>) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
-
Sets the atomTypes attribute of the ForceFieldConfigurator object
- setB(Vector3d) - Method in class org.openscience.cdk.Crystal
-
Sets the B unit cell axes in Cartesian coordinates.
- setB(Vector3d) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Sets the B unit cell axes in Cartesian coordinates.
- setB(Vector3d) - Method in interface org.openscience.cdk.interfaces.ICrystal
-
Sets the B unit cell axes in carthesian coordinates.
- setB(Vector3d) - Method in class org.openscience.cdk.silent.Crystal
-
Sets the B unit cell axes in Cartesian coordinates.
- setBasis(int[], int[], int[], double[], Vector[], IAtom[]) - Method in class org.openscience.cdk.math.qm.GaussiansBasis
-
Set up basis with gauss funktions
f(x,y,z) = (x-rx)^nx * (y-ry)^ny * (z-rz)^nz * exp(-alpha*(r-ri)^2).
- setBehaveAsBitFingerprint(boolean) - Method in interface org.openscience.cdk.fingerprint.ICountFingerprint
-
Changes behaviour, if true is given the count fingerprint will
behave as a bit fingerprint and return 0 or 1 for counts.
- setBehaveAsBitFingerprint(boolean) - Method in class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
-
- setBondInSensitiveTimeOut(double) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
set timeout in mins (default 1.00 min) for bond insensitive searches
- setBondInSensitiveTimeOut(double) - Method in class org.openscience.cdk.smsd.Isomorphism
-
set timeout in mins (default 1.00 min) for bond insensitive searches
- setBondLength(double) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
-
Set the bond length used for laying out the molecule.
- setBondMatchFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultBondMatcher
-
- setBondMatchFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultMCSPlusAtomMatcher
-
- setBondMatchFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultRGraphAtomMatcher
-
- setBondMatchFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFAtomMatcher
-
- setBondMatchFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFBondMatcher
-
- setBondMatchFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler
-
- setBondMatchFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler
-
- setBondMatchFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler
-
- setBondOrderSum(Double) - Method in class org.openscience.cdk.AtomType
-
Sets the the exact bond order sum attribute of the AtomType object.
- setBondOrderSum(Double) - Method in class org.openscience.cdk.debug.DebugAtom
-
Sets the the exact bond order sum attribute of the AtomType object.
- setBondOrderSum(Double) - Method in class org.openscience.cdk.debug.DebugAtomType
-
Sets the the exact bond order sum attribute of the AtomType object.
- setBondOrderSum(Double) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Sets the the exact bond order sum attribute of the AtomType object.
- setBondOrderSum(Double) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Sets the the exact bond order sum attribute of the AtomType object.
- setBondOrderSum(Double) - Method in interface org.openscience.cdk.interfaces.IAtomType
-
Sets the the exact bond order sum attribute of the AtomType object.
- setBondOrderSum(Double) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets the the exact bond order sum attribute of the AtomType object.
- setBondOrderSum(Double) - Method in class org.openscience.cdk.silent.AtomType
-
Sets the the exact bond order sum attribute of the AtomType object.
- setBonds(IBond[]) - Method in class org.openscience.cdk.AtomContainer
-
Sets the array of bonds of this AtomContainer.
- setBonds(IBond[]) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Sets the array of bonds of this AtomContainer.
- setBonds(IBond[]) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Sets the array of bonds of this AtomContainer.
- setBonds(IBond[]) - Method in class org.openscience.cdk.silent.AtomContainer
-
Sets the array of bonds of this AtomContainer.
- setBondSensitiveTimeOut(double) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
set timeout in mins (default 0.10 min) for bond sensitive searches
- setBondSensitiveTimeOut(double) - Method in class org.openscience.cdk.smsd.Isomorphism
-
set timeout in mins (default 0.10 min) for bond sensitive searches
- setBuilder(IChemObjectBuilder) - Method in class org.openscience.cdk.stereo.DoubleBondStereochemistry
-
- setBuilder(IChemObjectBuilder) - Method in class org.openscience.cdk.stereo.TetrahedralChirality
-
- setC(Vector3d) - Method in class org.openscience.cdk.Crystal
-
Sets the C unit cell axes in Cartesian coordinates.
- setC(Vector3d) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Sets the C unit cell axes in Cartesian coordinates.
- setC(Vector3d) - Method in interface org.openscience.cdk.interfaces.ICrystal
-
Sets the C unit cell axes in carthesian coordinates.
- setC(Vector3d) - Method in class org.openscience.cdk.silent.Crystal
-
Sets the C unit cell axes in Cartesian coordinates.
- setChainID(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
set the Chain identifier of this atom.
- setChainID(String) - Method in class org.openscience.cdk.debug.DebugPDBMonomer
-
Sets the Chain ID of this monomer.
- setChainID(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
set the Chain identifier of this atom.
- setChainID(String) - Method in interface org.openscience.cdk.interfaces.IPDBMonomer
-
Sets the Chain ID of this monomer.
- setChainID(String) - Method in class org.openscience.cdk.protein.data.PDBAtom
-
set the Chain identifier of this atom.
- setChainID(String) - Method in class org.openscience.cdk.protein.data.PDBMonomer
-
- setChainID(String) - Method in class org.openscience.cdk.silent.PDBAtom
-
set the Chain identifier of this atom.
- setChainID(String) - Method in class org.openscience.cdk.silent.PDBMonomer
-
- setCharge(Double) - Method in class org.openscience.cdk.Atom
-
Sets the partial charge of this atom.
- setCharge(Integer) - Method in class org.openscience.cdk.debug.DebugAdductFormula
-
No use this method.
- setCharge(Double) - Method in class org.openscience.cdk.debug.DebugAtom
-
Sets the partial charge of this atom.
- setCharge(Double) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Sets the partial charge of this atom.
- setCharge(Integer) - Method in class org.openscience.cdk.debug.DebugMolecularFormula
-
Sets the partial charge of this IMolecularFormula.
- setCharge(Double) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Sets the partial charge of this atom.
- setCharge(Integer) - Method in class org.openscience.cdk.formula.AdductFormula
-
Deprecated.
- setCharge(double) - Method in class org.openscience.cdk.formula.IsotopePattern
-
Set the charge in this pattern.
- setCharge(Integer) - Method in class org.openscience.cdk.formula.MolecularFormula
-
Sets the 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(Double) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets the partial charge of this atom.
- setCharge(Integer) - Method in class org.openscience.cdk.silent.AdductFormula
-
Deprecated.
- setCharge(Double) - Method in class org.openscience.cdk.silent.Atom
-
Sets the partial charge of this atom.
- setCharge(Integer) - Method in class org.openscience.cdk.silent.MolecularFormula
-
Sets the partial charge of this IMolecularFormula.
- 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.
- setChemFilters(boolean, boolean, boolean) - Method in class org.openscience.cdk.smsd.interfaces.AbstractMCS
-
initialize query and target molecules.
- setChemFilters(boolean, boolean, boolean) - Method in class org.openscience.cdk.smsd.Isomorphism
-
initialize query and target molecules.
- setChemObjectReader(ISimpleChemObjectReader) - Method in class org.openscience.cdk.io.random.RandomAccessReader
-
- setChiCatHydrogen(double) - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
-
Sets chi_cat value for hydrogen, because H poses a special problem due to lack of possible second ionisation.
- setClassName(String) - Method in class org.openscience.cdk.dict.Entry
-
- setClipboardContent(IAtomContainer) - Method in class org.openscience.cdk.renderer.RendererModel
-
Sets the atoms and bonds on the Renderer2D clipboard.
- setClockwise(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom
-
- setCoefficients(Matrix) - Method in class org.openscience.cdk.math.qm.Orbitals
-
Set a coefficient matrix
- setColumn(int, GIMatrix) - Method in class org.openscience.cdk.graph.invariant.GIMatrix
-
Sets the column of the matrix at the specified index to a new value.
- setCountElectrons(int) - Method in class org.openscience.cdk.math.qm.Orbitals
-
Sets the count of electrons, which occupies the orbitals
- setCovalentRadius(Double) - Method in class org.openscience.cdk.AtomType
-
Sets the covalent radius for this AtomType.
- setCovalentRadius(Double) - Method in class org.openscience.cdk.debug.DebugAtom
-
Sets the covalent radius for this AtomType.
- setCovalentRadius(Double) - Method in class org.openscience.cdk.debug.DebugAtomType
-
Sets the covalent radius for this AtomType.
- setCovalentRadius(Double) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Sets the covalent radius for this AtomType.
- setCovalentRadius(Double) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Sets the covalent radius for this AtomType.
- setCovalentRadius(Double) - Method in interface org.openscience.cdk.interfaces.IAtomType
-
Sets the covalent radius for this AtomType.
- setCovalentRadius(Double) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets the covalent radius for this AtomType.
- setCovalentRadius(Double) - Method in class org.openscience.cdk.silent.AtomType
-
Sets the covalent radius for this AtomType.
- setCreator(String) - Method in class org.openscience.cdk.io.RssWriter
-
- setCreatormap(Map) - Method in class org.openscience.cdk.io.RssWriter
-
- setCrystal(ICrystal) - Method in class org.openscience.cdk.ChemModel
-
Sets the Crystal contained in this ChemModel.
- setCrystal(ICrystal) - Method in class org.openscience.cdk.debug.DebugChemModel
-
Sets the Crystal contained in this ChemModel.
- setCrystal(ICrystal) - Method in interface org.openscience.cdk.interfaces.IChemModel
-
Sets the Crystal contained in this ChemModel.
- setCrystal(ICrystal) - Method in class org.openscience.cdk.silent.ChemModel
-
Sets the Crystal contained in this ChemModel.
- setCurr(long) - Method in class org.openscience.cdk.smiles.InvPair
-
Set the value of the seed.
- setDatemap(Map) - Method in class org.openscience.cdk.io.RssWriter
-
- setDebugEnabled(boolean) - Method in class org.openscience.cdk.tools.SystemOutLoggingTool
-
Protected method which must not be used, except for testing purposes.
- setDebugStream(PrintStream) - Method in class org.openscience.cdk.iupac.parser.NomParserTokenManager
-
Set debug output.
- setDebugStream(PrintStream) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager
-
Set debug output.
- setDefaultReactions() - Method in class org.openscience.cdk.tools.StructureResonanceGenerator
-
Set the default reactions that must be presents to generate the resonance.
- setDefaultRestrictions() - Method in class org.openscience.cdk.formula.MassToFormulaTool
-
Deprecated.
Set the default restrictions that must be presents in the molecular formula.
- setDefinition(String) - Method in class org.openscience.cdk.dict.Entry
-
- setDegree(int) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom
-
- setDescription(String) - Method in class org.openscience.cdk.dict.Entry
-
- setDescription(String) - Method in class org.openscience.cdk.io.RssWriter
-
- setDescriptorInstances(List<IDescriptor>) - Method in class org.openscience.cdk.qsar.DescriptorEngine
-
Set the list of Descriptor
objects.
- setDescriptorMetadata(String) - Method in class org.openscience.cdk.dict.Entry
-
- setDescriptorSpecifications(List<IImplementationSpecification>) - Method in class org.openscience.cdk.qsar.DescriptorEngine
-
Set the list of DescriptorSpecification
objects.
- setDetails(String) - Method in class org.openscience.cdk.validate.ValidationTest
-
- setDim(int[]) - Method in class org.openscience.cdk.tools.GridGenerator
-
- setDimension(double, double) - Method in class org.openscience.cdk.tools.GridGenerator
-
Method sets the maximal 3d dimensions to given min and max values.
- setDimension(double[], boolean) - Method in class org.openscience.cdk.tools.GridGenerator
-
Method sets the maximal 3d dimensions to given min and max values.
- setDimension(double, double, double, double, double, double) - Method in class org.openscience.cdk.tools.GridGenerator
-
Method sets the maximal 3d dimensions to given min and max values.
- setDirection(IReaction.Direction) - Method in class org.openscience.cdk.debug.DebugReaction
-
Sets the direction of the reaction.
- setDirection(IReaction.Direction) - Method in interface org.openscience.cdk.interfaces.IReaction
-
Sets the direction of the reaction.
- setDirection(IReaction.Direction) - Method in class org.openscience.cdk.Reaction
-
Sets the direction of the reaction.
- setDirection(IReaction.Direction) - Method in class org.openscience.cdk.silent.Reaction
-
Sets the direction of the reaction.
- setDisplayMode(int) - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Set the display mode
- setDocumentProperty(String, String) - Method in class org.openscience.cdk.io.iterator.event.EventCMLHandler
-
Procedure required by the CDOInterface.
- setDrawCenter(double, double) - Method in class org.openscience.cdk.renderer.AbstractRenderer
-
Set the point on the screen to draw the diagram.
- setElectronCount(Integer) - Method in class org.openscience.cdk.debug.DebugBond
-
Sets the number of electrons in this electron container.
- setElectronCount(Integer) - Method in class org.openscience.cdk.debug.DebugElectronContainer
-
Sets the number of electrons in this electron container.
- setElectronCount(Integer) - Method in class org.openscience.cdk.debug.DebugLonePair
-
Sets the number of electrons in this electron container.
- setElectronCount(Integer) - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
Sets the number of electrons in this electron container.
- setElectronCount(Integer) - Method in class org.openscience.cdk.ElectronContainer
-
Sets the number of electrons in this electron container.
- setElectronCount(Integer) - Method in interface org.openscience.cdk.interfaces.IElectronContainer
-
Sets the number of electrons in this electron container.
- setElectronCount(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Sets the number of electrons in this bond
- setElectronCount(Integer) - Method in class org.openscience.cdk.silent.ElectronContainer
-
Sets the number of electrons in this electron container.
- setEndChainID(Character) - Method in class org.openscience.cdk.debug.DebugPDBStructure
-
set the ending Chain identifier of this structure.
- setEndChainID(Character) - Method in interface org.openscience.cdk.interfaces.IPDBStructure
-
set the ending Chain identifier of this structure.
- setEndChainID(Character) - Method in class org.openscience.cdk.protein.data.PDBStructure
-
set the ending Chain identifier of this structure.
- setEndChainID(Character) - Method in class org.openscience.cdk.silent.PDBStructure
-
set the ending Chain identifier of this structure.
- setEndInsertionCode(Character) - Method in class org.openscience.cdk.debug.DebugPDBStructure
-
set the ending Code for insertion of residues of this structure.
- setEndInsertionCode(Character) - Method in interface org.openscience.cdk.interfaces.IPDBStructure
-
set the ending Code for insertion of residues of this structure.
- setEndInsertionCode(Character) - Method in class org.openscience.cdk.protein.data.PDBStructure
-
set the ending Code for insertion of residues of this structure.
- setEndInsertionCode(Character) - Method in class org.openscience.cdk.silent.PDBStructure
-
set the ending Code for insertion of residues of this structure.
- setEndSequenceNumber(Integer) - Method in class org.openscience.cdk.debug.DebugPDBStructure
-
set the ending sequence number of this structure.
- setEndSequenceNumber(Integer) - Method in interface org.openscience.cdk.interfaces.IPDBStructure
-
set the ending sequence number of this structure.
- setEndSequenceNumber(Integer) - Method in class org.openscience.cdk.protein.data.PDBStructure
-
set the ending sequence number of this structure.
- setEndSequenceNumber(Integer) - Method in class org.openscience.cdk.silent.PDBStructure
-
set the ending sequence number of this structure.
- setEqual(BinaryTree) - Method in class org.openscience.cdk.smsd.helper.BinaryTree
-
Set equal node
- setErrorHandler(IChemObjectReaderErrorHandler) - Method in class org.openscience.cdk.io.DefaultChemObjectReader
-
Sets an error handler that is sent events when file format issues occur.
- setErrorHandler(IChemObjectReaderErrorHandler) - Method in interface org.openscience.cdk.io.IChemObjectReader
-
Sets an error handler that is sent events when file format issues occur.
- setErrorHandler(IChemObjectReaderErrorHandler) - Method in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader
-
Sets an error handler that is sent events when file format issues occur.
- setExactMass(Double) - Method in class org.openscience.cdk.debug.DebugAtom
-
Sets the ExactMass attribute of the Isotope object.
- setExactMass(Double) - Method in class org.openscience.cdk.debug.DebugAtomType
-
Sets the ExactMass attribute of the Isotope object.
- setExactMass(Double) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Sets the ExactMass attribute of the Isotope object.
- setExactMass(Double) - Method in class org.openscience.cdk.debug.DebugIsotope
-
Sets the ExactMass attribute of the Isotope object.
- setExactMass(Double) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Sets the ExactMass attribute of the Isotope object.
- setExactMass(Double) - Method in class org.openscience.cdk.FragmentAtom
-
- setExactMass(Double) - Method in interface org.openscience.cdk.interfaces.IIsotope
-
Sets the ExactMass attribute of the Isotope object.
- setExactMass(Double) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets the ExactMass attribute of the Isotope object.
- setExactMass(Double) - Method in class org.openscience.cdk.Isotope
-
Sets the ExactMass attribute of the Isotope object.
- setExactMass(Double) - Method in class org.openscience.cdk.silent.FragmentAtom
-
- setExactMass(Double) - Method in class org.openscience.cdk.silent.Isotope
-
Sets the ExactMass attribute of the Isotope object.
- setExpanded(boolean) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Sets whether this atom is to be fully drawn and not just in the abbreviated form.
- setExpanded(boolean) - Method in class org.openscience.cdk.FragmentAtom
-
- setExpanded(boolean) - Method in interface org.openscience.cdk.interfaces.IFragmentAtom
-
Sets whether this atom is to be fully drawn and not just in the abbreviated form.
- setExpanded(boolean) - Method in class org.openscience.cdk.silent.FragmentAtom
-
- setExtendGrid(double) - Method in class org.openscience.cdk.tools.GridGenerator
-
- setExtension(BitSet) - Method in class org.openscience.cdk.isomorphism.mcss.RNode
-
Sets the extension attribute of the RNode object.
- setExtension(BitSet) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode
-
Sets the extension attribute of the RNode object
- setExternalSelectedPart(IAtomContainer) - Method in class org.openscience.cdk.renderer.RendererModel
-
Set externally selected atoms.
- setFirstAttachmentPoint(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.RGroup
-
- setFirstGraphSize(int) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
-
Sets the size of the first of the two
compared graphs.
- setFirstGraphSize(int) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
-
Sets the size of the first of the two
compared graphs.
- setFlag(int, boolean) - Method in class org.openscience.cdk.ChemObject
-
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Sets the value of some flag.
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugAtom
-
Sets the value of some flag.
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Sets the value of some flag.
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
Sets the value of some flag.
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugAtomType
-
Sets the value of some flag.
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Sets the value of some flag.
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugBond
-
Sets the value of some flag.
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugChemFile
-
Sets the value of some flag.
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugChemModel
-
Sets the value of some flag.
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugChemObject
-
Sets the value of some flag.
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugChemSequence
-
Sets the value of some flag.
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Sets the value of some flag.
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugElectronContainer
-
Sets the value of some flag.
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugElement
-
Sets the value of some flag.
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Sets the value of some flag.
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugIsotope
-
Sets the value of some flag.
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugLonePair
-
Sets the value of some flag.
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugMapping
-
Sets the value of some flag.
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Sets the value of some flag.
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Sets the value of some flag.
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Sets the value of some flag.
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugReaction
-
Sets the value of some flag.
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugReactionScheme
-
Sets the value of some flag.
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugReactionSet
-
Sets the value of some flag.
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugRing
-
Sets the value of some flag.
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
Sets the value of some flag.
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugStrand
-
Sets the value of some flag.
- setFlag(int, boolean) - Method in class org.openscience.cdk.debug.DebugSubstance
-
Sets the value of some flag.
- setFlag(int, boolean) - Method in interface org.openscience.cdk.interfaces.IChemObject
-
Sets the value of some flag.
- setFlag(int, boolean) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
- setFlag(int, boolean) - Method in class org.openscience.cdk.silent.ChemObject
-
- setFlags(boolean[]) - Method in class org.openscience.cdk.ChemObject
-
Sets the whole set of flags.
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Sets the whole set of flags.
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugAtom
-
Sets the whole set of flags.
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Sets the whole set of flags.
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
Sets the whole set of flags.
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugAtomType
-
Sets the whole set of flags.
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Sets the whole set of flags.
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugBond
-
Sets the whole set of flags.
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugChemFile
-
Sets the whole set of flags.
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugChemModel
-
Sets the whole set of flags.
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugChemObject
-
Sets the whole set of flags.
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugChemSequence
-
Sets the whole set of flags.
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Sets the whole set of flags.
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugElectronContainer
-
Sets the whole set of flags.
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugElement
-
Sets the whole set of flags.
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Sets the whole set of flags.
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugIsotope
-
Sets the whole set of flags.
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugLonePair
-
Sets the whole set of flags.
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugMapping
-
Sets the whole set of flags.
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Sets the whole set of flags.
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Sets the whole set of flags.
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Sets the whole set of flags.
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugReaction
-
Sets the whole set of flags.
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugReactionScheme
-
Sets the whole set of flags.
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugReactionSet
-
Sets the whole set of flags.
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugRing
-
Sets the whole set of flags.
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
Sets the whole set of flags.
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugStrand
-
Sets the whole set of flags.
- setFlags(boolean[]) - Method in class org.openscience.cdk.debug.DebugSubstance
-
Sets the whole set of flags.
- setFlags(boolean[]) - Method in interface org.openscience.cdk.interfaces.IChemObject
-
Sets the whole set of flags.
- setFlags(boolean[]) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
- setFlags(boolean[]) - Method in class org.openscience.cdk.silent.ChemObject
-
- setFontForZoom(double) - Method in class org.openscience.cdk.renderer.font.AWTFontManager
-
For a particular zoom level, set the appropriate font size to use.
- setFontForZoom(double) - Method in interface org.openscience.cdk.renderer.font.IFontManager
-
For a particular zoom level, set the appropriate font size to use.
- setFontManager(IFontManager) - Method in class org.openscience.cdk.renderer.visitor.AWTDrawVisitor
-
The font manager must be set by any renderer that uses this class!
This manager is needed to keep track of fonts of the right size.
- setFontManager(IFontManager) - Method in interface org.openscience.cdk.renderer.visitor.IDrawVisitor
-
- setFontName(String) - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
-
Set the font name ('Arial', 'Times New Roman') and so on.
- setFontName(String) - Method in interface org.openscience.cdk.renderer.font.IFontManager
-
Set the font name ('Arial', 'Times New Roman') and so on.
- setFontStyle(IFontManager.FontStyle) - Method in class org.openscience.cdk.renderer.font.AbstractFontManager
-
Set the font style.
- setFontStyle(IFontManager.FontStyle) - Method in interface org.openscience.cdk.renderer.font.IFontManager
-
Set the font style.
- setForbidden(BitSet) - Method in class org.openscience.cdk.isomorphism.mcss.RNode
-
Sets the forbidden attribute of the RNode object.
- setForbidden(BitSet) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode
-
Sets the forbidden attribute of the RNode object
- setForceFieldConfigurator(String, IChemObjectBuilder) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
-
Constructor for the ForceFieldConfigurator object
- setFormalCharge(Integer) - Method in class org.openscience.cdk.AtomType
-
Sets the formal charge of this atom.
- setFormalCharge(Integer) - Method in class org.openscience.cdk.debug.DebugAtom
-
Sets the formal charge of this atom.
- setFormalCharge(Integer) - Method in class org.openscience.cdk.debug.DebugAtomType
-
Sets the formal charge of this atom.
- setFormalCharge(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Sets the formal charge of this atom.
- setFormalCharge(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Sets the formal charge of this atom.
- setFormalCharge(Integer) - Method in interface org.openscience.cdk.interfaces.IAtomType
-
Sets the formal charge of this atom.
- setFormalCharge(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets the formal charge of this atom.
- setFormalCharge(Integer) - Method in class org.openscience.cdk.silent.AtomType
-
Sets the formal charge of this atom.
- setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.AtomType
-
Sets the formal neighbour count of this atom.
- setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.debug.DebugAtom
-
Sets the formal neighbour count of this atom.
- setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.debug.DebugAtomType
-
Sets the formal neighbour count of this atom.
- setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Sets the formal neighbour count of this atom.
- setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Sets the formal neighbour count of this atom.
- setFormalNeighbourCount(Integer) - Method in interface org.openscience.cdk.interfaces.IAtomType
-
Sets the formal neighbour count of this atom.
- setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets the formal neighbour count of this atom.
- setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.silent.AtomType
-
Sets the formal neighbour count of this atom.
- setFormula(IMolecularFormula) - Method in class org.openscience.cdk.formula.IsotopeContainer
-
Set IMolecularFormula object of this container.
- setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.Atom
-
Sets a point specifying the location of this
atom in a Crystal unit cell.
- setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugAtom
-
Sets a point specifying the location of this
atom in a Crystal unit cell.
- setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Sets a point specifying the location of this
atom in a Crystal unit cell.
- setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Sets a point specifying the location of this
atom in a Crystal unit cell.
- setFractionalPoint3d(Point3d) - Method in interface org.openscience.cdk.interfaces.IAtom
-
Sets a point specifying the location of this
atom in a Crystal unit cell.
- setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets a point specifying the location of this
atom in a Crystal unit cell.
- setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.silent.Atom
-
Sets a point specifying the location of this
atom in a Crystal unit cell.
- setFragment(IAtomContainer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Sets the fully expended form of the IFragmentAtom.
- setFragment(IAtomContainer) - Method in class org.openscience.cdk.FragmentAtom
-
- setFragment(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IFragmentAtom
-
Sets the fully expended form of the IFragmentAtom.
- setFragment(IAtomContainer) - Method in class org.openscience.cdk.silent.FragmentAtom
-
- setGrid(double[][][]) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- setGrid(double[][][]) - Method in class org.openscience.cdk.tools.GridGenerator
-
- setGroup(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.matchers.RGroup
-
- setHCount(int) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom
-
- setHetAtom(Boolean) - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
Mark the atom as a heteroatom.
- setHetAtom(Boolean) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
Mark the atom as a heteroatom.
- setHetAtom(Boolean) - Method in class org.openscience.cdk.protein.data.PDBAtom
-
- setHetAtom(Boolean) - Method in class org.openscience.cdk.silent.PDBAtom
-
- setHighlightedAtom(IAtom) - Method in class org.openscience.cdk.renderer.RendererModel
-
Sets the atom currently highlighted.
- setHighlightedBond(IBond) - Method in class org.openscience.cdk.renderer.RendererModel
-
Sets the Bond currently highlighted.
- setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.AtomType
-
Sets the hybridization of this atom.
- setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.debug.DebugAtom
-
Sets the hybridization of this atom.
- setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.debug.DebugAtomType
-
Sets the hybridization of this atom.
- setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Sets the hybridization of this atom.
- setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Sets the hybridization of this atom.
- setHybridization(IAtomType.Hybridization) - Method in interface org.openscience.cdk.interfaces.IAtomType
-
Sets the hybridization of this atom.
- setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets the hybridization of this atom.
- setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.silent.AtomType
-
Sets the hybridization of this atom.
- setICode(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
set the Code for insertion of residues of this atom.
- setICode(String) - Method in class org.openscience.cdk.debug.DebugPDBMonomer
-
Sets the ICode of this monomer.
- setICode(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
set the Code for insertion of residues of this atom.
- setICode(String) - Method in interface org.openscience.cdk.interfaces.IPDBMonomer
-
Sets the ICode of this monomer.
- setICode(String) - Method in class org.openscience.cdk.protein.data.PDBAtom
-
set the Code for insertion of residues of this atom.
- setICode(String) - Method in class org.openscience.cdk.protein.data.PDBMonomer
-
- setICode(String) - Method in class org.openscience.cdk.silent.PDBAtom
-
set the Code for insertion of residues of this atom.
- setICode(String) - Method in class org.openscience.cdk.silent.PDBMonomer
-
- setID(String) - Method in class org.openscience.cdk.ChemObject
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.debug.DebugAtom
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.debug.DebugAtomType
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.debug.DebugBond
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.debug.DebugChemFile
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.debug.DebugChemModel
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.debug.DebugChemObject
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.debug.DebugChemSequence
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.debug.DebugElectronContainer
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.debug.DebugElement
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.debug.DebugIsotope
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.debug.DebugLonePair
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.debug.DebugMapping
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.debug.DebugReaction
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.debug.DebugReactionScheme
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.debug.DebugReactionSet
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.debug.DebugRing
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.debug.DebugStrand
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.debug.DebugSubstance
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.dict.Entry
-
- setID(String) - Method in interface org.openscience.cdk.interfaces.IChemObject
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
Sets the identifier (ID) of this object.
- setID(String) - Method in class org.openscience.cdk.silent.ChemObject
-
Sets the identifier (ID) of this object.
- setId1(int) - Method in class org.openscience.cdk.isomorphism.mcss.RMap
-
Sets the id1 attribute of the RMap object.
- setId1(int) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMap
-
Sets the id1 attribute of the CDKRMap object
- setId2(int) - Method in class org.openscience.cdk.isomorphism.mcss.RMap
-
Sets the id2 attribute of the RMap object.
- setId2(int) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMap
-
Sets the id2 attribute of the CDKRMap object
- setIDPolicy(int) - Static method in class org.openscience.cdk.tools.IDCreator
-
Alters the policy of ID generation.
- setIgnoreAromaticBonds(boolean) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory
-
Deprecated.
"the use of aromatic bonds is strongly discouraged" - InChI
FAQ, the InChI will fail for many compounds if ignore
aromatic bonds is not enabled and the compound have aromatic
flags.
- setImagelink(String) - Method in class org.openscience.cdk.io.RssWriter
-
- setImaginaryPart(double) - Method in class org.openscience.cdk.math.Complex
-
Sets the imaginary part of this value
- setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.Atom
-
Sets the number of implicit hydrogen count of this atom.
- setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.debug.DebugAtom
-
Sets the number of implicit hydrogen count of this atom.
- setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Sets the number of implicit hydrogen count of this atom.
- setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Sets the number of implicit hydrogen count of this atom.
- setImplicitHydrogenCount(Integer) - Method in interface org.openscience.cdk.interfaces.IAtom
-
Sets the implicit hydrogen count of this atom.
- setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets the number of implicit hydrogen count of this atom.
- setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.silent.Atom
-
Sets the number of implicit hydrogen count of this atom.
- setInchimap(Map) - Method in class org.openscience.cdk.io.RssWriter
-
- setIndexCreated(boolean) - Method in class org.openscience.cdk.io.random.RandomAccessReader
-
- setInputReader(Reader) - Method in class org.openscience.cdk.io.listener.TextGUIListener
-
Overwrites the default reader from which the input is taken.
- setInputStream(InputStream) - Method in class org.openscience.cdk.config.CDKBasedAtomTypeConfigurator
-
Sets the file containing the configuration data.
- setInputStream(InputStream) - Method in interface org.openscience.cdk.config.IAtomTypeConfigurator
-
Sets the file containing the configuration data.
- setInputStream(InputStream) - Method in class org.openscience.cdk.config.OWLBasedAtomTypeConfigurator
-
Sets the file containing the configuration data.
- setInputStream(InputStream) - Method in class org.openscience.cdk.config.TXTBasedAtomTypeConfigurator
-
Sets the file containing the configuration data.
- setInputStream(InputStream) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
-
Sets the inputStream attribute of the ForceFieldConfigurator object
- setInputStream(InputStream) - Method in class org.openscience.cdk.modeling.builder3d.MM2BasedParameterSetReader
-
Sets the file containing the config data.
- setInputStream(InputStream) - Method in class org.openscience.cdk.modeling.builder3d.MMFF94BasedParameterSetReader
-
Sets the file containing the config data
- setIntensity(double) - Method in class org.openscience.cdk.formula.IsotopeContainer
-
Set the intensity value of this container.
- setInterrupted(boolean) - Method in class org.openscience.cdk.smiles.DeduceBondSystemTool
-
Sets if the calculation should be interrupted.
- setInterrupted(boolean) - Method in class org.openscience.cdk.smiles.FixBondOrdersTool
-
Sets if the calculation should be interrupted.
- setLabel(String) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Sets the label of this PseudoAtom.
- setLabel(String) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Sets the label of this PseudoAtom.
- setLabel(String) - Method in class org.openscience.cdk.dict.Entry
-
- setLabel(String) - Method in interface org.openscience.cdk.interfaces.IPseudoAtom
-
Sets the label of this PseudoAtom.
- setLabel(String) - Method in class org.openscience.cdk.PseudoAtom
-
Sets the label of this PseudoAtom.
- setLabel(String) - Method in class org.openscience.cdk.silent.PseudoAtom
-
Sets the label of this PseudoAtom.
- setLast(long) - Method in class org.openscience.cdk.smiles.InvPair
-
- setLatticeConstant(double) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- setLatticeConstant(double) - Method in class org.openscience.cdk.tools.GridGenerator
-
- setLeft(IQueryAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom
-
Deprecated.
- setLeft(IQueryBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond
-
- setLength(int) - Method in class org.openscience.cdk.iupac.parser.AttachedGroup
-
Setter for property length.
- setLevel(IOSetting.Importance) - Method in class org.openscience.cdk.io.listener.SwingGUIListener
-
- setLevel(IOSetting.Importance) - Method in class org.openscience.cdk.io.listener.TextGUIListener
-
- setLine(int, GIMatrix) - Method in class org.openscience.cdk.graph.invariant.GIMatrix
-
Sets the line of the matrix at the specified index to a new value.
- setLink(String) - Method in class org.openscience.cdk.io.RssWriter
-
- setLinkageRadius(double) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- setLinkmap(Map) - Method in class org.openscience.cdk.io.RssWriter
-
- setLocations(List<Token>) - Method in class org.openscience.cdk.iupac.parser.AttachedGroup
-
Setter for property locations.
- setLoggingToolClass(Class<? extends ILoggingTool>) - Static method in class org.openscience.cdk.tools.LoggingToolFactory
-
- setMappings(List<Map<Integer, Integer>>) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
-
Set mapping solutions
- setMass(double) - Method in class org.openscience.cdk.formula.IsotopeContainer
-
Set the mass value of this container.
- setMassNumber(Integer) - Method in class org.openscience.cdk.debug.DebugAtom
-
Sets the atomic mass of this element.
- setMassNumber(Integer) - Method in class org.openscience.cdk.debug.DebugAtomType
-
Sets the atomic mass of this element.
- setMassNumber(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Sets the atomic mass of this element.
- setMassNumber(Integer) - Method in class org.openscience.cdk.debug.DebugIsotope
-
Sets the atomic mass of this element.
- setMassNumber(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Sets the atomic mass of this element.
- setMassNumber(Integer) - Method in interface org.openscience.cdk.interfaces.IIsotope
-
Sets the atomic mass of this element.
- setMassNumber(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets the atomic mass of this element.
- setMassNumber(Integer) - Method in class org.openscience.cdk.Isotope
-
Sets the atomic mass of this element.
- setMassNumber(Integer) - Method in class org.openscience.cdk.silent.Isotope
-
Sets the atomic mass of this element.
- setMatchBond(boolean) - Method in class org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
- setMatchBonds(boolean) - Method in class org.openscience.cdk.smsd.Isomorphism
-
- setMatchingAtoms(int[]) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom
-
Set the atoms of a target molecule that correspond to this group.
- setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.AtomType
-
Sets the MaxBondOrder attribute of the AtomType object.
- setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.debug.DebugAtom
-
Sets the MaxBondOrder attribute of the AtomType object.
- setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.debug.DebugAtomType
-
Sets the MaxBondOrder attribute of the AtomType object.
- setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Sets the MaxBondOrder attribute of the AtomType object.
- setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Sets the MaxBondOrder attribute of the AtomType object.
- setMaxBondOrder(IBond.Order) - Method in interface org.openscience.cdk.interfaces.IAtomType
-
Sets the MaxBondOrder attribute of the AtomType object.
- setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets the MaxBondOrder attribute of the AtomType object.
- setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.silent.AtomType
-
Sets the MaxBondOrder attribute of the AtomType object.
- setMaxGasteigerDamp(double) - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
-
Sets the maxGasteigerDamp attribute of the GasteigerMarsiliPartialCharges
object.
- setMaxGasteigerIters(double) - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
-
Sets the maxGasteigerIters attribute of the GasteigerMarsiliPartialCharges
object.
- setMaxGasteigerIters(int) - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges
-
Sets the maxGasteigerIters attribute of the GasteigerPEPEPartialCharges
object.
- setMaximalStructures(int) - Method in class org.openscience.cdk.tools.StructureResonanceGenerator
-
Set the number maximal of resonance structures to be found.
- setMaximumNeighbors(int) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultMCSPlusAtomMatcher
-
- setMaximumNeighbors(int) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultRGraphAtomMatcher
-
- setMaximumNeighbors(int) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFAtomMatcher
-
- setMaxIteration(int) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
-
Sets the maxIteration for the RGraph parsing.
- setMaxIteration(int) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
-
Sets the maxIteration for the CDKRGraph parsing.
- setMaxIterations(int) - Method in class org.openscience.cdk.charges.Electronegativity
-
set the maximum number of Iterations.
- setMaxIterations(int) - Method in class org.openscience.cdk.charges.PiElectronegativity
-
set the maximum number of Iterations.
- setMaxResonStruc(int) - Method in class org.openscience.cdk.charges.Electronegativity
-
set the maximum number of resonance structures.
- setMaxResonStruc(int) - Method in class org.openscience.cdk.charges.PiElectronegativity
-
set the maximum number of resonance structures.
- setMaxResoStruc(int) - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges
-
Sets the maximum resonance structures to be searched.
- setMechanism(String) - Method in class org.openscience.cdk.dict.EntryReact
-
Set the mechanism of this reaction.
- setMinimumFragmentSize(int) - Method in class org.openscience.cdk.fragment.ExhaustiveFragmenter
-
Set the minimum fragment size.
- setMinPSCluster(int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- setMinPSPocket(int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- setMM2Parameters(IChemObjectBuilder) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
-
Sets the parameters attribute of the ForceFieldConfigurator object, default is mm2 force field
- setMMFF94Parameters(IChemObjectBuilder) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
-
- setModelCenter(double, double) - Method in class org.openscience.cdk.renderer.AbstractRenderer
-
Set the position of the center of the model.
- setMolecule(IAtomContainer) - Method in class org.openscience.cdk.layout.AtomPlacer
-
Sets the molecule the AtomPlacer currently works with
- setMolecule(IAtomContainer) - Method in class org.openscience.cdk.layout.RingPlacer
-
- setMolecule(IAtomContainer, boolean) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
-
Assings a molecule to be layed out.
- setMolecule(IAtomContainer) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
-
Assings a molecule to be layed out.
- setMolecule(IAtomContainer) - Method in class org.openscience.cdk.structgen.RandomGenerator
-
Assigns a starting structure to this generator.
- setMoleculeSet(IAtomContainerSet) - Method in class org.openscience.cdk.ChemModel
-
Sets the MoleculeSet of this ChemModel.
- setMoleculeSet(IAtomContainerSet) - Method in class org.openscience.cdk.debug.DebugChemModel
-
Sets the MoleculeSet of this ChemModel.
- setMoleculeSet(IAtomContainerSet) - Method in interface org.openscience.cdk.interfaces.IChemModel
-
Sets the IAtomContainerSet of this ChemModel.
- setMoleculeSet(IAtomContainerSet) - Method in class org.openscience.cdk.silent.ChemModel
-
Sets the MoleculeSet of this ChemModel.
- setMonoIsotope(IsotopeContainer) - Method in class org.openscience.cdk.formula.IsotopePattern
-
Set the mono isotope object.
- setMonomerName(String) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Sets the name of the Monomer object.
- setMonomerName(String) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Sets the name of the Monomer object.
- setMonomerName(String) - Method in interface org.openscience.cdk.interfaces.IMonomer
-
Set the name of the Monomer object.
- setMonomerName(String) - Method in class org.openscience.cdk.Monomer
-
Sets the name of the Monomer object.
- setMonomerName(String) - Method in class org.openscience.cdk.silent.Monomer
-
Sets the name of the Monomer object.
- setMonomerType(String) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Sets the type of the Monomer object.
- setMonomerType(String) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Sets the type of the Monomer object.
- setMonomerType(String) - Method in interface org.openscience.cdk.interfaces.IMonomer
-
Set the type of the Monomer object.
- setMonomerType(String) - Method in class org.openscience.cdk.Monomer
-
Sets the type of the Monomer object.
- setMonomerType(String) - Method in class org.openscience.cdk.silent.Monomer
-
Sets the type of the Monomer object.
- setMultiMap(Map) - Method in class org.openscience.cdk.io.RssWriter
-
- setMultiplier(IAtomContainer, Double) - Method in class org.openscience.cdk.AtomContainerSet
-
Sets the coefficient of a AtomContainer to a given value.
- setMultiplier(int, Double) - Method in class org.openscience.cdk.AtomContainerSet
-
Sets the coefficient of a AtomContainer to a given value.
- setMultiplier(IAtomContainer, Double) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
Sets the coefficient of a AtomContainer to a given value.
- setMultiplier(int, Double) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
Sets the coefficient of a AtomContainer to a given value.
- setMultiplier(IAtomContainer, Double) - Method in class org.openscience.cdk.debug.DebugSubstance
-
Sets the coefficient of a AtomContainer to a given value.
- setMultiplier(int, Double) - Method in class org.openscience.cdk.debug.DebugSubstance
-
Sets the coefficient of a AtomContainer to a given value.
- setMultiplier(IAtomContainer, Double) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
-
Sets the coefficient of a AtomContainer to a given value.
- setMultiplier(int, Double) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
-
Sets the coefficient of a AtomContainer to a given value.
- setMultiplier(IAtomContainer, Double) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Sets the coefficient of a AtomContainer to a given value.
- setMultiplier(int, Double) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Sets the coefficient of a AtomContainer to a given value.
- setMultipliers(Double[]) - Method in class org.openscience.cdk.AtomContainerSet
-
Sets the multipliers of the AtomContainers.
- setMultipliers(Double[]) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
Sets the multipliers of the AtomContainers.
- setMultipliers(Double[]) - Method in class org.openscience.cdk.debug.DebugSubstance
-
Sets the multipliers of the AtomContainers.
- setMultipliers(Double[]) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
-
Sets the multipliers of the AtomContainers.
- setMultipliers(Double[]) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Sets the multipliers of the AtomContainers.
- setName(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
set the Atom name of this atom.
- setName(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
set the Atom name of this atom.
- setName(String) - Method in class org.openscience.cdk.iupac.parser.AttachedGroup
-
Setter for property name.
- setName(String) - Method in class org.openscience.cdk.libio.md.Residue
-
- setName(String) - Method in class org.openscience.cdk.protein.data.PDBAtom
-
set the Atom name of this atom.
- setName(String) - Method in class org.openscience.cdk.silent.PDBAtom
-
set the Atom name of this atom.
- setNaturalAbundance(Double) - Method in class org.openscience.cdk.debug.DebugAtom
-
Sets the NaturalAbundance attribute of the Isotope object.
- setNaturalAbundance(Double) - Method in class org.openscience.cdk.debug.DebugAtomType
-
Sets the NaturalAbundance attribute of the Isotope object.
- setNaturalAbundance(Double) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Sets the NaturalAbundance attribute of the Isotope object.
- setNaturalAbundance(Double) - Method in class org.openscience.cdk.debug.DebugIsotope
-
Sets the NaturalAbundance attribute of the Isotope object.
- setNaturalAbundance(Double) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Sets the NaturalAbundance attribute of the Isotope object.
- setNaturalAbundance(Double) - Method in interface org.openscience.cdk.interfaces.IIsotope
-
Sets the NaturalAbundance attribute of the Isotope object.
- setNaturalAbundance(Double) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets the NaturalAbundance attribute of the Isotope object.
- setNaturalAbundance(Double) - Method in class org.openscience.cdk.Isotope
-
Sets the NaturalAbundance attribute of the Isotope object.
- setNaturalAbundance(Double) - Method in class org.openscience.cdk.silent.Isotope
-
Sets the NaturalAbundance attribute of the Isotope object.
- setNewMatrix(boolean) - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregor
-
set a new Matrix.
- setNotEqual(BinaryTree) - Method in class org.openscience.cdk.smsd.helper.BinaryTree
-
Set not equal node
- setNotification(boolean) - Method in class org.openscience.cdk.ChemObject
-
- setNotification(boolean) - Method in class org.openscience.cdk.debug.DebugChemObject
-
Set a flag to use or not use notification.
- setNotification(boolean) - Method in interface org.openscience.cdk.interfaces.IChemObject
-
Set a flag to use or not use notification.
- setNotification(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
- setNotification(boolean) - Method in class org.openscience.cdk.renderer.RendererModel
-
Dis- or enables sending around change notifications.
- setNotification(boolean) - Method in class org.openscience.cdk.silent.ChemObject
-
- setNS(String) - Method in class org.openscience.cdk.dict.Dictionary
-
- setNumAtoms(int) - Method in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
-
- setNumber(int) - Method in class org.openscience.cdk.libio.md.ChargeGroup
-
- setNumber(int) - Method in class org.openscience.cdk.libio.md.Residue
-
- setObjectProperty(String, String, String) - Method in class org.openscience.cdk.io.iterator.event.EventCMLHandler
-
Procedure required by the CDOInterface.
- setOccupancy(Double) - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
set the Occupancy of this atom.
- setOccupancy(Double) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
set the Occupancy of this atom.
- setOccupancy(Double) - Method in class org.openscience.cdk.protein.data.PDBAtom
-
set the Occupancy of this atom.
- setOccupancy(Double) - Method in class org.openscience.cdk.silent.PDBAtom
-
set the Occupancy of this atom.
- setOccurrence(String) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
-
Picky setter for occurrence fields.
- setOfMolecules - Variable in class org.openscience.cdk.ChemModel
-
A MoleculeSet.
- setOfMolecules - Variable in class org.openscience.cdk.silent.ChemModel
-
A MoleculeSet.
- setOfReactions - Variable in class org.openscience.cdk.ChemModel
-
A ReactionSet.
- setOfReactions - Variable in class org.openscience.cdk.silent.ChemModel
-
A ReactionSet.
- seTolerance(double) - Method in class org.openscience.cdk.formula.IsotopePatternSimilarity
-
Set the tolerance of the mass accuracy.
- setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom
-
- setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom
-
- setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond
-
- setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolAndChargeQueryAtom
-
- setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolChargeIDQueryAtom
-
- setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom
-
- setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom
-
- setOrder(IBond.Order) - Method in class org.openscience.cdk.Bond
-
Sets the bond order of this bond.
- setOrder(IBond.Order) - Method in class org.openscience.cdk.debug.DebugBond
-
Sets the bond order of this bond.
- setOrder(IBond.Order) - Method in interface org.openscience.cdk.interfaces.IBond
-
Sets the bond order of this bond.
- setOrder(IBond.Order) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Sets the bond order of this query bond.
- setOrder(IBond.Order) - Method in class org.openscience.cdk.silent.Bond
-
Sets the bond order of this bond.
- setOutputWriter(Writer) - Method in class org.openscience.cdk.io.listener.PropertiesListener
-
Overwrites the default writer to which the output is directed.
- setOutputWriter(Writer) - Method in class org.openscience.cdk.io.listener.TextGUIListener
-
Overwrites the default writer to which the output is directed.
- setOverrideBondWidth(double) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
-
Set the width to use for all bonds, overriding any standard bond widths.
- setOverrideColor(Color) - Method in class org.openscience.cdk.renderer.generators.BasicBondGenerator
-
Set the color to use for all bonds, overriding the standard bond colors.
- setOxt(Boolean) - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
Change the state of this atom in being the PDB OXT atom.
- setOxt(Boolean) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
Change the state of this atom in being the PDB OXT atom.
- setOxt(Boolean) - Method in class org.openscience.cdk.protein.data.PDBAtom
-
- setOxt(Boolean) - Method in class org.openscience.cdk.silent.PDBAtom
-
- setParameter(boolean) - Method in interface org.openscience.cdk.reaction.type.parameters.IParameterReact
-
Set the parameter to take account.
- setParameter(boolean) - Method in class org.openscience.cdk.reaction.type.parameters.ParameterReact
-
Set the parameter to take account.
- setParameterList(List<IParameterReact>) - Method in interface org.openscience.cdk.reaction.IReactionProcess
-
Sets the parameters for this reaction.
- setParameterList(List<IParameterReact>) - Method in class org.openscience.cdk.reaction.ReactionEngine
-
Returns the current parameter Map for this reaction.
- setParameters(String, String, String) - Method in class org.openscience.cdk.dict.EntryReact
-
Set the parameters of the reaction.
- setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.ChargeRule
-
Sets the parameters attribute of the ChargeRule object.
- setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.ElementRule
-
Sets the parameters attribute of the ElementRule object.
- setParameters(Object[]) - Method in interface org.openscience.cdk.formula.rules.IRule
-
Sets the parameters for this rule.
- setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.IsotopePatternRule
-
Sets the parameters attribute of the IsotopePatternRule object.
- setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.MMElementRule
-
Sets the parameters attribute of the MMElementRule object.
- setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.NitrogenRule
-
Sets the parameters attribute of the NitrogenRule object.
- setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.RDBERule
-
Sets the parameters attribute of the RDBE object.
- setParameters(Object[]) - Method in class org.openscience.cdk.formula.rules.ToleranceRangeRule
-
Sets the parameters attribute of the ToleranceRangeRule object.
- setParameters(Map<String, Object>) - Method in class org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
-
Sets the parameters attribute of the ForceFieldConfigurator object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor
-
This descriptor does not have any parameter to be set.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor
-
This descriptor does have any parameter.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor
-
This descriptor does have any parameter.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor
-
This descriptor does have any parameter.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor
-
Sets the parameters attribute of the BondsToAtomDescriptor object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor
-
This descriptor does have any parameter.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor
-
Sets the parameters attribute of the DistanceToAtomDescriptor object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor
-
This descriptor does have any parameter.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor
-
This descriptor does have any parameter.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor
-
This descriptor does have any parameter.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor
-
This descriptor does have any parameter.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor
-
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.AcidicGroupCountDescriptor
-
Sets the parameters for this descriptor.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
-
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor
-
Sets the parameters attribute of the AminoAcidsCountDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor
-
Sets the parameters attribute of the APolDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor
-
Sets the parameters attribute of the AromaticAtomsCountDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor
-
Sets the parameters attribute of the AromaticBondsCountDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor
-
Sets the parameters attribute of the AtomCountDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
-
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
-
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
-
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor
-
Sets the parameters for this descriptor.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor
-
Sets the parameters attribute of the BCUTDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor
-
Sets the parameters attribute of the BondCountDescriptor object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor
-
Sets the parameters attribute of the BPolDescriptor object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor
-
Sets the parameters attribute of the GravitationalIndexDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
-
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
-
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
-
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
-
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor
-
Sets the parameters attribute of the CPSADescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor
-
Sets the parameters attribute of the EccentricConnectivityIndexDescriptor object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor
-
Sets the parameters for this descriptor.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor
-
Sets the parameters for this descriptor.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor
-
Sets the parameters attribute of the FragmentComplexityDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor
-
Sets the parameters attribute of the GravitationalIndexDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor
-
Sets the parameters attribute of the HBondAcceptorCountDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor
-
Sets the parameter of this HBondDonorCountDescriptor instance.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor
-
Sets the parameters attribute of the HybridizationRatioDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor
-
Sets the parameters attribute of the IPMolecularLearningDescriptor object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor
-
Sets the parameters attribute of the
KappaShapeIndicesDescriptor object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor
-
Sets the parameters attribute of the descriptor.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor
-
Sets the parameters attribute of the LargestChain object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor
-
Sets the parameters attribute of the LargestPiSystemDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor
-
Sets the parameters attribute of the PetitjeanNumberDescriptor object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor
-
Sets the parameters attribute of the LongestAliphaticChainDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor
-
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
-
Sets the parameters attribute of the WeightDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor
-
Sets the parameters attribute of the MomentOfInertiaDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor
-
Sets the parameters attribute of the PetitjeanNumberDescriptor object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor
-
Sets the parameters attribute of the PetitjeanShapeIndexDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor
-
Sets the parameters attribute of the RotatableBondsCountDescriptor object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor
-
Sets the parameters attribute of the RuleOfFiveDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor
-
Set parameters: ignored, there are none.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor
-
Sets the parameters attribute of the TPSADescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor
-
Sets the parameters for this descriptor.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor
-
Sets the parameters attribute of the VAdjMaDescriptor object
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor
-
Sets the parameters attribute of the WeightDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor
-
Sets the parameters attribute of the WeightedPathDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor
-
Sets the parameters attribute of the WHIMDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor
-
Sets the parameters attribute of the WienerNumbersDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor
-
Sets the parameters attribute of the XLogPDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor
-
Sets the parameters attribute of the ZagrebIndexDescriptor object.
- setParameters(Object[]) - Method in class org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor
-
Sets the parameters attribute of the TaeAminoAcidDescriptor object.
- setParameters(Object[]) - Method in interface org.openscience.cdk.qsar.IDescriptor
-
Sets the parameters for this descriptor.
- setParameterSet(Map) - Method in class org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
-
Constructor for the setParameterSet object.
- setParentMolecule(MDMolecule) - Method in class org.openscience.cdk.libio.md.ChargeGroup
-
- setParentMolecule(MDMolecule) - Method in class org.openscience.cdk.libio.md.Residue
-
- setPermutation(int[]) - Method in class org.openscience.cdk.graph.Permutor
-
Set the currently used permutation.
- setPermutation(int[]) - Method in class org.openscience.cdk.smsd.labelling.Permutor
-
Set the currently used permutation.
- setPharmacophoreQuery(PharmacophoreQuery) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreMatcher
-
Set a pharmacophore query.
- setPocketSize(int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- setPoint2d(Point2d) - Method in class org.openscience.cdk.Atom
-
Sets a point specifying the location of this
atom in a 2D space.
- setPoint2d(Point2d) - Method in class org.openscience.cdk.debug.DebugAtom
-
Sets a point specifying the location of this
atom in a 2D space.
- setPoint2d(Point2d) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Sets a point specifying the location of this
atom in a 2D space.
- setPoint2d(Point2d) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Sets a point specifying the location of this
atom in a 2D space.
- setPoint2d(Point2d) - Method in interface org.openscience.cdk.interfaces.IAtom
-
Sets a point specifying the location of this
atom in a 2D space.
- setPoint2d(Point2d) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets a point specifying the location of this
atom in a 2D space.
- setPoint2d(Point2d) - Method in class org.openscience.cdk.silent.Atom
-
Sets a point specifying the location of this
atom in a 2D space.
- setPoint3d(Point3d) - Method in class org.openscience.cdk.Atom
-
Sets a point specifying the location of this
atom in 3D space.
- setPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugAtom
-
Sets a point specifying the location of this
atom in 3D space.
- setPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Sets a point specifying the location of this
atom in 3D space.
- setPoint3d(Point3d) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Sets a point specifying the location of this
atom in 3D space.
- setPoint3d(Point3d) - Method in interface org.openscience.cdk.interfaces.IAtom
-
Sets a point specifying the location of this
atom in 3D space.
- setPoint3d(Point3d) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets a point specifying the location of this
atom in 3D space.
- setPoint3d(Point3d) - Method in class org.openscience.cdk.silent.Atom
-
Sets a point specifying the location of this
atom in 3D space.
- setPreservingAromaticity(boolean) - Method in class org.openscience.cdk.smiles.SmilesParser
-
Deprecated.
- setPrime() - Method in class org.openscience.cdk.smiles.InvPair
-
Sets the prime number based on the current seed.
- setProductCoefficient(IAtomContainer, Double) - Method in class org.openscience.cdk.debug.DebugReaction
-
Sets the coefficient of a a product to a given value.
- setProductCoefficient(IAtomContainer, Double) - Method in interface org.openscience.cdk.interfaces.IReaction
-
Sets the coefficient of a a product to a given value.
- setProductCoefficient(IAtomContainer, Double) - Method in class org.openscience.cdk.Reaction
-
Sets the coefficient of a a product to a given value.
- setProductCoefficient(IAtomContainer, Double) - Method in class org.openscience.cdk.silent.Reaction
-
Sets the coefficient of a a product to a given value.
- setProductCoefficients(Double[]) - Method in class org.openscience.cdk.debug.DebugReaction
-
Sets the coefficient of the products.
- setProductCoefficients(Double[]) - Method in interface org.openscience.cdk.interfaces.IReaction
-
Sets the coefficient of the products.
- setProductCoefficients(Double[]) - Method in class org.openscience.cdk.Reaction
-
Sets the coefficient of the products.
- setProductCoefficients(Double[]) - Method in class org.openscience.cdk.silent.Reaction
-
Sets the coefficient of the products.
- setProducts(IAtomContainerSet) - Method in class org.openscience.cdk.debug.DebugReaction
-
Assigns a MoleculeSet to the products of this reaction.
- setProducts(IAtomContainerSet) - Method in interface org.openscience.cdk.interfaces.IReaction
-
Assigns a IAtomContaineSet to the products of this reaction.
- setProducts(IAtomContainerSet) - Method in class org.openscience.cdk.Reaction
-
Assigns a MoleculeSet to the products of this reaction.
- setProducts(IAtomContainerSet) - Method in class org.openscience.cdk.silent.Reaction
-
Assigns a MoleculeSet to the products of this reaction.
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.ChemObject
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugChemObject
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.debug.DebugMolecularFormula
-
Sets the properties of this object.
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.formula.MolecularFormula
-
Sets the properties of this object.
- setProperties(Map<Object, Object>) - Method in interface org.openscience.cdk.interfaces.IChemObject
-
Set the properties of this object to the provided map (shallow copy).
- setProperties(Map<Object, Object>) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
-
Sets the properties of this object.I should
integrate into ChemObject.
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.silent.ChemObject
-
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.silent.MolecularFormula
-
Sets the properties of this object.
- setProperty(Object, Object) - Method in class org.openscience.cdk.ChemObject
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugAtom
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugAtomContainerSet
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugAtomType
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugBond
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugChemFile
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugChemModel
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugChemObject
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugChemSequence
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugElectronContainer
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugElement
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugIsotope
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugLonePair
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugMapping
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugMolecularFormula
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugReaction
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugReactionScheme
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugReactionSet
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugRing
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugSingleElectron
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugStrand
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.debug.DebugSubstance
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.formula.MolecularFormula
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in interface org.openscience.cdk.interfaces.IChemObject
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.silent.ChemObject
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.silent.MolecularFormula
-
Sets a property for a IChemObject.
- setProtein(IBioPolymer) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- setProteinInterior(int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- setPublisher(String) - Method in class org.openscience.cdk.io.RssWriter
-
- setQueryCacheSize(int) - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool
-
Set the maximum size of the query cache.
- setRandom(Random) - Static method in class org.openscience.cdk.math.RandomNumbersTool
-
Sets the base generator to be used by this class.
- setRandomSeed(long) - Static method in class org.openscience.cdk.math.RandomNumbersTool
-
Sets the seed of this random number generator using a single
long
seed.
- setRank(int) - Method in class org.openscience.cdk.graph.Permutor
-
Set the permutation to use, given its rank.
- setRank(int) - Method in class org.openscience.cdk.smsd.labelling.Permutor
-
Set the permutation to use, given its rank.
- setRAtom(double) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- setRawContent(Object) - Method in class org.openscience.cdk.dict.Entry
-
- setRdFields(Map<String, Object>) - Method in class org.openscience.cdk.io.MDLRXNWriter
-
Here you can set a map which will be used to build rd fields in the file.
- setReactantCoefficient(IAtomContainer, Double) - Method in class org.openscience.cdk.debug.DebugReaction
-
Sets the coefficient of a a reactant to a given value.
- setReactantCoefficient(IAtomContainer, Double) - Method in interface org.openscience.cdk.interfaces.IReaction
-
Sets the coefficient of a a reactant to a given value.
- setReactantCoefficient(IAtomContainer, Double) - Method in class org.openscience.cdk.Reaction
-
Sets the coefficient of a a reactant to a given value.
- setReactantCoefficient(IAtomContainer, Double) - Method in class org.openscience.cdk.silent.Reaction
-
Sets the coefficient of a a reactant to a given value.
- setReactantCoefficients(Double[]) - Method in class org.openscience.cdk.debug.DebugReaction
-
Sets the coefficients of the reactants.
- setReactantCoefficients(Double[]) - Method in interface org.openscience.cdk.interfaces.IReaction
-
Sets the coefficients of the reactants.
- setReactantCoefficients(Double[]) - Method in class org.openscience.cdk.Reaction
-
Sets the coefficients of the reactants.
- setReactantCoefficients(Double[]) - Method in class org.openscience.cdk.silent.Reaction
-
Sets the coefficients of the reactants.
- setReactants(IAtomContainerSet) - Method in class org.openscience.cdk.debug.DebugReaction
-
Assigns a MoleculeSet to the reactants in this reaction.
- setReactants(IAtomContainerSet) - Method in interface org.openscience.cdk.interfaces.IReaction
-
Assigns a IAtomContaineSet to the reactants in this reaction.
- setReactants(IAtomContainerSet) - Method in class org.openscience.cdk.Reaction
-
Assigns a MoleculeSet to the reactants in this reaction.
- setReactants(IAtomContainerSet) - Method in class org.openscience.cdk.silent.Reaction
-
Assigns a MoleculeSet to the reactants in this reaction.
- SetReactionCenter - Class in org.openscience.cdk.reaction.type.parameters
-
Class extension of ParameterReact class which defines if a reaction is set already the reaction center
in the reactants.
- SetReactionCenter() - Constructor for class org.openscience.cdk.reaction.type.parameters.SetReactionCenter
-
- setReactionMetadata(String) - Method in class org.openscience.cdk.dict.EntryReact
-
- setReactions(List<IReactionProcess>) - Method in class org.openscience.cdk.tools.StructureResonanceGenerator
-
Set the reactions that must be used in the generation of the resonance.
- setReactionSet(IReactionSet) - Method in class org.openscience.cdk.ChemModel
-
Sets the ReactionSet contained in this ChemModel.
- setReactionSet(IReactionSet) - Method in class org.openscience.cdk.debug.DebugChemModel
-
Sets the ReactionSet contained in this ChemModel.
- setReactionSet(IReactionSet) - Method in interface org.openscience.cdk.interfaces.IChemModel
-
Sets the ReactionSet contained in this ChemModel.
- setReactionSet(IReactionSet) - Method in class org.openscience.cdk.silent.ChemModel
-
Sets the ReactionSet contained in this ChemModel.
- setReader(Reader) - Method in class org.openscience.cdk.io.CIFReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.CIFReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.CMLReader
-
This method must not be used; XML reading requires the use of an InputStream.
- setReader(InputStream) - Method in class org.openscience.cdk.io.CMLReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.CrystClustReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.CrystClustReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.CTXReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.CTXReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.GamessReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.GamessReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.Gaussian03Reader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.Gaussian03Reader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.Gaussian98Reader
-
Sets the reader attribute of the Gaussian98Reader object.
- setReader(InputStream) - Method in class org.openscience.cdk.io.Gaussian98Reader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.GhemicalMMReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.GhemicalMMReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.HINReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.HINReader
-
- setReader(Reader) - Method in interface org.openscience.cdk.io.IChemObjectReader
-
Sets the Reader from which this ChemObjectReader should read
the contents.
- setReader(InputStream) - Method in interface org.openscience.cdk.io.IChemObjectReader
-
Sets the InputStream from which this ChemObjectReader should read
the contents.
- setReader(Reader) - Method in class org.openscience.cdk.io.INChIPlainTextReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.INChIPlainTextReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.INChIReader
-
This method must not be used; XML reading requires the use of an InputStream.
- setReader(InputStream) - Method in class org.openscience.cdk.io.INChIReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.iterator.event.EventCMLReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundASNReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundASNReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.iterator.IteratingSDFReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.iterator.IteratingSDFReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.iterator.IteratingSMILESReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.iterator.IteratingSMILESReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.MDLReader
-
- 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.Mopac7Reader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.Mopac7Reader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.MoSSOutputReader
-
Sets the Reader from which this ChemObjectReader should read
the contents.
- setReader(InputStream) - Method in class org.openscience.cdk.io.MoSSOutputReader
-
Sets the InputStream from which this ChemObjectReader should read
the contents.
- setReader(Reader) - Method in class org.openscience.cdk.io.PCCompoundASNReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.PCCompoundASNReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.PCCompoundXMLReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.PCCompoundXMLReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.PCSubstanceXMLReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.PCSubstanceXMLReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.PDBReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.PDBReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.PMPReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.PMPReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.random.RandomAccessSDFReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.random.RandomAccessSDFReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.rdf.CDKOWLReader
-
Deprecated.
- setReader(InputStream) - Method in class org.openscience.cdk.io.rdf.CDKOWLReader
-
Sets the InputStream from which this ChemObjectReader should read
the contents.
- setReader(Reader) - Method in class org.openscience.cdk.io.RGroupQueryReader
-
Sets the input Reader.
- setReader(InputStream) - Method in class org.openscience.cdk.io.RGroupQueryReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.ShelXReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.ShelXReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.SMILESReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.SMILESReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.VASPReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.VASPReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.XYZReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.XYZReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.ZMatrixReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.ZMatrixReader
-
- setReaderMode(IChemObjectReader.Mode) - Method in class org.openscience.cdk.io.DefaultChemObjectReader
-
- setReaderMode(IChemObjectReader.Mode) - Method in interface org.openscience.cdk.io.IChemObjectReader
-
Sets the reader mode.
- setReaderMode(IChemObjectReader.Mode) - Method in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader
-
- setReaderMode(IChemObjectReader.Mode) - Method in class org.openscience.cdk.io.random.DefaultRandomAccessChemObjectReader
-
- setRealPart(double) - Method in class org.openscience.cdk.math.Complex
-
Sets the real part of this complex value
- setRecord(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
set one entire line from the PDB entry file which describe the IPDBAtom.
- setRecord(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
Set one entire line from the PDB entry file which describe the IPDBAtom.
- setRecord(String) - Method in class org.openscience.cdk.protein.data.PDBAtom
-
set one entire line from the PDB entry file which describe the IPDBAtom.
- setRecord(String) - Method in class org.openscience.cdk.silent.PDBAtom
-
set one entire line from the PDB entry file which describe the IPDBAtom.
- setRendererModel(RendererModel) - Method in class org.openscience.cdk.renderer.visitor.AWTDrawVisitor
-
- setRendererModel(RendererModel) - Method in interface org.openscience.cdk.renderer.visitor.IDrawVisitor
-
- setRepresentation(String) - Method in class org.openscience.cdk.dict.EntryReact
-
Set the representation of the reaction.
- setRequiredRGroupNumber(int) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
-
- setResidues(List) - Method in class org.openscience.cdk.libio.md.MDMolecule
-
- setResName(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
set the Residue name of this atom.
- setResName(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
set the Residue name of this atom.
- setResName(String) - Method in class org.openscience.cdk.protein.data.PDBAtom
-
set the Residue name of this atom.
- setResName(String) - Method in class org.openscience.cdk.silent.PDBAtom
-
set the Residue name of this atom.
- setResSeq(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
set the Residue sequence number of this atom.
- setResSeq(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
set the Residue sequence number of this atom.
- setResSeq(String) - Method in interface org.openscience.cdk.interfaces.IPDBMonomer
-
Sets the sequence identifier of this monomer.
- setResSeq(String) - Method in class org.openscience.cdk.protein.data.PDBAtom
-
set the Residue sequence number of this atom.
- setResSeq(String) - Method in class org.openscience.cdk.protein.data.PDBMonomer
-
- setResSeq(String) - Method in class org.openscience.cdk.silent.PDBAtom
-
set the Residue sequence number of this atom.
- setResSeq(String) - Method in class org.openscience.cdk.silent.PDBMonomer
-
- setRestH(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
-
- setRestrictions(List<IRule>) - Method in class org.openscience.cdk.formula.MassToFormulaTool
-
Deprecated.
Set the restrictions that must be presents in the molecular formula.
- setRGroupDefinitions(Map<Integer, RGroupList>) - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
-
Setter for the R-group definitions (substituents).
- setRGroupDefinitions(Map<Integer, RGroupList>) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
- setRGroupNumber(int) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
-
Setter for rGroupNumber, checks for valid range.
- setRGroups(List<RGroup>) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
-
- setRight(IQueryAtom) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom
-
Deprecated.
- setRight(IQueryBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond
-
- setRingBond(IQueryBond) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.RingIdentifierAtom
-
- setRingSet(IRingSet) - Method in class org.openscience.cdk.atomtype.EStateAtomTypeMatcher
-
- setRingSet(IRingSet) - Method in class org.openscience.cdk.ChemModel
-
Sets the RingSet of this ChemModel.
- setRingSet(IRingSet) - Method in class org.openscience.cdk.debug.DebugChemModel
-
Sets the RingSet of this ChemModel.
- setRingSet(IRingSet) - Method in interface org.openscience.cdk.interfaces.IChemModel
-
Sets the RingSet of this ChemModel.
- setRingSet(IRingSet) - Method in class org.openscience.cdk.silent.ChemModel
-
Sets the RingSet of this ChemModel.
- setRMap(RMap) - Method in class org.openscience.cdk.isomorphism.mcss.RNode
-
Sets the rMap attribute of the RNode object.
- setRMap(CDKRMap) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode
-
Sets the rMap attribute of the RNode object
- setrMap(CDKRMap) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode
-
Sets resolution map/graph
- setRootAttachmentPoints(Map<IAtom, Map<Integer, IBond>>) - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
-
Setter for root attachment points = bonds that connect R pseudo-atoms to the scaffold.
- setRootAttachmentPoints(Map<IAtom, Map<Integer, IBond>>) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
- setRootStructure(IAtomContainer) - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
-
Setter for the root structure of this R-Group.
- setRootStructure(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
- setRSolvent(double) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- setScale(IAtomContainer) - Method in class org.openscience.cdk.renderer.AtomContainerRenderer
-
Set the scale for an IAtomContainer.
- setScale(IChemModel) - Method in class org.openscience.cdk.renderer.ChemModelRenderer
-
Set the scale for an IChemModel.
- setScale(T) - Method in interface org.openscience.cdk.renderer.IRenderer
-
- setScale(IAtomContainerSet) - Method in class org.openscience.cdk.renderer.MoleculeSetRenderer
-
- setScale(IReaction) - Method in class org.openscience.cdk.renderer.ReactionRenderer
-
Set the scale for an IReaction.
- setScale(IReactionSet) - Method in class org.openscience.cdk.renderer.ReactionSetRenderer
-
Set the scale for an IReactionSet.
- setSecondAttachmentPoint(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.RGroup
-
- setSecondGraphSize(int) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
-
Returns the size of the second of the two
compared graphs.
- setSecondGraphSize(int) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
-
Returns the size of the second of the two
compared graphs.
- setSegID(String) - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
set the Segment identifier, left-justified of this atom.
- setSegID(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
set the Segment identifier, left-justified of this atom.
- setSegID(String) - Method in class org.openscience.cdk.protein.data.PDBAtom
-
set the Segment identifier, left-justified of this atom.
- setSegID(String) - Method in class org.openscience.cdk.silent.PDBAtom
-
set the Segment identifier, left-justified of this atom.
- setSelection(IChemObjectSelection) - Method in class org.openscience.cdk.renderer.RendererModel
-
- setSerial(Integer) - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
set the Atom serial number of this atom.
- setSerial(Integer) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
set the Atom serial number of this atom.
- setSerial(Integer) - Method in class org.openscience.cdk.protein.data.PDBAtom
-
set the Atom serial number of this atom.
- setSerial(Integer) - Method in class org.openscience.cdk.silent.PDBAtom
-
set the Atom serial number of this atom.
- setSetting(String) - Method in class org.openscience.cdk.io.setting.BooleanIOSetting
-
Sets the setting for a certain question.
- setSetting(String) - Method in class org.openscience.cdk.io.setting.IntegerIOSetting
-
Sets the setting for a certain question.
- setSetting(String) - Method in class org.openscience.cdk.io.setting.IOSetting
-
Sets the setting for a certain question.
- setSetting(String) - Method in class org.openscience.cdk.io.setting.OptionIOSetting
-
Sets the setting for a certain question.
- setSetting(int) - Method in class org.openscience.cdk.io.setting.OptionIOSetting
-
Sets the setting for a certain question.
- setSetting(String) - Method in class org.openscience.cdk.io.setting.StringIOSetting
-
Sets the setting for a certain question.
- setSingleOrDoubleFlags(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
- setSkip(boolean) - Method in class org.openscience.cdk.io.iterator.IteratingSDFReader
-
Indicate whether the reader should skip over SDF records
that cause problems.
- setSmarts(String) - Method in class org.openscience.cdk.pharmacophore.PharmacophoreAtom
-
Set the SMARTS for the group.
- setSmarts(String) - Method in class org.openscience.cdk.smiles.smarts.SMARTSQueryTool
-
Set a new SMARTS pattern.
- setSolvantValue(int) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- setSource(IAtomContainer) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
-
Set source molecule
- setSpaceGroup(String) - Method in class org.openscience.cdk.Crystal
-
Sets the space group of this crystal.
- setSpaceGroup(String) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Sets the space group of this crystal.
- setSpaceGroup(String) - Method in interface org.openscience.cdk.interfaces.ICrystal
-
Sets the space group of this crystal.
- setSpaceGroup(String) - Method in class org.openscience.cdk.silent.Crystal
-
Sets the space group of this crystal.
- setSplitOrder(AbstractEquitablePartitionRefiner.SplitOrder) - Method in class org.openscience.cdk.group.AbstractEquitablePartitionRefiner
-
Set the preference for splitting cells.
- setStackLength(int) - Method in interface org.openscience.cdk.tools.ILoggingTool
-
Sets the number of StackTraceElements to be printed in DEBUG mode when
calling debug(Throwable)
.
- setStackLength(int) - Method in class org.openscience.cdk.tools.LoggingTool
-
Sets the number of StackTraceElements to be printed in DEBUG mode when
calling debug(Throwable)
.
- setStackLength(int) - Method in class org.openscience.cdk.tools.SystemOutLoggingTool
-
Sets the number of StackTraceElements to be printed in DEBUG mode when
calling debug(Throwable)
.
- setStart(long) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
-
- setStartChainID(Character) - Method in class org.openscience.cdk.debug.DebugPDBStructure
-
set the start Chain identifier of this structure.
- setStartChainID(Character) - Method in interface org.openscience.cdk.interfaces.IPDBStructure
-
set the start Chain identifier of this structure.
- setStartChainID(Character) - Method in class org.openscience.cdk.protein.data.PDBStructure
-
set the start Chain identifier of this structure.
- setStartChainID(Character) - Method in class org.openscience.cdk.silent.PDBStructure
-
set the start Chain identifier of this structure.
- setStartInsertionCode(Character) - Method in class org.openscience.cdk.debug.DebugPDBStructure
-
set the start Chain identifier of this structure.
- setStartInsertionCode(Character) - Method in interface org.openscience.cdk.interfaces.IPDBStructure
-
set the start Chain identifier of this structure.
- setStartInsertionCode(Character) - Method in class org.openscience.cdk.protein.data.PDBStructure
-
set the start Chain identifier of this structure.
- setStartInsertionCode(Character) - Method in class org.openscience.cdk.silent.PDBStructure
-
set the start Chain identifier of this structure.
- setStartSequenceNumber(Integer) - Method in class org.openscience.cdk.debug.DebugPDBStructure
-
set the start sequence number of this structure.
- setStartSequenceNumber(Integer) - Method in interface org.openscience.cdk.interfaces.IPDBStructure
-
set the start sequence number of this structure.
- setStartSequenceNumber(Integer) - Method in class org.openscience.cdk.protein.data.PDBStructure
-
set the start sequence number of this structure.
- setStartSequenceNumber(Integer) - Method in class org.openscience.cdk.silent.PDBStructure
-
set the start sequence number of this structure.
- setStepSize(int) - Method in class org.openscience.cdk.charges.GasteigerMarsiliPartialCharges
-
Set the StepSize attribute of the GasteigerMarsiliPartialCharges
object.
- setStepSize(int) - Method in class org.openscience.cdk.charges.GasteigerPEPEPartialCharges
-
Set the StepSize attribute of the GasteigerMarsiliPartialCharges
object.
- setStereo(IBond.Stereo) - Method in class org.openscience.cdk.Bond
-
Sets the stereo descriptor for this bond.
- setStereo(IBond.Stereo) - Method in class org.openscience.cdk.debug.DebugBond
-
Sets the stereo descriptor for this bond.
- setStereo(IBond.Stereo) - Method in interface org.openscience.cdk.interfaces.IBond
-
Sets the stereo descriptor for this bond.
- setStereo(IBond.Stereo) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Sets the stereo descriptor for this query bond.
- setStereo(IBond.Stereo) - Method in class org.openscience.cdk.silent.Bond
-
Sets the stereo descriptor for this bond.
- setStereoElements(List<IStereoElement>) - Method in class org.openscience.cdk.AtomContainer
-
- setStereoElements(List<IStereoElement>) - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
- setStereoElements(List<IStereoElement>) - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Set the stereo elements - this will replace the existing instance
with a new instance.
- setStereoElements(List<IStereoElement>) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
- setStereoElements(List<IStereoElement>) - Method in class org.openscience.cdk.silent.AtomContainer
-
- setStereoParity(Integer) - Method in class org.openscience.cdk.Atom
-
Sets the stereo parity for this atom.
- setStereoParity(Integer) - Method in class org.openscience.cdk.debug.DebugAtom
-
Sets the stereo parity for this atom.
- setStereoParity(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Dummy method: the stereo parity is undefined, final.
- setStereoParity(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Dummy method: the stereo parity is undefined, final.
- setStereoParity(Integer) - Method in interface org.openscience.cdk.interfaces.IAtom
-
Sets the stereo parity for this atom.
- setStereoParity(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets the stereo parity for this atom.
- setStereoParity(Integer) - Method in class org.openscience.cdk.PseudoAtom
-
Dummy method: the stereo parity is undefined, final.
- setStereoParity(Integer) - Method in class org.openscience.cdk.silent.Atom
-
Sets the stereo parity for this atom.
- setStereoParity(Integer) - Method in class org.openscience.cdk.silent.PseudoAtom
-
Dummy method: the stereo parity is undefined, final.
- setStrandName(String) - Method in class org.openscience.cdk.debug.DebugStrand
-
Sets the name of the Strand object.
- setStrandName(String) - Method in interface org.openscience.cdk.interfaces.IStrand
-
Set the name of the Strand object.
- setStrandName(String) - Method in class org.openscience.cdk.silent.Strand
-
Sets the name of the Strand object.
- setStrandName(String) - Method in class org.openscience.cdk.Strand
-
Sets the name of the Strand object.
- setStrandType(String) - Method in class org.openscience.cdk.debug.DebugStrand
-
Sets the type of the Strand object.
- setStrandType(String) - Method in interface org.openscience.cdk.interfaces.IStrand
-
Set the type of the Strand object.
- setStrandType(String) - Method in class org.openscience.cdk.silent.Strand
-
Sets the type of the Strand object.
- setStrandType(String) - Method in class org.openscience.cdk.Strand
-
Sets the type of the Strand object.
- setStructureType(String) - Method in class org.openscience.cdk.debug.DebugPDBStructure
-
set the Structure Type of this structure.
- setStructureType(String) - Method in interface org.openscience.cdk.interfaces.IPDBStructure
-
set the Structure Type of this structure.
- setStructureType(String) - Method in class org.openscience.cdk.protein.data.PDBStructure
-
set the Structure Type of this structure.
- setStructureType(String) - Method in class org.openscience.cdk.silent.PDBStructure
-
set the Structure Type of this structure.
- setSubgraph(List<Integer>) - Method in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
-
- setSwitchingAtom(IAtom) - Method in class org.openscience.cdk.libio.md.ChargeGroup
-
- setSymbol(String) - Method in class org.openscience.cdk.debug.DebugAtom
-
Sets the element symbol of this element.
- setSymbol(String) - Method in class org.openscience.cdk.debug.DebugAtomType
-
Sets the element symbol of this element.
- setSymbol(String) - Method in class org.openscience.cdk.debug.DebugElement
-
Sets the element symbol of this element.
- setSymbol(String) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Sets the element symbol of this element.
- setSymbol(String) - Method in class org.openscience.cdk.debug.DebugIsotope
-
Sets the element symbol of this element.
- setSymbol(String) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Sets the element symbol of this element.
- setSymbol(String) - Method in class org.openscience.cdk.Element
-
Sets the element symbol of this element.
- setSymbol(String) - Method in interface org.openscience.cdk.interfaces.IElement
-
Sets the element symbol of this element.
- setSymbol(String) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets the element symbol of this element.
- setSymbol(String) - Method in class org.openscience.cdk.silent.Element
-
Sets the element symbol of this element.
- setSymbol(String) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultMCSPlusAtomMatcher
-
- setSymbol(String) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultRGraphAtomMatcher
-
- setSymbol(String) - Method in class org.openscience.cdk.smsd.algorithm.matchers.DefaultVFAtomMatcher
-
- setTabSize(int) - Method in class org.openscience.cdk.iupac.parser.SimpleCharStream
-
- setTabSize(int) - Method in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
- setTarget(IAtomContainer) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
-
Set target molecule
- setTempFactor(Double) - Method in class org.openscience.cdk.debug.DebugPDBAtom
-
set the Temperature factor of this atom.
- setTempFactor(Double) - Method in interface org.openscience.cdk.interfaces.IPDBAtom
-
set the Temperature factor of this atom.
- setTempFactor(Double) - Method in class org.openscience.cdk.protein.data.PDBAtom
-
set the Temperature factor of this atom.
- setTempFactor(Double) - Method in class org.openscience.cdk.silent.PDBAtom
-
set the Temperature factor of this atom.
- setTemplateHandler(TemplateHandler) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
-
Sets the templateHandler attribute of the StructureDiagramGenerator object
- setTimeManager(TimeManager) - Static method in class org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlus
-
- setTimeManager(TimeManager) - Static method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
-
- setTimeManager(TimeManager) - Static method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper
-
- setTimeManager(TimeManager) - Static method in class org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper
-
- setTimeout(long) - Method in class org.openscience.cdk.isomorphism.mcss.RGraph
-
Sets the time in milliseconds until the substructure search will be breaked.
- setTimeout(long) - Method in class org.openscience.cdk.isomorphism.UniversalIsomorphismTester
-
Sets the time in milliseconds until the substructure search will be breaked.
- setTimeout(long) - Method in class org.openscience.cdk.ringsearch.AllRingsFinder
-
Deprecated.
use the new threshold (during construction)
- setTimeOut(double) - Method in class org.openscience.cdk.smsd.global.TimeOut
-
set cutoff value for time out eg.
- setTimeoutFlag(boolean) - Method in class org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
-
Set time out flag
- setTimeOutFlag(boolean) - Method in class org.openscience.cdk.smsd.global.TimeOut
-
Set true if timeout occures else false
- setTimezone(String) - Method in class org.openscience.cdk.io.RssWriter
-
- setting - Variable in class org.openscience.cdk.io.setting.IOSetting
-
- SettingManager<T extends ISetting> - Class in org.openscience.cdk.io.setting
-
Provides dynamic management of settings.
- SettingManager() - Constructor for class org.openscience.cdk.io.setting.SettingManager
-
- setTitle(String) - Method in class org.openscience.cdk.io.RssWriter
-
- setTitle(String) - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Set the main title
- setTitlemap(Map) - Method in class org.openscience.cdk.io.RssWriter
-
- setTo(Permutation) - Method in class org.openscience.cdk.group.Permutation
-
Alter a permutation by setting it to the values in the other permutation.
- setToolTipTextMap(Map<IAtom, String>) - Method in class org.openscience.cdk.renderer.RendererModel
-
Sets the toolTipTextMap.
- setTransform(AffineTransform) - Method in interface org.openscience.cdk.renderer.elements.IRenderingVisitor
-
Sets the affine transformations used.
- setTransform(AffineTransform) - Method in class org.openscience.cdk.renderer.visitor.AbstractAWTDrawVisitor
-
Sets a new affine transformation to convert world coordinates into
screen coordinates.
- setType(CTFileQueryBond.Type) - Method in class org.openscience.cdk.isomorphism.matchers.CTFileQueryBond
-
Getter for bond type
- setUnspecified(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom
-
- setup(PermutationGroup, IEquitablePartitionRefiner) - Method in class org.openscience.cdk.group.AbstractDiscretePartitionRefiner
-
- setup() - Method in class org.openscience.cdk.renderer.AbstractRenderer
-
Creates the transform using the scale, zoom, drawCenter, and modelCenter.
- setup(IAtomContainer, Rectangle) - Method in class org.openscience.cdk.renderer.AtomContainerRenderer
-
Setup the transformations necessary to draw this Atom Container.
- setup(IChemModel, Rectangle) - Method in class org.openscience.cdk.renderer.ChemModelRenderer
-
Setup the transformations necessary to draw this Chem Model.
- setup(T, Rectangle) - Method in interface org.openscience.cdk.renderer.IRenderer
-
- setup(IAtomContainerSet, Rectangle) - Method in class org.openscience.cdk.renderer.MoleculeSetRenderer
-
- setup(IReaction, Rectangle) - Method in class org.openscience.cdk.renderer.ReactionRenderer
-
Setup the transformations necessary to draw this Reaction.
- setup(IReactionSet, Rectangle) - Method in class org.openscience.cdk.renderer.ReactionSetRenderer
-
Setup the transformations necessary to draw this Reaction Set.
- setupTransformNatural(Rectangle2D) - Method in class org.openscience.cdk.renderer.AbstractRenderer
-
Set the transform for a non-fit to screen paint.
- setupTransformToFit(Rectangle2D, Rectangle2D, double, boolean) - Method in class org.openscience.cdk.renderer.AbstractRenderer
-
Sets the transformation needed to draw the model on the canvas when
the diagram needs to fit the screen.
- setUseAromaticityFlag(boolean) - Method in class org.openscience.cdk.smiles.SmilesGenerator
-
- setUseIdentityTemplates(boolean) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
-
Set whether identity templates are used.
- setUseTemplates(boolean) - Method in class org.openscience.cdk.layout.StructureDiagramGenerator
-
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
-
Sets the the exact electron valency of the AtomType object.
- setValency(Integer) - Method in class org.openscience.cdk.debug.DebugAtomType
-
Sets the the exact electron valency of the AtomType object.
- setValency(Integer) - Method in class org.openscience.cdk.debug.DebugFragmentAtom
-
Sets the the exact electron valency of the AtomType object.
- setValency(Integer) - Method in class org.openscience.cdk.debug.DebugPseudoAtom
-
Sets the the exact electron valency of the AtomType object.
- setValency(Integer) - Method in interface org.openscience.cdk.interfaces.IAtomType
-
Sets the the exact electron valency of the AtomType object.
- setValency(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets the the exact electron valency of the AtomType object.
- setValency(Integer) - Method in class org.openscience.cdk.silent.AtomType
-
Sets the the exact electron valency of the AtomType object.
- setValue(Object) - Method in interface org.openscience.cdk.reaction.type.parameters.IParameterReact
-
Set the value of the parameter.
- setValue(Object) - Method in class org.openscience.cdk.reaction.type.parameters.ParameterReact
-
Set the value of the parameter.
- setValue(T) - Method in interface org.openscience.cdk.renderer.generators.IGeneratorParameter
-
Sets the value for this parameter.
- setValue(T) - Method in class org.openscience.cdk.renderer.generators.parameter.AbstractGeneratorParameter
-
Sets the value for this parameter.
- setValueAt(int, int, double) - Method in class org.openscience.cdk.graph.invariant.GIMatrix
-
Sets the value of the element at the given index.
- setVanDerWaalsFile(String) - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
- setWriter(Writer) - Method in class org.openscience.cdk.io.CDKSourceCodeWriter
-
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.CDKSourceCodeWriter
-
- setWriter(Writer) - Method in class org.openscience.cdk.io.CMLWriter
-
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.CMLWriter
-
- setWriter(Writer) - Method in class org.openscience.cdk.io.CrystClustWriter
-
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.CrystClustWriter
-
- setWriter(Writer) - Method in class org.openscience.cdk.io.HINWriter
-
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.HINWriter
-
- setWriter(Writer) - Method in interface org.openscience.cdk.io.IChemObjectWriter
-
Sets the Writer from which this ChemObjectWriter should write
the contents.
- setWriter(OutputStream) - Method in interface org.openscience.cdk.io.IChemObjectWriter
-
Sets the OutputStream from which this ChemObjectWriter should write
the contents.
- setWriter(Writer) - Method in class org.openscience.cdk.io.MDLRXNWriter
-
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.MDLRXNWriter
-
- setWriter(Writer) - Method in class org.openscience.cdk.io.MDLV2000Writer
-
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.MDLV2000Writer
-
- setWriter(Writer) - Method in class org.openscience.cdk.io.Mol2Writer
-
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.Mol2Writer
-
- setWriter(Writer) - Method in class org.openscience.cdk.io.PDBWriter
-
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.PDBWriter
-
- setWriter(Writer) - Method in class org.openscience.cdk.io.program.GaussianInputWriter
-
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.program.GaussianInputWriter
-
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.program.Mopac7Writer
-
- setWriter(Writer) - Method in class org.openscience.cdk.io.program.Mopac7Writer
-
- setWriter(Writer) - Method in class org.openscience.cdk.io.rdf.CDKOWLWriter
-
Sets the Writer from which this ChemObjectWriter should write
the contents.
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.rdf.CDKOWLWriter
-
Sets the OutputStream from which this ChemObjectWriter should write
the contents.
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.RGroupQueryWriter
-
Sets the writer to given output stream.
- setWriter(Writer) - Method in class org.openscience.cdk.io.RGroupQueryWriter
-
Sets the writer.
- setWriter(Writer) - Method in class org.openscience.cdk.io.RssWriter
-
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.RssWriter
-
- setWriter(Writer) - Method in class org.openscience.cdk.io.SDFWriter
-
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.SDFWriter
-
- setWriter(Writer) - Method in class org.openscience.cdk.io.ShelXWriter
-
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.ShelXWriter
-
- setWriter(Writer) - Method in class org.openscience.cdk.io.SMILESWriter
-
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.SMILESWriter
-
- setWriter(Writer) - Method in class org.openscience.cdk.io.XYZWriter
-
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.XYZWriter
-
- setX(double, double) - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Sets the function area, which will painted
- setXTitle(String) - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Set the title of the x axis
- setY(double, double) - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Sets the function area, which will painted
- setYTitle(String) - Method in class org.openscience.cdk.renderer.GraphRendererModel
-
Set the title of the y axis
- setZ(Integer) - Method in class org.openscience.cdk.Crystal
-
Sets the number of asymmetric parts in the unit cell.
- setZ(Integer) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Sets the number of asymmetric parts in the unit cell.
- setZ(Integer) - Method in interface org.openscience.cdk.interfaces.ICrystal
-
Sets the number of assymmetric parts in the unit cell.
- setZ(Integer) - Method in class org.openscience.cdk.silent.Crystal
-
Sets the number of asymmetric parts in the unit cell.
- setZoom(double) - Method in class org.openscience.cdk.renderer.AbstractRenderer
-
Set the zoom, where 1.0 is 100% zoom.
- setZoom(double) - Method in interface org.openscience.cdk.renderer.IRenderer
-
Set a new zoom factor.
- setZoomToFit(double, double, double, double) - Method in class org.openscience.cdk.renderer.AbstractRenderer
-
Calculate and set the zoom factor needed to completely fit the diagram
onto the screen bounds.
- shallowCopy() - Method in class org.openscience.cdk.ChemObject
-
Clones this IChemObject
, but preserves references to Object
s.
- shallowCopy() - Method in class org.openscience.cdk.silent.ChemObject
-
Clones this IChemObject
, but preserves references to Object
s.
- shapeOf(Shape, Color) - Static method in class org.openscience.cdk.renderer.elements.GeneralPath
-
Create a filled path of the specified Java 2D Shape and color.
- SharingAnionReaction - Class in org.openscience.cdk.reaction.type
-
IReactionProcess which participate in movement resonance.
- SharingAnionReaction() - Constructor for class org.openscience.cdk.reaction.type.SharingAnionReaction
-
Constructor of the SharingAnionReaction object.
- SharingChargeDBReaction - Class in org.openscience.cdk.reaction.type
-
IReactionProcess which participate in movement resonance.
- SharingChargeDBReaction() - Constructor for class org.openscience.cdk.reaction.type.SharingChargeDBReaction
-
Constructor of the SharingChargeDBReaction object.
- SharingChargeSBReaction - Class in org.openscience.cdk.reaction.type
-
IReactionProcess which participate in movement resonance.
- SharingChargeSBReaction() - Constructor for class org.openscience.cdk.reaction.type.SharingChargeSBReaction
-
Constructor of the SharingChargeSBReaction object.
- SharingElectronMechanism - Class in org.openscience.cdk.reaction.mechanism
-
This mechanism displaces the charge (lonePair) because of
deficiency of charge.
- SharingElectronMechanism() - Constructor for class org.openscience.cdk.reaction.mechanism.SharingElectronMechanism
-
- SharingLonePairReaction - Class in org.openscience.cdk.reaction.type
-
IReactionProcess which participate in movement resonance.
- SharingLonePairReaction() - Constructor for class org.openscience.cdk.reaction.type.SharingLonePairReaction
-
Constructor of the SharingLonePairReaction object.
- SHEET - Static variable in class org.openscience.cdk.protein.data.PDBStructure
-
- SHEET - Static variable in class org.openscience.cdk.silent.PDBStructure
-
- ShelXFormat - Class in org.openscience.cdk.io.formats
-
- ShelXFormat() - Constructor for class org.openscience.cdk.io.formats.ShelXFormat
-
- ShelXReader - Class in org.openscience.cdk.io
-
A reader for ShelX output (RES) files.
- ShelXReader(Reader) - Constructor for class org.openscience.cdk.io.ShelXReader
-
Create an ShelX file reader.
- ShelXReader(InputStream) - Constructor for class org.openscience.cdk.io.ShelXReader
-
- ShelXReader() - Constructor for class org.openscience.cdk.io.ShelXReader
-
- ShelXWriter - Class in org.openscience.cdk.io
-
Serializes a MoleculeSet or a Molecule object to ShelX code.
- ShelXWriter(Writer) - Constructor for class org.openscience.cdk.io.ShelXWriter
-
Constructs a new ShelXWriter class.
- ShelXWriter(OutputStream) - Constructor for class org.openscience.cdk.io.ShelXWriter
-
- ShelXWriter() - Constructor for class org.openscience.cdk.io.ShelXWriter
-
- shift(Rectangle, Rectangle) - Method in class org.openscience.cdk.renderer.AbstractRenderer
-
Determine the overlap of the diagram with the screen, and shift (if
necessary) the diagram draw center.
- shift(Rectangle, Rectangle) - Method in class org.openscience.cdk.renderer.MoleculeSetRenderer
-
Determine the overlap of the diagram with the screen, and shift (if
necessary) the diagram draw center.
- shiftContainer(IAtomContainer, Rectangle2D, Rectangle2D, double) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Shift the container horizontally to the right to make its bounds not
overlap with the other bounds.
- shiftContainer(IAtomContainer, double[], double[], double) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Shift the container horizontally to the right to make its bounds not overlap with the other
bounds.
- shiftDrawCenter(double, double) - Method in class org.openscience.cdk.renderer.AbstractRenderer
-
Move the draw center by dx and dy.
- shiftDrawCenter(double, double) - Method in interface org.openscience.cdk.renderer.IRenderer
-
Set a new drawing center in screen coordinates.
- shiftReactionVertical(IReaction, Rectangle2D, Rectangle2D, double) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Shift the containers in a reaction vertically upwards to not overlap
with the reference Rectangle2D.
- shiftReactionVertical(IReaction, double[], double[], double) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Shift the containers in a reaction vertically upwards to not overlap with the reference
rectangle.
- ShortestPathFingerprinter - Class in org.openscience.cdk.fingerprint
-
- ShortestPathFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.ShortestPathFingerprinter
-
Creates a fingerprint generator of length
DEFAULT_SIZE
- ShortestPathFingerprinter(int) - Constructor for class org.openscience.cdk.fingerprint.ShortestPathFingerprinter
-
Constructs a fingerprint generator that creates fingerprints of the given fingerprintLength, using a generation
algorithm with shortest paths.
- ShortestPaths - Class in org.openscience.cdk.graph
-
Find and reconstruct the shortest paths from a given start atom to any other
connected atom.
- ShortestPaths(IAtomContainer, IAtom) - Constructor for class org.openscience.cdk.graph.ShortestPaths
-
Create a new shortest paths tool for a single start atom.
- ShortestPathWalker - Class in org.openscience.cdk.fingerprint
-
- ShortestPathWalker(IAtomContainer) - Constructor for class org.openscience.cdk.fingerprint.ShortestPathWalker
-
Create a new shortest path walker for a given container.
- shouldBeLinear(IAtom, IAtomContainer) - Static method in class org.openscience.cdk.layout.AtomPlacer
-
- showCarbon(IAtom, IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.AtomMassGenerator
-
Returns true if the mass number of this element is set and not
equal the mass number of the most abundant isotope of this element.
- showCarbon(IAtom, IAtomContainer, RendererModel) - Method in class org.openscience.cdk.renderer.generators.BasicAtomGenerator
-
Checks a carbon atom to see if it should be shown.
- SI - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- SigmaElectronegativityDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
-
Atomic descriptor that reflects that Gasteiger-Marsili sigma electronegativity.
- SigmaElectronegativityDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor
-
Constructor for the SigmaElectronegativityDescriptor object
- SignatureFingerprinter - Class in org.openscience.cdk.fingerprint
-
- SignatureFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.SignatureFingerprinter
-
Initialize the fingerprinter with a defult signature depth of 1.
- SignatureFingerprinter(int) - Constructor for class org.openscience.cdk.fingerprint.SignatureFingerprinter
-
Initialize the fingerprinter with a certain signature depth.
- signatureForVertex(int) - Method in class org.openscience.cdk.signature.MoleculeSignature
-
- SignatureQuotientGraph - Class in org.openscience.cdk.signature
-
A signature quotient graph has a vertex for every signature symmetry class
and an edge for each bond in the molecule between atoms in their class.
- SignatureQuotientGraph(IAtomContainer) - Constructor for class org.openscience.cdk.signature.SignatureQuotientGraph
-
Construct a quotient graph from the symmetry classes generated from the
atom container.
- SignatureQuotientGraph(IAtomContainer, int) - Constructor for class org.openscience.cdk.signature.SignatureQuotientGraph
-
Construct a quotient graph using symmetry classes defined by signatures
of height height
.
- SignatureReactionCanoniser - Class in org.openscience.cdk.smsd.labelling
-
- SignatureReactionCanoniser() - Constructor for class org.openscience.cdk.smsd.labelling.SignatureReactionCanoniser
-
- signatureStringForVertex(int) - Method in class org.openscience.cdk.signature.MoleculeSignature
-
- signatureStringForVertex(int, int) - Method in class org.openscience.cdk.signature.MoleculeSignature
-
- signedDistanceToPlane(Vector3d, Point3d, Point3d) - Static method in class org.openscience.cdk.stereo.StereoTool
-
Given a normalized normal for a plane, any point in that plane, and
a point, will return the distance between the plane and that point.
- SilentChemObjectBuilder - Class in org.openscience.cdk.silent
-
A factory class to provide implementation independent
ICDKObject
s.
- SILICON - Static variable in enum org.openscience.cdk.config.Elements
-
- SILVER - Static variable in enum org.openscience.cdk.config.Elements
-
- SILVER - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- similar(IMatrix) - Method in class org.openscience.cdk.math.IMatrix
-
Similar transformation
Ut * M * U
- similar(IMatrix, IMatrix) - Method in class org.openscience.cdk.math.IMatrix
-
Similar transformation
Ut * M * U
- similar(Matrix) - Method in class org.openscience.cdk.math.Matrix
-
Similar transformation
Ut * M * U
- SimpleAtomCanonicalizer - Class in org.openscience.cdk.fingerprint
-
This code returns a sorted set of atoms for a container according to its
symbol and hybridization states.
- SimpleAtomCanonicalizer() - Constructor for class org.openscience.cdk.fingerprint.SimpleAtomCanonicalizer
-
- SimpleAtomComparator - Class in org.openscience.cdk.fingerprint
-
This code returns a sorted set of atoms for a container according to its
symbol and hybridization states.
- SimpleAtomComparator() - Constructor for class org.openscience.cdk.fingerprint.SimpleAtomComparator
-
- SimpleBasisSet - Class in org.openscience.cdk.math.qm
-
This class will generate a simple base set for a atom container.
- SimpleBasisSet(IAtom[]) - Constructor for class org.openscience.cdk.math.qm.SimpleBasisSet
-
Create a base set
- SimpleBond() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
- SimpleCharStream - Class in org.openscience.cdk.iupac.parser
-
An implementation of interface CharStream, where the stream is assumed to
contain only ASCII characters (without unicode processing).
- SimpleCharStream(Reader, int, int, int) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(Reader, int, int) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(Reader) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(InputStream, String, int, int, int) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(InputStream, int, int, int) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(InputStream, String, int, int) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(InputStream, int, int) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(InputStream, String) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(InputStream) - Constructor for class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream - Class in org.openscience.cdk.smiles.smarts.parser
-
An implementation of interface CharStream, where the stream is assumed to
contain only ASCII characters (without unicode processing).
- SimpleCharStream(Reader, int, int, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(Reader, int, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(Reader) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(InputStream, String, int, int, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(InputStream, int, int, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(InputStream, String, int, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(InputStream, int, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(InputStream, String) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Constructor.
- SimpleCharStream(InputStream) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Constructor.
- SimpleCycle - Class in org.openscience.cdk.ringsearch.cyclebasis
-
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<SimpleCycle>, List, UndirectedGraph) - Constructor for class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis
-
- SimpleCycleBasis(UndirectedGraph) - Constructor for class org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis
-
- simplifyMolecularFormula(String) - Static method in class org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
-
Simplify the molecular formula.
- SINGLE_ELECTRON_COUNT - Static variable in class org.openscience.cdk.CDKConstants
-
Used as property key for indicating the number of single electrons on the atom type.
- SINGLE_OR_DOUBLE - Static variable in class org.openscience.cdk.CDKConstants
-
Flag used for marking uncertainty of the bond order.
- SINGLEBOND - Static variable in class org.openscience.cdk.libio.jena.CDK
-
- SingleElectron - Class in org.openscience.cdk.silent
-
A Single Electron is an orbital which is occupied by only one electron.
- SingleElectron(IAtom) - Constructor for class org.openscience.cdk.silent.SingleElectron
-
Constructs an single electron orbital on an Atom.
- SingleElectron() - Constructor for class org.openscience.cdk.silent.SingleElectron
-
Constructs an single electron orbital with an associated Atom.
- SingleElectron - Class in org.openscience.cdk
-
A Single Electron is an orbital which is occupied by only one electron.
- SingleElectron(IAtom) - Constructor for class org.openscience.cdk.SingleElectron
-
Constructs an single electron orbital on an Atom.
- SingleElectron() - Constructor for class org.openscience.cdk.SingleElectron
-
Constructs an single electron orbital with an associated Atom.
- singleElectronCount - Variable in class org.openscience.cdk.AtomContainer
-
Number of single electrons contained by this object.
- singleElectronCount - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Number of single electrons contained by this object.
- singleElectronCount - Variable in class org.openscience.cdk.silent.AtomContainer
-
Number of single electrons contained by this object.
- SingleElectronDiff - Class in org.openscience.cdk.tools.diff
-
- singleElectrons - Variable in class org.openscience.cdk.AtomContainer
-
Internal array of single electrons.
- singleElectrons() - Method in class org.openscience.cdk.AtomContainer
-
Returns an Iterable for looping over all single electrons in this container.
- singleElectrons() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns an Iterable for looping over all single electrons in this container.
- singleElectrons() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns an Iterable for looping over all single electrons in this container.
- singleElectrons() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns an Iterable for looping over all single electrons in this container.
- singleElectrons() - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns an Iterable for looping over all single electrons in this container.
- singleElectrons() - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns an Iterable for looping over all single electrons in this container.
- singleElectrons() - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns an Iterable for looping over all single electrons in this container.
- singleElectrons() - Method in class org.openscience.cdk.debug.DebugRing
-
Returns an Iterable for looping over all single electrons in this container.
- singleElectrons() - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns an Iterable for looping over all single electrons in this container.
- singleElectrons() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns an Iterable for looping over all single electrons in this container.
- singleElectrons - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Internal array of single electrons.
- singleElectrons() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns an Iterable for looping over all single electrons in this container.
- singleElectrons - Variable in class org.openscience.cdk.silent.AtomContainer
-
Internal array of single electrons.
- singleElectrons() - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns an Iterable for looping over all single electrons in this container.
- SingleMapping - Class in org.openscience.cdk.smsd.algorithm.single
-
This class handles single atom mapping.
- SingleMapping() - Constructor for class org.openscience.cdk.smsd.algorithm.single.SingleMapping
-
Default
- SingleMappingHandler - Class in org.openscience.cdk.smsd.algorithm.single
-
- SingleMappingHandler(boolean) - Constructor for class org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler
-
- SingleStructureRandomGenerator - Class in org.openscience.cdk.structgen
-
Randomly generates a single, connected, correctly bonded structure for
a given molecular formula.
- SingleStructureRandomGenerator(long) - Constructor for class org.openscience.cdk.structgen.SingleStructureRandomGenerator
-
Constructor for the SingleStructureRandomGenerator object.
- SingleStructureRandomGenerator() - Constructor for class org.openscience.cdk.structgen.SingleStructureRandomGenerator
-
Constructor for the SingleStructureRandomGenerator object.
- sitefinder() - Method in class org.openscience.cdk.protein.ProteinPocketFinder
-
Main method which calls the methods: assignProteinToGrid,
GridScan, and FindPockets.
- size() - Method in class org.openscience.cdk.ConformerContainer
-
Get the number of conformers stored.
- size() - Method in class org.openscience.cdk.debug.DebugAdductFormula
-
Returns the number of MolecularFormulas in this AdductFormula.
- size() - Method in class org.openscience.cdk.debug.DebugMolecularFormulaSet
-
Returns the number of MolecularFormulas in this MolecularFormulaSet.
- size() - Method in class org.openscience.cdk.dict.Dictionary
-
- size() - Method in class org.openscience.cdk.fingerprint.BitSetFingerprint
-
- size() - Method in interface org.openscience.cdk.fingerprint.IBitFingerprint
-
Returns the size of the fingerprint, i.e., the number of hash bins.
- size() - Method in interface org.openscience.cdk.fingerprint.ICountFingerprint
-
Returns the number of bits of this fingerprint.
- size() - Method in class org.openscience.cdk.fingerprint.IntArrayCountFingerprint
-
- size() - Method in class org.openscience.cdk.fingerprint.IntArrayFingerprint
-
- size() - Method in class org.openscience.cdk.formula.AdductFormula
-
Returns the number of MolecularFormulas in this AdductFormula.
- size() - Method in class org.openscience.cdk.formula.MolecularFormulaSet
-
Returns the number of MolecularFormulas in this MolecularFormulaSet.
- size() - Method in class org.openscience.cdk.graph.AllCycles
-
Cardinality of the set.
- size() - Method in class org.openscience.cdk.graph.EssentialCycles
-
Number of essential cycles.
- size() - Method in class org.openscience.cdk.graph.MinimumCycleBasis
-
The number of the cycles in the minimum cycle basis.
- size() - Method in class org.openscience.cdk.graph.RelevantCycles
-
The number of the relevant cycles.
- size() - Method in class org.openscience.cdk.graph.TripletShortCycles
-
Size of the cycle basis, cardinality of the ESSSR.
- size() - Method in class org.openscience.cdk.group.Partition
-
Gets the size of the partition, in terms of the number of cells.
- size() - Method in class org.openscience.cdk.group.Permutation
-
Get the number of elements in the permutation.
- size() - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet
-
Returns the number of MolecularFormulas in this IMolecularFormulaSet.
- size() - Method in interface org.openscience.cdk.io.random.IRandomAccessChemObjectReader
-
- size() - Method in class org.openscience.cdk.io.random.RandomAccessReader
-
- size - Variable in class org.openscience.cdk.math.IVector
-
Size of this vector
- size - Variable in class org.openscience.cdk.math.Vector
-
The size of this vector
- size() - Method in class org.openscience.cdk.silent.AdductFormula
-
Returns the number of MolecularFormulas in this AdductFormula.
- size() - Method in class org.openscience.cdk.silent.MolecularFormulaSet
-
Returns the number of MolecularFormulas in this MolecularFormulaSet.
- skeleton(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Create a skeleton copy of the provided structure.
- SM - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- SMALL_FIRST - Static variable in class org.openscience.cdk.silent.RingSet
-
Flag to denote that the set is order with the smallest ring first?
- SMALL_FIRST - Static variable in class org.openscience.cdk.tools.manipulator.RingSizeComparator
-
Flag to denote that the set is order with the smallest ring first
- SMALLEST_RINGS - Static variable in class org.openscience.cdk.CDKConstants
-
A smallest set of smallest rings computed for this molecule.
- SmallestRingAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
-
Match an atom in a specific size ring.
- SmallestRingAtom(int, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.SmallestRingAtom
-
Creates a matcher for specified ring size.
- SmallestRingSize() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
- SmallRingDescriptor - Class in org.openscience.cdk.qsar.descriptors.molecular
-
Small ring descriptors: these are based on enumeration of all the small rings (sizes 3 to 9) in a molecule,
which can be obtained quickly and deterministically.
- SmallRingDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor
-
- Smarts2MQLVisitor - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST tree visitor.
- Smarts2MQLVisitor() - Constructor for class org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor
-
- SMARTSAtom - Class in org.openscience.cdk.isomorphism.matchers.smarts
-
Abstract smarts atom.
- SMARTSAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom
-
- SMARTSBond - Class in org.openscience.cdk.isomorphism.matchers.smarts
-
Abstract smarts bond.
- SMARTSBond(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.SMARTSBond
-
- SMARTSBond(IQueryAtom, IQueryAtom, IBond.Order, IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.SMARTSBond
-
- SmartsDumpVisitor - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST Tree visitor.
- SmartsDumpVisitor() - Constructor for class org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor
-
- SmartsExpression() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
- SMARTSFormat - Class in org.openscience.cdk.io.formats
-
- SMARTSFormat() - Constructor for class org.openscience.cdk.io.formats.SMARTSFormat
-
- SmartsMatchers - Class in org.openscience.cdk.isomorphism.matchers.smarts
-
Bridging class between the SMARTS matcher and the parser/query tool.
- SmartsMatchers() - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.SmartsMatchers
-
- SMARTSParser - Class in org.openscience.cdk.smiles.smarts.parser
-
This parser implements a nearly complete subset of the SMARTS syntax as defined on
the
Daylight website.
- SMARTSParser(InputStream) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
Constructor with InputStream.
- SMARTSParser(InputStream, String) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
Constructor with InputStream and supplied encoding
- SMARTSParser(Reader) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
Constructor.
- SMARTSParser(SMARTSParserTokenManager) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
Constructor with generated Token Manager.
- SMARTSParserConstants - Interface in org.openscience.cdk.smiles.smarts.parser
-
Token literal values and constants.
- SMARTSParserTokenManager - Class in org.openscience.cdk.smiles.smarts.parser
-
Token Manager.
- SMARTSParserTokenManager(SimpleCharStream) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager
-
Constructor.
- SMARTSParserTokenManager(SimpleCharStream, int) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager
-
Constructor.
- SMARTSParserTreeConstants - Interface in org.openscience.cdk.smiles.smarts.parser
-
- SMARTSParserVisitor - Interface in org.openscience.cdk.smiles.smarts.parser
-
- SmartsPattern - Class in org.openscience.cdk.smiles.smarts
-
A
Pattern
for matching a single SMARTS query against multiple target
compounds.
- SMARTSQueryTool - Class in org.openscience.cdk.smiles.smarts
-
This class provides a easy to use wrapper around SMARTS matching functionality.
- SMARTSQueryTool(String, IChemObjectBuilder) - Constructor for class org.openscience.cdk.smiles.smarts.SMARTSQueryTool
-
Create a new SMARTS query tool for the specified SMARTS string.
- SmartsQueryVisitor - Class in org.openscience.cdk.smiles.smarts.parser
-
An AST tree visitor.
- SmartsQueryVisitor(IChemObjectBuilder) - Constructor for class org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor
-
- SmartsStereoMatch - Class in org.openscience.cdk.isomorphism
-
Filters SMARTS matches for those that have valid stereochemistry
configuration.
- SmartsStereoMatch(IAtomContainer, IAtomContainer) - Constructor for class org.openscience.cdk.isomorphism.SmartsStereoMatch
-
Create a predicate for checking mappings between a provided
query
and target
.
- SMILES - Static variable in class org.openscience.cdk.CDKConstants
-
The Daylight SMILES.
- SMILESFIXFormat - Class in org.openscience.cdk.io.formats
-
- SMILESFIXFormat() - Constructor for class org.openscience.cdk.io.formats.SMILESFIXFormat
-
- SMILESFormat - Class in org.openscience.cdk.io.formats
-
- SMILESFormat() - Constructor for class org.openscience.cdk.io.formats.SMILESFormat
-
- SmilesGenerator - Class in org.openscience.cdk.smiles
-
Generate a SMILES [Weininger, David, SMILES, a Chemical Language and Information System. 1.
Introduction to Methodology and Encoding Rules, Journal of Chemical Information and Computer
Sciences, 1988, 28:31-36, Weininger, David and Weininger, Arthur and Weininger, Joseph
L., SMILES 2. Algorithm for Generation of Unique SMILES
Notation, Journal of Chemical Information and Computer
Sciences, 1989, 29:97-101] string for a provided structure.
- SmilesGenerator() - Constructor for class org.openscience.cdk.smiles.SmilesGenerator
-
Create the generic SMILES generator.
- SmilesParser - Class in org.openscience.cdk.smiles
-
Read molecules and reactions from a SMILES [?Authors?, SMILES Tutorial] string.
- SmilesParser(IChemObjectBuilder) - Constructor for class org.openscience.cdk.smiles.SmilesParser
-
Create a new SMILES parser which will create
IAtomContainer
s with
the specified builder.
- SmilesReactionCanoniser - Class in org.openscience.cdk.smsd.labelling
-
- SmilesReactionCanoniser() - Constructor for class org.openscience.cdk.smsd.labelling.SmilesReactionCanoniser
-
- SMILESReader - Class in org.openscience.cdk.io
-
This Reader reads files which has one SMILES string on each
line, where the format is given as below:
- SMILESReader(Reader) - Constructor for class org.openscience.cdk.io.SMILESReader
-
Construct a new reader from a Reader and a specified builder object.
- SMILESReader(InputStream) - Constructor for class org.openscience.cdk.io.SMILESReader
-
- SMILESReader() - Constructor for class org.openscience.cdk.io.SMILESReader
-
- SmilesValencyChecker - Class in org.openscience.cdk.tools
-
Small customization of ValencyHybridChecker suggested by Todd Martin
specially tuned for SMILES parsing.
- SmilesValencyChecker() - Constructor for class org.openscience.cdk.tools.SmilesValencyChecker
-
- SmilesValencyChecker(String) - Constructor for class org.openscience.cdk.tools.SmilesValencyChecker
-
- SMILESWriter - Class in org.openscience.cdk.io
-
Writes the SMILES strings to a plain text file.
- SMILESWriter(Writer) - Constructor for class org.openscience.cdk.io.SMILESWriter
-
Constructs a new SMILESWriter that can write a list of SMILES to a Writer
- SMILESWriter(OutputStream) - Constructor for class org.openscience.cdk.io.SMILESWriter
-
- SMILESWriter() - Constructor for class org.openscience.cdk.io.SMILESWriter
-
- SMILESWriter(FileOutputStream) - Constructor for class org.openscience.cdk.io.SMILESWriter
-
Constructs a new SMILESWriter that can write an list of SMILES to a given OutputStream
- SMSDNormalizer - Class in org.openscience.cdk.normalize
-
This class containes set of modules required to clean a molecule
before subjecting it for MCS search.
- SMSDNormalizer() - Constructor for class org.openscience.cdk.normalize.SMSDNormalizer
-
- SN - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- SODIUM - Static variable in enum org.openscience.cdk.config.Elements
-
- SODIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- sort() - Method in class org.openscience.cdk.signature.Orbit
-
Sorts the atom indices in this orbit.
- sort(IAtomContainerSet) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
-
Sorts the IAtomContainers in the given IAtomContainerSet by the following
criteria with decreasing priority:
- sort(IRingSet) - Static method in class org.openscience.cdk.tools.manipulator.RingSetManipulator
-
Sorts the rings in the set by size.
- sortAndNormalizedByIntensity(IsotopePattern) - Static method in class org.openscience.cdk.formula.IsotopePatternManipulator
-
Return the isotope pattern sorted and normalized by intensity
to the highest abundance.
- sortAtomContainers(Comparator<IAtomContainer>) - Method in class org.openscience.cdk.AtomContainerSet
-
Sort the AtomContainers and multipliers using a provided Comparator.
- sortAtomContainers(Comparator<IAtomContainer>) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet
-
Sort the AtomContainers using a provided Comparator.
- sortAtomContainers(Comparator<IAtomContainer>) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Sort the AtomContainers and multipliers using a provided Comparator
- sortBy2DDistance(IAtom[], Point2d) - Static method in class org.openscience.cdk.geometry.GeometryTools
-
Sorts a Vector of atoms such that the 2D distances of the atom locations
from a given point are smallest for the first atoms in the vector.
- sortBy2DDistance(IAtom[], Point2d) - Static method in class org.openscience.cdk.geometry.GeometryUtil
-
Sorts a Vector of atoms such that the 2D distances of the atom locations from a given point
are smallest for the first atoms in the vector.
- sortByIntensity(IsotopePattern) - Static method in class org.openscience.cdk.formula.IsotopePatternManipulator
-
Return the isotope pattern sorted by intensity
to the highest abundance.
- sortByMass(IsotopePattern) - Static method in class org.openscience.cdk.formula.IsotopePatternManipulator
-
Return the isotope pattern sorted by mass
to the highest abundance.
- sortResultsByEnergies() - Method in class org.openscience.cdk.smsd.filters.ChemicalFilters
-
Sort MCS solution by bond breaking energy.
- sortResultsByFragments() - Method in class org.openscience.cdk.smsd.filters.ChemicalFilters
-
Sort solution by ascending order of the fragment count.
- sortResultsByStereoAndBondMatch() - Method in class org.openscience.cdk.smsd.filters.ChemicalFilters
-
Sort MCS solution by stereo and bond type matches.
- SPACE - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- SpanningTree - Class in org.openscience.cdk.graph
-
Spanning tree of a molecule.
- SpanningTree(IAtomContainer) - Constructor for class org.openscience.cdk.graph.SpanningTree
-
Create a new spanning tree for the provided molecule.
- SpartanFormat - Class in org.openscience.cdk.io.formats
-
- SpartanFormat() - Constructor for class org.openscience.cdk.io.formats.SpartanFormat
-
- specialCase() - Method in class org.openscience.cdk.iupac.parser.NomParser
-
Deprecated.
Deal with special cases where the rules don't apply.
- specialToken - Variable in class org.openscience.cdk.iupac.parser.Token
-
This field is used to access special tokens that occur prior to this
token, but after the immediately preceding regular (non-special) token.
- specialToken - Variable in class org.openscience.cdk.smiles.smarts.parser.Token
-
This field is used to access special tokens that occur prior to this
token, but after the immediately preceding regular (non-special) token.
- sphere - Variable in class org.openscience.cdk.tools.HOSECodeGenerator
-
Counter for the sphere in which we currently work.
- sphereDelimiters - Variable in class org.openscience.cdk.tools.HOSECodeGenerator
-
Delimiters used to separate spheres in the output string.
- sphereNodes - Variable in class org.openscience.cdk.tools.HOSECodeGenerator
-
Container for the nodes in a sphere.
- sphereNodesWithAtoms - Variable in class org.openscience.cdk.tools.HOSECodeGenerator
-
- spheres - Variable in class org.openscience.cdk.tools.HOSECodeGenerator
-
Here we store the spheres that we assemble, in order to parse them into a
code later.
- spheresWithAtoms - Variable in class org.openscience.cdk.tools.HOSECodeGenerator
-
- SPHERICAL_MATCHER - Static variable in class org.openscience.cdk.CDKConstants
-
Used as property key for indicating the HOSE code for a certain atom type.
- spinMultiplicities - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- splice(PathEdge) - Method in class org.openscience.cdk.smsd.ring.PathEdge
-
- SPLIT_MODE_BREADTH_FIRST - Static variable in class org.openscience.cdk.structgen.stochastic.operator.CrossoverMachine
-
Indicates that crossover
is using SPLIT_MODE_BREADTH_FIRST mode.
- SPLIT_MODE_DEPTH_FIRST - Static variable in class org.openscience.cdk.structgen.stochastic.operator.CrossoverMachine
-
Indicates that crossover
is using SPLIT_MODE_DEPTH_FIRST mode.
- SPLIT_MODE_RADNDOM - Static variable in class org.openscience.cdk.structgen.stochastic.operator.CrossoverMachine
-
Indicates that crossover
is using SPLIT_MODE_RADNDOM mode.
- splitAfter(int, int) - Method in class org.openscience.cdk.group.Partition
-
Splits this partition by taking the cell at cellIndex and making two
new cells - the first with the the rest of the elements from that cell
and the second with the singleton splitElement.
- splitBefore(int, int) - Method in class org.openscience.cdk.group.Partition
-
Splits this partition by taking the cell at cellIndex and making two
new cells - the first with the singleton splitElement and the second
with the rest of the elements from that cell.
- splitMolecule(IAtomContainer, IBond) - Static method in class org.openscience.cdk.fragment.FragmentUtils
-
Non destructively split a molecule into two parts at the specified bond.
- sqrt() - Method in class org.openscience.cdk.math.Quaternion
-
- SR - Static variable in interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
-
RegularExpression Id.
- sssr(IAtomContainer) - Static method in class org.openscience.cdk.graph.Cycles
-
Find the smallest set of smallest rings (SSSR) - aka minimum cycle basis
(MCB) of a molecule.
- SSSRFinder - Class in org.openscience.cdk.ringsearch
-
Finds the Smallest Set of Smallest Rings.
- SSSRFinder(IAtomContainer) - Constructor for class org.openscience.cdk.ringsearch.SSSRFinder
-
Constructs a SSSRFinder for a specified molecule.
- st - Variable in class org.openscience.cdk.io.VASPReader
-
- StabilizationCharges - Class in org.openscience.cdk.charges
-
The stabilization of the positive and the negative charge
obtained (e.g in the polar breaking of a bond) is calculated from the sigma- and
lone pair-electronegativity values of the atoms that are in conjugation to the atoms
obtaining the charges.
- StabilizationCharges() - Constructor for class org.openscience.cdk.charges.StabilizationCharges
-
Constructor for the StabilizationCharges object.
- StabilizationPlusChargeDescriptor - Class in org.openscience.cdk.qsar.descriptors.atomic
-
The stabilization of the positive charge
(e.g.) obtained in the polar breaking of a bond is calculated from the sigma- and
lone pair-electronegativity values of the atoms that are in conjugation to the atoms
obtaining the charges.
- StabilizationPlusChargeDescriptor() - Constructor for class org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor
-
Constructor for the StabilizationPlusChargeDescriptor object
- StandardGenerator - Class in org.openscience.cdk.renderer.generators.standard
-
The standard generator creates
IRenderingElement
s for the atoms and bonds of a structure
diagram.
- StandardGenerator(Font) - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator
-
Create a new standard generator that utilises the specified font to display atom symbols.
- StandardGenerator.AnnotationColor - Class in org.openscience.cdk.renderer.generators.standard
-
The color of the atom numbers.
- StandardGenerator.AnnotationColor() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.AnnotationColor
-
- StandardGenerator.AnnotationDistance - Class in org.openscience.cdk.renderer.generators.standard
-
The distance of atom numbers from their parent atom as a percentage of bond length, default
value is 0.25 (25%)
- StandardGenerator.AnnotationDistance() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.AnnotationDistance
-
- StandardGenerator.AnnotationFontScale - Class in org.openscience.cdk.renderer.generators.standard
-
Annotation font size relative to element symbols, default = 0.4 (40%).
- StandardGenerator.AnnotationFontScale() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.AnnotationFontScale
-
- StandardGenerator.AtomColor - Class in org.openscience.cdk.renderer.generators.standard
-
Defines the color of unselected atoms (and bonds).
- StandardGenerator.AtomColor() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.AtomColor
-
- StandardGenerator.BondSeparation - Class in org.openscience.cdk.renderer.generators.standard
-
Defines the ratio of the separation between lines in double bonds as a percentage of length
(BasicSceneGenerator.BondLength
).
- StandardGenerator.BondSeparation() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.BondSeparation
-
- StandardGenerator.DashSection - Class in org.openscience.cdk.renderer.generators.standard
-
The number of sections to render in a dashed 'unknown' bond, default = 4;
- StandardGenerator.DashSection() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.DashSection
-
- StandardGenerator.FancyBoldWedges - Class in org.openscience.cdk.renderer.generators.standard
-
Modify bold wedges to be flush with adjacent bonds, default = true.
- StandardGenerator.FancyBoldWedges() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.FancyBoldWedges
-
- StandardGenerator.FancyHashedWedges - Class in org.openscience.cdk.renderer.generators.standard
-
Modify hashed wedges to be flush when there is a single adjacent bond, default = true.
- StandardGenerator.FancyHashedWedges() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.FancyHashedWedges
-
- StandardGenerator.HashSpacing - Class in org.openscience.cdk.renderer.generators.standard
-
The preferred spacing between lines in hashed bonds.
- StandardGenerator.HashSpacing() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.HashSpacing
-
- StandardGenerator.Highlighting - Class in org.openscience.cdk.renderer.generators.standard
-
Parameter defines the style of highlight used to emphasis atoms and bonds.
- StandardGenerator.Highlighting() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.Highlighting
-
- StandardGenerator.HighlightStyle - Enum in org.openscience.cdk.renderer.generators.standard
-
Enumeration of highlight style.
- StandardGenerator.OuterGlowWidth - Class in org.openscience.cdk.renderer.generators.standard
-
The width of outer glow as a percentage of stroke width.
- StandardGenerator.OuterGlowWidth() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.OuterGlowWidth
-
- StandardGenerator.StrokeRatio - Class in org.openscience.cdk.renderer.generators.standard
-
Defines the ratio of the stroke to the width of the stroke of the font used to depict atom
symbols.
- StandardGenerator.StrokeRatio() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.StrokeRatio
-
- StandardGenerator.SymbolMarginRatio - Class in org.openscience.cdk.renderer.generators.standard
-
Defines the margin between an atom symbol and a connected bond based on the stroke width.
- StandardGenerator.SymbolMarginRatio() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.SymbolMarginRatio
-
- StandardGenerator.Visibility - Class in org.openscience.cdk.renderer.generators.standard
-
Defines which atoms have their symbol displayed.
- StandardGenerator.Visibility() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.Visibility
-
- StandardGenerator.WaveSpacing - Class in org.openscience.cdk.renderer.generators.standard
-
The spacing of waves (semi circles) drawn in wavy bonds with.
- StandardGenerator.WaveSpacing() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.WaveSpacing
-
- StandardGenerator.WedgeRatio - Class in org.openscience.cdk.renderer.generators.standard
-
Ratio of the wide end of wedge compared to the narrow end (stroke width).
- StandardGenerator.WedgeRatio() - Constructor for class org.openscience.cdk.renderer.generators.standard.StandardGenerator.WedgeRatio
-
- StandardSubstructureSets - Class in org.openscience.cdk.fingerprint
-
Default sets of atom containers aimed for use with the substructure.
- StandardSubstructureSets() - Constructor for class org.openscience.cdk.fingerprint.StandardSubstructureSets
-
- Start() - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParser
-
Start ::=
<#_WS>
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.isotopes.IsotopeHandler
- startDocument() - Method in class org.openscience.cdk.dict.DictionaryHandler
-
- startDocument() - Method in class org.openscience.cdk.io.cml.CDKConvention
-
- startDocument() - Method in class org.openscience.cdk.io.cml.CMLCoreModule
-
- startDocument() - Method in class org.openscience.cdk.io.cml.CMLHandler
-
- startDocument() - Method in interface org.openscience.cdk.io.cml.ICMLModule
-
- startDocument() - Method in class org.openscience.cdk.io.cml.MDLMolConvention
-
- startDocument() - Method in class org.openscience.cdk.io.cml.PMPConvention
-
- startDocument() - Method in class org.openscience.cdk.io.inchi.INChIHandler
-
- startDocument() - Method in class org.openscience.cdk.io.iterator.event.EventCMLHandler
-
Procedure required by the CDOInterface.
- startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.config.atomtypes.AtomTypeHandler
- startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeHandler
- startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingHandler
- startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.config.isotopes.IsotopeHandler
- startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.dict.DictionaryHandler
-
- startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.CDKConvention
-
- startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.CMLCoreModule
-
- startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.CMLHandler
-
- startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.CMLReactionModule
-
- startElement(CMLStack, String, String, String, Attributes) - Method in interface org.openscience.cdk.io.cml.ICMLModule
-
- startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.JMOLANIMATIONConvention
-
- startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.MDLMolConvention
-
- startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.MDMoleculeConvention
-
Add parsing of elements in mdmolecule:
mdmolecule
chargeGroup
id
cgNumber
atomArray
switchingAtom
residue
id
title
resNumber
atomArray
- startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.PDBConvention
-
- startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.PMPConvention
-
- startElement(CMLStack, String, String, String, Attributes) - Method in class org.openscience.cdk.io.cml.QSARConvention
-
- startElement(String, String, String, Attributes) - Method in class org.openscience.cdk.io.inchi.INChIHandler
-
Implementation of the startElement() procedure overwriting the
DefaultHandler interface.
- startMcGregorIteration(int, Map<Integer, Integer>) - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregor
-
Start McGregor search and extend the mappings if possible.
- startMcGregorIteration(int, List<Integer>, List<Integer>) - Method in class org.openscience.cdk.smsd.algorithm.mcgregor.McGregor
-
Start McGregor search and extend the mappings if possible.
- startObject(String) - Method in class org.openscience.cdk.io.iterator.event.EventCMLHandler
-
Procedure required by the CDOInterface.
- startX - Variable in class org.openscience.cdk.renderer.elements.ArrowElement
-
X coordinate of the point where the arrow starts.
- startY - Variable in class org.openscience.cdk.renderer.elements.ArrowElement
-
Y coordinate of the point where the arrow starts.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.AtomContainer
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.AtomContainerSet
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.ChemFile
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.ChemModel
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.ChemSequence
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugCrystal
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugMonomer
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugPolymer
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugRing
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.debug.DebugStrand
-
Called by objects to which this object has
registered as a listener.
- stateChanged(EventObject) - Method in interface org.openscience.cdk.event.ICDKChangeListener
-
Invoked when the target of the listener has changed its state.
- stateChanged(EventObject) - Method in interface org.openscience.cdk.event.ICDKSelectionChangeListener
-
Invoked when the target of the listener has changed its state.
- stateChanged(IChemObjectChangeEvent) - Method in interface org.openscience.cdk.interfaces.IChemObjectListener
-
Called by objects to notify objects that implemented this interface
and registered with them as ChemObjectListeners.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.ReactionSet
-
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.AtomContainer
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.ChemFile
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.ChemModel
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.ChemSequence
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.ReactionSet
-
- stateChanged(List) - Method in interface org.openscience.cdk.structgen.IStructureGenerationListener
-
- staticFlag - Static variable in class org.openscience.cdk.iupac.parser.SimpleCharStream
-
Whether parser is static.
- staticFlag - Static variable in class org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
-
Whether parser is static.
- STDOUT_LOGGING_TOOL_CLASS - Static variable in class org.openscience.cdk.tools.LoggingToolFactory
-
Back-up logging tool.
- stereo - Variable in class org.openscience.cdk.Bond
-
A descriptor the stereochemical orientation of this bond.
- stereo - Variable in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
A descriptor the stereochemical orientation of this query bond.
- stereo - Variable in class org.openscience.cdk.silent.Bond
-
A descriptor the stereochemical orientation of this bond.
- STEREO_ATOM_PARITY_MINUS - Static variable in class org.openscience.cdk.CDKConstants
-
A negative atom parity.
- STEREO_ATOM_PARITY_PLUS - Static variable in class org.openscience.cdk.CDKConstants
-
A positive atom parity.
- STEREO_ATOM_PARITY_UNDEFINED - Static variable in class org.openscience.cdk.CDKConstants
-
A undefined atom parity.
- StereoBond - Class in org.openscience.cdk.isomorphism.matchers.smarts
-
This query bond indicates a particular geometric stereo configuration.
- StereoBond(IChemObjectBuilder, StereoBond.Direction, boolean) - Constructor for class org.openscience.cdk.isomorphism.matchers.smarts.StereoBond
-
- StereoBond.Direction - Enum in org.openscience.cdk.isomorphism.matchers.smarts
-
- Stereocenters - Class in org.openscience.cdk.stereo
-
Find atoms which can support stereo chemistry based on the connectivity.
- Stereocenters.Stereocenter - Enum in org.openscience.cdk.stereo
-
Defines the type of a stereocenter.
- Stereocenters.Type - Enum in org.openscience.cdk.stereo
-
- stereocenterType(int) - Method in class org.openscience.cdk.stereo.Stereocenters
-
Determine the type of stereocenter is the atom at index v
.
- stereochemistry() - Method in class org.openscience.cdk.isomorphism.Mappings
-
Filter the mappings for those which preserve stereochemistry specified in
the query.
- StereoElementFactory - Class in org.openscience.cdk.stereo
-
Create stereo elements for a structure with 2D and 3D coordinates.
- StereoElementFactory(IAtomContainer, int[][], GraphUtil.EdgeToBondMap) - Constructor for class org.openscience.cdk.stereo.StereoElementFactory
-
Internal constructor.
- stereoElements - Variable in class org.openscience.cdk.AtomContainer
-
Internal list of atom parities.
- stereoElements() - Method in class org.openscience.cdk.AtomContainer
-
Returns the stereo elements defined for this atom container.
- stereoElements() - Method in class org.openscience.cdk.debug.DebugAminoAcid
-
Returns the stereo elements defined for this atom container.
- stereoElements() - Method in class org.openscience.cdk.debug.DebugAtomContainer
-
Returns the stereo elements defined for this atom container.
- stereoElements() - Method in class org.openscience.cdk.debug.DebugBioPolymer
-
Returns the stereo elements defined for this atom container.
- stereoElements() - Method in class org.openscience.cdk.debug.DebugCrystal
-
Returns the stereo elements defined for this atom container.
- stereoElements() - Method in class org.openscience.cdk.debug.DebugMonomer
-
Returns the stereo elements defined for this atom container.
- stereoElements() - Method in class org.openscience.cdk.debug.DebugPolymer
-
Returns the stereo elements defined for this atom container.
- stereoElements() - Method in class org.openscience.cdk.debug.DebugRing
-
Returns the stereo elements defined for this atom container.
- stereoElements() - Method in class org.openscience.cdk.debug.DebugStrand
-
Returns the stereo elements defined for this atom container.
- stereoElements() - Method in interface org.openscience.cdk.interfaces.IAtomContainer
-
Returns the stereo elements defined for this atom container.
- stereoElements - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Internal list of atom parities.
- stereoElements() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the stereo elements defined for this atom container.
- stereoElements - Variable in class org.openscience.cdk.silent.AtomContainer
-
Internal list of atom parities.
- stereoElements() - Method in class org.openscience.cdk.silent.AtomContainer
-
Returns the stereo elements defined for this atom container.
- StereoEncoder - Interface in org.openscience.cdk.hash.stereo
-
An encoder for stereo chemistry.
- StereoEncoderFactory - Interface in org.openscience.cdk.hash.stereo
-
Describes a factory for stereo elements.
- stereoGiven - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- stereoParity - Variable in class org.openscience.cdk.Atom
-
A stereo parity descriptor for the stereochemistry of this atom.
- stereoParity - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
A stereo parity descriptor for the stereochemistry of this atom.
- stereoParity - Variable in class org.openscience.cdk.silent.Atom
-
A stereo parity descriptor for the stereochemistry of this atom.
- stereosAreOpposite(IAtomContainer, IAtom) - Static method in class org.openscience.cdk.geometry.BondTools
-
Says if of four atoms connected two one atom the up and down bonds are
opposite or not, i.
- StereoTool - Class in org.openscience.cdk.stereo
-
Methods to determine or check the stereo class of a set of atoms.
- StereoTool() - Constructor for class org.openscience.cdk.stereo.StereoTool
-
- StereoTool.SquarePlanarShape - Enum in org.openscience.cdk.stereo
-
The shape that four atoms take in a plane.
- StereoTool.StereoClass - Enum in org.openscience.cdk.stereo
-
Currently unused, but intended for the StereoTool to indicate what it
'means' by an assignment of some atoms to a class.
- StereoTool.TetrahedralSign - Enum in org.openscience.cdk.stereo
-
The handedness of a tetrahedron, in terms of the point-plane distance
of three of the corners, compared to the fourth.
- storeAtomData() - Method in class org.openscience.cdk.io.cml.CMLCoreModule
-
- storeAtomData() - Method in class org.openscience.cdk.io.cml.PDBConvention
-
- storeBondData() - Method in class org.openscience.cdk.io.cml.CMLCoreModule
-
- storeData() - Method in class org.openscience.cdk.io.cml.CMLCoreModule
-
- storeData() - Method in class org.openscience.cdk.io.cml.PDBConvention
-
- Strand - Class in org.openscience.cdk.silent
-
A Strand is an AtomContainer which stores additional strand specific
informations for a group of Atoms.
- Strand() - Constructor for class org.openscience.cdk.silent.Strand
-
Constructs a new Strand.
- Strand - Class in org.openscience.cdk
-
A Strand is an AtomContainer which stores additional strand specific
informations for a group of Atoms.
- Strand() - Constructor for class org.openscience.cdk.Strand
-
Constructs a new Strand.
- StringDifference - Class in org.openscience.cdk.tools.diff.tree
-
- StringIOSetting - Class in org.openscience.cdk.io.setting
-
An class for a reader setting which must be of type String.
- StringIOSetting(String, IOSetting.Importance, String, String) - Constructor for class org.openscience.cdk.io.setting.StringIOSetting
-
- stroke - Variable in class org.openscience.cdk.renderer.elements.GeneralPath
-
The width of the stroke.
- STRONTIUM - Static variable in enum org.openscience.cdk.config.Elements
-
- STRONTIUM - Static variable in interface org.openscience.cdk.iupac.parser.NomParserConstants
-
RegularExpression Id.
- structgenATF - Variable in class org.openscience.cdk.tools.SmilesValencyChecker
-
- StructGenAtomTypeGuesser - Class in org.openscience.cdk.atomtype
-
AtomTypeMatcher that finds an AtomType by matching the Atom's element symbol.
- StructGenAtomTypeGuesser() - Constructor for class org.openscience.cdk.atomtype.StructGenAtomTypeGuesser
-
Constructor for the StructGenMatcher object.
- StructGenMatcher - Class in org.openscience.cdk.atomtype
-
AtomTypeMatcher that finds an AtomType by matching the Atom's element symbol.
- StructGenMatcher() - Constructor for class org.openscience.cdk.atomtype.StructGenMatcher
-
Constructor for the StructGenMatcher object.
- StructureDiagramGenerator - Class in org.openscience.cdk.layout
-
Generates 2D coordinates for a molecule for which only connectivity is known
or the coordinates have been discarded for some reason.
- StructureDiagramGenerator() - Constructor for class org.openscience.cdk.layout.StructureDiagramGenerator
-
The empty constructor.
- StructureDiagramGenerator(IAtomContainer) - Constructor for class org.openscience.cdk.layout.StructureDiagramGenerator
-
Creates an instance of this class while assigning a molecule to be layed
out.
- StructureResonanceGenerator - Class in org.openscience.cdk.tools
-
This class try to generate resonance structure for a determinate molecule.
- StructureResonanceGenerator() - Constructor for class org.openscience.cdk.tools.StructureResonanceGenerator
-
Construct an instance of StructureResonanceGenerator.
- StructureResonanceGenerator(boolean) - Constructor for class org.openscience.cdk.tools.StructureResonanceGenerator
-
Construct an instance of StructureResonanceGenerator.
- sub(Complex) - Method in class org.openscience.cdk.math.Complex
-
Subtracs a complex value
- sub(IMatrix) - Method in class org.openscience.cdk.math.IMatrix
-
Subtraktion from two matrices
- sub(IMatrix, IMatrix) - Method in class org.openscience.cdk.math.IMatrix
-
Subtraktion from two matrices
- sub(IVector) - Method in class org.openscience.cdk.math.IVector
-
Subtraction from two vectors
- sub(IVector, IVector) - Method in class org.openscience.cdk.math.IVector
-
Subtraction from two vectors
- sub(Matrix) - Method in class org.openscience.cdk.math.Matrix
-
Subtracts from two matrices.
- sub(Quaternion) - Method in class org.openscience.cdk.math.Quaternion
-
- sub(Vector) - Method in class org.openscience.cdk.math.Vector
-
Subtraktion from two vectors
- subChain() - Method in class org.openscience.cdk.iupac.parser.NomParser
-
Deprecated.
The substituent part of the prefix
- subgraph(int[][], int[]) - Static method in class org.openscience.cdk.graph.GraphUtil
-
Create a subgraph by specifying the vertices from the original graph to include in the subgraph.
- subGraph - Variable in class org.openscience.cdk.structgen.stochastic.operator.ChemGraph
-
- subList(int, int) - Method in class org.openscience.cdk.ConformerContainer
-
- subscript - Variable in class org.openscience.cdk.renderer.elements.TextGroupElement.Child
-
A subscript (if any) for the child.
- Substance - Class in org.openscience.cdk.silent
-
- Substance() - Constructor for class org.openscience.cdk.silent.Substance
-
- Substance - Class in org.openscience.cdk
-
- Substance() - Constructor for class org.openscience.cdk.Substance
-
- SubstructureFingerprinter - Class in org.openscience.cdk.fingerprint
-
IFingerprinter
that gives a bit set which has a size equal to the number
of substructures it was constructed from.
- SubstructureFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.SubstructureFingerprinter
-
- SubstructureFingerprinter(String[]) - Constructor for class org.openscience.cdk.fingerprint.SubstructureFingerprinter
-
Set up the fingerprinter to use a user-defined set of fragments.
- suggest(Class<?>) - Method in class org.openscience.cdk.DynamicFactory
-
Provides a list of all possible constructor keys for the provided
interface.
- SULFUR - Static variable in enum org.openscience.cdk.config.Elements
-
- suppressHydrogens() - Method in class org.openscience.cdk.hash.HashGeneratorMaker
-
Suppress any explicit hydrogens in the encoding of hash values.
- suppressHydrogens(IAtomContainer) - Static method in class org.openscience.cdk.tools.manipulator.AtomContainerManipulator
-
Suppress any explicit hydrogens in the provided container.
- SVGFormat - Class in org.openscience.cdk.io.formats
-
- SVGFormat() - Constructor for class org.openscience.cdk.io.formats.SVGFormat
-
- SwingEventRelay - Class in org.openscience.cdk.controller
-
- SwingEventRelay(JComponent) - Constructor for class org.openscience.cdk.controller.SwingEventRelay
-
- SwingGUIListener - Class in org.openscience.cdk.io.listener
-
Allows processing of IOSetting quesions which are passed to the user
by using Swing dialogs.
- SwingGUIListener(Component, IOSetting.Importance) - Constructor for class org.openscience.cdk.io.listener.SwingGUIListener
-
0 = ask no questions
3 = ask all questions
- SwingMouseEventRelay - Class in org.openscience.cdk.controller
-
- SwingMouseEventRelay(IMouseEventRelay) - Constructor for class org.openscience.cdk.controller.SwingMouseEventRelay
-
- SwissArmyKnife - Class in org.openscience.cdk.tools
-
Deprecated.
- SwissArmyKnife() - Constructor for class org.openscience.cdk.tools.SwissArmyKnife
-
Deprecated.
- SwitchTo(int) - Method in class org.openscience.cdk.iupac.parser.NomParserTokenManager
-
Switch to specified lex state.
- SwitchTo(int) - Method in class org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager
-
Switch to specified lex state.
- SybylAtomTypeMatcher - Class in org.openscience.cdk.atomtype
-
Atom Type matcher for Sybyl atom types.
- SybylDescriptorFormat - Class in org.openscience.cdk.io.formats
-
- SybylDescriptorFormat() - Constructor for class org.openscience.cdk.io.formats.SybylDescriptorFormat
-
- symbol() - Method in enum org.openscience.cdk.config.Elements
-
The element symbol, C for carbon, N for nitrogen, Na for sodium, etc.
- symbol - Variable in class org.openscience.cdk.Element
-
The element symbol for this element as listed in the periodic table.
- symbol - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
The element symbol for this element as listed in the periodic table.
- SYMBOL - Static variable in class org.openscience.cdk.libio.jena.CDK
-
- symbol - Variable in class org.openscience.cdk.silent.Element
-
The element symbol for this element as listed in the periodic table.
- SymbolAndChargeQueryAtom - Class in org.openscience.cdk.isomorphism.matchers
-
- SymbolAndChargeQueryAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolAndChargeQueryAtom
-
- SymbolAndChargeQueryAtom(IAtom) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolAndChargeQueryAtom
-
- SymbolChargeIDQueryAtom - Class in org.openscience.cdk.isomorphism.matchers
-
- SymbolChargeIDQueryAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolChargeIDQueryAtom
-
- SymbolChargeIDQueryAtom(IAtom) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolChargeIDQueryAtom
-
- SymbolQueryAtom - Class in org.openscience.cdk.isomorphism.matchers
-
- SymbolQueryAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom
-
- SymbolQueryAtom(IAtom) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom
-
- SymbolSetQueryAtom - Class in org.openscience.cdk.isomorphism.matchers
-
A QueryAtom that matches all symbols in this container.
- SymbolSetQueryAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom
-
Constructor for the SymbolSetQueryAtom object
- SymbolVisibility - Class in org.openscience.cdk.renderer
-
Predicate that defines whether an atom symbol is displayed in a structure diagram.
- SymbolVisibility() - Constructor for class org.openscience.cdk.renderer.SymbolVisibility
-
- symmetry(IAtomContainer, int[][]) - Static method in class org.openscience.cdk.graph.invariant.Canon
-
Compute the symmetry classes for the provided structure.
- SYSTEMID - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
-
- SystemOutLoggingTool - Class in org.openscience.cdk.tools
-
- SystemOutLoggingTool(Class<?>) - Constructor for class org.openscience.cdk.tools.SystemOutLoggingTool
-
Constructs a ILoggingTool which produces log lines indicating them to be
for the given Class.