Cdk Keyword List

Keyword List The keyword list is an overview of CDK functionality organized by keyword. For each keyword a reference is made to the CDK class that implements that functionality. To simplify the list, the common prefix org.openscience.cdk has been removed. For example, the class org.openscience.cdk.layout.StructureDiagramGenerator has to do with 2D coordinates. 2D layout.StructureDiagramGenerator 2D coordinates layout.StructureDiagramGenerator 2D-coordinates layout.TemplateHandler layout.OverlapResolver 3D modeling.builder3d.ModelBuilder3D similarity.DistanceMoment 3D coordinates modeling.builder3d.ModelBuilder3D 3D isomorphism pharmacophore.PharmacophoreQueryAtom pharmacophore.PharmacophoreBond pharmacophore.PharmacophoreUtils pharmacophore.PharmacophoreMatcher pharmacophore.PharmacophoreAtom pharmacophore.PharmacophoreAngleBond pharmacophore.PharmacophoreQueryAngleBond pharmacophore.PharmacophoreQueryBond 3D model geometry.AtomTools.add3DCoordinates1() modeling.builder3d.AtomTetrahedralLigandPlacer3D.add3DCoordinatesForSinglyBondedLigands() 3D-coordinates modeling.forcefield.GeometricMinimizer adding tools.CDKHydrogenAdder.addImplicitHydrogens() tools.manipulator.AtomContainerManipulator.convertImplicitToExplicitHydrogens() adjacency matrix graph.matrix.AdjacencyMatrix amino acid AminoAcid interfaces.IAminoAcid amino acids stuctures templates.AminoAcids animation

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2 ChemSequence interfaces.IChemSequence aromatic ring bond order adjustment tools.DeAromatizationTool aromaticity detector aromaticity.AromaticityCalculator ASN io.iterator.IteratingPCSubstancesXMLReader io.iterator.IteratingPCCompoundASNReader io.iterator.IteratingPCCompoundXMLReader association Association atom Atom Bond interfaces.IAtom interfaces.IBond type AtomType config.TXTBasedAtomTypeConfigurator config.AtomTypeFactory interfaces.IAtomType valency tools.LonePairElectronChecker tools.SaturationChecker tools.SmilesValencyChecker chemical validation validate.ValidationTest atom coloring partial charges renderer.color.PartialAtomicChargeColors CPK renderer.color.CPKAtomColors atom mapping Mapping atom parity AtomParity interfaces.IAtomParity atom type E-state atomtype.EStateAtomTypeMatcher mmff94 modeling.builder3d.MMFF94BasedParameterSetReader MM2 modeling.builder3d.MM2BasedParameterSetReader atom types Sybyl atomtype.SybylAtomTypeMatcher atomic interfaces.IElement qsar.descriptors.molecular.APolDescriptor atomic number interfaces.IElement AtomPlacer3D modeling.builder3d.AtomPlacer3D BCUT qsar.descriptors.molecular.BCUTDescriptor Binary Space Partitioning Tree graph.rebond.Bspt biopolymer BioPolymer

KEYWORD LIST

3 interfaces.IBioPolymer interfaces.IPDBPolymer bond ElectronContainer Association Bond LonePair interfaces.ILonePair interfaces.IBond recalculation graph.rebond.RebondTool bond count rotatable qsar.descriptors.molecular.RotatableBondsCountDescriptor bond creation geometry.BondTools.closeEnoughToBond() bond order CDKConstants smiles.DeduceBondSystemTool calculation tools.SaturationChecker.newSaturate() tools.SmilesValencyChecker.saturate() bond order adjustment tools.DeAromatizationTool calculation tools.SaturationChecker.newSaturate() tools.SmilesValencyChecker.saturate() canonicalization graph.invariant.CanonicalLabeler CAS number index.CASNumber index.CASNumber.isValid() CDK source code io.CDKSourceCodeWriter center of mass geometry.GeometryTools.get2DCentreOfMass() geometry.GeometryTools.get3DCentreOfMass() charge distribution charges.InductivePartialCharges charges.GasteigerMarsiliPartialCharges charges.GasteigerPEPEPartialCharges chemical identifier io.INChIPlainTextReader io.INChIReader chemical validation validate.ValidationTest chi chain index qsar.descriptors.molecular.ChiChainDescriptor chi cluster index qsar.descriptors.molecular.ChiClusterDescriptor chi path cluster index qsar.descriptors.molecular.ChiPathClusterDescriptor chi path index qsar.descriptors.molecular.ChiPathDescriptor CIF io.CIFReader class convertor libio.cml.Convertor classification qsar.model.R.CNNClassificationModel CML

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KEYWORD LIST

io.CMLWriter io.CMLReader io.iterator.event.EventCMLReader libio.cml.Convertor conformer conformation io.iterator.IteratingMDLConformerReader connection matrix graph.matrix.ConnectionMatrix connectivity graph.ConnectivityChecker coordinate calculation geometry.AtomTools.add3DCoordinates1() modeling.builder3d.AtomTetrahedralLigandPlacer3D.add3DCoordinatesForSinglyBondedLigands() coordinate generation geometry.AtomTools.calculate3DCoordinatesForLigands() modeling.builder3d.AtomTetrahedralLigandPlacer3D.get3DCoordinatesForLigands() 3D modeling.builder3d.ModelBuilder3D CPK renderer.color.CPKAtomColors creation tools.IDCreator crystal Crystal geometry.CrystalGeometryTools interfaces.ICrystal DBE tools.manipulator.MolecularFormulaManipulator.getDBE() descriptor qsar.descriptors.molecular.RuleOfFiveDescriptor qsar.descriptors.molecular.BCUTDescriptor qsar.descriptors.molecular.WHIMDescriptor qsar.descriptors.molecular.ChiChainDescriptor qsar.descriptors.molecular.GravitationalIndexDescriptor qsar.descriptors.molecular.XLogPDescriptor qsar.descriptors.molecular.KappaShapeIndicesDescriptor qsar.descriptors.molecular.RotatableBondsCountDescriptor qsar.descriptors.molecular.ChiPathDescriptor qsar.descriptors.molecular.ChiPathClusterDescriptor qsar.descriptors.molecular.ChiClusterDescriptor qsar.descriptors.molecular.ZagrebIndexDescriptor qsar.descriptors.molecular.CarbonTypesDescriptor qsar.descriptors.molecular.TPSADescriptor diagonalization math.Matrix.diagonalize() dictionary dict.OWLFile dict.Dictionary dict.DictionaryDatabase dict.Entry dict.OWLReact dict.EntryReact implicit CDK references dict.CDKDictionaryReferences double bond equivalent tools.manipulator.MolecularFormulaManipulator.getDBE() E-state atomtype.EStateAtomTypeMatcher

5 EAID number graph.invariant.HuLuIndexTool.getEAIDNumber() electron Bond interfaces.IElectronContainer interfaces.IBond unpaired SingleElectron interfaces.ISingleElectron electronegativities partial equalization of orbital charges.GasteigerMarsiliPartialCharges charges.GasteigerPEPEPartialCharges electronegativity charges.InductivePartialCharges charges.PiElectronegativity charges.Electronegativity tools.PeriodicTable element PeriodicTableElement Element config.IsotopeFactory interfaces.IElement tools.PeriodicTable sorting tools.ElementComparator estate config.fragments.EStateFragments fingerprint.EStateFingerprinter file format io.SMILESWriter io.GamessReader INChI io.INChIPlainTextReader io.INChIReader XYZ io.XYZReader Polymorph Predictor (tm) io.PMPReader CML io.CMLWriter io.CMLReader io.iterator.event.EventCMLReader Mol2 io.Mol2Reader Z-matrix io.ZMatrixReader ShelX io.ShelXWriter HIN io.HINReader MDL SD file io.SDFWriter ShelXL io.ShelXReader PDB io.PDBReader PubChem Compound ASN

6 io.PCSubstanceXMLReader io.PCCompoundASNReader CIF io.CIFReader mmCIF io.CIFReader MDL RXN io.MDLRXNReader io.MDLRXNV2000Reader CDK source code io.CDKSourceCodeWriter MDL RXN file io.MDLRXNWriter MDL molfile io.MDLWriter io.MDLV2000Reader io.MDLReader io.iterator.IteratingMDLReader PubChem Compound XML io.PCCompoundXMLReader SDF io.MDLV2000Reader io.MDLReader io.iterator.IteratingMDLReader SMILES io.SMILESReader io.iterator.IteratingSMILESReader ASN io.iterator.IteratingPCSubstancesXMLReader io.iterator.IteratingPCCompoundASNReader io.iterator.IteratingPCCompoundXMLReader file format SDF io.iterator.IteratingMDLConformerReader fingerprint fingerprint.FingerprinterTool fingerprint.MACCSFingerprinter fingerprint.Fingerprinter fingerprint.IFingerprinter fingerprint.SubstructureFingerprinter fingerprint.EStateFingerprinter fingerprint.ExtendedFingerprinter fingerprint.GraphOnlyFingerprinter force field modeling.forcefield.MMFF94EnergyFunction fractional coordinates crystal geometry.CrystalGeometryTools fragment config.fragments.EStateFragments Gamess io.GamessReader Gauss elimination math.Matrix.elimination() Gaussian (tm) input file io.program.GaussianInputWriter Gaussian basis set math.qm.GaussiansBasis generator smiles.SmilesGenerator geometry modeling.forcefield.GeometricMinimizer

KEYWORD LIST

7 Gram-Schmidt algorithm math.Matrix.orthonormalize() graph path ringsearch.Path graph matrix molecular graph.matrix.IGraphMatrix gravitational index qsar.descriptors.molecular.GravitationalIndexDescriptor HIN io.HINReader HOSE code tools.BremserOneSphereHOSECodePredictor spherical atom search tools.HOSECodeGenerator hydrogen removal tools.manipulator.AtomContainerManipulator.removeHydrogens() tools.manipulator.AtomContainerManipulator.removeHydrogensPreserveMultiplyBonded() tools.manipulator.AtomContainerManipulator.getHeavyAtoms() tools.manipulator.MolecularFormulaManipulator.getHeavyElements() hydrogens adding tools.CDKHydrogenAdder.addImplicitHydrogens() tools.manipulator.AtomContainerManipulator.convertImplicitToExplicitHydrogens() id creation tools.IDCreator implicit CDK references dict.CDKDictionaryReferences INChI io.INChIPlainTextReader io.INChIReader input file io.program.GaussianInputWriter ionization potential qsar.descriptors.molecular.IPMolecularLearningDescriptor isomorphism isomorphism.IsomorphismTester isotope Isotope config.IsotopeFactory interfaces.IIsotope isotope pattern formula.IsotopePatternGenerator IUPAC name iupac.parser.NomParser jaccard similarity.Tanimoto Jacobi algorithm math.Matrix.diagonalize() join-the-dots geometry.BondTools.closeEnoughToBond() graph.rebond.Bspt JRI qsar.model.R2.RModel Kappe shape index qsar.descriptors.molecular.KappaShapeIndicesDescriptor Layout layout.StructureDiagramGenerator layout.TemplateHandler layout.OverlapResolver line search modeling.forcefield.LineSearch linear qsar.model.R.LinearRegressionModel

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KEYWORD LIST

linear regression qsar.model.R2.LinearRegressionModel Lipinski qsar.descriptors.molecular.RuleOfFiveDescriptor lipophilicity qsar.descriptors.molecular.ALOGPDescriptor log file io.GamessReader logP qsar.descriptors.molecular.ALOGPDescriptor lone-pair ElectronContainer LonePair interfaces.ILonePair mass interfaces.IIsotope molecular tools.manipulator.AtomContainerManipulator.getNaturalExactMass() mass number interfaces.IIsotope MDL molfile io.MDLWriter io.MDLV2000Reader io.MDLReader io.iterator.IteratingMDLReader MDL molfile V3000 io.MDLV3000Reader MDL RXN io.MDLRXNReader io.MDLRXNV2000Reader MDL RXN file io.MDLRXNWriter MDL SD file io.SDFWriter MDL V3000 io.MDLRXNV3000Reader MM2 modeling.builder3d.MM2BasedParameterSetReader mmCIF io.CIFReader mmff94 modeling.builder3d.MMFF94BasedParameterSetReader modeling.forcefield.MMFF94EnergyFunction Mol2 io.Mol2Reader molecular graph.matrix.IGraphMatrix tools.manipulator.AtomContainerManipulator.getNaturalExactMass() molecular formula formula.MolecularFormula formula.AdductFormula formula.MolecularFormulaChecker formula.MolecularFormulaRange formula.MolecularFormulaSet interfaces.IMolecularFormulaSet interfaces.IAdductFormula interfaces.IMolecularFormula molecule Molecule MoleculeSet molecular formula formula.MolecularFormulaChecker moment of inertia qsar.descriptors.molecular.MomentOfInertiaDescriptor

9 monomer Monomer interfaces.IMonomer Morgan number graph.invariant.MorganNumbersTools Murcko fragments tools.GenerateFragments neural network qsar.model.R.CNNClassificationModel qsar.model.R.CNNRegressionModel qsar.model.R2.CNNRegressionModel Newton-Raphson modeling.forcefield.NewtonRaphsonMethod notional coordinates geometry.CrystalGeometryTools.notionalToCartesian() number qsar.descriptors.molecular.PetitjeanNumberDescriptor mass interfaces.IIsotope atomic interfaces.IElement orbital ElectronContainer Association LonePair interfaces.ILonePair orthonormalization math.Matrix.orthonormalize() output io.GamessReader parser smiles.SmilesParser partial atomic charges charges.InductivePartialCharges charges.GasteigerMarsiliPartialCharges charges.GasteigerPEPEPartialCharges partial charges renderer.color.PartialAtomicChargeColors partial equalization of orbital charges.GasteigerMarsiliPartialCharges charges.GasteigerPEPEPartialCharges partial least squares qsar.model.R.PLSRegressionModel path ringsearch.Path PDB io.PDBReader pdbpolymer interfaces.IPDBMonomer interfaces.IPDBAtom interfaces.IPDBStructure interfaces.IPDBPolymer PEOE charges.GasteigerMarsiliPartialCharges PEPE charges.GasteigerPEPEPartialCharges periodic table tools.PeriodicTable permutation graph.AtomContainerPermutor graph.AtomContainerBondPermutor graph.AtomContainerAtomPermutor Petit-Jean shape index qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor

10 number qsar.descriptors.molecular.PetitjeanNumberDescriptor pharmacophore pharmacophore.PharmacophoreQueryAtom pharmacophore.PharmacophoreBond pharmacophore.PharmacophoreUtils pharmacophore.PharmacophoreMatcher pharmacophore.PharmacophoreAtom pharmacophore.PharmacophoreAngleBond pharmacophore.PharmacophoreQueryAngleBond pharmacophore.PharmacophoreQueryBond physical properties PhysicalConstants PLS qsar.model.R.PLSRegressionModel pocket protein.ProteinPocketFinder polarizability charges.Polarizability atomic qsar.descriptors.molecular.APolDescriptor polymer BioPolymer Polymer interfaces.IBioPolymer interfaces.IPolymer interfaces.IPDBPolymer protein.data.PDBStrand protein.data.PDBPolymer Polymorph Predictor (tm) io.PMPReader prime numbers math.Primes projection in 2D geometry.Projector protein protein.ProteinPocketFinder PubChem io.iterator.IteratingPCSubstancesXMLReader io.iterator.IteratingPCCompoundASNReader io.iterator.IteratingPCCompoundXMLReader PubChem Compound ASN io.PCSubstanceXMLReader io.PCCompoundASNReader PubChem Compound XML io.PCCompoundXMLReader R qsar.model.R2.CNNRegressionModel qsar.model.R2.RModel qsar.model.R2.LinearRegressionModel radial distribution function geometry.RDFCalculator radical SingleElectron interfaces.ISingleElectron radius vanderwaals tools.PeriodicTable RDF geometry.RDFCalculator reaction

KEYWORD LIST

11 ReactionSet ChemSequence Reaction ReactionScheme MoleculeSet interfaces.IReaction interfaces.IChemSequence interfaces.IReactionSet atom mapping Mapping rebonding graph.rebond.RebondTool graph.rebond.Bspt recalculation graph.rebond.RebondTool refractivity qsar.descriptors.molecular.ALOGPDescriptor regression qsar.model.R.CNNRegressionModel qsar.model.R.PLSRegressionModel linear qsar.model.R.LinearRegressionModel removal tools.manipulator.AtomContainerManipulator.removeHydrogens() tools.manipulator.AtomContainerManipulator.removeHydrogensPreserveMultiplyBonded() tools.manipulator.AtomContainerManipulator.getHeavyAtoms() tools.manipulator.MolecularFormulaManipulator.getHeavyElements() ring Ring interfaces.IRing set of RingSet interfaces.IRingSet ring finding graph.SpanningTree ring search ringsearch.FiguerasSSSRFinder ringsearch.SSSRFinder ringsearch.cyclebasis.SimpleCycle rotatable qsar.descriptors.molecular.RotatableBondsCountDescriptor RSS io.RssWriter rule-of-five qsar.descriptors.molecular.RuleOfFiveDescriptor saturation tools.LonePairElectronChecker tools.SaturationChecker SDF io.MDLV2000Reader io.MDLReader io.iterator.IteratingMDLReader set of RingSet interfaces.IRingSet

12 shape index qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor ShelX io.ShelXWriter ShelXL io.ShelXReader similarity fingerprint.MACCSFingerprinter fingerprint.Fingerprinter fingerprint.SubstructureFingerprinter fingerprint.EStateFingerprinter fingerprint.ExtendedFingerprinter fingerprint.GraphOnlyFingerprinter 3D similarity.DistanceMoment tanimoto similarity.Tanimoto smallest-set-of-rings ringsearch.FiguerasSSSRFinder ringsearch.SSSRFinder ringsearch.cyclebasis.SimpleCycle SMARTS isomorphism.matchers.smarts.RingMembershipAtom isomorphism.matchers.smarts.HybridizationNumberAtom isomorphism.matchers.smarts.AromaticOrSingleQueryBond isomorphism.matchers.smarts.TotalValencyAtom isomorphism.matchers.smarts.ChiralityAtom isomorphism.matchers.smarts.SMARTSBond isomorphism.matchers.smarts.AnyAtom isomorphism.matchers.smarts.ExplicitConnectionAtom isomorphism.matchers.smarts.AromaticAtom isomorphism.matchers.smarts.AtomicNumberAtom isomorphism.matchers.smarts.AnyOrderQueryBond isomorphism.matchers.smarts.OrderQueryBond isomorphism.matchers.smarts.RingIdentifierAtom isomorphism.matchers.smarts.RingBond isomorphism.matchers.smarts.TotalConnectionAtom isomorphism.matchers.smarts.FormalChargeAtom isomorphism.matchers.smarts.DegreeAtom isomorphism.matchers.smarts.RecursiveSmartsAtom isomorphism.matchers.smarts.AliphaticAtom isomorphism.matchers.smarts.AromaticQueryBond isomorphism.matchers.smarts.PeriodicGroupNumberAtom isomorphism.matchers.smarts.NonCHHeavyAtom isomorphism.matchers.smarts.TotalRingConnectionAtom isomorphism.matchers.smarts.TotalHCountAtom isomorphism.matchers.smarts.LogicalOperatorAtom isomorphism.matchers.smarts.AromaticSymbolAtom isomorphism.matchers.smarts.SmallestRingAtom isomorphism.matchers.smarts.MassAtom isomorphism.matchers.smarts.LogicalOperatorBond isomorphism.matchers.smarts.AliphaticSymbolAtom

KEYWORD LIST

13 isomorphism.matchers.smarts.ImplicitHCountAtom isomorphism.matchers.smarts.HydrogenAtom isomorphism.matchers.smarts.SMARTSAtom isomorphism.matchers.smarts.ConnectionCountAtom isomorphism.matchers.smarts.StereoBond isomorphism.matchers.smarts.RingAtom smiles.smarts.SMARTSQueryTool smiles.smarts.parser.SMARTSParser smiles.smarts.parser.ASTOrExpression smiles.smarts.parser.ASTElement smiles.smarts.parser.ASTChirality smiles.smarts.parser.ASTPrimitiveAtomExpression smiles.smarts.parser.ASTAtomicMass smiles.smarts.parser.ASTNotBond smiles.smarts.parser.ASTCharge smiles.smarts.parser.ASTLowAndBond smiles.smarts.parser.ASTAtom smiles.smarts.parser.ASTLowAndExpression SMARTS AST smiles.smarts.parser.ASTPeriodicGroupNumber smiles.smarts.parser.ASTExplicitHighAndExpression smiles.smarts.parser.ASTAtomicNumber smiles.smarts.parser.ASTStart smiles.smarts.parser.ASTOrBond smiles.smarts.parser.ASTSmarts smiles.smarts.parser.ASTImplicitHCount smiles.smarts.parser.SimpleNode smiles.smarts.parser.ASTAliphatic smiles.smarts.parser.ASTHybrdizationNumber smiles.smarts.parser.Node smiles.smarts.parser.ASTSmallestRingSize smiles.smarts.parser.ASTRingIdentifier smiles.smarts.parser.ASTExplicitAtom smiles.smarts.parser.ASTRingConnectivity smiles.smarts.parser.ASTAromatic smiles.smarts.parser.ASTReaction smiles.smarts.parser.ASTTotalHCount smiles.smarts.parser.ASTExplicitConnectivity smiles.smarts.parser.ASTTotalConnectivity smiles.smarts.parser.ASTSimpleBond smiles.smarts.parser.ASTValence smiles.smarts.parser.ASTImplicitHighAndExpression smiles.smarts.parser.ASTGroup smiles.smarts.parser.ASTImplicitHighAndBond smiles.smarts.parser.ASTRecursiveSmartsExpression smiles.smarts.parser.ASTNotExpression smiles.smarts.parser.ASTRingMembership

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KEYWORD LIST

smiles.smarts.parser.ASTAnyAtom smiles.smarts.parser.ASTNonCHHeavyAtom smiles.smarts.parser.ASTExplicitHighAndBond smiles.smarts.parser.visitor.Smarts2MQLVisitor smiles.smarts.parser.visitor.SmartsQueryVisitor smiles.smarts.parser.visitor.SmartsDumpVisitor SMILES io.SMILESReader io.iterator.IteratingSMILESReader generator smiles.SmilesGenerator parser smiles.SmilesParser sorting tools.ElementComparator spanning tree graph.SpanningTree spherical atom search tools.HOSECodeGenerator stabilization charge charges.StabilizationCharges stack io.cml.CMLStack steepest descent modeling.forcefield.SteepestDescentsMethod stereochemistry CDKConstants AtomParity interfaces.IAtomParity structure diagram generation layout.TemplateHandler Structure Diagram Generation (SDG) layout.StructureDiagramGenerator structure generator structgen.RandomGenerator structgen.VicinitySampler stuctures templates.AminoAcids substructure search fingerprint.FingerprinterTool.isSubset() smiles.smarts.SMARTSQueryTool smiles.smarts.parser.SMARTSParser Sybyl atomtype.SybylAtomTypeMatcher tanimoto similarity.Tanimoto templates templates.AminoAcids templates.MoleculeFactory templates.saturatedhydrocarbons.IsoAlkanes topological bond order ctypes qsar.descriptors.molecular.CarbonTypesDescriptor total polar surface area qsar.descriptors.molecular.TPSADescriptor TPSA qsar.descriptors.molecular.TPSADescriptor type AtomType config.TXTBasedAtomTypeConfigurator config.AtomTypeFactory interfaces.IAtomType unpaired SingleElectron

15 interfaces.ISingleElectron valency tools.LonePairElectronChecker tools.SaturationChecker tools.SmilesValencyChecker validation index.CASNumber.isValid() vanderwaals tools.PeriodicTable WHIM qsar.descriptors.molecular.WHIMDescriptor Wiener number qsar.descriptors.molecular.WienerNumbersDescriptor XLogP qsar.descriptors.molecular.XLogPDescriptor XYZ io.XYZReader Z Matrix geometry.ZMatrixTools Z-matrix io.ZMatrixReader Zagreb index qsar.descriptors.molecular.ZagrebIndexDescriptor