Hierarchy For All Packages

Package Hierarchies:

• net.sf.jniinchi,
• org.openscience.cdk,
• org.openscience.cdk.aromaticity,
• org.openscience.cdk.atomtype,
• org.openscience.cdk.atomtype.mapper,
• org.openscience.cdk.charges,
• org.openscience.cdk.config,
• org.openscience.cdk.config.atomtypes,
• org.openscience.cdk.config.fragments,
• org.openscience.cdk.config.isotopes,
• org.openscience.cdk.controller,
• org.openscience.cdk.debug,
• org.openscience.cdk.depict,
• org.openscience.cdk.dict,
• org.openscience.cdk.event,
• org.openscience.cdk.exception,
• org.openscience.cdk.fingerprint,
• org.openscience.cdk.fingerprint.model,
• org.openscience.cdk.forcefield.mmff,
• org.openscience.cdk.formula,
• org.openscience.cdk.formula.rules,
• org.openscience.cdk.fragment,
• org.openscience.cdk.geometry,
• org.openscience.cdk.geometry.alignment,
• org.openscience.cdk.geometry.cip,
• org.openscience.cdk.geometry.cip.rules,
• org.openscience.cdk.geometry.surface,
• org.openscience.cdk.geometry.volume,
• org.openscience.cdk.graph,
• org.openscience.cdk.graph.invariant,
• org.openscience.cdk.graph.invariant.exception,
• org.openscience.cdk.graph.matrix,
• org.openscience.cdk.graph.rebond,
• org.openscience.cdk.group,
• org.openscience.cdk.hash,
• org.openscience.cdk.hash.stereo,
• org.openscience.cdk.inchi,
• org.openscience.cdk.index,
• org.openscience.cdk.interfaces,
• org.openscience.cdk.io,
• org.openscience.cdk.io.cml,
• org.openscience.cdk.io.formats,
• org.openscience.cdk.io.inchi,
• org.openscience.cdk.io.iterator,
• org.openscience.cdk.io.iterator.event,
• org.openscience.cdk.io.listener,
• org.openscience.cdk.io.program,
• org.openscience.cdk.io.pubchemxml,
• org.openscience.cdk.io.random,
• org.openscience.cdk.io.rdf,
• org.openscience.cdk.io.setting,
• org.openscience.cdk.isomorphism,
• org.openscience.cdk.isomorphism.matchers,
• org.openscience.cdk.isomorphism.matchers.smarts,
• org.openscience.cdk.isomorphism.mcss,
• org.openscience.cdk.iupac.parser,
• org.openscience.cdk.layout,
• org.openscience.cdk.libio.cml,
• org.openscience.cdk.libio.jena,
• org.openscience.cdk.libio.md,
• org.openscience.cdk.math,
• org.openscience.cdk.math.qm,
• org.openscience.cdk.modeling.builder3d,
• org.openscience.cdk.normalize,
• org.openscience.cdk.pharmacophore,
• org.openscience.cdk.protein,
• org.openscience.cdk.protein.data,
• org.openscience.cdk.qsar,
• org.openscience.cdk.qsar.descriptors.atomic,
• org.openscience.cdk.qsar.descriptors.atompair,
• org.openscience.cdk.qsar.descriptors.bond,
• org.openscience.cdk.qsar.descriptors.molecular,
• org.openscience.cdk.qsar.descriptors.protein,
• org.openscience.cdk.qsar.descriptors.substance,
• org.openscience.cdk.qsar.result,
• org.openscience.cdk.reaction,
• org.openscience.cdk.reaction.mechanism,
• org.openscience.cdk.reaction.type,
• org.openscience.cdk.reaction.type.parameters,
• org.openscience.cdk.renderer,
• org.openscience.cdk.renderer.color,
• org.openscience.cdk.renderer.elements,
• org.openscience.cdk.renderer.elements.path,
• org.openscience.cdk.renderer.font,
• org.openscience.cdk.renderer.generators,
• org.openscience.cdk.renderer.generators.parameter,
• org.openscience.cdk.renderer.generators.standard,
• org.openscience.cdk.renderer.selection,
• org.openscience.cdk.renderer.visitor,
• org.openscience.cdk.ringsearch,
• org.openscience.cdk.ringsearch.cyclebasis,
• org.openscience.cdk.sgroup,
• org.openscience.cdk.signature,
• org.openscience.cdk.silent,
• org.openscience.cdk.similarity,
• org.openscience.cdk.smarts,
• org.openscience.cdk.smiles,
• org.openscience.cdk.smiles.smarts,
• org.openscience.cdk.smiles.smarts.parser,
• org.openscience.cdk.smsd,
• org.openscience.cdk.smsd.algorithm.matchers,
• org.openscience.cdk.smsd.algorithm.mcgregor,
• org.openscience.cdk.smsd.algorithm.mcsplus,
• org.openscience.cdk.smsd.algorithm.rgraph,
• org.openscience.cdk.smsd.algorithm.single,
• org.openscience.cdk.smsd.algorithm.vflib,
• org.openscience.cdk.smsd.algorithm.vflib.builder,
• org.openscience.cdk.smsd.algorithm.vflib.interfaces,
• org.openscience.cdk.smsd.algorithm.vflib.map,
• org.openscience.cdk.smsd.algorithm.vflib.query,
• org.openscience.cdk.smsd.filters,
• org.openscience.cdk.smsd.global,
• org.openscience.cdk.smsd.helper,
• org.openscience.cdk.smsd.interfaces,
• org.openscience.cdk.smsd.labelling,
• org.openscience.cdk.smsd.ring,
• org.openscience.cdk.smsd.tools,
• org.openscience.cdk.stereo,
• org.openscience.cdk.structgen,
• org.openscience.cdk.structgen.maygen,
• org.openscience.cdk.structgen.stochastic,
• org.openscience.cdk.structgen.stochastic.operator,
• org.openscience.cdk.tautomers,
• org.openscience.cdk.templates,
• org.openscience.cdk.templates.saturatedhydrocarbons,
• org.openscience.cdk.tools,
• org.openscience.cdk.tools.diff,
• org.openscience.cdk.tools.diff.tree,
• org.openscience.cdk.tools.features,
• org.openscience.cdk.tools.manipulator,
• org.openscience.cdk.tools.periodictable,
• org.openscience.cdk.validate

Class Hierarchy

• java.lang.Object
  • org.openscience.cdk.depict.Abbreviations (implements java.lang.Iterable<T>)
  • org.openscience.cdk.qsar.AbstractAtomicDescriptor (implements org.openscience.cdk.qsar.IAtomicDescriptor)
    • org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor (implements org.openscience.cdk.qsar.IAtomicDescriptor)
    • org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationDescriptor (implements org.openscience.cdk.qsar.IAtomicDescriptor)
    • org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptor (implements org.openscience.cdk.qsar.IAtomicDescriptor)
    • org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor (implements org.openscience.cdk.qsar.IAtomicDescriptor)
    • org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor (implements org.openscience.cdk.qsar.IAtomicDescriptor)
    • org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor (implements org.openscience.cdk.qsar.IAtomicDescriptor)
    • org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor (implements org.openscience.cdk.qsar.IAtomicDescriptor)
    • org.openscience.cdk.qsar.descriptors.atomic.EffectiveAtomPolarizabilityDescriptor (implements org.openscience.cdk.qsar.IAtomicDescriptor)
    • org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicHardnessDescriptor (implements org.openscience.cdk.qsar.IAtomicDescriptor)
    • org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor (implements org.openscience.cdk.qsar.IAtomicDescriptor)
    • org.openscience.cdk.qsar.descriptors.atomic.IPAtomicHOSEDescriptor
    • org.openscience.cdk.qsar.descriptors.atomic.IPAtomicLearningDescriptor
    • org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor (implements org.openscience.cdk.qsar.IAtomicDescriptor)
    • org.openscience.cdk.qsar.descriptors.atomic.IsProtonInConjugatedPiSystemDescriptor (implements org.openscience.cdk.qsar.IAtomicDescriptor)
    • org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor
    • org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor
    • org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor
    • org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor
    • org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor (implements org.openscience.cdk.qsar.IAtomicDescriptor)
    • org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor (implements org.openscience.cdk.qsar.IAtomicDescriptor)
    • org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor
    • org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor (implements org.openscience.cdk.qsar.IAtomicDescriptor)
    • org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_G3R (implements org.openscience.cdk.qsar.IAtomicDescriptor)
    • org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GDR (implements org.openscience.cdk.qsar.IAtomicDescriptor)
    • org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR (implements org.openscience.cdk.qsar.IAtomicDescriptor)
    • org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GHR_topol (implements org.openscience.cdk.qsar.IAtomicDescriptor)
    • org.openscience.cdk.qsar.descriptors.atomic.RDFProtonDescriptor_GSR (implements org.openscience.cdk.qsar.IAtomicDescriptor)
    • org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor (implements org.openscience.cdk.qsar.IAtomicDescriptor)
    • org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor (implements org.openscience.cdk.qsar.IAtomicDescriptor)
    • org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor (implements org.openscience.cdk.qsar.IAtomicDescriptor)
  • org.openscience.cdk.qsar.AbstractAtomPairDescriptor (implements org.openscience.cdk.qsar.IAtomPairDescriptor)
    • org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor (implements org.openscience.cdk.qsar.IAtomPairDescriptor)
  • org.openscience.cdk.renderer.visitor.AbstractAWTDrawVisitor (implements org.openscience.cdk.renderer.visitor.IDrawVisitor)
    • org.openscience.cdk.renderer.visitor.AWTDrawVisitor
  • org.openscience.cdk.qsar.AbstractBondDescriptor (implements org.openscience.cdk.qsar.IBondDescriptor)
    • org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptor (implements org.openscience.cdk.qsar.IBondDescriptor)
    • org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor
    • org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor
    • org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor
    • org.openscience.cdk.qsar.descriptors.bond.BondSigmaElectronegativityDescriptor (implements org.openscience.cdk.qsar.IBondDescriptor)
    • org.openscience.cdk.qsar.descriptors.bond.IPBondLearningDescriptor
  • java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    • java.util.AbstractList<E> (implements java.util.List<E>)
      • java.util.Vector<E> (implements java.lang.Cloneable, java.util.List<E>, java.util.RandomAccess, java.io.Serializable)
        • org.openscience.cdk.ringsearch.Queue
  • org.openscience.cdk.tools.diff.tree.AbstractDifference (implements org.openscience.cdk.tools.diff.tree.IDifference)
  • org.openscience.cdk.tools.diff.tree.AbstractDifferenceList (implements org.openscience.cdk.tools.diff.tree.IDifferenceList)
    • org.openscience.cdk.tools.diff.tree.BooleanArrayDifference (implements org.openscience.cdk.tools.diff.tree.IDifferenceList)
    • org.openscience.cdk.tools.diff.tree.ChemObjectDifference (implements org.openscience.cdk.tools.diff.tree.IDifferenceList)
    • org.openscience.cdk.tools.diff.tree.Point2dDifference (implements org.openscience.cdk.tools.diff.tree.IDifferenceList)
    • org.openscience.cdk.tools.diff.tree.Point3dDifference (implements org.openscience.cdk.tools.diff.tree.IDifferenceList)
  • org.openscience.cdk.fingerprint.AbstractFingerprinter (implements org.openscience.cdk.fingerprint.IFingerprinter)
    • org.openscience.cdk.fingerprint.AtomPairs2DFingerprinter (implements org.openscience.cdk.fingerprint.IFingerprinter)
    • org.openscience.cdk.fingerprint.CircularFingerprinter (implements org.openscience.cdk.fingerprint.IFingerprinter)
    • org.openscience.cdk.fingerprint.EStateFingerprinter (implements org.openscience.cdk.fingerprint.IFingerprinter)
    • org.openscience.cdk.fingerprint.Fingerprinter (implements org.openscience.cdk.fingerprint.IFingerprinter)
      • org.openscience.cdk.fingerprint.GraphOnlyFingerprinter
      • org.openscience.cdk.fingerprint.HybridizationFingerprinter (implements org.openscience.cdk.fingerprint.IFingerprinter)
    • org.openscience.cdk.fingerprint.LingoFingerprinter (implements org.openscience.cdk.fingerprint.IFingerprinter)
    • org.openscience.cdk.fingerprint.MACCSFingerprinter (implements org.openscience.cdk.fingerprint.IFingerprinter)
    • org.openscience.cdk.fingerprint.PubchemFingerprinter (implements org.openscience.cdk.fingerprint.IFingerprinter)
    • org.openscience.cdk.fingerprint.ShortestPathFingerprinter (implements org.openscience.cdk.fingerprint.IFingerprinter, java.io.Serializable)
    • org.openscience.cdk.fingerprint.SignatureFingerprinter (implements org.openscience.cdk.fingerprint.IFingerprinter)
    • org.openscience.cdk.fingerprint.SubstructureFingerprinter (implements org.openscience.cdk.fingerprint.IFingerprinter)
      • org.openscience.cdk.fingerprint.KlekotaRothFingerprinter
  • org.openscience.cdk.renderer.font.AbstractFontManager (implements org.openscience.cdk.renderer.font.IFontManager)
    • org.openscience.cdk.renderer.font.AWTFontManager
  • org.openscience.cdk.renderer.generators.parameter.AbstractGeneratorParameter<T> (implements org.openscience.cdk.renderer.generators.IGeneratorParameter<T>)
    • org.openscience.cdk.renderer.generators.AtomNumberGenerator.AtomColorer
    • org.openscience.cdk.renderer.generators.AtomNumberGenerator.AtomNumberTextColor
    • org.openscience.cdk.renderer.generators.AtomNumberGenerator.ColorByType
    • org.openscience.cdk.renderer.generators.AtomNumberGenerator.Offset
    • org.openscience.cdk.renderer.generators.AtomNumberGenerator.WillDrawAtomNumbers
    • org.openscience.cdk.renderer.generators.BasicAtomGenerator.AtomColor
    • org.openscience.cdk.renderer.generators.BasicAtomGenerator.AtomColorer
    • org.openscience.cdk.renderer.generators.BasicAtomGenerator.AtomRadius
    • org.openscience.cdk.renderer.generators.BasicAtomGenerator.ColorByType
    • org.openscience.cdk.renderer.generators.BasicAtomGenerator.CompactAtom
    • org.openscience.cdk.renderer.generators.BasicAtomGenerator.CompactShape
    • org.openscience.cdk.renderer.generators.BasicAtomGenerator.KekuleStructure
    • org.openscience.cdk.renderer.generators.BasicAtomGenerator.ShowEndCarbons
    • org.openscience.cdk.renderer.generators.BasicAtomGenerator.ShowExplicitHydrogens
    • org.openscience.cdk.renderer.generators.BasicBondGenerator.BondDistance
    • org.openscience.cdk.renderer.generators.BasicBondGenerator.BondWidth
    • org.openscience.cdk.renderer.generators.BasicBondGenerator.DefaultBondColor
    • org.openscience.cdk.renderer.generators.BasicBondGenerator.TowardsRingCenterProportion
    • org.openscience.cdk.renderer.generators.BasicBondGenerator.WedgeWidth
    • org.openscience.cdk.renderer.generators.BasicSceneGenerator.ArrowHeadWidth
    • org.openscience.cdk.renderer.generators.BasicSceneGenerator.BackgroundColor
    • org.openscience.cdk.renderer.generators.BasicSceneGenerator.BondLength
    • org.openscience.cdk.renderer.generators.BasicSceneGenerator.FitToScreen
    • org.openscience.cdk.renderer.generators.BasicSceneGenerator.FontName
    • org.openscience.cdk.renderer.generators.BasicSceneGenerator.ForegroundColor
    • org.openscience.cdk.renderer.generators.BasicSceneGenerator.Margin
    • org.openscience.cdk.renderer.generators.BasicSceneGenerator.Scale
    • org.openscience.cdk.renderer.generators.BasicSceneGenerator.ShowMoleculeTitle
    • org.openscience.cdk.renderer.generators.BasicSceneGenerator.ShowReactionTitle
    • org.openscience.cdk.renderer.generators.BasicSceneGenerator.ShowTooltip
    • org.openscience.cdk.renderer.generators.BasicSceneGenerator.UseAntiAliasing
    • org.openscience.cdk.renderer.generators.BasicSceneGenerator.UsedFontStyle
    • org.openscience.cdk.renderer.generators.BasicSceneGenerator.ZoomFactor
    • org.openscience.cdk.renderer.generators.BoundsGenerator.BoundsColor
    • org.openscience.cdk.renderer.generators.ExtendedAtomGenerator.ShowAtomTypeNames
    • org.openscience.cdk.renderer.generators.ExtendedAtomGenerator.ShowImplicitHydrogens
    • org.openscience.cdk.renderer.generators.HighlightGenerator.HighlightPalette
    • org.openscience.cdk.renderer.generators.HighlightGenerator.HighlightRadius
    • org.openscience.cdk.renderer.generators.MappingGenerator.AtomAtomMappingLineColor
    • org.openscience.cdk.renderer.generators.MappingGenerator.MappingLineWidth
    • org.openscience.cdk.renderer.generators.MappingGenerator.ShowAtomAtomMapping
    • org.openscience.cdk.renderer.generators.ReactionSceneGenerator.ArrowHeadWidth
    • org.openscience.cdk.renderer.generators.ReactionSceneGenerator.ShowReactionBoxes
    • org.openscience.cdk.renderer.RendererModel.ColorHash
    • org.openscience.cdk.renderer.RendererModel.ExternalHighlightColor
    • org.openscience.cdk.renderer.RendererModel.MarkedOutput
    • org.openscience.cdk.renderer.RendererModel.Padding
    • org.openscience.cdk.renderer.RendererModel.SelectionColor
    • org.openscience.cdk.renderer.RendererModel.TitleColor
    • org.openscience.cdk.renderer.RendererModel.TitleFontScale
    • org.openscience.cdk.renderer.generators.RingGenerator.CDKStyleAromaticity
    • org.openscience.cdk.renderer.generators.RingGenerator.MaxDrawableAromaticRing
    • org.openscience.cdk.renderer.generators.RingGenerator.RingProportion
    • org.openscience.cdk.renderer.generators.RingGenerator.ShowAromaticity
    • org.openscience.cdk.renderer.generators.standard.StandardGenerator.AnnotationColor
    • org.openscience.cdk.renderer.generators.standard.StandardGenerator.AnnotationDistance
    • org.openscience.cdk.renderer.generators.standard.StandardGenerator.AnnotationFontScale
    • org.openscience.cdk.renderer.generators.standard.StandardGenerator.AtomColor
    • org.openscience.cdk.renderer.generators.standard.StandardGenerator.BondSeparation
    • org.openscience.cdk.renderer.generators.standard.StandardGenerator.DashSection
    • org.openscience.cdk.renderer.generators.standard.StandardGenerator.DelocalisedDonutsBondDisplay
    • org.openscience.cdk.renderer.generators.standard.StandardGenerator.DeuteriumSymbol
    • org.openscience.cdk.renderer.generators.standard.StandardGenerator.FancyBoldWedges
    • org.openscience.cdk.renderer.generators.standard.StandardGenerator.FancyHashedWedges
    • org.openscience.cdk.renderer.generators.standard.StandardGenerator.ForceDelocalisedBondDisplay
    • org.openscience.cdk.renderer.generators.standard.StandardGenerator.HashSpacing
    • org.openscience.cdk.renderer.generators.standard.StandardGenerator.Highlighting
    • org.openscience.cdk.renderer.generators.standard.StandardGenerator.OmitMajorIsotopes
    • org.openscience.cdk.renderer.generators.standard.StandardGenerator.OuterGlowWidth
    • org.openscience.cdk.renderer.generators.standard.StandardGenerator.PseudoFontStyle
    • org.openscience.cdk.renderer.generators.standard.StandardGenerator.SgroupBracketDepth
    • org.openscience.cdk.renderer.generators.standard.StandardGenerator.SgroupFontScale
    • org.openscience.cdk.renderer.generators.standard.StandardGenerator.StrokeRatio
    • org.openscience.cdk.renderer.generators.standard.StandardGenerator.SymbolMarginRatio
    • org.openscience.cdk.renderer.generators.standard.StandardGenerator.Visibility
    • org.openscience.cdk.renderer.generators.standard.StandardGenerator.WaveSpacing
    • org.openscience.cdk.renderer.generators.standard.StandardGenerator.WedgeRatio
  • org._3pq.jgrapht.graph.AbstractGraph (implements org._3pq.jgrapht.Graph)
    • org._3pq.jgrapht.graph.Subgraph (implements java.io.Serializable)
      • org._3pq.jgrapht.graph.UndirectedSubgraph (implements org._3pq.jgrapht.UndirectedGraph)
        • org.openscience.cdk.ringsearch.cyclebasis.SimpleCycle
  • signature.AbstractGraphBuilder
    • org.openscience.cdk.signature.MoleculeFromSignatureBuilder
  • signature.AbstractGraphSignature
    • org.openscience.cdk.signature.MoleculeSignature
  • org.openscience.cdk.smsd.interfaces.AbstractMCS
    • org.openscience.cdk.smsd.Isomorphism (implements java.io.Serializable)
  • org.openscience.cdk.smsd.interfaces.AbstractMCSAlgorithm
    • org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler (implements org.openscience.cdk.smsd.interfaces.IMCSBase)
    • org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler (implements org.openscience.cdk.smsd.interfaces.IMCSBase)
    • org.openscience.cdk.smsd.algorithm.single.SingleMappingHandler (implements org.openscience.cdk.smsd.interfaces.IMCSBase)
    • org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler (implements org.openscience.cdk.smsd.interfaces.IMCSBase)
  • org.openscience.cdk.qsar.AbstractMolecularDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.AcidicGroupCountDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.FractionalCSP3Descriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.HybridizationRatioDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor
    • org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.SpiroAtomCountDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.protein.TaeAminoAcidDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.VABCDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
    • org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
  • signature.AbstractQuotientGraph
    • org.openscience.cdk.signature.SignatureQuotientGraph
  • org.openscience.cdk.smsd.labelling.AbstractReactionLabeller
    • org.openscience.cdk.smsd.labelling.SignatureReactionCanoniser (implements org.openscience.cdk.smsd.labelling.ICanonicalReactionLabeller)
    • org.openscience.cdk.smsd.labelling.SmilesReactionCanoniser (implements org.openscience.cdk.smsd.labelling.ICanonicalReactionLabeller)
  • org.openscience.cdk.renderer.AbstractRenderer<T>
    • org.openscience.cdk.renderer.AtomContainerRenderer (implements org.openscience.cdk.renderer.IRenderer<T>)
    • org.openscience.cdk.renderer.ChemModelRenderer (implements org.openscience.cdk.renderer.IRenderer<T>)
    • org.openscience.cdk.renderer.MoleculeSetRenderer (implements org.openscience.cdk.renderer.IRenderer<T>)
    • org.openscience.cdk.renderer.ReactionRenderer (implements org.openscience.cdk.renderer.IRenderer<T>)
    • org.openscience.cdk.renderer.ReactionSetRenderer (implements org.openscience.cdk.renderer.IRenderer<T>)
  • org.openscience.cdk.io.formats.AbstractResourceFormat (implements org.openscience.cdk.io.formats.IResourceFormat)
    • org.openscience.cdk.io.formats.ABINITFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.Aces2Format (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.ADFFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.AlchemyFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.BGFFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.BSFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.CacaoCartesianFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.CacaoInternalFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.CACheFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.CDKOWLFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.CDKSourceCodeFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.Chem3D_Cartesian_1Format (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.Chem3D_Cartesian_2Format (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.ChemDrawFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.ChemtoolFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.CIFFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.CMLFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.CMLRSSFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.CRK2DFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.CRK3DFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.CrystClustFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.CTXFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.DaltonFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.DMol3Format (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.DOCK5Format (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.FenskeHall_ZMatrixFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.FingerprintFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.GamessFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.Gaussian03Format (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.Gaussian90Format (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.Gaussian92Format (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.Gaussian94Format (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.Gaussian95Format (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.Gaussian98Format (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.GaussianInputFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.GhemicalMMFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.GhemicalSPMFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.GROMOS96Format (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.HINFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.INChIFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.INChIPlainTextFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.JaguarFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.JMEFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.MacroModelFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.MDLFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.MDLRXNFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.MDLRXNV2000Format (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.MDLRXNV3000Format (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.MDLV2000Format (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.MDLV3000Format (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.MMODFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.Mol2Format (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.MOPAC2002Format (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.MOPAC2007Format (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.MOPAC2009Format (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.MOPAC2012Format (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.MOPAC7Format (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.MOPAC7InputFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.MOPAC93Format (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.MOPAC97Format (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.MoSSOutputFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.MPQCFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.NWChemFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.PCModelFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.PDBFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.PDBMLFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.PMPFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.POVRayFormat (implements org.openscience.cdk.io.formats.IResourceFormat)
    • org.openscience.cdk.io.formats.PQSChemFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.PubChemASNFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.PubChemCompoundsXMLFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.PubChemCompoundXMLFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.PubChemFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.PubChemSubstancesASNFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.QChemFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.RawCopyFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.RGroupQueryFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.SDFFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.ShelXFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.SMARTSFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.SMILESFIXFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.SMILESFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.SpartanFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.SVGFormat (implements org.openscience.cdk.io.formats.IResourceFormat)
    • org.openscience.cdk.io.formats.SybylDescriptorFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.TinkerMM2Format (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.TinkerXYZFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.TurboMoleFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.UniChemXYZFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.VASPFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
    • org.openscience.cdk.io.formats.ViewmolFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.XEDFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.XYZFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.YasaraFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.ZindoFormat (implements org.openscience.cdk.io.formats.IChemFormat)
    • org.openscience.cdk.io.formats.ZMatrixFormat (implements org.openscience.cdk.io.formats.IChemFormatMatcher)
  • org.openscience.cdk.renderer.selection.AbstractSelection (implements org.openscience.cdk.renderer.selection.IChemObjectSelection)
  • org.openscience.cdk.smsd.interfaces.AbstractSubGraph
    • org.openscience.cdk.smsd.algorithm.rgraph.CDKSubGraphHandler (implements org.openscience.cdk.smsd.interfaces.IMCSBase)
    • org.openscience.cdk.smsd.algorithm.vflib.VFlibSubStructureHandler (implements org.openscience.cdk.smsd.interfaces.IMCSBase)
    • org.openscience.cdk.smsd.algorithm.vflib.VFlibTurboHandler (implements org.openscience.cdk.smsd.interfaces.IMCSBase)
  • org.openscience.cdk.validate.AbstractValidator (implements org.openscience.cdk.validate.IValidator)
    • org.openscience.cdk.validate.BasicValidator
    • org.openscience.cdk.validate.CDKValidator
    • org.openscience.cdk.validate.DictionaryValidator
    • org.openscience.cdk.validate.Geometry3DValidator
  • signature.AbstractVertexSignature
    • org.openscience.cdk.signature.AtomSignature
  • org.openscience.cdk.formula.AdductFormula (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IAdductFormula, java.lang.Iterable<T>)
    • org.openscience.cdk.debug.DebugAdductFormula (implements org.openscience.cdk.interfaces.IAdductFormula)
  • org.openscience.cdk.silent.AdductFormula (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IAdductFormula, java.lang.Iterable<T>)
  • org.openscience.cdk.reaction.mechanism.AdductionLPMechanism (implements org.openscience.cdk.reaction.IReactionMechanism)
  • org.openscience.cdk.reaction.mechanism.AdductionPBMechanism (implements org.openscience.cdk.reaction.IReactionMechanism)
  • org.openscience.cdk.graph.matrix.AdjacencyMatrix (implements org.openscience.cdk.graph.matrix.IGraphMatrix)
  • org.openscience.cdk.graph.AllCycles
  • org.openscience.cdk.graph.AllPairsShortestPaths
  • org.openscience.cdk.ringsearch.AllRingsFinder
  • org.openscience.cdk.tools.manipulator.AminoAcidManipulator
  • org.openscience.cdk.templates.AminoAcids
  • org.openscience.cdk.math.qm.AngularMomentum
  • org.openscience.cdk.aromaticity.Aromaticity
  • org.openscience.cdk.aromaticity.AromaticityCalculator
  • org.openscience.cdk.renderer.elements.ArrowElement (implements org.openscience.cdk.renderer.elements.IRenderingElement)
  • org.openscience.cdk.renderer.generators.AtomContainerBoundsGenerator (implements org.openscience.cdk.renderer.generators.IGenerator<T>)
  • org.openscience.cdk.tools.manipulator.AtomContainerComparator (implements java.util.Comparator<T>)
  • org.openscience.cdk.tools.manipulator.AtomContainerComparatorBy2DCenter (implements java.util.Comparator<T>)
  • org.openscience.cdk.tools.diff.AtomContainerDiff
  • org.openscience.cdk.tools.manipulator.AtomContainerManipulator
    • org.openscience.cdk.smsd.tools.ExtAtomContainerManipulator
    • org.openscience.cdk.normalize.SMSDNormalizer
  • org.openscience.cdk.smsd.labelling.AtomContainerPrinter
  • org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator
  • org.openscience.cdk.tools.diff.AtomDiff
  • org.openscience.cdk.tools.AtomicProperties
  • org.openscience.cdk.isomorphism.AtomMappingTools
  • org.openscience.cdk.isomorphism.AtomMatcher
  • org.openscience.cdk.renderer.generators.AtomNumberGenerator (implements org.openscience.cdk.renderer.generators.IGenerator<T>)
  • org.openscience.cdk.layout.AtomPlacer
  • org.openscience.cdk.modeling.builder3d.AtomPlacer3D
  • org.openscience.cdk.AtomRef (implements org.openscience.cdk.interfaces.IAtom)
  • org.openscience.cdk.modeling.builder3d.AtomTetrahedralLigandPlacer3D
  • org.openscience.cdk.geometry.AtomTools
  • org.openscience.cdk.tools.AtomTypeAwareSaturationChecker (implements org.openscience.cdk.tools.IDeduceBondOrderTool, org.openscience.cdk.tools.IValencyChecker)
  • org.openscience.cdk.charges.AtomTypeCharges (implements org.openscience.cdk.charges.IChargeCalculator)
  • org.openscience.cdk.tools.diff.AtomTypeDiff
  • org.openscience.cdk.config.AtomTypeFactory
  • org.openscience.cdk.tools.diff.tree.AtomTypeHybridizationDifference (implements org.openscience.cdk.tools.diff.tree.IDifference)
  • org.openscience.cdk.tools.manipulator.AtomTypeManipulator
  • org.openscience.cdk.atomtype.mapper.AtomTypeMapper
  • org.openscience.cdk.config.atomtypes.AtomTypeReader
  • org.openscience.cdk.tools.AtomTypeTools
  • org.openscience.cdk.qsar.AtomValenceTool
  • org.openscience.cdk.stereo.Atropisomeric
  • org.openscience.cdk.iupac.parser.AttachedGroup
  • org.openscience.cdk.renderer.AverageBondLengthCalculator
  • org.openscience.cdk.renderer.generators.BasicAtomGenerator (implements org.openscience.cdk.renderer.generators.IGenerator<T>)
    • org.openscience.cdk.renderer.generators.AtomMassGenerator
    • org.openscience.cdk.renderer.generators.ExtendedAtomGenerator
  • org.openscience.cdk.renderer.generators.BasicBondGenerator (implements org.openscience.cdk.renderer.generators.IGenerator<T>)
    • org.openscience.cdk.renderer.generators.RingGenerator
  • org.openscience.cdk.renderer.generators.BasicGenerator (implements org.openscience.cdk.renderer.generators.IGenerator<T>)
  • org.openscience.cdk.renderer.generators.BasicSceneGenerator (implements org.openscience.cdk.renderer.generators.IGenerator<T>)
  • org.openscience.cdk.fingerprint.model.Bayesian
  • org.openscience.cdk.graph.BFSShortestPath
  • org.openscience.cdk.graph.BiconnectivityInspector
  • org.openscience.cdk.smsd.helper.BinaryTree
  • org.openscience.cdk.fingerprint.BitSetFingerprint (implements org.openscience.cdk.fingerprint.IBitFingerprint)
  • org.openscience.cdk.smsd.algorithm.mcsplus.BKKCKCF
  • org.openscience.cdk.tools.diff.BondDiff
  • org.openscience.cdk.smsd.tools.BondEnergies
  • org.openscience.cdk.smsd.helper.BondEnergy
  • org.openscience.cdk.tools.manipulator.BondManipulator
  • org.openscience.cdk.isomorphism.BondMatcher
  • org.openscience.cdk.tools.diff.tree.BondOrderDifference (implements org.openscience.cdk.tools.diff.tree.IDifference)
  • org.openscience.cdk.BondRef (implements org.openscience.cdk.interfaces.IBond)
  • org.openscience.cdk.geometry.BondTools
  • org.openscience.cdk.tools.diff.tree.BooleanDifference (implements org.openscience.cdk.tools.diff.tree.IDifference)
  • org.openscience.cdk.qsar.result.BooleanResultType (implements org.openscience.cdk.qsar.result.IDescriptorResult)
    • org.openscience.cdk.qsar.result.BooleanResult
  • org.openscience.cdk.renderer.elements.Bounds (implements org.openscience.cdk.renderer.elements.IRenderingElement)
  • org.openscience.cdk.renderer.BoundsCalculator
  • org.openscience.cdk.renderer.generators.BoundsGenerator (implements org.openscience.cdk.renderer.generators.IGenerator<T>)
  • org.openscience.cdk.tools.BremserOneSphereHOSECodePredictor (implements java.io.Serializable)
  • org.openscience.cdk.graph.rebond.Bspt
  • org.openscience.cdk.graph.invariant.Canon
  • org.openscience.cdk.graph.invariant.CanonicalLabeler
  • org.openscience.cdk.smsd.labelling.CanonicalLabellingAdaptor (implements org.openscience.cdk.smsd.labelling.ICanonicalMoleculeLabeller)
  • org.openscience.cdk.graph.invariant.CanonOpts
  • org.openscience.cdk.index.CASNumber
  • org.openscience.cdk.CDK
  • org.openscience.cdk.libio.jena.CDK
  • org.openscience.cdk.renderer.color.CDK2DAtomColors (implements org.openscience.cdk.renderer.color.IAtomColorer, java.io.Serializable)
  • org.openscience.cdk.renderer.color.CDKAtomColors (implements org.openscience.cdk.renderer.color.IAtomColorer)
  • org.openscience.cdk.atomtype.CDKAtomTypeMatcher (implements org.openscience.cdk.atomtype.IAtomTypeMatcher)
  • org.openscience.cdk.config.CDKBasedAtomTypeConfigurator (implements org.openscience.cdk.config.IAtomTypeConfigurator)
  • org.openscience.cdk.CDKConstants
  • org.openscience.cdk.dict.CDKDictionaryReferences
  • org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector
  • org.openscience.cdk.tools.CDKHydrogenAdder
  • org.openscience.cdk.smsd.algorithm.rgraph.CDKMCS
  • org.openscience.cdk.smsd.algorithm.rgraph.CDKRGraph
  • org.openscience.cdk.smsd.algorithm.rgraph.CDKRMap
  • org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler
  • org.openscience.cdk.smsd.algorithm.rgraph.CDKRNode
  • org.openscience.cdk.tools.CDKUtilities
  • org.openscience.cdk.tools.CDKValencyChecker (implements org.openscience.cdk.tools.IValencyChecker)
  • org.openscience.cdk.formula.rules.ChargeRule (implements org.openscience.cdk.formula.rules.IRule)
  • org.openscience.cdk.tools.manipulator.ChemFileManipulator
  • org.openscience.cdk.structgen.stochastic.operator.ChemGraph
  • org.openscience.cdk.smsd.filters.ChemicalFilters
  • org.openscience.cdk.tools.manipulator.ChemModelManipulator
  • org.openscience.cdk.ChemObject (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IChemObject, java.io.Serializable)
    • org.openscience.cdk.AtomContainer (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IAtomContainer, org.openscience.cdk.interfaces.IChemObjectListener, java.io.Serializable)
      • org.openscience.cdk.libio.md.ChargeGroup
      • org.openscience.cdk.Crystal (implements java.lang.Cloneable, org.openscience.cdk.interfaces.ICrystal, java.io.Serializable)
        • org.openscience.cdk.debug.DebugCrystal (implements org.openscience.cdk.interfaces.ICrystal)
      • org.openscience.cdk.debug.DebugAtomContainer (implements org.openscience.cdk.interfaces.IAtomContainer)
      • org.openscience.cdk.libio.md.MDMolecule
      • org.openscience.cdk.Monomer (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IMonomer, java.io.Serializable)
        • org.openscience.cdk.AminoAcid (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IAminoAcid, java.io.Serializable)
          • org.openscience.cdk.debug.DebugAminoAcid (implements org.openscience.cdk.interfaces.IAminoAcid)
        • org.openscience.cdk.debug.DebugMonomer (implements org.openscience.cdk.interfaces.IMonomer)
        • org.openscience.cdk.protein.data.PDBMonomer (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IPDBMonomer)
          • org.openscience.cdk.debug.DebugPDBMonomer (implements org.openscience.cdk.interfaces.IPDBMonomer)
      • org.openscience.cdk.Polymer (implements org.openscience.cdk.interfaces.IPolymer, java.io.Serializable)
        • org.openscience.cdk.BioPolymer (implements org.openscience.cdk.interfaces.IBioPolymer, java.io.Serializable)
          • org.openscience.cdk.debug.DebugBioPolymer (implements org.openscience.cdk.interfaces.IBioPolymer)
          • org.openscience.cdk.protein.data.PDBPolymer (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IPDBPolymer)
            • org.openscience.cdk.debug.DebugPDBPolymer (implements org.openscience.cdk.interfaces.IBioPolymer)
        • org.openscience.cdk.debug.DebugPolymer (implements org.openscience.cdk.interfaces.IPolymer)
      • org.openscience.cdk.libio.md.Residue
      • org.openscience.cdk.Ring (implements org.openscience.cdk.interfaces.IRing, java.io.Serializable)
        • org.openscience.cdk.debug.DebugRing (implements org.openscience.cdk.interfaces.IRing)
      • org.openscience.cdk.Strand (implements org.openscience.cdk.interfaces.IStrand, java.io.Serializable)
        • org.openscience.cdk.debug.DebugStrand (implements org.openscience.cdk.interfaces.IStrand)
        • org.openscience.cdk.protein.data.PDBStrand
    • org.openscience.cdk.AtomContainerSet (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IAtomContainerSet, org.openscience.cdk.interfaces.IChemObjectListener, java.io.Serializable)
      • org.openscience.cdk.debug.DebugAtomContainerSet (implements org.openscience.cdk.interfaces.IAtomContainerSet)
      • org.openscience.cdk.debug.DebugSubstance (implements org.openscience.cdk.interfaces.ISubstance)
      • org.openscience.cdk.RingSet (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IRingSet, java.io.Serializable)
        • org.openscience.cdk.debug.DebugRingSet (implements org.openscience.cdk.interfaces.IRingSet)
      • org.openscience.cdk.Substance (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IChemObjectListener, org.openscience.cdk.interfaces.ISubstance, java.io.Serializable)
    • org.openscience.cdk.ChemFile (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IChemFile, org.openscience.cdk.interfaces.IChemObjectListener, java.io.Serializable)
      • org.openscience.cdk.debug.DebugChemFile (implements org.openscience.cdk.interfaces.IChemFile)
    • org.openscience.cdk.ChemModel (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IChemModel, org.openscience.cdk.interfaces.IChemObjectListener, java.io.Serializable)
      • org.openscience.cdk.debug.DebugChemModel (implements org.openscience.cdk.interfaces.IChemModel)
    • org.openscience.cdk.ChemSequence (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IChemObjectListener, org.openscience.cdk.interfaces.IChemSequence, java.io.Serializable)
      • org.openscience.cdk.debug.DebugChemSequence (implements org.openscience.cdk.interfaces.IChemSequence)
    • org.openscience.cdk.debug.DebugChemObject (implements org.openscience.cdk.interfaces.IChemObject)
    • org.openscience.cdk.ElectronContainer (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IElectronContainer, java.io.Serializable)
      • org.openscience.cdk.Association (implements java.lang.Cloneable, java.io.Serializable)
      • org.openscience.cdk.Bond (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IBond, java.io.Serializable)
        • org.openscience.cdk.debug.DebugBond (implements org.openscience.cdk.interfaces.IBond)
        • org.openscience.cdk.pharmacophore.PharmacophoreAngleBond
        • org.openscience.cdk.pharmacophore.PharmacophoreBond
        • org.openscience.cdk.pharmacophore.PharmacophoreQueryAngleBond (implements org.openscience.cdk.isomorphism.matchers.IQueryBond)
        • org.openscience.cdk.pharmacophore.PharmacophoreQueryBond (implements org.openscience.cdk.isomorphism.matchers.IQueryBond)
      • org.openscience.cdk.debug.DebugElectronContainer (implements org.openscience.cdk.interfaces.IElectronContainer)
      • org.openscience.cdk.LonePair (implements java.lang.Cloneable, org.openscience.cdk.interfaces.ILonePair, java.io.Serializable)
        • org.openscience.cdk.debug.DebugLonePair (implements org.openscience.cdk.interfaces.ILonePair)
      • org.openscience.cdk.SingleElectron (implements java.lang.Cloneable, org.openscience.cdk.interfaces.ISingleElectron, java.io.Serializable)
        • org.openscience.cdk.debug.DebugSingleElectron (implements org.openscience.cdk.interfaces.ISingleElectron)
    • org.openscience.cdk.Element (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IElement, java.io.Serializable)
      • org.openscience.cdk.debug.DebugElement (implements org.openscience.cdk.interfaces.IElement)
      • org.openscience.cdk.Isotope (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IIsotope, java.io.Serializable)
        • org.openscience.cdk.AtomType (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IAtomType, java.io.Serializable)
          • org.openscience.cdk.Atom (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IAtom, java.io.Serializable)
            • org.openscience.cdk.debug.DebugAtom (implements org.openscience.cdk.interfaces.IAtom)
            • org.openscience.cdk.protein.data.PDBAtom (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IPDBAtom)
              • org.openscience.cdk.debug.DebugPDBAtom (implements org.openscience.cdk.interfaces.IPDBAtom)
            • org.openscience.cdk.pharmacophore.PharmacophoreAtom
            • org.openscience.cdk.pharmacophore.PharmacophoreQueryAtom (implements org.openscience.cdk.isomorphism.matchers.IQueryAtom)
            • org.openscience.cdk.PseudoAtom (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IPseudoAtom, java.io.Serializable)
              • org.openscience.cdk.debug.DebugPseudoAtom (implements org.openscience.cdk.interfaces.IPseudoAtom)
              • org.openscience.cdk.EnzymeResidueLocator
              • org.openscience.cdk.FragmentAtom (implements org.openscience.cdk.interfaces.IFragmentAtom)
                • org.openscience.cdk.debug.DebugFragmentAtom
          • org.openscience.cdk.debug.DebugAtomType (implements org.openscience.cdk.interfaces.IAtomType)
        • org.openscience.cdk.debug.DebugIsotope (implements org.openscience.cdk.interfaces.IIsotope)
    • org.openscience.cdk.Mapping (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IMapping, java.io.Serializable)
      • org.openscience.cdk.debug.DebugMapping (implements org.openscience.cdk.interfaces.IMapping)
    • org.openscience.cdk.protein.data.PDBStructure (implements org.openscience.cdk.interfaces.IPDBStructure)
      • org.openscience.cdk.debug.DebugPDBStructure
    • org.openscience.cdk.Reaction (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IReaction, java.io.Serializable)
      • org.openscience.cdk.debug.DebugReaction (implements org.openscience.cdk.interfaces.IReaction)
    • org.openscience.cdk.ReactionSet (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IChemObjectListener, org.openscience.cdk.interfaces.IReactionSet, java.io.Serializable)
      • org.openscience.cdk.debug.DebugReactionSet (implements org.openscience.cdk.interfaces.IReactionSet)
      • org.openscience.cdk.reaction.ReactionChain
      • org.openscience.cdk.ReactionScheme (implements org.openscience.cdk.interfaces.IReactionScheme)
        • org.openscience.cdk.debug.DebugReactionScheme (implements org.openscience.cdk.interfaces.IReactionScheme)
  • org.openscience.cdk.silent.ChemObject (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IChemObject, java.io.Serializable)
    • org.openscience.cdk.silent.AtomContainer (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IAtomContainer, org.openscience.cdk.interfaces.IChemObjectListener, java.io.Serializable)
      • org.openscience.cdk.silent.Crystal (implements java.lang.Cloneable, org.openscience.cdk.interfaces.ICrystal, java.io.Serializable)
      • org.openscience.cdk.silent.Monomer (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IMonomer, java.io.Serializable)
        • org.openscience.cdk.silent.AminoAcid (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IAminoAcid, java.io.Serializable)
        • org.openscience.cdk.silent.PDBMonomer (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IPDBMonomer)
      • org.openscience.cdk.silent.Polymer (implements org.openscience.cdk.interfaces.IPolymer, java.io.Serializable)
        • org.openscience.cdk.silent.BioPolymer (implements org.openscience.cdk.interfaces.IBioPolymer, java.io.Serializable)
          • org.openscience.cdk.silent.PDBPolymer (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IPDBPolymer)
      • org.openscience.cdk.silent.Ring (implements org.openscience.cdk.interfaces.IRing, java.io.Serializable)
      • org.openscience.cdk.silent.Strand (implements org.openscience.cdk.interfaces.IStrand, java.io.Serializable)
    • org.openscience.cdk.silent.AtomContainerSet (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IAtomContainerSet, org.openscience.cdk.interfaces.IChemObjectListener, java.io.Serializable)
      • org.openscience.cdk.silent.RingSet (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IRingSet, java.io.Serializable)
      • org.openscience.cdk.silent.Substance (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IChemObjectListener, org.openscience.cdk.interfaces.ISubstance, java.io.Serializable)
    • org.openscience.cdk.silent.ChemFile (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IChemFile, org.openscience.cdk.interfaces.IChemObjectListener, java.io.Serializable)
    • org.openscience.cdk.silent.ChemModel (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IChemModel, org.openscience.cdk.interfaces.IChemObjectListener, java.io.Serializable)
    • org.openscience.cdk.silent.ChemSequence (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IChemObjectListener, org.openscience.cdk.interfaces.IChemSequence, java.io.Serializable)
    • org.openscience.cdk.silent.ElectronContainer (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IElectronContainer, java.io.Serializable)
      • org.openscience.cdk.silent.Bond (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IBond, java.io.Serializable)
      • org.openscience.cdk.silent.LonePair (implements java.lang.Cloneable, org.openscience.cdk.interfaces.ILonePair, java.io.Serializable)
      • org.openscience.cdk.silent.SingleElectron (implements java.lang.Cloneable, org.openscience.cdk.interfaces.ISingleElectron, java.io.Serializable)
    • org.openscience.cdk.silent.Element (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IElement, java.io.Serializable)
      • org.openscience.cdk.silent.Isotope (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IIsotope, java.io.Serializable)
        • org.openscience.cdk.silent.AtomType (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IAtomType, java.io.Serializable)
          • org.openscience.cdk.silent.Atom (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IAtom, java.io.Serializable)
            • org.openscience.cdk.silent.PDBAtom (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IPDBAtom)
            • org.openscience.cdk.silent.PseudoAtom (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IPseudoAtom, java.io.Serializable)
              • org.openscience.cdk.silent.FragmentAtom (implements org.openscience.cdk.interfaces.IFragmentAtom)
    • org.openscience.cdk.silent.Mapping (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IMapping, java.io.Serializable)
    • org.openscience.cdk.silent.PDBStructure (implements org.openscience.cdk.interfaces.IPDBStructure)
    • org.openscience.cdk.silent.Reaction (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IReaction, java.io.Serializable)
    • org.openscience.cdk.silent.ReactionSet (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IChemObjectListener, org.openscience.cdk.interfaces.IReactionSet, java.io.Serializable)
      • org.openscience.cdk.silent.ReactionScheme (implements org.openscience.cdk.interfaces.IReactionScheme)
  • org.openscience.cdk.tools.diff.ChemObjectDiff
  • org.openscience.cdk.io.ChemObjectIO (implements org.openscience.cdk.io.IChemObjectIO)
    • org.openscience.cdk.io.DefaultChemObjectReader (implements org.openscience.cdk.io.ISimpleChemObjectReader)
      • org.openscience.cdk.io.rdf.CDKOWLReader
      • org.openscience.cdk.io.CIFReader
      • org.openscience.cdk.io.CMLReader
      • org.openscience.cdk.io.CrystClustReader
      • org.openscience.cdk.io.CTXReader
      • org.openscience.cdk.io.GamessReader
      • org.openscience.cdk.io.Gaussian03Reader
      • org.openscience.cdk.io.Gaussian98Reader
      • org.openscience.cdk.io.GhemicalMMReader
      • org.openscience.cdk.io.HINReader
      • org.openscience.cdk.io.INChIPlainTextReader
      • org.openscience.cdk.io.INChIReader
      • org.openscience.cdk.io.MDLReader
      • org.openscience.cdk.io.MDLRXNReader
      • org.openscience.cdk.io.MDLRXNV2000Reader
      • org.openscience.cdk.io.MDLRXNV3000Reader
      • org.openscience.cdk.io.MDLV2000Reader
      • org.openscience.cdk.io.MDLV3000Reader
      • org.openscience.cdk.io.Mol2Reader
      • org.openscience.cdk.io.Mopac7Reader
      • org.openscience.cdk.io.MoSSOutputReader
      • org.openscience.cdk.io.PCCompoundASNReader
      • org.openscience.cdk.io.PCCompoundXMLReader
      • org.openscience.cdk.io.PCSubstanceXMLReader
      • org.openscience.cdk.io.PDBReader
      • org.openscience.cdk.io.PMPReader
      • org.openscience.cdk.io.RGroupQueryReader
      • org.openscience.cdk.io.ShelXReader
      • org.openscience.cdk.io.SMILESReader
      • org.openscience.cdk.io.VASPReader
      • org.openscience.cdk.io.XYZReader
      • org.openscience.cdk.io.ZMatrixReader
    • org.openscience.cdk.io.DefaultChemObjectWriter (implements org.openscience.cdk.io.IChemObjectWriter)
      • org.openscience.cdk.io.rdf.CDKOWLWriter
      • org.openscience.cdk.io.CDKSourceCodeWriter
      • org.openscience.cdk.io.CMLWriter
      • org.openscience.cdk.io.CrystClustWriter
      • org.openscience.cdk.io.program.GaussianInputWriter
      • org.openscience.cdk.io.HINWriter
      • org.openscience.cdk.io.MDLRXNWriter
      • org.openscience.cdk.io.MDLV2000Writer
      • org.openscience.cdk.io.MDLV3000Writer
      • org.openscience.cdk.io.Mol2Writer
      • org.openscience.cdk.io.program.Mopac7Writer
      • org.openscience.cdk.io.PDBWriter
      • org.openscience.cdk.io.RGroupQueryWriter
      • org.openscience.cdk.io.RssWriter
      • org.openscience.cdk.io.SDFWriter
      • org.openscience.cdk.io.ShelXWriter
      • org.openscience.cdk.io.SMILESWriter
      • org.openscience.cdk.io.XYZWriter
    • org.openscience.cdk.io.iterator.event.DefaultEventChemObjectReader (implements org.openscience.cdk.io.iterator.event.IEventChemObjectReader)
      • org.openscience.cdk.io.iterator.event.EventCMLReader
    • org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader<T> (implements org.openscience.cdk.io.iterator.IIteratingChemObjectReader<T>)
      • org.openscience.cdk.io.iterator.IteratingPCCompoundASNReader
      • org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader
      • org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader
      • org.openscience.cdk.io.iterator.IteratingSDFReader
      • org.openscience.cdk.io.iterator.IteratingSMILESReader
  • org.openscience.cdk.tools.manipulator.ChemSequenceManipulator
  • org.openscience.cdk.geometry.cip.rules.CIPLigandRule (implements org.openscience.cdk.geometry.cip.rules.ISequenceSubRule<ILigand>)
  • org.openscience.cdk.geometry.cip.CIPTool
  • org.openscience.cdk.fingerprint.CircularFingerprinter.FP
  • org.openscience.cdk.math.qm.ClosedShellJob
  • org.openscience.cdk.io.cml.CMLCoreModule (implements org.openscience.cdk.io.cml.ICMLModule)
    • org.openscience.cdk.io.cml.CDKConvention
    • org.openscience.cdk.io.cml.CMLReactionModule
    • org.openscience.cdk.io.cml.JMOLANIMATIONConvention
    • org.openscience.cdk.io.cml.MDLMolConvention
    • org.openscience.cdk.io.cml.MDMoleculeConvention
    • org.openscience.cdk.io.cml.PDBConvention
    • org.openscience.cdk.io.cml.PMPConvention
    • org.openscience.cdk.io.cml.QSARConvention
  • org.openscience.cdk.io.cml.CMLErrorHandler (implements org.xml.sax.ErrorHandler)
  • org.openscience.cdk.io.cml.CMLModuleStack
  • org.openscience.cdk.io.cml.CMLResolver (implements org.xml.sax.EntityResolver)
  • org.openscience.cdk.math.Complex
  • org.openscience.cdk.ConformerContainer (implements java.util.List<E>)
  • org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector
  • org.openscience.cdk.graph.ConnectedComponents
  • org.openscience.cdk.graph.matrix.ConnectionMatrix (implements org.openscience.cdk.graph.matrix.IGraphMatrix)
  • org.openscience.cdk.graph.ConnectivityChecker
  • org.openscience.cdk.libio.cml.Convertor
  • org.openscience.cdk.libio.jena.Convertor
  • org.openscience.cdk.renderer.color.CPKAtomColors (implements org.openscience.cdk.renderer.color.IAtomColorer, java.io.Serializable)
  • org.openscience.cdk.structgen.stochastic.operator.CrossoverMachine
  • org.openscience.cdk.geometry.CrystalGeometryTools
  • org.openscience.cdk.smiles.CxSmilesGenerator
  • org.openscience.cdk.ringsearch.cyclebasis.CycleBasis
  • org.openscience.cdk.graph.Cycles
  • org.openscience.cdk.tools.DataFeatures
  • org.openscience.cdk.tools.DataFeaturesTool
  • org.openscience.cdk.tools.DeAromatizationTool
  • org.openscience.cdk.debug.DebugChemObjectBuilder (implements org.openscience.cdk.interfaces.IChemObjectBuilder)
  • org.openscience.cdk.smiles.DeduceBondSystemTool
  • org.openscience.cdk.smsd.algorithm.matchers.DefaultBondMatcher (implements org.openscience.cdk.smsd.algorithm.matchers.BondMatcher)
  • org.openscience.cdk.DefaultChemObjectBuilder (implements org.openscience.cdk.interfaces.IChemObjectBuilder)
  • org.xml.sax.helpers.DefaultHandler (implements org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler)
    • org.openscience.cdk.config.atomtypes.AtomTypeHandler
    • org.openscience.cdk.io.cml.CMLHandler
      • org.openscience.cdk.io.iterator.event.EventCMLHandler
    • org.openscience.cdk.dict.DictionaryHandler
    • org.openscience.cdk.io.inchi.INChIHandler
    • org.openscience.cdk.config.isotopes.IsotopeHandler
    • org.openscience.cdk.config.atomtypes.OWLAtomTypeHandler
    • org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingHandler
  • org.openscience.cdk.smsd.algorithm.matchers.DefaultMatcher
  • org.openscience.cdk.smsd.algorithm.matchers.DefaultMCSPlusAtomMatcher (implements org.openscience.cdk.smsd.algorithm.matchers.AtomMatcher)
  • org.openscience.cdk.io.random.DefaultRandomAccessChemObjectReader (implements org.openscience.cdk.io.random.IRandomAccessChemObjectReader<T>)
    • org.openscience.cdk.io.random.RandomAccessReader (implements org.openscience.cdk.io.random.IRandomAccessChemObjectReader<T>)
      • org.openscience.cdk.io.random.RandomAccessSDFReader
  • org.openscience.cdk.smsd.algorithm.matchers.DefaultRGraphAtomMatcher (implements org.openscience.cdk.smsd.algorithm.matchers.AtomMatcher)
  • org.openscience.cdk.smsd.algorithm.matchers.DefaultVFAtomMatcher (implements org.openscience.cdk.smsd.algorithm.matchers.VFAtomMatcher)
  • org.openscience.cdk.smsd.algorithm.matchers.DefaultVFBondMatcher (implements org.openscience.cdk.smsd.algorithm.matchers.VFBondMatcher)
  • org.openscience.cdk.depict.Depiction
  • org.openscience.cdk.depict.DepictionGenerator
  • org.openscience.cdk.qsar.DescriptorEngine
  • org.openscience.cdk.qsar.DescriptorSpecification (implements org.openscience.cdk.IImplementationSpecification, java.io.Serializable)
  • org.openscience.cdk.qsar.DescriptorValue (implements java.io.Serializable)
  • org.openscience.cdk.dict.Dictionary
    • org.openscience.cdk.dict.OWLFile
    • org.openscience.cdk.dict.OWLReact
  • org.openscience.cdk.dict.DictionaryDatabase
  • org.openscience.cdk.dict.DictRef (implements java.lang.Cloneable, java.io.Serializable)
  • org.openscience.cdk.group.DisjointSetForest
  • org.openscience.cdk.similarity.DistanceMoment
  • org.openscience.cdk.qsar.result.DoubleArrayResultType (implements org.openscience.cdk.qsar.result.IDescriptorResult)
    • org.openscience.cdk.qsar.result.DoubleArrayResult
  • org.openscience.cdk.aromaticity.DoubleBondAcceptingAromaticityDetector
  • org.openscience.cdk.hash.stereo.DoubleBondElementEncoderFactory (implements org.openscience.cdk.hash.stereo.StereoEncoderFactory)
  • org.openscience.cdk.stereo.DoubleBondStereochemistry (implements org.openscience.cdk.interfaces.IDoubleBondStereochemistry)
  • org.openscience.cdk.tools.diff.tree.DoubleDifference (implements org.openscience.cdk.tools.diff.tree.IDifference)
  • org.openscience.cdk.qsar.result.DoubleResult (implements org.openscience.cdk.qsar.result.IDescriptorResult)
  • org.openscience.cdk.qsar.result.DoubleResultType (implements org.openscience.cdk.qsar.result.IDescriptorResult)
  • org.openscience.cdk.DynamicFactory
  • org.openscience.cdk.DynamicFactory.BasicCreator<T> (implements org.openscience.cdk.DynamicFactory.Creator<T>)
  • org.openscience.cdk.DynamicFactory.ConstructorKey (implements java.lang.Comparable<T>)
  • org.openscience.cdk.DynamicFactory.DefaultInterfaceProvider (implements org.openscience.cdk.DynamicFactory.InterfaceProvider)
  • org.openscience.cdk.smsd.algorithm.vflib.builder.EdgeBuilder (implements org.openscience.cdk.smsd.algorithm.vflib.interfaces.IEdge)
  • org.openscience.cdk.tools.diff.ElectronContainerDiff
  • org.openscience.cdk.aromaticity.ElectronDonation
  • org.openscience.cdk.charges.Electronegativity
  • org.openscience.cdk.tools.ElementComparator (implements java.util.Comparator<T>)
  • org.openscience.cdk.tools.diff.ElementDiff
  • org.openscience.cdk.renderer.elements.ElementGroup (implements org.openscience.cdk.renderer.elements.IRenderingElement, java.lang.Iterable<T>)
  • org.openscience.cdk.formula.rules.ElementRule (implements org.openscience.cdk.formula.rules.IRule)
  • org.openscience.cdk.dict.Entry
    • org.openscience.cdk.dict.EntryReact
  • org.openscience.cdk.graph.invariant.EquivalentClassPartitioner
  • org.openscience.cdk.graph.EssentialCycles
  • org.openscience.cdk.atomtype.EStateAtomTypeMatcher (implements org.openscience.cdk.atomtype.IAtomTypeMatcher)
  • org.openscience.cdk.config.fragments.EStateFragments
  • java.util.EventObject (implements java.io.Serializable)
    • org.openscience.cdk.event.ChemObjectChangeEvent (implements org.openscience.cdk.interfaces.IChemObjectChangeEvent)
    • org.openscience.cdk.io.ReaderEvent
  • org.openscience.cdk.smsd.algorithm.mcsplus.ExactMapping
  • org.openscience.cdk.fragment.ExhaustiveFragmenter (implements org.openscience.cdk.fragment.IFragmenter)
  • org.openscience.cdk.isomorphism.matchers.Expr
  • org.openscience.cdk.stereo.ExtendedCisTrans
  • org.openscience.cdk.fingerprint.ExtendedFingerprinter (implements org.openscience.cdk.fingerprint.IFingerprinter)
  • org.openscience.cdk.stereo.ExtendedTetrahedral
  • org.openscience.cdk.ringsearch.FiguerasSSSRFinder
  • org.openscience.cdk.smsd.helper.FinalMappings (implements org.openscience.cdk.smsd.interfaces.IFinalMapping)
  • org.openscience.cdk.fingerprint.FingerprinterTool
  • org.openscience.cdk.smiles.FixBondOrdersTool
  • org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator
  • org.openscience.cdk.io.FormatFactory
  • org.openscience.cdk.tools.FormatStringBuffer
  • org.openscience.cdk.math.FortranFormat
  • org.openscience.cdk.math.qm.FourierGridBasis (implements org.openscience.cdk.math.qm.IBasis)
  • org.openscience.cdk.qsar.descriptors.molecular.FractionalPSADescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
  • org.openscience.cdk.fragment.FragmentUtils
  • org.openscience.cdk.charges.GasteigerMarsiliPartialCharges (implements org.openscience.cdk.charges.IChargeCalculator)
  • org.openscience.cdk.charges.GasteigerPEPEPartialCharges (implements org.openscience.cdk.charges.IChargeCalculator)
  • org.openscience.cdk.math.qm.GaussiansBasis (implements org.openscience.cdk.math.qm.IBasis)
    • org.openscience.cdk.math.qm.SimpleBasisSet
  • org.openscience.cdk.renderer.elements.GeneralPath (implements org.openscience.cdk.renderer.elements.IRenderingElement)
  • org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
  • org.openscience.cdk.hash.stereo.GeometricCumulativeDoubleBondFactory (implements org.openscience.cdk.hash.stereo.StereoEncoderFactory)
  • org.openscience.cdk.hash.stereo.GeometricDoubleBondEncoderFactory (implements org.openscience.cdk.hash.stereo.StereoEncoderFactory)
  • org.openscience.cdk.hash.stereo.GeometricTetrahedralEncoderFactory (implements org.openscience.cdk.hash.stereo.StereoEncoderFactory)
  • org.openscience.cdk.geometry.GeometryTools
  • org.openscience.cdk.geometry.GeometryUtil
  • org.openscience.cdk.graph.invariant.GIMatrix
  • org.openscience.cdk.renderer.GraphRendererModel
  • org.openscience.cdk.graph.GraphUtil
  • org.openscience.cdk.graph.GraphUtil.EdgeToBondMap
  • org.openscience.cdk.tools.GridGenerator
  • org.openscience.cdk.smsd.ring.HanserRingFinder (implements org.openscience.cdk.smsd.ring.RingFinder)
  • org.openscience.cdk.hash.HashGeneratorMaker
  • org.openscience.cdk.reaction.mechanism.HeterolyticCleavageMechanism (implements org.openscience.cdk.reaction.IReactionMechanism)
  • org.openscience.cdk.renderer.generators.HighlightGenerator (implements org.openscience.cdk.renderer.generators.IGenerator<T>)
  • org.openscience.cdk.reaction.mechanism.HomolyticCleavageMechanism (implements org.openscience.cdk.reaction.IReactionMechanism)
  • org.openscience.cdk.tools.HOSECodeAnalyser
  • org.openscience.cdk.tools.HOSECodeGenerator (implements java.io.Serializable)
  • org.openscience.cdk.graph.invariant.HuLuIndexTool
  • org.openscience.cdk.layout.HydrogenPlacer
  • org.openscience.cdk.io.formats.IChemFormatMatcher.MatchResult (implements java.lang.Comparable<T>)
  • org.openscience.cdk.tools.IDCreator
  • org.openscience.cdk.math.IMatrix
  • org.openscience.cdk.io.inchi.INChIContentProcessorTool
  • org.openscience.cdk.inchi.InChIGenerator
  • org.openscience.cdk.inchi.InChIGeneratorFactory
  • org.openscience.cdk.graph.invariant.InChINumbersTools
  • org.openscience.cdk.tautomers.InChITautomerGenerator
  • org.openscience.cdk.inchi.InChIToStructure
  • org.openscience.cdk.charges.InductivePartialCharges (implements org.openscience.cdk.charges.IChargeCalculator)
  • org.openscience.cdk.fingerprint.IntArrayCountFingerprint (implements org.openscience.cdk.fingerprint.ICountFingerprint)
  • org.openscience.cdk.fingerprint.IntArrayFingerprint (implements org.openscience.cdk.fingerprint.IBitFingerprint)
  • org.openscience.cdk.qsar.result.IntegerArrayResultType (implements org.openscience.cdk.qsar.result.IDescriptorResult)
    • org.openscience.cdk.qsar.result.IntegerArrayResult
  • org.openscience.cdk.tools.diff.tree.IntegerDifference (implements org.openscience.cdk.tools.diff.tree.IDifference)
  • org.openscience.cdk.qsar.result.IntegerResult (implements org.openscience.cdk.qsar.result.IDescriptorResult)
  • org.openscience.cdk.qsar.result.IntegerResultType (implements org.openscience.cdk.qsar.result.IDescriptorResult)
  • org.openscience.cdk.smiles.InvPair (implements java.io.Serializable)
  • org.openscience.cdk.tools.IonizationPotentialTool
  • org.openscience.cdk.io.setting.IOSetting (implements org.openscience.cdk.interfaces.ISetting)
    • org.openscience.cdk.io.setting.BooleanIOSetting
    • org.openscience.cdk.io.setting.IntegerIOSetting
    • org.openscience.cdk.io.setting.OptionIOSetting
    • org.openscience.cdk.io.setting.StringIOSetting
  • org.openscience.cdk.templates.saturatedhydrocarbons.IsoAlkanes
  • org.openscience.cdk.isomorphism.IsomorphismTester (implements java.io.Serializable)
  • org.openscience.cdk.formula.IsotopeContainer
  • org.openscience.cdk.tools.diff.IsotopeDiff
  • org.openscience.cdk.config.IsotopeFactory
    • org.openscience.cdk.config.Isotopes
    • org.openscience.cdk.config.XMLIsotopeFactory
  • org.openscience.cdk.formula.IsotopePattern
  • org.openscience.cdk.formula.IsotopePatternGenerator
  • org.openscience.cdk.formula.IsotopePatternManipulator
  • org.openscience.cdk.formula.rules.IsotopePatternRule (implements org.openscience.cdk.formula.rules.IRule)
  • org.openscience.cdk.formula.IsotopePatternSimilarity
  • org.openscience.cdk.config.isotopes.IsotopeReader
  • org.openscience.cdk.io.iterator.IteratingMDLConformerReader (implements java.util.Iterator<E>)
  • org.openscience.cdk.math.IVector
  • org.openscience.cdk.smiles.smarts.parser.JJTSMARTSParserState
  • org.openscience.cdk.renderer.color.JmolColors (implements org.openscience.cdk.renderer.color.IAtomColorer)
  • org.openscience.cdk.qsar.descriptors.molecular.JPlogPDescriptor.JPlogPCalculator
  • org.openscience.cdk.geometry.alignment.KabschAlignment
  • org.openscience.cdk.aromaticity.Kekulization
  • org.openscience.cdk.smsd.helper.LabelContainer
  • org.openscience.cdk.geometry.cip.Ligand (implements org.openscience.cdk.geometry.cip.ILigand)
    • org.openscience.cdk.geometry.cip.ImplicitHydrogenLigand
  • org.openscience.cdk.renderer.elements.LineElement (implements org.openscience.cdk.renderer.elements.IRenderingElement)
    • org.openscience.cdk.renderer.elements.WedgeLineElement
  • org.openscience.cdk.similarity.LingoSimilarity
  • org.openscience.cdk.tools.LoggingToolFactory
  • org.openscience.cdk.tools.diff.LonePairDiff
  • org.openscience.cdk.tools.LonePairElectronChecker
  • org.openscience.cdk.renderer.generators.LonePairGenerator (implements org.openscience.cdk.renderer.generators.IGenerator<T>)
  • org.openscience.cdk.renderer.generators.MappingGenerator (implements org.openscience.cdk.renderer.generators.IGenerator<T>)
  • org.openscience.cdk.isomorphism.Mappings (implements java.lang.Iterable<T>)
  • org.openscience.cdk.renderer.elements.MarkedElement (implements org.openscience.cdk.renderer.elements.IRenderingElement)
  • org.openscience.cdk.formula.MassToFormulaTool
  • org.openscience.cdk.smsd.algorithm.vflib.map.Match
  • org.openscience.cdk.graph.Matching
  • org.openscience.cdk.math.Matrix
  • org.openscience.cdk.structgen.maygen.Maygen
  • org.openscience.cdk.smsd.algorithm.mcgregor.McGregor
  • org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks
  • org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper
  • org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlus
  • org.openscience.cdk.libio.cml.MDMoleculeCustomizer (implements org.openscience.cdk.libio.cml.ICMLCustomizer)
  • org.openscience.cdk.graph.MinimalPathIterator (implements java.util.Iterator<E>)
  • org.openscience.cdk.graph.MinimumCycleBasis
  • org.openscience.cdk.atomtype.MM2AtomTypeMatcher (implements org.openscience.cdk.atomtype.IAtomTypeMatcher)
  • org.openscience.cdk.modeling.builder3d.MM2BasedAtomTypePattern
  • org.openscience.cdk.modeling.builder3d.MM2BasedParameterSetReader
  • org.openscience.cdk.formula.rules.MMElementRule (implements org.openscience.cdk.formula.rules.IRule)
  • org.openscience.cdk.forcefield.mmff.Mmff
  • org.openscience.cdk.atomtype.MMFF94AtomTypeMatcher (implements org.openscience.cdk.atomtype.IAtomTypeMatcher)
  • org.openscience.cdk.modeling.builder3d.MMFF94BasedAtomTypePattern
  • org.openscience.cdk.modeling.builder3d.MMFF94BasedParameterSetReader
  • org.openscience.cdk.modeling.builder3d.MMFF94ParametersCall
  • org.openscience.cdk.charges.MMFF94PartialCharges (implements org.openscience.cdk.charges.IChargeCalculator)
  • org.openscience.cdk.modeling.builder3d.ModelBuilder3D
  • org.openscience.cdk.formula.MolecularFormula (implements org.openscience.cdk.interfaces.IMolecularFormula)
    • org.openscience.cdk.debug.DebugMolecularFormula (implements org.openscience.cdk.interfaces.IMolecularFormula)
  • org.openscience.cdk.silent.MolecularFormula (implements org.openscience.cdk.interfaces.IMolecularFormula)
  • org.openscience.cdk.formula.MolecularFormulaChecker
  • org.openscience.cdk.formula.MolecularFormulaGenerator
  • org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator
  • org.openscience.cdk.formula.MolecularFormulaRange (implements java.lang.Cloneable)
  • org.openscience.cdk.tools.manipulator.MolecularFormulaRangeManipulator
  • org.openscience.cdk.formula.MolecularFormulaSet (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IMolecularFormulaSet, java.lang.Iterable<T>)
    • org.openscience.cdk.debug.DebugMolecularFormulaSet (implements org.openscience.cdk.interfaces.IMolecularFormulaSet)
  • org.openscience.cdk.silent.MolecularFormulaSet (implements java.lang.Cloneable, org.openscience.cdk.interfaces.IMolecularFormulaSet, java.lang.Iterable<T>)
  • org.openscience.cdk.tools.manipulator.MolecularFormulaSetManipulator
  • org.openscience.cdk.iupac.parser.MoleculeBuilder
  • org.openscience.cdk.templates.MoleculeFactory
  • org.openscience.cdk.tools.features.MoleculeFeaturesTool
  • org.openscience.cdk.graph.MoleculeGraphs
  • org.openscience.cdk.smsd.tools.MoleculeSanityCheck
  • org.openscience.cdk.tools.manipulator.MoleculeSetManipulator
  • org.openscience.cdk.smsd.labelling.MoleculeSignatureLabellingAdaptor (implements org.openscience.cdk.smsd.labelling.ICanonicalMoleculeLabeller)
  • org.openscience.cdk.smsd.tools.MolHandler
  • org.openscience.cdk.graph.invariant.MorganNumbersTools
  • org.openscience.cdk.fragment.MurckoFragmenter (implements org.openscience.cdk.fragment.IFragmenter)
  • org.openscience.cdk.geometry.surface.NeighborList
  • org.openscience.cdk.formula.rules.NitrogenRule (implements org.openscience.cdk.formula.rules.IRule)
  • org.openscience.cdk.smsd.algorithm.vflib.builder.NodeBuilder (implements org.openscience.cdk.smsd.algorithm.vflib.interfaces.INode)
  • org.openscience.cdk.iupac.parser.NomParser (implements org.openscience.cdk.iupac.parser.NomParserConstants)
  • org.openscience.cdk.iupac.parser.NomParserTokenManager (implements org.openscience.cdk.iupac.parser.NomParserConstants)
  • org.openscience.cdk.normalize.Normalizer
  • org.openscience.cdk.geometry.surface.NumericalSurface
  • org.openscience.cdk.stereo.Octahedral
  • org.openscience.cdk.math.qm.OneElectronJob
  • org.openscience.cdk.signature.Orbit (implements java.lang.Cloneable, java.lang.Iterable<T>)
  • org.openscience.cdk.math.qm.Orbitals
  • org.openscience.cdk.renderer.elements.OvalElement (implements org.openscience.cdk.renderer.elements.IRenderingElement)
    • org.openscience.cdk.renderer.elements.RingElement (implements org.openscience.cdk.renderer.elements.IRenderingElement)
  • org.openscience.cdk.layout.OverlapResolver
  • org.openscience.cdk.layout.OverlapResolver.OverlapPair
  • org.openscience.cdk.config.atomtypes.OWLAtomTypeMappingReader
  • org.openscience.cdk.config.atomtypes.OWLAtomTypeReader
  • org.openscience.cdk.config.OWLBasedAtomTypeConfigurator (implements org.openscience.cdk.config.IAtomTypeConfigurator)
  • org.openscience.cdk.qsar.descriptors.substance.OxygenAtomCountDescriptor (implements org.openscience.cdk.qsar.descriptors.substance.ISubstanceDescriptor)
  • org.openscience.cdk.reaction.type.parameters.ParameterReact (implements org.openscience.cdk.reaction.type.parameters.IParameterReact)
    • org.openscience.cdk.reaction.type.parameters.SetReactionCenter
  • org.openscience.cdk.renderer.color.PartialAtomicChargeColors (implements org.openscience.cdk.renderer.color.IAtomColorer)
  • org.openscience.cdk.structgen.stochastic.PartialFilledStructureMerger
  • org.openscience.cdk.group.Partition
  • org.openscience.cdk.group.PartitionRefinement
  • org.openscience.cdk.group.PartitionRefinement.AtomRefinerBuilder
  • org.openscience.cdk.group.PartitionRefinement.BondRefinerBuilder
  • org.openscience.cdk.renderer.elements.path.PathBuilder
  • org.openscience.cdk.smsd.ring.PathEdge
  • org.openscience.cdk.renderer.elements.path.PathElement
    • org.openscience.cdk.renderer.elements.path.Close
    • org.openscience.cdk.renderer.elements.path.CubicTo
    • org.openscience.cdk.renderer.elements.path.LineTo
    • org.openscience.cdk.renderer.elements.path.MoveTo
    • org.openscience.cdk.renderer.elements.path.QuadTo
  • org.openscience.cdk.renderer.elements.PathElement (implements org.openscience.cdk.renderer.elements.IRenderingElement)
  • org.openscience.cdk.smsd.ring.PathGraph
  • org.openscience.cdk.graph.PathTools
  • org.openscience.cdk.isomorphism.Pattern
    • org.openscience.cdk.isomorphism.DfPattern
    • org.openscience.cdk.smarts.SmartsPattern
    • org.openscience.cdk.smiles.smarts.SmartsPattern
    • org.openscience.cdk.isomorphism.Ullmann
    • org.openscience.cdk.isomorphism.VentoFoggia
  • org.openscience.cdk.libio.cml.PDBAtomCustomizer (implements org.openscience.cdk.libio.cml.ICMLCustomizer)
  • org.openscience.cdk.tools.periodictable.PeriodicTable
  • org.openscience.cdk.group.Permutation
  • org.openscience.cdk.group.PermutationGroup
  • org.openscience.cdk.graph.Permutor
    • org.openscience.cdk.graph.AtomContainerPermutor (implements java.util.Iterator<E>)
      • org.openscience.cdk.graph.AtomContainerAtomPermutor
      • org.openscience.cdk.graph.AtomContainerBondPermutor
  • org.openscience.cdk.smsd.labelling.Permutor
    • org.openscience.cdk.smsd.labelling.AtomContainerAtomPermutor (implements java.util.Iterator<E>)
  • org.openscience.cdk.pharmacophore.PharmacophoreMatcher
  • org.openscience.cdk.pharmacophore.PharmacophoreUtils
  • org.openscience.cdk.PhysicalConstants
  • org.openscience.cdk.charges.PiElectronegativity
  • org.openscience.cdk.graph.rebond.Point (implements org.openscience.cdk.graph.rebond.Bspt.Tuple)
  • org.openscience.cdk.charges.Polarizability
  • org.openscience.cdk.smsd.filters.PostFilter
  • org.openscience.cdk.math.Primes
  • org.openscience.cdk.validate.ProblemMarker
  • org.openscience.cdk.renderer.generators.ProductsBoxGenerator (implements org.openscience.cdk.renderer.generators.IGenerator<T>)
  • org.openscience.cdk.geometry.Projector
  • org.openscience.cdk.io.listener.PropertiesListener (implements org.openscience.cdk.io.listener.IReaderListener, org.openscience.cdk.io.listener.IWriterListener)
  • org.openscience.cdk.tools.ProteinBuilderTool
  • org.openscience.cdk.protein.ProteinPocketFinder
  • org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
  • org.openscience.cdk.libio.cml.QSARCustomizer (implements org.openscience.cdk.libio.cml.ICMLCustomizer)
  • org.openscience.cdk.math.Quaternion
  • org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
  • org.openscience.cdk.isomorphism.matchers.QueryChemObject (implements org.openscience.cdk.interfaces.IChemObject)
    • org.openscience.cdk.isomorphism.matchers.QueryAtom (implements org.openscience.cdk.isomorphism.matchers.IQueryAtom)
      • org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom (implements org.openscience.cdk.isomorphism.matchers.IQueryAtom)
      • org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom (implements org.openscience.cdk.isomorphism.matchers.IQueryAtom)
        • org.openscience.cdk.isomorphism.matchers.smarts.AliphaticAtom
        • org.openscience.cdk.isomorphism.matchers.smarts.AliphaticSymbolAtom
        • org.openscience.cdk.isomorphism.matchers.smarts.AnyAtom
        • org.openscience.cdk.isomorphism.matchers.smarts.AromaticAtom
        • org.openscience.cdk.isomorphism.matchers.smarts.AromaticSymbolAtom
        • org.openscience.cdk.isomorphism.matchers.smarts.AtomicNumberAtom
        • org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom
        • org.openscience.cdk.isomorphism.matchers.smarts.ExplicitConnectionAtom
        • org.openscience.cdk.isomorphism.matchers.smarts.FormalChargeAtom
        • org.openscience.cdk.isomorphism.matchers.smarts.HybridizationNumberAtom
        • org.openscience.cdk.isomorphism.matchers.smarts.HydrogenAtom
        • org.openscience.cdk.isomorphism.matchers.smarts.ImplicitHCountAtom
        • org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom
        • org.openscience.cdk.isomorphism.matchers.smarts.MassAtom
        • org.openscience.cdk.isomorphism.matchers.smarts.NonCHHeavyAtom
        • org.openscience.cdk.isomorphism.matchers.smarts.PeriodicGroupNumberAtom
        • org.openscience.cdk.isomorphism.matchers.smarts.ReactionRoleQueryAtom
        • org.openscience.cdk.isomorphism.matchers.smarts.RecursiveSmartsAtom
        • org.openscience.cdk.isomorphism.matchers.smarts.RingIdentifierAtom
        • org.openscience.cdk.isomorphism.matchers.smarts.RingMembershipAtom
        • org.openscience.cdk.isomorphism.matchers.smarts.SmallestRingAtom
        • org.openscience.cdk.isomorphism.matchers.smarts.TotalConnectionAtom
        • org.openscience.cdk.isomorphism.matchers.smarts.TotalHCountAtom
        • org.openscience.cdk.isomorphism.matchers.smarts.TotalRingConnectionAtom
        • org.openscience.cdk.isomorphism.matchers.smarts.TotalValencyAtom
      • org.openscience.cdk.isomorphism.matchers.SymbolAndChargeQueryAtom (implements org.openscience.cdk.isomorphism.matchers.IQueryAtom)
      • org.openscience.cdk.isomorphism.matchers.SymbolChargeIDQueryAtom (implements org.openscience.cdk.isomorphism.matchers.IQueryAtom)
      • org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom (implements org.openscience.cdk.isomorphism.matchers.IQueryAtom)
      • org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom (implements org.openscience.cdk.isomorphism.matchers.IQueryAtom)
    • org.openscience.cdk.isomorphism.matchers.QueryAtomContainer (implements org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer)
      • org.openscience.cdk.pharmacophore.PharmacophoreQuery
    • org.openscience.cdk.isomorphism.matchers.QueryBond (implements org.openscience.cdk.isomorphism.matchers.IQueryBond)
      • org.openscience.cdk.isomorphism.matchers.CTFileQueryBond (implements org.openscience.cdk.isomorphism.matchers.IQueryBond)
      • org.openscience.cdk.isomorphism.matchers.OrderQueryBond (implements org.openscience.cdk.isomorphism.matchers.IQueryBond)
      • org.openscience.cdk.isomorphism.matchers.OrderQueryBondOrderOnly (implements org.openscience.cdk.isomorphism.matchers.IQueryBond)
      • org.openscience.cdk.isomorphism.matchers.smarts.SMARTSBond (implements org.openscience.cdk.isomorphism.matchers.IQueryBond)
        • org.openscience.cdk.isomorphism.matchers.smarts.AnyOrderQueryBond
        • org.openscience.cdk.isomorphism.matchers.smarts.AromaticOrSingleQueryBond
        • org.openscience.cdk.isomorphism.matchers.smarts.AromaticQueryBond
        • org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond
        • org.openscience.cdk.isomorphism.matchers.smarts.OrderQueryBond
        • org.openscience.cdk.isomorphism.matchers.smarts.RingBond
        • org.openscience.cdk.isomorphism.matchers.smarts.StereoBond
    • org.openscience.cdk.isomorphism.matchers.RGroupQuery (implements org.openscience.cdk.interfaces.IChemObject, org.openscience.cdk.isomorphism.matchers.IRGroupQuery)
  • org.openscience.cdk.smsd.algorithm.vflib.query.QueryCompiler (implements org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQueryCompiler)
  • org.openscience.cdk.smsd.algorithm.mcgregor.QueryProcessor
  • org.openscience.cdk.renderer.generators.RadicalGenerator (implements org.openscience.cdk.renderer.generators.IGenerator<T>)
  • org.openscience.cdk.reaction.mechanism.RadicalSiteIonizationMechanism (implements org.openscience.cdk.reaction.IReactionMechanism)
  • org.openscience.cdk.reaction.mechanism.RadicalSiteRearrangementMechanism (implements org.openscience.cdk.reaction.IReactionMechanism)
  • java.util.Random (implements java.io.Serializable)
    • org.openscience.cdk.math.RandomNumbersTool
  • org.openscience.cdk.structgen.RandomGenerator
  • org.openscience.cdk.renderer.color.RasmolColors (implements org.openscience.cdk.renderer.color.IAtomColorer, java.io.Serializable)
  • org.openscience.cdk.formula.rules.RDBERule (implements org.openscience.cdk.formula.rules.IRule)
  • org.openscience.cdk.formula.rules.RDBERule.Combinations
  • org.openscience.cdk.geometry.RDFCalculator
  • org.openscience.cdk.renderer.generators.ReactantsBoxGenerator (implements org.openscience.cdk.renderer.generators.IGenerator<T>)
  • org.openscience.cdk.renderer.generators.ReactionArrowGenerator (implements org.openscience.cdk.renderer.generators.IGenerator<T>)
  • org.openscience.cdk.renderer.generators.ReactionBoxGenerator (implements org.openscience.cdk.renderer.generators.IGenerator<T>)
  • org.openscience.cdk.reaction.ReactionEngine
    • org.openscience.cdk.reaction.type.AdductionProtonLPReaction (implements org.openscience.cdk.reaction.IReactionProcess)
    • org.openscience.cdk.reaction.type.AdductionProtonPBReaction (implements org.openscience.cdk.reaction.IReactionProcess)
    • org.openscience.cdk.reaction.type.AdductionSodiumLPReaction (implements org.openscience.cdk.reaction.IReactionProcess)
    • org.openscience.cdk.reaction.type.CarbonylEliminationReaction (implements org.openscience.cdk.reaction.IReactionProcess)
    • org.openscience.cdk.reaction.type.ElectronImpactNBEReaction (implements org.openscience.cdk.reaction.IReactionProcess)
    • org.openscience.cdk.reaction.type.ElectronImpactPDBReaction (implements org.openscience.cdk.reaction.IReactionProcess)
    • org.openscience.cdk.reaction.type.ElectronImpactSDBReaction (implements org.openscience.cdk.reaction.IReactionProcess)
    • org.openscience.cdk.reaction.type.HeterolyticCleavagePBReaction (implements org.openscience.cdk.reaction.IReactionProcess)
    • org.openscience.cdk.reaction.type.HeterolyticCleavageSBReaction (implements org.openscience.cdk.reaction.IReactionProcess)
    • org.openscience.cdk.reaction.type.HomolyticCleavageReaction (implements org.openscience.cdk.reaction.IReactionProcess)
    • org.openscience.cdk.reaction.type.HyperconjugationReaction (implements org.openscience.cdk.reaction.IReactionProcess)
    • org.openscience.cdk.reaction.type.PiBondingMovementReaction (implements org.openscience.cdk.reaction.IReactionProcess)
    • org.openscience.cdk.reaction.type.RadicalChargeSiteInitiationHReaction (implements org.openscience.cdk.reaction.IReactionProcess)
    • org.openscience.cdk.reaction.type.RadicalChargeSiteInitiationReaction (implements org.openscience.cdk.reaction.IReactionProcess)
    • org.openscience.cdk.reaction.type.RadicalSiteHrAlphaReaction (implements org.openscience.cdk.reaction.IReactionProcess)
    • org.openscience.cdk.reaction.type.RadicalSiteHrBetaReaction (implements org.openscience.cdk.reaction.IReactionProcess)
    • org.openscience.cdk.reaction.type.RadicalSiteHrDeltaReaction (implements org.openscience.cdk.reaction.IReactionProcess)
    • org.openscience.cdk.reaction.type.RadicalSiteHrGammaReaction (implements org.openscience.cdk.reaction.IReactionProcess)
    • org.openscience.cdk.reaction.type.RadicalSiteInitiationHReaction (implements org.openscience.cdk.reaction.IReactionProcess)
    • org.openscience.cdk.reaction.type.RadicalSiteInitiationReaction (implements org.openscience.cdk.reaction.IReactionProcess)
    • org.openscience.cdk.reaction.type.RadicalSiteRrAlphaReaction (implements org.openscience.cdk.reaction.IReactionProcess)
    • org.openscience.cdk.reaction.type.RadicalSiteRrBetaReaction (implements org.openscience.cdk.reaction.IReactionProcess)
    • org.openscience.cdk.reaction.type.RadicalSiteRrDeltaReaction (implements org.openscience.cdk.reaction.IReactionProcess)
    • org.openscience.cdk.reaction.type.RadicalSiteRrGammaReaction (implements org.openscience.cdk.reaction.IReactionProcess)
    • org.openscience.cdk.reaction.type.RearrangementAnionReaction (implements org.openscience.cdk.reaction.IReactionProcess)
    • org.openscience.cdk.reaction.type.RearrangementCationReaction (implements org.openscience.cdk.reaction.IReactionProcess)
    • org.openscience.cdk.reaction.type.RearrangementLonePairReaction (implements org.openscience.cdk.reaction.IReactionProcess)
    • org.openscience.cdk.reaction.type.RearrangementRadicalReaction (implements org.openscience.cdk.reaction.IReactionProcess)
    • org.openscience.cdk.reaction.type.SharingAnionReaction (implements org.openscience.cdk.reaction.IReactionProcess)
    • org.openscience.cdk.reaction.type.SharingChargeDBReaction (implements org.openscience.cdk.reaction.IReactionProcess)
    • org.openscience.cdk.reaction.type.SharingChargeSBReaction (implements org.openscience.cdk.reaction.IReactionProcess)
    • org.openscience.cdk.reaction.type.SharingLonePairReaction (implements org.openscience.cdk.reaction.IReactionProcess)
    • org.openscience.cdk.reaction.type.TautomerizationReaction (implements org.openscience.cdk.reaction.IReactionProcess)
  • org.openscience.cdk.tools.manipulator.ReactionManipulator
  • org.openscience.cdk.renderer.generators.ReactionPlusGenerator (implements org.openscience.cdk.renderer.generators.IGenerator<T>)
  • org.openscience.cdk.renderer.generators.ReactionSceneGenerator (implements org.openscience.cdk.renderer.generators.IGenerator<T>)
  • org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator
  • org.openscience.cdk.tools.manipulator.ReactionSetManipulator
  • org.openscience.cdk.reaction.ReactionSpecification (implements org.openscience.cdk.IImplementationSpecification)
  • org.openscience.cdk.io.ReaderFactory
  • org.openscience.cdk.reaction.mechanism.RearrangementChargeMechanism (implements org.openscience.cdk.reaction.IReactionMechanism)
  • org.openscience.cdk.graph.rebond.RebondTool
  • org.openscience.cdk.renderer.elements.RectangleElement (implements org.openscience.cdk.renderer.elements.IRenderingElement)
  • org.openscience.cdk.graph.RelevantCycles
  • org.openscience.cdk.reaction.mechanism.RemovingSEofBMechanism (implements org.openscience.cdk.reaction.IReactionMechanism)
  • org.openscience.cdk.reaction.mechanism.RemovingSEofNBMechanism (implements org.openscience.cdk.reaction.IReactionMechanism)
  • org.openscience.cdk.renderer.RendererModel (implements java.lang.Cloneable, java.io.Serializable)
  • org.openscience.cdk.isomorphism.mcss.RGraph
  • org.openscience.cdk.isomorphism.matchers.RGroup (implements org.openscience.cdk.isomorphism.matchers.IRGroup)
  • org.openscience.cdk.isomorphism.matchers.RGroupList (implements org.openscience.cdk.isomorphism.matchers.IRGroupList)
  • org.openscience.cdk.smsd.ring.RingFilter
  • org.openscience.cdk.tools.manipulator.RingManipulator
  • org.openscience.cdk.ringsearch.RingPartitioner
  • org.openscience.cdk.layout.RingPlacer
  • org.openscience.cdk.ringsearch.RingSearch
  • org.openscience.cdk.tools.manipulator.RingSetManipulator
  • org.openscience.cdk.tools.manipulator.RingSizeComparator (implements java.util.Comparator<T>)
  • org.openscience.cdk.isomorphism.mcss.RMap
  • org.openscience.cdk.isomorphism.mcss.RNode
  • org.openscience.cdk.tools.SaturationChecker (implements org.openscience.cdk.tools.IDeduceBondOrderTool, org.openscience.cdk.tools.IValencyChecker)
  • nu.xom.Serializer
    • org.openscience.cdk.io.cml.CustomSerializer
  • org.openscience.cdk.io.setting.SettingManager<T>
  • org.openscience.cdk.sgroup.Sgroup
  • org.openscience.cdk.sgroup.SgroupBracket
  • org.openscience.cdk.tools.manipulator.SgroupManipulator
  • org.openscience.cdk.reaction.mechanism.SharingElectronMechanism (implements org.openscience.cdk.reaction.IReactionMechanism)
  • org.openscience.cdk.graph.ShortestPaths
  • org.openscience.cdk.fingerprint.ShortestPathWalker
  • org.openscience.cdk.silent.SilentChemObjectBuilder (implements org.openscience.cdk.interfaces.IChemObjectBuilder)
  • org.openscience.cdk.fingerprint.SimpleAtomCanonicalizer
  • org.openscience.cdk.fingerprint.SimpleAtomComparator (implements java.util.Comparator<T>, java.io.Serializable)
  • org.openscience.cdk.iupac.parser.SimpleCharStream
  • org.openscience.cdk.smiles.smarts.parser.SimpleCharStream
  • org.openscience.cdk.ringsearch.cyclebasis.SimpleCycleBasis
  • org.openscience.cdk.tools.diff.SingleElectronDiff
  • org.openscience.cdk.smsd.algorithm.single.SingleMapping
  • org.openscience.cdk.structgen.SingleStructureRandomGenerator
  • org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor (implements org.openscience.cdk.qsar.IMolecularDescriptor)
  • org.openscience.cdk.smarts.Smarts
  • org.openscience.cdk.smiles.smarts.parser.Smarts2MQLVisitor (implements org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor)
  • org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor (implements org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor)
  • org.openscience.cdk.smarts.SmartsFragmentExtractor
  • org.openscience.cdk.isomorphism.matchers.smarts.SmartsMatchers
  • org.openscience.cdk.smiles.smarts.parser.SMARTSParser (implements org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants, org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants)
  • org.openscience.cdk.smiles.smarts.parser.SMARTSParserDefaultVisitor (implements org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor)
  • org.openscience.cdk.smiles.smarts.parser.SMARTSParserTokenManager (implements org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants)
  • org.openscience.cdk.smiles.smarts.SMARTSQueryTool
  • org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor (implements org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor)
  • org.openscience.cdk.smarts.SmartsResult
  • org.openscience.cdk.isomorphism.SmartsStereoMatch (implements java.util.function.Predicate<T>)
  • org.openscience.cdk.smiles.SmiFlavor
  • org.openscience.cdk.smiles.SmilesGenerator
  • org.openscience.cdk.smiles.SmilesParser
  • org.openscience.cdk.tools.SmilesValencyChecker (implements org.openscience.cdk.tools.IDeduceBondOrderTool, org.openscience.cdk.tools.IValencyChecker)
  • org.openscience.cdk.graph.SpanningTree
  • org.openscience.cdk.stereo.SquarePlanar
  • org.openscience.cdk.ringsearch.SSSRFinder
  • org.openscience.cdk.charges.StabilizationCharges
  • org.openscience.cdk.renderer.generators.standard.StandardGenerator (implements org.openscience.cdk.renderer.generators.IGenerator<T>)
  • org.openscience.cdk.fingerprint.StandardSubstructureSets
  • org.openscience.cdk.stereo.Stereocenters
  • org.openscience.cdk.stereo.StereoElementFactory
  • org.openscience.cdk.stereo.StereoTool
  • org.openscience.cdk.tools.diff.tree.StringDifference (implements org.openscience.cdk.tools.diff.tree.IDifference)
  • org.openscience.cdk.atomtype.StructGenAtomTypeGuesser (implements org.openscience.cdk.atomtype.IAtomTypeGuesser)
  • org.openscience.cdk.atomtype.StructGenMatcher (implements org.openscience.cdk.atomtype.IAtomTypeMatcher)
  • org.openscience.cdk.layout.StructureDiagramGenerator
  • org.openscience.cdk.tools.StructureResonanceGenerator
  • org.openscience.cdk.controller.SwingEventRelay (implements org.openscience.cdk.controller.IViewEventRelay)
  • org.openscience.cdk.io.listener.SwingGUIListener (implements org.openscience.cdk.io.listener.IReaderListener, org.openscience.cdk.io.listener.IWriterListener)
  • org.openscience.cdk.controller.SwingMouseEventRelay (implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
  • org.openscience.cdk.tools.SwissArmyKnife
  • org.openscience.cdk.atomtype.SybylAtomTypeMatcher (implements org.openscience.cdk.atomtype.IAtomTypeMatcher)
  • org.openscience.cdk.renderer.SymbolVisibility
    • org.openscience.cdk.renderer.generators.standard.SelectionVisibility
  • org.openscience.cdk.tools.SystemOutLoggingTool (implements org.openscience.cdk.tools.ILoggingTool)
  • org.openscience.cdk.similarity.Tanimoto
  • org.openscience.cdk.smsd.algorithm.mcgregor.TargetProcessor
  • org.openscience.cdk.smsd.algorithm.vflib.builder.TargetProperties (implements java.io.Serializable)
  • org.openscience.cdk.reaction.mechanism.TautomerizationMechanism (implements org.openscience.cdk.reaction.IReactionMechanism)
  • org.openscience.cdk.modeling.builder3d.TemplateExtractor
  • org.openscience.cdk.layout.TemplateHandler
  • org.openscience.cdk.modeling.builder3d.TemplateHandler3D
  • org.openscience.cdk.geometry.surface.Tessellate
  • org.openscience.cdk.templates.TestMoleculeFactory
  • org.openscience.cdk.stereo.TetrahedralChirality (implements org.openscience.cdk.interfaces.ITetrahedralChirality)
  • org.openscience.cdk.hash.stereo.TetrahedralElementEncoderFactory (implements org.openscience.cdk.hash.stereo.StereoEncoderFactory)
  • org.openscience.cdk.renderer.elements.TextElement (implements org.openscience.cdk.renderer.elements.IRenderingElement)
    • org.openscience.cdk.renderer.elements.AtomSymbolElement
      • org.openscience.cdk.renderer.elements.AtomMassSymbolElement
    • org.openscience.cdk.renderer.elements.TextGroupElement
  • org.openscience.cdk.renderer.elements.TextGroupElement.Child
  • org.openscience.cdk.io.listener.TextGUIListener (implements org.openscience.cdk.io.listener.IReaderListener, org.openscience.cdk.io.listener.IWriterListener)
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Error
      • org.openscience.cdk.exception.IncorrectUseOfCDKCoreClassError
      • org.openscience.cdk.iupac.parser.TokenMgrError
      • org.openscience.cdk.smiles.smarts.parser.TokenMgrError
    • java.lang.Exception
      • org.openscience.cdk.graph.invariant.exception.BadMatrixFormatException
      • org.openscience.cdk.exception.CDKException
        • org.openscience.cdk.qsar.DescriptorException
        • org.openscience.cdk.exception.Intractable
        • org.openscience.cdk.exception.InvalidSmilesException
        • org.openscience.cdk.exception.NoSuchAtomTypeException
        • org.openscience.cdk.exception.UnsupportedChemObjectException
      • org.openscience.cdk.graph.invariant.exception.IndexOutOfBoundsException
      • org.openscience.cdk.graph.invariant.exception.MatrixNotInvertibleException
      • org.openscience.cdk.iupac.parser.ParseException
      • org.openscience.cdk.smiles.smarts.parser.ParseException
      • java.lang.RuntimeException
        • org.openscience.cdk.exception.NoSuchAtomException
        • org.openscience.cdk.exception.NoSuchBondException
  • org.openscience.cdk.smsd.tools.TimeManager
  • org.openscience.cdk.smsd.global.TimeOut
  • org.openscience.cdk.iupac.parser.Token (implements java.io.Serializable)
  • org.openscience.cdk.smiles.smarts.parser.Token (implements java.io.Serializable)
  • org.openscience.cdk.formula.rules.ToleranceRangeRule (implements org.openscience.cdk.formula.rules.IRule)
  • org.openscience.cdk.graph.matrix.TopologicalMatrix (implements org.openscience.cdk.graph.matrix.IGraphMatrix)
  • org.openscience.cdk.geometry.surface.Triangle
  • org.openscience.cdk.stereo.TrigonalBipyramidal
  • org.openscience.cdk.graph.TripletShortCycles
  • org.openscience.cdk.config.TXTBasedAtomTypeConfigurator (implements org.openscience.cdk.config.IAtomTypeConfigurator)
  • org.openscience.cdk.controller.UndoAdapter (implements javax.swing.event.UndoableEditListener)
  • org.openscience.cdk.renderer.color.UniColor (implements org.openscience.cdk.renderer.color.IAtomColorer)
  • org.openscience.cdk.isomorphism.UniversalIsomorphismTester
  • org.openscience.cdk.geometry.volume.VABCVolume
  • org.openscience.cdk.validate.ValidationReport
  • org.openscience.cdk.validate.ValidationTest
  • org.openscience.cdk.validate.ValidatorEngine (implements org.openscience.cdk.validate.IValidator)
  • org.openscience.cdk.math.Vector
  • org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper (implements org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper)
  • org.openscience.cdk.smsd.algorithm.vflib.map.VFMCSMapper (implements org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper)
  • org.openscience.cdk.smsd.algorithm.vflib.builder.VFQueryBuilder (implements org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQuery)
  • org.openscience.cdk.smsd.algorithm.vflib.map.VFState (implements org.openscience.cdk.smsd.algorithm.vflib.interfaces.IState)
  • org.openscience.cdk.Vibration
  • org.openscience.cdk.structgen.VicinitySampler
  • org.openscience.cdk.geometry.cip.VisitedAtoms
  • org.openscience.cdk.io.WriterFactory
  • org.openscience.cdk.geometry.ZMatrixTools

Interface Hierarchy

• org.openscience.cdk.hash.AtomEncoder
• org.openscience.cdk.hash.AtomHashGenerator
• org.openscience.cdk.smsd.algorithm.matchers.AtomMatcher
• java.lang.AutoCloseable
  • java.io.Closeable
    • org.openscience.cdk.io.IChemObjectIO
      • org.openscience.cdk.io.IChemObjectReader
        • org.openscience.cdk.io.iterator.IIteratingChemObjectReader<T> (also extends java.util.Iterator<E>)
        • org.openscience.cdk.io.ISimpleChemObjectReader
      • org.openscience.cdk.io.IChemObjectWriter
      • org.openscience.cdk.io.iterator.event.IEventChemObjectReader
    • org.openscience.cdk.structgen.maygen.Maygen.Consumer
• org.openscience.cdk.smsd.algorithm.matchers.BondMatcher
• org.openscience.cdk.graph.rebond.Bspt.Tuple
• java.lang.Cloneable
  • org.openscience.cdk.interfaces.ICDKObject
    • org.openscience.cdk.interfaces.IChemObject
      • org.openscience.cdk.interfaces.IAtomContainer (also extends org.openscience.cdk.interfaces.IChemObjectListener)
        • org.openscience.cdk.interfaces.ICrystal
        • org.openscience.cdk.interfaces.IMonomer
          • org.openscience.cdk.interfaces.IAminoAcid
          • org.openscience.cdk.interfaces.IPDBMonomer
        • org.openscience.cdk.interfaces.IPolymer
          • org.openscience.cdk.interfaces.IBioPolymer
            • org.openscience.cdk.interfaces.IPDBPolymer
        • org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer
        • org.openscience.cdk.interfaces.IRing
        • org.openscience.cdk.interfaces.IStrand
      • org.openscience.cdk.interfaces.IAtomContainerSet
        • org.openscience.cdk.interfaces.IRingSet
        • org.openscience.cdk.interfaces.ISubstance
      • org.openscience.cdk.interfaces.IChemFile
      • org.openscience.cdk.interfaces.IChemModel
      • org.openscience.cdk.interfaces.IChemSequence
      • org.openscience.cdk.interfaces.IElectronContainer
        • org.openscience.cdk.interfaces.IBond
          • org.openscience.cdk.isomorphism.matchers.IQueryBond
        • org.openscience.cdk.interfaces.ILonePair
        • org.openscience.cdk.interfaces.ISingleElectron
      • org.openscience.cdk.interfaces.IElement
        • org.openscience.cdk.interfaces.IIsotope
          • org.openscience.cdk.interfaces.IAtomType
            • org.openscience.cdk.interfaces.IAtom
              • org.openscience.cdk.interfaces.IPDBAtom
              • org.openscience.cdk.interfaces.IPseudoAtom
                • org.openscience.cdk.interfaces.IFragmentAtom
              • org.openscience.cdk.isomorphism.matchers.IQueryAtom
      • org.openscience.cdk.interfaces.IMapping
      • org.openscience.cdk.interfaces.IReaction
      • org.openscience.cdk.interfaces.IReactionSet
        • org.openscience.cdk.interfaces.IReactionScheme
      • org.openscience.cdk.isomorphism.matchers.IRGroupQuery
    • org.openscience.cdk.interfaces.IMolecularFormula
    • org.openscience.cdk.interfaces.IMolecularFormulaSet
      • org.openscience.cdk.interfaces.IAdductFormula
    • org.openscience.cdk.interfaces.IPDBStructure
    • org.openscience.cdk.interfaces.IStereoElement<F,C>
      • org.openscience.cdk.interfaces.IDoubleBondStereochemistry
      • org.openscience.cdk.interfaces.ITetrahedralChirality
• java.lang.Comparable<T>
  • org.openscience.cdk.group.Invariant
• java.util.Comparator<T>
  • org.openscience.cdk.geometry.cip.rules.ISequenceSubRule<ILigand>
• org.openscience.cdk.graph.CycleFinder
• org.openscience.cdk.ringsearch.CyclicVertexSearch
• org.openscience.cdk.group.DiscretePartitionRefiner
  • org.openscience.cdk.group.AtomContainerDiscretePartitionRefiner
• org.openscience.cdk.DynamicFactory.CreationModifier<T>
• org.openscience.cdk.DynamicFactory.Creator<T>
• org.openscience.cdk.DynamicFactory.InterfaceProvider
• org.openscience.cdk.hash.EnsembleHashGenerator
• java.util.EventListener
  • org.openscience.cdk.event.ICDKChangeListener
  • org.openscience.cdk.event.ICDKSelectionChangeListener
  • org.openscience.cdk.io.listener.IChemObjectIOListener
    • org.openscience.cdk.io.listener.IReaderListener
    • org.openscience.cdk.io.listener.IWriterListener
• org.openscience.cdk.renderer.generators.HighlightGenerator.Palette
• org.openscience.cdk.renderer.color.IAtomColorer
• org.openscience.cdk.config.IAtomTypeConfigurator
• org.openscience.cdk.atomtype.IAtomTypeGuesser
• org.openscience.cdk.atomtype.IAtomTypeMatcher
• org.openscience.cdk.math.qm.IBasis
• org.openscience.cdk.smsd.labelling.ICanonicalMoleculeLabeller
• org.openscience.cdk.smsd.labelling.ICanonicalReactionLabeller
• org.openscience.cdk.interfaces.IChemObjectBuilder
• org.openscience.cdk.interfaces.IChemObjectChangeEvent
• org.openscience.cdk.interfaces.IChemObjectListener
  • org.openscience.cdk.interfaces.IAtomContainer (also extends org.openscience.cdk.interfaces.IChemObject)
    • org.openscience.cdk.interfaces.ICrystal
    • org.openscience.cdk.interfaces.IMonomer
      • org.openscience.cdk.interfaces.IAminoAcid
      • org.openscience.cdk.interfaces.IPDBMonomer
    • org.openscience.cdk.interfaces.IPolymer
      • org.openscience.cdk.interfaces.IBioPolymer
        • org.openscience.cdk.interfaces.IPDBPolymer
    • org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer
    • org.openscience.cdk.interfaces.IRing
    • org.openscience.cdk.interfaces.IStrand
• org.openscience.cdk.io.IChemObjectReaderErrorHandler
• org.openscience.cdk.renderer.selection.IChemObjectSelection
• org.openscience.cdk.libio.cml.ICMLCustomizer
• org.openscience.cdk.io.cml.ICMLModule
  • org.openscience.cdk.io.cml.ICMLConvention
• org.openscience.cdk.tools.IDeduceBondOrderTool
• org.openscience.cdk.qsar.IDescriptor
  • org.openscience.cdk.qsar.IAtomicDescriptor
  • org.openscience.cdk.qsar.IAtomPairDescriptor
  • org.openscience.cdk.qsar.IBondDescriptor
  • org.openscience.cdk.qsar.IMolecularDescriptor
  • org.openscience.cdk.qsar.descriptors.substance.ISubstanceDescriptor
• org.openscience.cdk.tools.diff.tree.IDifference
  • org.openscience.cdk.tools.diff.tree.IDifferenceList
• org.openscience.cdk.smsd.algorithm.vflib.interfaces.IEdge
• org.openscience.cdk.charges.IElectronicPropertyCalculator
  • org.openscience.cdk.charges.IChargeCalculator
• org.openscience.cdk.smsd.interfaces.IFinalMapping
• org.openscience.cdk.fingerprint.IFingerprinter
• org.openscience.cdk.renderer.font.IFontManager
• org.openscience.cdk.fragment.IFragmenter
• org.openscience.cdk.math.IFunction
• org.openscience.cdk.renderer.generators.IGenerator<T>
• org.openscience.cdk.renderer.generators.IGeneratorParameter<T>
• org.openscience.cdk.graph.matrix.IGraphMatrix
• org.openscience.cdk.IImplementationSpecification
• org.openscience.cdk.geometry.cip.ILigand
• org.openscience.cdk.tools.ILoggingTool
• org.openscience.cdk.smsd.algorithm.vflib.interfaces.IMapper
• org.openscience.cdk.smsd.interfaces.IMCSBase
• org.openscience.cdk.controller.IMouseEventRelay
• org.openscience.cdk.smsd.algorithm.vflib.interfaces.INode
• org.openscience.cdk.reaction.type.parameters.IParameterReact
• org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQuery
• org.openscience.cdk.smsd.algorithm.vflib.interfaces.IQueryCompiler
• org.openscience.cdk.geometry.IRDFWeightFunction
• org.openscience.cdk.reaction.IReactionMechanism
• org.openscience.cdk.reaction.IReactionProcess
• org.openscience.cdk.renderer.IRenderer<T>
• org.openscience.cdk.renderer.elements.IRenderingElement
• org.openscience.cdk.renderer.elements.IRenderingVisitor
  • org.openscience.cdk.renderer.visitor.IDrawVisitor
• org.openscience.cdk.io.formats.IResourceFormat
  • org.openscience.cdk.io.formats.IChemFormat
    • org.openscience.cdk.io.formats.IChemFormatMatcher
• org.openscience.cdk.isomorphism.matchers.IRGroup
• org.openscience.cdk.isomorphism.matchers.IRGroupList
• org.openscience.cdk.formula.rules.IRule
• org.openscience.cdk.interfaces.ISetting
• org.openscience.cdk.smsd.algorithm.vflib.interfaces.IState
• org.openscience.cdk.structgen.IStructureGenerationListener
• java.util.Iterator<E>
  • org.openscience.cdk.io.iterator.IIteratingChemObjectReader<T> (also extends org.openscience.cdk.io.IChemObjectReader)
  • java.util.ListIterator<E>
    • org.openscience.cdk.io.random.IRandomAccessChemObjectReader<T>
• org.openscience.cdk.tools.IValencyChecker
• org.openscience.cdk.validate.IValidator
• org.openscience.cdk.controller.IViewEventRelay
• org.openscience.cdk.hash.MoleculeHashGenerator
• org.openscience.cdk.smiles.smarts.parser.Node
• org.openscience.cdk.iupac.parser.NomParserConstants
• org.openscience.cdk.group.PermutationGroup.Backtracker
• org.openscience.cdk.group.Refinable
• org.openscience.cdk.smsd.ring.RingFinder
• java.io.Serializable
  • org.openscience.cdk.fingerprint.IBitFingerprint
  • org.openscience.cdk.fingerprint.ICountFingerprint
  • org.openscience.cdk.qsar.result.IDescriptorResult
• org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants
• org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants
• org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor
• org.openscience.cdk.hash.stereo.StereoEncoder
• org.openscience.cdk.hash.stereo.StereoEncoderFactory
• org.openscience.cdk.smsd.algorithm.matchers.VFAtomMatcher
• org.openscience.cdk.smsd.algorithm.matchers.VFBondMatcher

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • org.openscience.cdk.depict.Abbreviations.Option
    • org.openscience.cdk.smsd.interfaces.Algorithm
    • org.openscience.cdk.ringsearch.AllRingsFinder.Threshold
    • org.openscience.cdk.hash.BasicAtomEncoder (implements org.openscience.cdk.hash.AtomEncoder)
    • org.openscience.cdk.renderer.generators.BasicAtomGenerator.Shape
    • org.openscience.cdk.geometry.cip.CIPTool.CIP_CHIRALITY
    • org.openscience.cdk.isomorphism.matchers.CTFileQueryBond.Type
    • org.openscience.cdk.config.Elements
    • org.openscience.cdk.isomorphism.matchers.Expr.Type
    • org.openscience.cdk.geometry.GeometryTools.CoordinateCoverage
    • org.openscience.cdk.geometry.GeometryUtil.CoordinateCoverage
    • org.openscience.cdk.interfaces.IAtomType.Hybridization
    • org.openscience.cdk.interfaces.IBond.Display
    • org.openscience.cdk.interfaces.IBond.Order
    • org.openscience.cdk.interfaces.IBond.Stereo
    • org.openscience.cdk.io.IChemObjectReader.Mode
    • org.openscience.cdk.interfaces.IDoubleBondStereochemistry.Conformation
    • org.openscience.cdk.renderer.font.IFontManager.FontStyle
    • net.sf.jniinchi.INCHI_OPTION
    • net.sf.jniinchi.INCHI_RET
    • org.openscience.cdk.io.setting.IOSetting.Importance
    • org.openscience.cdk.interfaces.IReaction.Direction
    • org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo
    • org.openscience.cdk.renderer.elements.LineElement.LineType
    • org.openscience.cdk.io.MDLV2000Writer.SPIN_MULTIPLICITY
    • org.openscience.cdk.formula.rules.MMElementRule.Database
    • org.openscience.cdk.formula.rules.MMElementRule.RangeMass
    • org.openscience.cdk.stereo.Projection
    • org.openscience.cdk.ReactionRole
    • org.openscience.cdk.sgroup.SgroupKey
    • org.openscience.cdk.sgroup.SgroupType
    • org.openscience.cdk.renderer.generators.standard.StandardGenerator.HighlightStyle
    • org.openscience.cdk.isomorphism.matchers.smarts.StereoBond.Direction
    • org.openscience.cdk.stereo.Stereocenters.Stereocenter
    • org.openscience.cdk.stereo.Stereocenters.Type
    • org.openscience.cdk.stereo.StereoTool.SquarePlanarShape
    • org.openscience.cdk.stereo.StereoTool.StereoClass
    • org.openscience.cdk.stereo.StereoTool.TetrahedralSign
    • org.openscience.cdk.renderer.elements.TextGroupElement.Position
    • org.openscience.cdk.renderer.elements.path.Type
    • org.openscience.cdk.renderer.elements.WedgeLineElement.Direction
    • org.openscience.cdk.renderer.elements.WedgeLineElement.TYPE