- Abbreviations
- Abbreviations.Option
- ABINITFormat
- AbstractAtomicDescriptor
- AbstractAtomPairDescriptor
- AbstractAWTDrawVisitor
- AbstractBondDescriptor
- AbstractDifference
- AbstractDifferenceList
- AbstractFingerprinter
- AbstractFontManager
- AbstractGeneratorParameter
- AbstractMCS
- AbstractMCSAlgorithm
- AbstractMolecularDescriptor
- AbstractReactionLabeller
- AbstractRenderer
- AbstractResourceFormat
- AbstractSelection
- AbstractSubGraph
- AbstractValidator
- Aces2Format
- AcidicGroupCountDescriptor
- AdductFormula
- AdductFormula
- AdductionLPMechanism
- AdductionPBMechanism
- AdductionProtonLPReaction
- AdductionProtonPBReaction
- AdductionSodiumLPReaction
- ADFFormat
- AdjacencyMatrix
- AlchemyFormat
- Algorithm
- AliphaticAtom
- AliphaticSymbolAtom
- AllCycles
- AllPairsShortestPaths
- AllRingsFinder
- AllRingsFinder.Threshold
- ALOGPDescriptor
- AminoAcid
- AminoAcid
- AminoAcidCountDescriptor
- AminoAcidManipulator
- AminoAcids
- AngularMomentum
- AnyAtom
- AnyOrderQueryBond
- APolDescriptor
- AromaticAtom
- AromaticAtomsCountDescriptor
- AromaticBondsCountDescriptor
- Aromaticity
- Aromaticity.Model
- AromaticityCalculator
- AromaticOrSingleQueryBond
- AromaticQueryBond
- AromaticSymbolAtom
- ArrowElement
- Association
- Atom
- Atom
- AtomContainer
- AtomContainer
- AtomContainerAtomPermutor
- AtomContainerAtomPermutor
- AtomContainerBondPermutor
- AtomContainerBoundsGenerator
- AtomContainerComparator
- AtomContainerComparatorBy2DCenter
- AtomContainerDiff
- AtomContainerDiscretePartitionRefiner
- AtomContainerLegacy
- AtomContainerLegacy
- AtomContainerManipulator
- AtomContainerPermutor
- AtomContainerPrinter
- AtomContainerRenderer
- AtomContainerSet
- AtomContainerSet
- AtomContainerSetManipulator
- AtomCountDescriptor
- AtomDegreeDescriptor
- AtomDiff
- AtomEncoder
- AtomHashGenerator
- AtomHybridizationDescriptor
- AtomHybridizationVSEPRDescriptor
- AtomicNumberAtom
- AtomicNumberDifferenceDescriptor
- AtomicProperties
- AtomMappingTools
- AtomMassGenerator
- AtomMassSymbolElement
- AtomMatcher
- AtomMatcher
- AtomNumberGenerator
- AtomNumberGenerator.AtomColorer
- AtomNumberGenerator.AtomNumberTextColor
- AtomNumberGenerator.ColorByType
- AtomNumberGenerator.Offset
- AtomNumberGenerator.WillDrawAtomNumbers
- AtomPairs2DFingerprinter
- AtomPlacer
- AtomPlacer3D
- AtomRef
- AtomSignature
- AtomSymbolElement
- AtomTetrahedralLigandPlacer3D
- AtomTools
- AtomType
- AtomType
- AtomTypeAwareSaturationChecker
- AtomTypeCharges
- AtomTypeDiff
- AtomTypeFactory
- AtomTypeHandler
- AtomTypeHybridizationDifference
- AtomTypeManipulator
- AtomTypeMapper
- AtomTypeReader
- AtomTypeTools
- AtomValenceDescriptor
- AtomValenceTool
- Atropisomeric
- AttachedGroup
- AutocorrelationDescriptorCharge
- AutocorrelationDescriptorMass
- AutocorrelationDescriptorPolarizability
- AverageBondLengthCalculator
- AWTDrawVisitor
- AWTFontManager
- BadMatrixFormatException
- BasicAtomEncoder
- BasicAtomGenerator
- BasicAtomGenerator.AtomColor
- BasicAtomGenerator.AtomColorer
- BasicAtomGenerator.AtomRadius
- BasicAtomGenerator.ColorByType
- BasicAtomGenerator.CompactAtom
- BasicAtomGenerator.CompactShape
- BasicAtomGenerator.KekuleStructure
- BasicAtomGenerator.Shape
- BasicAtomGenerator.ShowEndCarbons
- BasicAtomGenerator.ShowExplicitHydrogens
- BasicBondGenerator
- BasicBondGenerator.BondDistance
- BasicBondGenerator.BondWidth
- BasicBondGenerator.DefaultBondColor
- BasicBondGenerator.TowardsRingCenterProportion
- BasicBondGenerator.WedgeWidth
- BasicGenerator
- BasicGroupCountDescriptor
- BasicSceneGenerator
- BasicSceneGenerator.ArrowHeadWidth
- BasicSceneGenerator.BackgroundColor
- BasicSceneGenerator.BondLength
- BasicSceneGenerator.FitToScreen
- BasicSceneGenerator.FontName
- BasicSceneGenerator.ForegroundColor
- BasicSceneGenerator.Margin
- BasicSceneGenerator.Scale
- BasicSceneGenerator.ShowMoleculeTitle
- BasicSceneGenerator.ShowReactionTitle
- BasicSceneGenerator.ShowTooltip
- BasicSceneGenerator.UseAntiAliasing
- BasicSceneGenerator.UsedFontStyle
- BasicSceneGenerator.ZoomFactor
- BasicValidator
- Bayesian
- BCUTDescriptor
- BFSShortestPath
- BGFFormat
- BiconnectivityInspector
- BinaryTree
- BioPolymer
- BioPolymer
- BitSetFingerprint
- BKKCKCF
- Bond
- Bond
- BondCountDescriptor
- BondDiff
- BondEnergies
- BondEnergy
- BondManipulator
- BondMatcher
- BondMatcher
- BondOrderDifference
- BondPartialPiChargeDescriptor
- BondPartialSigmaChargeDescriptor
- BondPartialTChargeDescriptor
- BondRef
- BondSigmaElectronegativityDescriptor
- BondsToAtomDescriptor
- BondTools
- BooleanArrayDifference
- BooleanDifference
- BooleanIOSetting
- BooleanResult
- BooleanResultType
- Bounds
- BoundsCalculator
- BoundsGenerator
- BoundsGenerator.BoundsColor
- BPolDescriptor
- BremserOneSphereHOSECodePredictor
- BSFormat
- Bspt
- Bspt.Tuple
- CacaoCartesianFormat
- CacaoInternalFormat
- CACheFormat
- Canon
- CanonicalLabeler
- CanonicalLabellingAdaptor
- CanonOpts
- CarbonTypesDescriptor
- CarbonylEliminationReaction
- CASNumber
- CDK
- CDK
- CDK2DAtomColors
- CDKAtomColors
- CDKAtomTypeMatcher
- CDKBasedAtomTypeConfigurator
- CDKConstants
- CDKConvention
- CDKDictionaryReferences
- CDKException
- CDKHueckelAromaticityDetector
- CDKHydrogenAdder
- CDKMCS
- CDKMCSHandler
- CDKOWLFormat
- CDKOWLReader
- CDKOWLWriter
- CDKRGraph
- CDKRMap
- CDKRMapHandler
- CDKRNode
- CDKSourceCodeFormat
- CDKSourceCodeWriter
- CDKSubGraphHandler
- CDKUtilities
- CDKValencyChecker
- CDKValidator
- ChargeGroup
- ChargeRule
- Chem3D_Cartesian_1Format
- Chem3D_Cartesian_2Format
- ChemDrawFormat
- ChemFile
- ChemFile
- ChemFileManipulator
- ChemGraph
- ChemicalFilters
- ChemModel
- ChemModel
- ChemModelManipulator
- ChemModelRenderer
- ChemObject
- ChemObject
- ChemObjectChangeEvent
- ChemObjectDiff
- ChemObjectDifference
- ChemObjectIO
- ChemSequence
- ChemSequence
- ChemSequenceManipulator
- ChemtoolFormat
- ChiChainDescriptor
- ChiClusterDescriptor
- ChiPathClusterDescriptor
- ChiPathDescriptor
- ChiralityAtom
- CIFFormat
- CIFReader
- CIPLigandRule
- CIPTool
- CIPTool.CIP_CHIRALITY
- CircularFingerprinter
- CircularFingerprinter.FP
- Close
- ClosedShellJob
- CMLCoreModule
- CMLErrorHandler
- CMLFormat
- CMLHandler
- CMLModuleStack
- CMLReactionModule
- CMLReader
- CMLResolver
- CMLRSSFormat
- CMLWriter
- Complex
- ConformerContainer
- ConjugatedPiSystemsDetector
- ConnectedComponents
- ConnectionMatrix
- ConnectivityChecker
- Convertor
- Convertor
- CovalentRadiusDescriptor
- CPKAtomColors
- CPSADescriptor
- CRK2DFormat
- CRK3DFormat
- CrossoverMachine
- Crystal
- Crystal
- CrystalGeometryTools
- CrystClustFormat
- CrystClustReader
- CrystClustWriter
- CTFileQueryBond
- CTFileQueryBond.Type
- CTXFormat
- CTXReader
- CubicTo
- CustomSerializer
- CxSmilesGenerator
- CycleBasis
- CycleFinder
- Cycles
- CyclicVertexSearch
- DaltonFormat
- DataFeatures
- DataFeaturesTool
- DeAromatizationTool
- DebugAdductFormula
- DebugAminoAcid
- DebugAtom
- DebugAtomContainer
- DebugAtomContainerSet
- DebugAtomType
- DebugBioPolymer
- DebugBond
- DebugChemFile
- DebugChemModel
- DebugChemObject
- DebugChemObjectBuilder
- DebugChemSequence
- DebugCrystal
- DebugElectronContainer
- DebugElement
- DebugFragmentAtom
- DebugIsotope
- DebugLonePair
- DebugMapping
- DebugMolecularFormula
- DebugMolecularFormulaSet
- DebugMonomer
- DebugPDBAtom
- DebugPDBMonomer
- DebugPDBPolymer
- DebugPDBStructure
- DebugPolymer
- DebugPseudoAtom
- DebugReaction
- DebugReactionScheme
- DebugReactionSet
- DebugRing
- DebugRingSet
- DebugSingleElectron
- DebugStrand
- DebugSubstance
- DeduceBondSystemTool
- DefaultBondMatcher
- DefaultChemObjectBuilder
- DefaultChemObjectReader
- DefaultChemObjectReaderErrorHandler
- DefaultChemObjectWriter
- DefaultEventChemObjectReader
- DefaultIteratingChemObjectReader
- DefaultMatcher
- DefaultMCSPlusAtomMatcher
- DefaultRandomAccessChemObjectReader
- DefaultRGraphAtomMatcher
- DefaultVFAtomMatcher
- DefaultVFBondMatcher
- Depiction
- DepictionGenerator
- DescriptorEngine
- DescriptorException
- DescriptorSpecification
- DescriptorValue
- DfPattern
- Dictionary
- DictionaryDatabase
- DictionaryHandler
- DictionaryValidator
- DictRef
- DiscretePartitionRefiner
- DisjointSetForest
- DistanceMoment
- DistanceToAtomDescriptor
- DMol3Format
- DOCK5Format
- DoubleArrayResult
- DoubleArrayResultType
- DoubleBondAcceptingAromaticityDetector
- DoubleBondElementEncoderFactory
- DoubleBondStereochemistry
- DoubleDifference
- DoubleResult
- DoubleResultType
- DynamicFactory
- DynamicFactory.BasicCreator
- DynamicFactory.ConstructorKey
- DynamicFactory.CreationModifier
- DynamicFactory.Creator
- DynamicFactory.DefaultInterfaceProvider
- DynamicFactory.InterfaceProvider
- EccentricConnectivityIndexDescriptor
- EdgeBuilder
- EffectiveAtomPolarizabilityDescriptor
- ElectronContainer
- ElectronContainer
- ElectronContainerDiff
- ElectronDonation
- Electronegativity
- ElectronImpactNBEReaction
- ElectronImpactPDBReaction
- ElectronImpactSDBReaction
- Element
- Element
- ElementComparator
- ElementDiff
- ElementGroup
- ElementRule
- Elements
- EnsembleHashGenerator
- Entry
- EntryReact
- EnzymeResidueLocator
- EquivalentClassPartitioner
- EssentialCycles
- EStateAtomTypeMatcher
- EStateFingerprinter
- EStateFragments
- EventCMLHandler
- EventCMLReader
- ExactMapping
- ExhaustiveFragmenter
- ExplicitConnectionAtom
- Expr
- Expr.Type
- ExtAtomContainerManipulator
- ExtendedAtomGenerator
- ExtendedAtomGenerator.ShowAtomTypeNames
- ExtendedAtomGenerator.ShowImplicitHydrogens
- ExtendedCisTrans
- ExtendedFingerprinter
- ExtendedTetrahedral
- FenskeHall_ZMatrixFormat
- FiguerasSSSRFinder
- FinalMappings
- Fingerprinter
- FingerprinterTool
- FingerprintFormat
- FixBondOrdersTool
- FMFDescriptor
- ForceFieldConfigurator
- FormalChargeAtom
- FormatFactory
- FormatStringBuffer
- FortranFormat
- FourierGridBasis
- FractionalCSP3Descriptor
- FractionalPSADescriptor
- FragmentAtom
- FragmentAtom
- FragmentComplexityDescriptor
- FragmentUtils
- FunctionalGroupsFinder
- GamessFormat
- GamessReader
- GasteigerMarsiliPartialCharges
- GasteigerPEPEPartialCharges
- Gaussian03Format
- Gaussian03Reader
- Gaussian90Format
- Gaussian92Format
- Gaussian94Format
- Gaussian95Format
- Gaussian98Format
- Gaussian98Reader
- GaussianInputFormat
- GaussianInputWriter
- GaussiansBasis
- GeneralPath
- GenerateCompatibilityGraph
- GeometricCumulativeDoubleBondFactory
- GeometricDoubleBondEncoderFactory
- GeometricTetrahedralEncoderFactory
- Geometry3DValidator
- GeometryTools
- GeometryTools.CoordinateCoverage
- GeometryUtil
- GeometryUtil.CoordinateCoverage
- GhemicalMMFormat
- GhemicalMMReader
- GhemicalSPMFormat
- GIMatrix
- GraphOnlyFingerprinter
- GraphRendererModel
- GraphUtil
- GraphUtil.EdgeToBondMap
- GravitationalIndexDescriptor
- GridGenerator
- GROMOS96Format
- HanserRingFinder
- HashGeneratorMaker
- HBondAcceptorCountDescriptor
- HBondDonorCountDescriptor
- HeterolyticCleavageMechanism
- HeterolyticCleavagePBReaction
- HeterolyticCleavageSBReaction
- HighlightGenerator
- HighlightGenerator.HighlightPalette
- HighlightGenerator.HighlightRadius
- HighlightGenerator.Palette
- HINFormat
- HINReader
- HINWriter
- HomolyticCleavageMechanism
- HomolyticCleavageReaction
- HOSECodeAnalyser
- HOSECodeGenerator
- HuLuIndexTool
- HybridizationFingerprinter
- HybridizationNumberAtom
- HybridizationRatioDescriptor
- HydrogenAtom
- HydrogenPlacer
- HyperconjugationReaction
- IAdductFormula
- IAminoAcid
- IAtom
- IAtomColorer
- IAtomContainer
- IAtomContainerSet
- IAtomicDescriptor
- IAtomPairDescriptor
- IAtomType
- IAtomType.Hybridization
- IAtomTypeConfigurator
- IAtomTypeGuesser
- IAtomTypeMatcher
- IBasis
- IBioPolymer
- IBitFingerprint
- IBond
- IBond.Display
- IBond.Order
- IBond.Stereo
- IBondDescriptor
- ICanonicalMoleculeLabeller
- ICanonicalReactionLabeller
- ICDKChangeListener
- ICDKObject
- ICDKSelectionChangeListener
- IChargeCalculator
- IChemFile
- IChemFormat
- IChemFormatMatcher
- IChemFormatMatcher.MatchResult
- IChemModel
- IChemObject
- IChemObjectBuilder
- IChemObjectChangeEvent
- IChemObjectIO
- IChemObjectIOListener
- IChemObjectListener
- IChemObjectReader
- IChemObjectReader.Mode
- IChemObjectReaderErrorHandler
- IChemObjectSelection
- IChemObjectWriter
- IChemSequence
- ICMLConvention
- ICMLCustomizer
- ICMLModule
- ICountFingerprint
- ICrystal
- IDCreator
- IDeduceBondOrderTool
- IDescriptor
- IDescriptorResult
- IDifference
- IDifferenceList
- IDoubleBondStereochemistry
- IDoubleBondStereochemistry.Conformation
- IDrawVisitor
- IEdge
- IElectronContainer
- IElectronicPropertyCalculator
- IElement
- IEventChemObjectReader
- IFinalMapping
- IFingerprinter
- IFontManager
- IFontManager.FontStyle
- IFragmentAtom
- IFragmenter
- IFunction
- IGenerator
- IGeneratorParameter
- IGraphMatrix
- IImplementationSpecification
- IIsotope
- IIteratingChemObjectReader
- ILigand
- ILoggingTool
- ILonePair
- IMapper
- IMapping
- IMatrix
- IMCSBase
- IMolecularDescriptor
- IMolecularFormula
- IMolecularFormulaSet
- IMonomer
- IMouseEventRelay
- ImplicitHCountAtom
- ImplicitHydrogenLigand
- INCHI_OPTION
- INCHI_RET
- INChIContentProcessorTool
- INChIFormat
- InChIGenerator
- InChIGeneratorFactory
- INChIHandler
- InChINumbersTools
- INChIPlainTextFormat
- INChIPlainTextReader
- INChIReader
- InChITautomerGenerator
- InChIToStructure
- IncorrectUseOfCDKCoreClassError
- IndexOutOfBoundsException
- InductiveAtomicHardnessDescriptor
- InductiveAtomicSoftnessDescriptor
- InductivePartialCharges
- INode
- IntArrayCountFingerprint
- IntArrayFingerprint
- IntegerArrayResult
- IntegerArrayResultType
- IntegerDifference
- IntegerIOSetting
- IntegerResult
- IntegerResultType
- Intractable
- InvalidSmilesException
- Invariant
- InverseSymbolSetQueryAtom
- InvPair
- IonizationPotentialTool
- IOSetting
- IOSetting.Importance
- IParameterReact
- IPAtomicHOSEDescriptor
- IPAtomicLearningDescriptor
- IPBondLearningDescriptor
- IPDBAtom
- IPDBMonomer
- IPDBPolymer
- IPDBStructure
- IPMolecularLearningDescriptor
- IPolymer
- IPseudoAtom
- IQuery
- IQueryAtom
- IQueryAtomContainer
- IQueryBond
- IQueryCompiler
- IRandomAccessChemObjectReader
- IRDFWeightFunction
- IReaction
- IReaction.Direction
- IReactionMechanism
- IReactionProcess
- IReactionScheme
- IReactionSet
- IReaderListener
- IRenderer
- IRenderingElement
- IRenderingVisitor
- IResourceFormat
- IRGroup
- IRGroupList
- IRGroupQuery
- IRing
- IRingSet
- IRule
- ISequenceSubRule
- ISetting
- ISimpleChemObjectReader
- ISingleElectron
- IsoAlkanes
- Isomorphism
- IsomorphismTester
- Isotope
- Isotope
- IsotopeContainer
- IsotopeDiff
- IsotopeFactory
- IsotopeHandler
- IsotopePattern
- IsotopePatternGenerator
- IsotopePatternManipulator
- IsotopePatternRule
- IsotopePatternSimilarity
- IsotopeReader
- Isotopes
- IsProtonInAromaticSystemDescriptor
- IsProtonInConjugatedPiSystemDescriptor
- IState
- IStereoElement
- IStrand
- IStructureGenerationListener
- ISubstance
- ISubstanceDescriptor
- IteratingMDLConformerReader
- IteratingPCCompoundASNReader
- IteratingPCCompoundXMLReader
- IteratingPCSubstancesXMLReader
- IteratingSDFReader
- IteratingSMILESReader
- ITetrahedralChirality
- ITetrahedralChirality.Stereo
- IValencyChecker
- IValidator
- IVector
- IViewEventRelay
- IWriterListener
- JaguarFormat
- JJTSMARTSParserState
- JMEFormat
- JMOLANIMATIONConvention
- JmolColors
- JPlogPDescriptor
- KabschAlignment
- KappaShapeIndicesDescriptor
- Kekulization
- KierHallSmartsDescriptor
- KlekotaRothFingerprinter
- LabelContainer
- LargestChainDescriptor
- LargestPiSystemDescriptor
- LengthOverBreadthDescriptor
- Ligand
- LineElement
- LineElement.LineType
- LineTo
- LingoFingerprinter
- LingoSimilarity
- LoggingToolFactory
- LogicalOperatorAtom
- LogicalOperatorBond
- LonePair
- LonePair
- LonePairDiff
- LonePairElectronChecker
- LonePairGenerator
- LongestAliphaticChainDescriptor
- MACCSFingerprinter
- MacroModelFormat
- Main
- MannholdLogPDescriptor
- Mapping
- Mapping
- MappingGenerator
- MappingGenerator.AtomAtomMappingLineColor
- MappingGenerator.MappingLineWidth
- MappingGenerator.ShowAtomAtomMapping
- Mappings
- MarkedElement
- MassAtom
- MassToFormulaTool
- Match
- Matching
- Matrix
- MatrixNotInvertibleException
- Maygen
- Maygen.Consumer
- McGregor
- McGregorChecks
- McgregorHelper
- MCSPlus
- MCSPlusHandler
- MDEDescriptor
- MDLFormat
- MDLMolConvention
- MDLReader
- MDLRXNFormat
- MDLRXNReader
- MDLRXNV2000Format
- MDLRXNV2000Reader
- MDLRXNV3000Format
- MDLRXNV3000Reader
- MDLRXNWriter
- MDLV2000Format
- MDLV2000Reader
- MDLV2000Writer
- MDLV2000Writer.SPIN_MULTIPLICITY
- MDLV3000Format
- MDLV3000Reader
- MDLV3000Writer
- MDMolecule
- MDMoleculeConvention
- MDMoleculeCustomizer
- MinimalPathIterator
- MinimumCycleBasis
- MM2AtomTypeMatcher
- MM2BasedAtomTypePattern
- MM2BasedParameterSetReader
- MMElementRule
- MMElementRule.Database
- MMElementRule.RangeMass
- Mmff
- MMFF94AtomTypeMatcher
- MMFF94BasedAtomTypePattern
- MMFF94BasedParameterSetReader
- MMFF94ParametersCall
- MMFF94PartialCharges
- MMODFormat
- ModelBuilder3D
- Mol2Format
- Mol2Reader
- Mol2Writer
- MolecularFormula
- MolecularFormula
- MolecularFormulaChecker
- MolecularFormulaGenerator
- MolecularFormulaManipulator
- MolecularFormulaRange
- MolecularFormulaRangeManipulator
- MolecularFormulaSet
- MolecularFormulaSet
- MolecularFormulaSetManipulator
- MoleculeBuilder
- MoleculeFactory
- MoleculeFeaturesTool
- MoleculeFromSignatureBuilder
- MoleculeGraphs
- MoleculeHashGenerator
- MoleculeSanityCheck
- MoleculeSetManipulator
- MoleculeSetRenderer
- MoleculeSignature
- MoleculeSignatureLabellingAdaptor
- MolHandler
- MomentOfInertiaDescriptor
- Monomer
- Monomer
- MOPAC2002Format
- MOPAC2007Format
- MOPAC2009Format
- MOPAC2012Format
- MOPAC7Format
- MOPAC7InputFormat
- Mopac7Reader
- Mopac7Writer
- MOPAC93Format
- MOPAC97Format
- MorganNumbersTools
- MoSSOutputFormat
- MoSSOutputReader
- MoveTo
- MPQCFormat
- MurckoFragmenter
- NeighborList
- NitrogenRule
- Node
- NodeBuilder
- NomParser
- NomParserConstants
- NomParserTokenManager
- NonCHHeavyAtom
- Normalizer
- NoSuchAtomException
- NoSuchAtomTypeException
- NoSuchBondException
- NumericalSurface
- NWChemFormat
- Octahedral
- OneElectronJob
- OptionIOSetting
- Orbit
- Orbitals
- OrderQueryBond
- OrderQueryBond
- OrderQueryBondOrderOnly
- OvalElement
- OverlapResolver
- OWLAtomTypeHandler
- OWLAtomTypeMappingHandler
- OWLAtomTypeMappingReader
- OWLAtomTypeReader
- OWLBasedAtomTypeConfigurator
- OWLFile
- OWLReact
- OxygenAtomCountDescriptor
- ParameterReact
- ParseException
- ParseException
- PartialAtomicChargeColors
- PartialFilledStructureMerger
- PartialPiChargeDescriptor
- PartialSigmaChargeDescriptor
- PartialTChargeMMFF94Descriptor
- PartialTChargePEOEDescriptor
- Partition
- PartitionRefinement
- PartitionRefinement.AtomRefinerBuilder
- PartitionRefinement.BondRefinerBuilder
- PathBuilder
- PathEdge
- PathElement
- PathElement
- PathGraph
- PathTools
- Pattern
- PCCompoundASNReader
- PCCompoundXMLReader
- PCModelFormat
- PCSubstanceXMLReader
- PDBAtom
- PDBAtom
- PDBAtomCustomizer
- PDBConvention
- PDBFormat
- PDBMLFormat
- PDBMonomer
- PDBMonomer
- PDBPolymer
- PDBPolymer
- PDBReader
- PDBStrand
- PDBStructure
- PDBStructure
- PDBWriter
- PeriodicGroupNumberAtom
- PeriodicTable
- PeriodicTablePositionDescriptor
- Permutation
- PermutationGroup
- PermutationGroup.Backtracker
- Permutor
- Permutor
- PetitjeanNumberDescriptor
- PetitjeanShapeIndexDescriptor
- PharmacophoreAngleBond
- PharmacophoreAtom
- PharmacophoreBond
- PharmacophoreMatcher
- PharmacophoreQuery
- PharmacophoreQueryAngleBond
- PharmacophoreQueryAtom
- PharmacophoreQueryBond
- PharmacophoreUtils
- PhysicalConstants
- PiBondingMovementReaction
- PiContactDetectionDescriptor
- PiElectronegativity
- PiElectronegativityDescriptor
- PMPConvention
- PMPFormat
- PMPReader
- Point
- Point2dDifference
- Point3dDifference
- Polarizability
- Polymer
- Polymer
- PostFilter
- POVRayFormat
- PQSChemFormat
- Primes
- ProblemMarker
- ProductsBoxGenerator
- Projection
- Projector
- PropertiesListener
- ProteinBuilderTool
- ProteinPocketFinder
- ProtonAffinityHOSEDescriptor
- ProtonTotalPartialChargeDescriptor
- PseudoAtom
- PseudoAtom
- PubChemASNFormat
- PubChemCompoundsXMLFormat
- PubChemCompoundXMLFormat
- PubchemFingerprinter
- PubChemFormat
- PubChemSubstancesASNFormat
- PubChemSubstancesXMLFormat
- PubChemSubstanceXMLFormat
- PubChemXMLHelper
- QChemFormat
- QSARConvention
- QSARCustomizer
- QuadTo
- Quaternion
- QueryAtom
- QueryAtomContainer
- QueryAtomContainerCreator
- QueryBond
- QueryChemObject
- QueryCompiler
- QueryProcessor
- Queue
- RadicalChargeSiteInitiationHReaction
- RadicalChargeSiteInitiationReaction
- RadicalGenerator
- RadicalSiteHrAlphaReaction
- RadicalSiteHrBetaReaction
- RadicalSiteHrDeltaReaction
- RadicalSiteHrGammaReaction
- RadicalSiteInitiationHReaction
- RadicalSiteInitiationReaction
- RadicalSiteIonizationMechanism
- RadicalSiteRearrangementMechanism
- RadicalSiteRrAlphaReaction
- RadicalSiteRrBetaReaction
- RadicalSiteRrDeltaReaction
- RadicalSiteRrGammaReaction
- RandomAccessReader
- RandomAccessSDFReader
- RandomGenerator
- RandomNumbersTool
- RasmolColors
- RawCopyFormat
- RDBERule
- RDFCalculator
- RdfileReader
- RdfileRecord
- RDFProtonDescriptor_G3R
- RDFProtonDescriptor_GDR
- RDFProtonDescriptor_GHR
- RDFProtonDescriptor_GHR_topol
- RDFProtonDescriptor_GSR
- ReactantsBoxGenerator
- Reaction
- Reaction
- ReactionArrowGenerator
- ReactionBoxGenerator
- ReactionChain
- ReactionEngine
- ReactionManipulator
- ReactionPlusGenerator
- ReactionRenderer
- ReactionRole
- ReactionRoleQueryAtom
- ReactionSceneGenerator
- ReactionSceneGenerator.ArrowHeadWidth
- ReactionSceneGenerator.ShowReactionBoxes
- ReactionScheme
- ReactionScheme
- ReactionSchemeManipulator
- ReactionSet
- ReactionSet
- ReactionSetManipulator
- ReactionSetRenderer
- ReactionSpecification
- ReaderEvent
- ReaderFactory
- RearrangementAnionReaction
- RearrangementCationReaction
- RearrangementChargeMechanism
- RearrangementLonePairReaction
- RearrangementRadicalReaction
- RebondTool
- RectangleElement
- RecursiveSmartsAtom
- Refinable
- RelevantCycles
- RemovingSEofBMechanism
- RemovingSEofNBMechanism
- RendererModel
- RendererModel.ColorHash
- RendererModel.ExternalHighlightColor
- RendererModel.MarkedOutput
- RendererModel.Padding
- RendererModel.SelectionColor
- RendererModel.TitleColor
- RendererModel.TitleFontScale
- Residue
- RGraph
- RGroup
- RGroupList
- RGroupQuery
- RGroupQueryFormat
- RGroupQueryReader
- RGroupQueryWriter
- RInChIExample
- RInChIException
- RInChIGenerator
- RInChIOptions
- RInChIOptions.RInChIOptionBuilder
- RInChIToReaction
- Ring
- Ring
- RingBond
- RingElement
- RingFilter
- RingFinder
- RingGenerator
- RingGenerator.CDKStyleAromaticity
- RingGenerator.MaxDrawableAromaticRing
- RingGenerator.RingProportion
- RingGenerator.ShowAromaticity
- RingIdentifierAtom
- RingManipulator
- RingMembershipAtom
- RingPartitioner
- RingPlacer
- RingSearch
- RingSet
- RingSet
- RingSetManipulator
- RingSizeComparator
- RMap
- RNode
- RotatableBondsCountDescriptor
- RssWriter
- RuleOfFiveDescriptor
- SaturationChecker
- SDFFormat
- SDFWriter
- SelectionVisibility
- SetReactionCenter
- SettingManager
- Sgroup
- SgroupBracket
- SgroupKey
- SgroupManipulator
- SgroupType
- SharingAnionReaction
- SharingChargeDBReaction
- SharingChargeSBReaction
- SharingElectronMechanism
- SharingLonePairReaction
- ShelXFormat
- ShelXReader
- ShelXWriter
- ShortestPathFingerprinter
- ShortestPaths
- ShortestPathWalker
- SigmaElectronegativityDescriptor
- SignatureFingerprinter
- SignatureQuotientGraph
- SignatureReactionCanoniser
- SilentChemObjectBuilder
- SimpleAtomCanonicalizer
- SimpleAtomComparator
- SimpleBasisSet
- SimpleCharStream
- SimpleCharStream
- SimpleCycle
- SimpleCycleBasis
- SingleElectron
- SingleElectron
- SingleElectronDiff
- SingleMapping
- SingleMappingHandler
- SingleStructureRandomGenerator
- SmallestRingAtom
- SmallRingDescriptor
- Smarts
- Smarts2MQLVisitor
- SMARTSAtom
- SMARTSBond
- SmartsDumpVisitor
- SMARTSFormat
- SmartsFragmentExtractor
- SmartsMatchers
- SMARTSParser
- SMARTSParserConstants
- SMARTSParserDefaultVisitor
- SMARTSParserTokenManager
- SMARTSParserTreeConstants
- SMARTSParserVisitor
- SmartsPattern
- SmartsPattern
- SMARTSQueryTool
- SmartsQueryVisitor
- SmartsResult
- SmartsStereoMatch
- SmiFlavor
- SMILESFIXFormat
- SMILESFormat
- SmilesGenerator
- SmilesParser
- SmilesReactionCanoniser
- SMILESReader
- SmilesValencyChecker
- SMILESWriter
- Smirks
- SmirksOption
- SmirksTransform
- SMSDNormalizer
- SpanningTree
- SpartanFormat
- SpiroAtomCountDescriptor
- SquarePlanar
- SSSRFinder
- StabilizationCharges
- StabilizationPlusChargeDescriptor
- StandardGenerator
- StandardGenerator.Alignment
- StandardGenerator.AnnotationColor
- StandardGenerator.AnnotationDistance
- StandardGenerator.AnnotationFontScale
- StandardGenerator.AtomColor
- StandardGenerator.BondSeparation
- StandardGenerator.DashSection
- StandardGenerator.DelocalisedDonutsBondDisplay
- StandardGenerator.DeuteriumSymbol
- StandardGenerator.FancyBoldWedges
- StandardGenerator.FancyHashedWedges
- StandardGenerator.ForceDelocalisedBondDisplay
- StandardGenerator.HashSpacing
- StandardGenerator.Highlighting
- StandardGenerator.HighlightStyle
- StandardGenerator.OmitMajorIsotopes
- StandardGenerator.OuterGlowWidth
- StandardGenerator.PseudoFontStyle
- StandardGenerator.SgroupBracketDepth
- StandardGenerator.SgroupFontScale
- StandardGenerator.StrokeRatio
- StandardGenerator.SymbolMarginRatio
- StandardGenerator.Visibility
- StandardGenerator.WaveSpacing
- StandardGenerator.WedgeRatio
- StandardSubstructureSets
- StatusMessagesOutput
- StatusMessagesOutput.Status
- StereoBond
- StereoBond.Direction
- Stereocenters
- Stereocenters.Stereocenter
- Stereocenters.Type
- StereoElementFactory
- StereoEncoder
- StereoEncoderFactory
- StereoTool
- StereoTool.SquarePlanarShape
- StereoTool.StereoClass
- StereoTool.TetrahedralSign
- Strand
- Strand
- StringDifference
- StringIOSetting
- StructGenAtomTypeGuesser
- StructGenMatcher
- StructureDiagramGenerator
- StructureResonanceGenerator
- Substance
- Substance
- SubstructureFingerprinter
- SugarRemovalUtility
- SugarRemovalUtility.PreservationMode
- SVGFormat
- SwingEventRelay
- SwingGUIListener
- SwingMouseEventRelay
- SwissArmyKnife
- SybylAtomTypeMatcher
- SybylDescriptorFormat
- SymbolAndChargeQueryAtom
- SymbolChargeIDQueryAtom
- SymbolQueryAtom
- SymbolSetQueryAtom
- SymbolVisibility
- SystemOutLoggingTool
- TaeAminoAcidDescriptor
- Tanimoto
- TargetProcessor
- TargetProperties
- TautomerizationMechanism
- TautomerizationReaction
- TemplateExtractor
- TemplateHandler
- TemplateHandler3D
- Tessellate
- TestMoleculeFactory
- TetrahedralChirality
- TetrahedralElementEncoderFactory
- TextElement
- TextGroupElement
- TextGroupElement.Position
- TextGUIListener
- TimeManager
- TimeOut
- TinkerMM2Format
- TinkerXYZFormat
- Token
- Token
- TokenMgrError
- TokenMgrError
- ToleranceRangeRule
- TopologicalMatrix
- TotalConnectionAtom
- TotalHCountAtom
- TotalRingConnectionAtom
- TotalValencyAtom
- TPSADescriptor
- Transform
- Transform.Mode
- TransformOp
- TransformOp.Type
- Triangle
- TrigonalBipyramidal
- TripletShortCycles
- TurboMoleFormat
- TXTBasedAtomTypeConfigurator
- Type
- Ullmann
- UndoAdapter
- UniChemXYZFormat
- UniColor
- UniversalIsomorphismTester
- UnsupportedChemObjectException
- VABCDescriptor
- VABCVolume
- VAdjMaDescriptor
- ValidationReport
- ValidationTest
- ValidatorEngine
- VASPFormat
- VASPReader
- VdWRadiusDescriptor
- Vector
- VentoFoggia
- VFAtomMatcher
- VFBondMatcher
- VFlibMCSHandler
- VFlibSubStructureHandler
- VFlibTurboHandler
- VFMapper
- VFMCSMapper
- VFQueryBuilder
- VFState
- Vibration
- VicinitySampler
- ViewmolFormat
- VisitedAtoms
- WedgeLineElement
- WedgeLineElement.Direction
- WedgeLineElement.TYPE
- WeightDescriptor
- WeightedPathDescriptor
- WHIMDescriptor
- WienerNumbersDescriptor
- WriterFactory
- XEDFormat
- XLogPDescriptor
- XMLIsotopeFactory
- XYZFormat
- XYZReader
- XYZWriter
- YasaraFormat
- ZagrebIndexDescriptor
- ZindoFormat
- ZMatrixFormat
- ZMatrixReader
- ZMatrixTools