cdk keyword list

Keyword List

The keyword list is an overview of CDK functionality organized by keyword. For each key-word a reference is made to the CDK class that implements that functionality. To simplifythe list, the common prefix org.openscience.cdk has been removed. For example, the classorg.openscience.cdk.layout.StructureDiagramGenerator has to do with 2D coordinates.

2D layout.StructureDiagramGenerator

2D coordinates layout.StructureDiagramGenerator

2D-coordinateslayout.TemplateHandler

layout.OverlapResolver

3Dmodeling.builder3d.ModelBuilder3D

similarity.DistanceMoment

3D coordinates modeling.builder3d.ModelBuilder3D

3D isomorphismpharmacophore.PharmacophoreQueryAtom

pharmacophore.PharmacophoreBond

pharmacophore.PharmacophoreUtils

pharmacophore.PharmacophoreMatcher

pharmacophore.PharmacophoreAtom

pharmacophore.PharmacophoreAngleBond

pharmacophore.PharmacophoreQueryAngleBond

pharmacophore.PharmacophoreQueryBond

3D modelgeometry.AtomTools.add3DCoordinates1()

modeling.builder3d.AtomTetrahedralLigandPlacer3D.add3DCoordinatesForSinglyBondedLigands()

3D-coordinates modeling.forcefield.GeometricMinimizer

addingtools.CDKHydrogenAdder.addImplicitHydrogens()

tools.manipulator.AtomContainerManipulator.convertImplicitToExplicitHydrogens()

adjacency matrix graph.matrix.AdjacencyMatrix

amino acidAminoAcid

interfaces.IAminoAcid

amino acidsstuctures templates.AminoAcids

animation

1

2 KEYWORD LIST

ChemSequence

interfaces.IChemSequence

aromatic ringbond order adjustment tools.DeAromatizationTool

aromaticity detector aromaticity.AromaticityCalculator

ASNio.iterator.IteratingPCSubstancesXMLReader

io.iterator.IteratingPCCompoundASNReader

io.iterator.IteratingPCCompoundXMLReader

association Association

atomAtom

Bond

interfaces.IAtom

interfaces.IBond

typeAtomType

config.TXTBasedAtomTypeConfigurator

config.AtomTypeFactory

interfaces.IAtomType

valencytools.LonePairElectronChecker

tools.SaturationChecker

tools.SmilesValencyChecker

chemical validation validate.ValidationTest

atom coloringpartial charges renderer.color.PartialAtomicChargeColors

CPK renderer.color.CPKAtomColors

atom mapping Mapping

atom parityAtomParity

interfaces.IAtomParity

atom typeE-state atomtype.EStateAtomTypeMatcher

mmff94 modeling.builder3d.MMFF94BasedParameterSetReader

MM2 modeling.builder3d.MM2BasedParameterSetReader

atom typesSybyl atomtype.SybylAtomTypeMatcher

atomicinterfaces.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

biopolymerBioPolymer

3

interfaces.IBioPolymer

interfaces.IPDBPolymer

bondElectronContainer

Association

Bond

LonePair

interfaces.ILonePair

interfaces.IBond

recalculation graph.rebond.RebondTool

bond countrotatable qsar.descriptors.molecular.RotatableBondsCountDescriptor

bond creation geometry.BondTools.closeEnoughToBond()

bond orderCDKConstants

smiles.DeduceBondSystemTool

calculationtools.SaturationChecker.newSaturate()

tools.SmilesValencyChecker.saturate()

bond order adjustment tools.DeAromatizationTool

calculationtools.SaturationChecker.newSaturate()

tools.SmilesValencyChecker.saturate()

canonicalization graph.invariant.CanonicalLabeler

CAS numberindex.CASNumber

index.CASNumber.isValid()

CDK source code io.CDKSourceCodeWriter

center of massgeometry.GeometryTools.get2DCentreOfMass()

geometry.GeometryTools.get3DCentreOfMass()

charge distributioncharges.InductivePartialCharges

charges.GasteigerMarsiliPartialCharges

charges.GasteigerPEPEPartialCharges

chemical identifierio.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

4 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 calculationgeometry.AtomTools.add3DCoordinates1()

modeling.builder3d.AtomTetrahedralLigandPlacer3D.add3DCoordinatesForSinglyBondedLigands()

coordinate generationgeometry.AtomTools.calculate3DCoordinatesForLigands()

modeling.builder3d.AtomTetrahedralLigandPlacer3D.get3DCoordinatesForLigands()

3D modeling.builder3d.ModelBuilder3D

CPK renderer.color.CPKAtomColors

creation tools.IDCreator

crystalCrystal

geometry.CrystalGeometryTools

interfaces.ICrystal

DBE tools.manipulator.MolecularFormulaManipulator.getDBE()

descriptorqsar.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()

dictionarydict.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()

electronBond

interfaces.IElectronContainer

interfaces.IBond

unpairedSingleElectron

interfaces.ISingleElectron

electronegativitiespartial equalization of orbital



electronegativitycharges.InductivePartialCharges

charges.PiElectronegativity

charges.Electronegativity

tools.PeriodicTable

elementPeriodicTableElement

Element

config.IsotopeFactory

interfaces.IElement

tools.PeriodicTable

sorting tools.ElementComparator

estateconfig.fragments.EStateFragments

fingerprint.EStateFingerprinter

file formatio.SMILESWriter

io.GamessReader

INChIio.INChIPlainTextReader

io.INChIReader

XYZ io.XYZReader

Polymorph Predictor (tm) io.PMPReader

CMLio.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 KEYWORD LIST

io.PCSubstanceXMLReader

io.PCCompoundASNReader

CIF io.CIFReader

mmCIF io.CIFReader

MDL RXNio.MDLRXNReader

io.MDLRXNV2000Reader

CDK source code io.CDKSourceCodeWriter

MDL RXN file io.MDLRXNWriter

MDL molfileio.MDLWriter

io.MDLV2000Reader

io.MDLReader

io.iterator.IteratingMDLReader

PubChem Compound XML io.PCCompoundXMLReader

SDFio.MDLV2000Reader

io.MDLReader


SMILESio.SMILESReader

io.iterator.IteratingSMILESReader

ASNio.iterator.IteratingPCSubstancesXMLReader



file format SDF io.iterator.IteratingMDLConformerReader

fingerprintfingerprint.FingerprinterTool

fingerprint.MACCSFingerprinter

fingerprint.Fingerprinter

fingerprint.IFingerprinter

fingerprint.SubstructureFingerprinter


fingerprint.ExtendedFingerprinter

fingerprint.GraphOnlyFingerprinter

force field modeling.forcefield.MMFF94EnergyFunction

fractional coordinatescrystal 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

7

Gram-Schmidt algorithm math.Matrix.orthonormalize()

graphpath ringsearch.Path

graph matrixmolecular graph.matrix.IGraphMatrix

gravitational index qsar.descriptors.molecular.GravitationalIndexDescriptor

HIN io.HINReader

HOSE code tools.BremserOneSphereHOSECodePredictor

spherical atom search tools.HOSECodeGenerator

hydrogenremoval

tools.manipulator.AtomContainerManipulator.removeHydrogens()

tools.manipulator.AtomContainerManipulator.removeHydrogensPreserveMultiplyBonded()

tools.manipulator.AtomContainerManipulator.getHeavyAtoms()

tools.manipulator.MolecularFormulaManipulator.getHeavyElements()

hydrogensadding

tools.CDKHydrogenAdder.addImplicitHydrogens()

tools.manipulator.AtomContainerManipulator.convertImplicitToExplicitHydrogens()

idcreation tools.IDCreator

implicit CDK references dict.CDKDictionaryReferences

INChIio.INChIPlainTextReader

io.INChIReader

input file io.program.GaussianInputWriter

ionization potential qsar.descriptors.molecular.IPMolecularLearningDescriptor

isomorphism isomorphism.IsomorphismTester

isotopeIsotope

config.IsotopeFactory

interfaces.IIsotope

isotope pattern formula.IsotopePatternGenerator

IUPAC name iupac.parser.NomParser

jaccard similarity.Tanimoto

Jacobi algorithm math.Matrix.diagonalize()

join-the-dotsgeometry.BondTools.closeEnoughToBond()

graph.rebond.Bspt

JRI qsar.model.R2.RModel

Kappe shape index qsar.descriptors.molecular.KappaShapeIndicesDescriptor

Layoutlayout.StructureDiagramGenerator

layout.TemplateHandler

layout.OverlapResolver

line search modeling.forcefield.LineSearch

linear qsar.model.R.LinearRegressionModel

8 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-pairElectronContainer

LonePair


mass interfaces.IIsotope

molecular tools.manipulator.AtomContainerManipulator.getNaturalExactMass()

mass number interfaces.IIsotope

MDL molfileio.MDLWriter

io.MDLV2000Reader

io.MDLReader


MDL molfile V3000 io.MDLV3000Reader

MDL RXNio.MDLRXNReader

io.MDLRXNV2000Reader

MDL RXN file io.MDLRXNWriter

MDL SD file io.SDFWriter

MDL V3000 io.MDLRXNV3000Reader

MM2 modeling.builder3d.MM2BasedParameterSetReader

mmCIF io.CIFReader

mmff94modeling.builder3d.MMFF94BasedParameterSetReader

modeling.forcefield.MMFF94EnergyFunction

Mol2 io.Mol2Reader

moleculargraph.matrix.IGraphMatrix

tools.manipulator.AtomContainerManipulator.getNaturalExactMass()

molecular formulaformula.MolecularFormula

formula.AdductFormula

formula.MolecularFormulaChecker

formula.MolecularFormulaRange

formula.MolecularFormulaSet

interfaces.IMolecularFormulaSet

interfaces.IAdductFormula

interfaces.IMolecularFormula

moleculeMolecule

MoleculeSet

molecular formula formula.MolecularFormulaChecker

moment of inertia qsar.descriptors.molecular.MomentOfInertiaDescriptor

9

monomerMonomer

interfaces.IMonomer

Morgan number graph.invariant.MorganNumbersTools

Murcko fragments tools.GenerateFragments

neural networkqsar.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

orbitalElectronContainer

Association

LonePair


orthonormalization math.Matrix.orthonormalize()

output io.GamessReader

parser smiles.SmilesParser

partial atomic chargescharges.InductivePartialCharges



partial charges renderer.color.PartialAtomicChargeColors

partial equalization of orbitalcharges.GasteigerMarsiliPartialCharges


partial least squares qsar.model.R.PLSRegressionModel

path ringsearch.Path

PDB io.PDBReader

pdbpolymerinterfaces.IPDBMonomer

interfaces.IPDBAtom

interfaces.IPDBStructure


PEOE charges.GasteigerMarsiliPartialCharges

PEPE charges.GasteigerPEPEPartialCharges

periodic table tools.PeriodicTable

permutationgraph.AtomContainerPermutor

graph.AtomContainerBondPermutor

graph.AtomContainerAtomPermutor

Petit-Jeanshape index qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor

10 KEYWORD LIST

number qsar.descriptors.molecular.PetitjeanNumberDescriptor

pharmacophorepharmacophore.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

polymerBioPolymer

Polymer

interfaces.IBioPolymer

interfaces.IPolymer


protein.data.PDBStrand

protein.data.PDBPolymer

Polymorph Predictor (tm) io.PMPReader

prime numbers math.Primes

projection in 2D geometry.Projector

protein protein.ProteinPocketFinder

PubChemio.iterator.IteratingPCSubstancesXMLReader



PubChem Compound ASNio.PCSubstanceXMLReader

io.PCCompoundASNReader

PubChem Compound XML io.PCCompoundXMLReader

Rqsar.model.R2.CNNRegressionModel

qsar.model.R2.RModel

qsar.model.R2.LinearRegressionModel

radial distribution function geometry.RDFCalculator

radicalSingleElectron


radiusvanderwaals tools.PeriodicTable

RDF geometry.RDFCalculator

reaction

11

ReactionSet

ChemSequence

Reaction

ReactionScheme

MoleculeSet

interfaces.IReaction

interfaces.IChemSequence

interfaces.IReactionSet

atom mapping Mapping

rebondinggraph.rebond.RebondTool

graph.rebond.Bspt

recalculation graph.rebond.RebondTool

refractivity qsar.descriptors.molecular.ALOGPDescriptor

regressionqsar.model.R.CNNRegressionModel

qsar.model.R.PLSRegressionModel

linear qsar.model.R.LinearRegressionModel

removaltools.manipulator.AtomContainerManipulator.removeHydrogens()

tools.manipulator.AtomContainerManipulator.removeHydrogensPreserveMultiplyBonded()

tools.manipulator.AtomContainerManipulator.getHeavyAtoms()

tools.manipulator.MolecularFormulaManipulator.getHeavyElements()

ringRing

interfaces.IRing

set ofRingSet

interfaces.IRingSet

ring finding graph.SpanningTree

ring searchringsearch.FiguerasSSSRFinder

ringsearch.SSSRFinder

ringsearch.cyclebasis.SimpleCycle

rotatable qsar.descriptors.molecular.RotatableBondsCountDescriptor

RSS io.RssWriter

rule-of-five qsar.descriptors.molecular.RuleOfFiveDescriptor

saturationtools.LonePairElectronChecker


SDFio.MDLV2000Reader

io.MDLReader


set ofRingSet

interfaces.IRingSet

12 KEYWORD LIST

shape index qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor

ShelX io.ShelXWriter

ShelXL io.ShelXReader

similarityfingerprint.MACCSFingerprinter

fingerprint.Fingerprinter

fingerprint.SubstructureFingerprinter


fingerprint.ExtendedFingerprinter

fingerprint.GraphOnlyFingerprinter

3D similarity.DistanceMoment

tanimoto similarity.Tanimoto

smallest-set-of-ringsringsearch.FiguerasSSSRFinder

ringsearch.SSSRFinder

ringsearch.cyclebasis.SimpleCycle

SMARTSisomorphism.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

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 ASTsmiles.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

14 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

SMILESio.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

stereochemistryCDKConstants

AtomParity

interfaces.IAtomParity

structure diagram generation layout.TemplateHandler

Structure Diagram Generation (SDG) layout.StructureDiagramGenerator

structure generatorstructgen.RandomGenerator

structgen.VicinitySampler

stuctures templates.AminoAcids

substructure searchfingerprint.FingerprinterTool.isSubset()

smiles.smarts.SMARTSQueryTool

smiles.smarts.parser.SMARTSParser

Sybyl atomtype.SybylAtomTypeMatcher

tanimoto similarity.Tanimoto

templatestemplates.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

typeAtomType

config.TXTBasedAtomTypeConfigurator

config.AtomTypeFactory

interfaces.IAtomType

unpairedSingleElectron

15


valencytools.LonePairElectronChecker


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

cdk keyword list

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