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  A  
ColumnAtom (org::openscience::cdk::isomorphism::matchers::smarts)   
  H  
  M  
RandomGenerator (org::openscience::cdk::structgen)   
ABINITFormat (org::openscience::cdk::io::formats)   Complex (org::openscience::cdk::math)   HBondAcceptorCountDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   MACiEFormat (org::openscience::cdk::io::formats)   RandomNumbersTool (org::openscience::cdk::math)   
AboutAction (org::openscience::cdk::applications::jchempaint::action)   ConjugatedPiSystemsDetector (org::openscience::cdk::graph::invariant)   HBondDonorCountDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   MACiEReader (org::openscience::cdk::io)   RawCopyFormat (org::openscience::cdk::io::formats)   
AboutDialog (org::openscience::cdk::applications::jchempaint::dialogs)   ConjugateGradientMethod (org::openscience::cdk::modeling::forcefield)   HelpAction (org::openscience::cdk::applications::jchempaint::action)   MacroModelFormat (org::openscience::cdk::io::formats)   RDFCalculator (org::openscience::cdk::geometry)   
AbstractAtomicDescriptor (org::openscience::cdk::qsar)   ConnectionCountAtom (org::openscience::cdk::isomorphism::matchers::smarts)   HelpDialog (org::openscience::cdk::applications::jchempaint::dialogs)   MakeJavafilesFiles (net::sf::cdk::tools)   RDFProtonDescriptor_G3R (org::openscience::cdk::qsar::descriptors::atomic)   
AbstractBondDescriptor (org::openscience::cdk::qsar)   ConnectionMatrix (org::openscience::cdk::graph::matrix)   HelpDialog::PageLoader (org::openscience::cdk::applications::jchempaint::dialogs)   MakeRequiresfilesFiles (net::sf::cdk::tools)   RDFProtonDescriptor_GDR (org::openscience::cdk::qsar::descriptors::atomic)   
AbstractController2D (org::openscience::cdk::controller)   ConnectivityChecker (org::openscience::cdk::graph)   HINFormat (org::openscience::cdk::io::formats)   Mapping (org::openscience::cdk)   RDFProtonDescriptor_GHR (org::openscience::cdk::qsar::descriptors::atomic)   
AbstractRenderer2D (org::openscience::cdk::renderer)   Controller2D (org::openscience::cdk::controller)   HINReader (org::openscience::cdk::io)   Mapping::ChemObjectIterator (org::openscience::cdk)   RDFProtonDescriptor_GHR_topol (org::openscience::cdk::qsar::descriptors::atomic)   
AbstractValidator (org::openscience::cdk::validate)   Controller2DModel (org::openscience::cdk::controller)   HINWriter (org::openscience::cdk::io)   MassAtom (org::openscience::cdk::isomorphism::matchers::smarts)   RDFProtonDescriptor_GSR (org::openscience::cdk::qsar::descriptors::atomic)   
Aces2Format (org::openscience::cdk::io::formats)   Controller2DModelEditor (org::openscience::cdk::applications::swing::editor)   HOSECodeAnalyser (org::openscience::cdk::tools)   MathTools (org::openscience::cdk::math)   Reaction (org::openscience::cdk)   
AddAtomsAndBondsEdit (org::openscience::cdk::applications::undoredo)   Convertor (org::openscience::cdk::libio::biojava)   HOSECodeGenerator (org::openscience::cdk::tools)   Matrix (org::openscience::cdk::math)   Reaction::MappingIterator (org::openscience::cdk)   
AddFuncGroupEdit (org::openscience::cdk::applications::undoredo)   Convertor (org::openscience::cdk::libio::cml)   HOSECodeGenerator::TreeNode (org::openscience::cdk::tools)   MDEDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   ReactionEditor (org::openscience::cdk::applications::swing::editor)   
AddHydrogenAction (org::openscience::cdk::applications::jchempaint::action)   ConvertToAction (org::openscience::cdk::applications::jchempaint::action)   HueckelAromaticityDetector (org::openscience::cdk::aromaticity)   MDLFormat (org::openscience::cdk::io::formats)   ReactionManipulator (org::openscience::cdk::tools::manipulator)   
AddHydrogenEdit (org::openscience::cdk::applications::undoredo)   ConvertToPseudoAtomAction (org::openscience::cdk::applications::jchempaint::action)   HuLuIndexTool (org::openscience::cdk::graph::invariant)   MDLMolConvention (org::openscience::cdk::io::cml)   ReactionSet (org::openscience::cdk)   
ADFFormat (org::openscience::cdk::io::formats)   ConvertToPseudoAtomEdit (org::openscience::cdk::applications::undoredo)   HybridizationMatcher (org::openscience::cdk::atomtype)   MDLReader (org::openscience::cdk::io)   ReactionSet::ReactionIterator (org::openscience::cdk)   
AdjacencyMatrix (org::openscience::cdk::graph::matrix)   ConvertToRadicalAction (org::openscience::cdk::applications::jchempaint::action)   HybridizationStateATMatcher (org::openscience::cdk::atomtype)   MDLRXNFormat (org::openscience::cdk::io::formats)   ReactionSetManipulator (org::openscience::cdk::tools::manipulator)   
AdjustBondOrdersAction (org::openscience::cdk::applications::jchempaint::action)   ConvertToRadicalEdit (org::openscience::cdk::applications::undoredo)   HydrogenAdder (org::openscience::cdk::tools)   MDLRXNReader (org::openscience::cdk::io)   ReactionSpecification (org::openscience::cdk::reaction)   
AdjustBondOrdersEdit (org::openscience::cdk::applications::undoredo)   CopyPasteAction (org::openscience::cdk::applications::jchempaint::action)   HydrogenAtom (org::openscience::cdk::isomorphism::matchers::smarts)   MDLRXNV2000Reader (org::openscience::cdk::io)   ReaderEvent (org::openscience::cdk::io)   
AlchemyFormat (org::openscience::cdk::io::formats)   CovalentRadiusDescriptor (org::openscience::cdk::qsar::descriptors::atomic)   HydrogenPlacer (org::openscience::cdk::layout)   MDLRXNV3000Format (org::openscience::cdk::io::formats)   ReaderFactory (org::openscience::cdk::io)   
AliphaticAtom (org::openscience::cdk::isomorphism::matchers::smarts)   CPKAtomColors (org::openscience::cdk::renderer::color)   HydrogenRearrangementDeltaReaction (org::openscience::cdk::reaction::type)   MDLRXNV3000Reader (org::openscience::cdk::io)   RearrangementAnion1Reaction (org::openscience::cdk::reaction::type)   
AliphaticSymbolAtom (org::openscience::cdk::isomorphism::matchers::smarts)   CPSADescriptor (org::openscience::cdk::qsar::descriptors::molecular)   HydrogenRearrangementGammaReaction (org::openscience::cdk::reaction::type)   MDLRXNWriter (org::openscience::cdk::io)   RearrangementAnion2Reaction (org::openscience::cdk::reaction::type)   
AllRingsFinder (org::openscience::cdk::ringsearch)   CreateCoordinatesForFileDialog (org::openscience::cdk::applications::jchempaint::dialogs)   HyperconjugationReaction (org::openscience::cdk::reaction::type)   MDLV2000Format (org::openscience::cdk::io::formats)   RearrangementAnion3Reaction (org::openscience::cdk::reaction::type)   
ALOGP (org::openscience::cdk::qsar::descriptors::molecular)   CreateCoordinatesForFileDialog::CreateAction (org::openscience::cdk::applications::jchempaint::dialogs)   
  I  
MDLV2000Reader (org::openscience::cdk::io)   RearrangementCation1Reaction (org::openscience::cdk::reaction::type)   
AlphaRenderer2D (org::openscience::cdk::renderer)   CreateInChIAction (org::openscience::cdk::applications::jchempaint::action)   IAminoAcid (org::openscience::cdk::interfaces)   MDLV3000Format (org::openscience::cdk::io::formats)   RearrangementCation2Reaction (org::openscience::cdk::reaction::type)   
AminoAcid (org::openscience::cdk)   CreateReactionAction (org::openscience::cdk::applications::jchempaint::action)   IAtom (org::openscience::cdk::interfaces)   MDLV3000Reader (org::openscience::cdk::io)   RearrangementCation3Reaction (org::openscience::cdk::reaction::type)   
AminoAcidCountDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   CreateSmilesAction (org::openscience::cdk::applications::jchempaint::action)   IAtomColorer (org::openscience::cdk::renderer::color)   MDLWriter (org::openscience::cdk::io)   RearrangementRadical1Reaction (org::openscience::cdk::reaction::type)   
AminoAcidManipulator (org::openscience::cdk::tools::manipulator)   CRK2DFormat (org::openscience::cdk::io::formats)   IAtomContainer (org::openscience::cdk::interfaces)   MDMolecule (org::openscience::cdk::libio::md)   RearrangementRadical2Reaction (org::openscience::cdk::reaction::type)   
AminoAcids (org::openscience::cdk::templates)   CRK3DFormat (org::openscience::cdk::io::formats)   IAtomContainerSet (org::openscience::cdk::interfaces)   MDMoleculeConvention (org::openscience::cdk::io::cml)   RearrangementRadical3Reaction (org::openscience::cdk::reaction::type)   
AngleBending (org::openscience::cdk::modeling::forcefield)   CrossoverMachine (org::openscience::cdk::structgen::stochastic::operator)   IAtomicDescriptor (org::openscience::cdk::qsar)   MDMoleculeCustomizer (org::openscience::cdk::libio::cml)   RebondTool (org::openscience::cdk::graph::rebond)   
AngularMomentum (org::openscience::cdk::math::qm)   Crystal (org::openscience::cdk)   IAtomPairDescriptor (org::openscience::cdk::qsar)   MenuBarAction (org::openscience::cdk::applications::jchempaint::action)   RecurseAtom (org::openscience::cdk::isomorphism::matchers::smarts)   
AnyAtom (org::openscience::cdk::isomorphism::matchers::smarts)   CrystalGeometryTools (org::openscience::cdk::geometry)   IAtomParity (org::openscience::cdk::interfaces)   MergeMoleculesEdit (org::openscience::cdk::applications::undoredo)   RecursiveSmartsAtom (org::openscience::cdk::isomorphism::matchers::smarts)   
AnyOrderQueryBond (org::openscience::cdk::isomorphism::matchers::smarts)   CrystClustFormat (org::openscience::cdk::io::formats)   IAtomType (org::openscience::cdk::interfaces)   MFAnalyser (org::openscience::cdk::tools)   RedoAction (org::openscience::cdk::applications::jchempaint::action)   
APIVersionTester (org::openscience::cdk::applications)   CrystClustReader (org::openscience::cdk::io)   IAtomTypeConfigurator (org::openscience::cdk::config)   MinimalPathIterator (org::openscience::cdk::graph)   RemoveAtomsAndBondsEdit (org::openscience::cdk::applications::undoredo)   
APolDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   CrystClustWriter (org::openscience::cdk::io)   IAtomTypeGuesser (org::openscience::cdk::atomtype)   MM2AtomTypeMatcher (org::openscience::cdk::atomtype)   Renderer2D (org::openscience::cdk::renderer)   
AppletCanvas (org::openscience::cdk::applications::jchempaint::applet)   CTXFormat (org::openscience::cdk::io::formats)   IAtomTypeMatcher (org::openscience::cdk::atomtype)   MM2BasedAtomTypePattern (org::openscience::cdk::modeling::builder3d)   Renderer2DModel (org::openscience::cdk::renderer)   
AromaticAtom (org::openscience::cdk::isomorphism::matchers::smarts)   CTXReader (org::openscience::cdk::io)   IBasis (org::openscience::cdk::math::qm)   MM2BasedParameterSetReader (org::openscience::cdk::modeling::builder3d)   Renderer2DModelEditor (org::openscience::cdk::applications::swing::editor)   
AromaticAtomsCountDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   CycleBasis (org::openscience::cdk::ringsearch::cyclebasis)   IBioPolymer (org::openscience::cdk::interfaces)   MMFF94AtomTypeMatcher (org::openscience::cdk::atomtype)   Residue (org::openscience::cdk::libio::md)   
AromaticBondsCountDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   
  D  
IBond (org::openscience::cdk::interfaces)   MMFF94BasedAtomTypePattern (org::openscience::cdk::modeling::builder3d)   ResonancePositiveChargeDescriptor (org::openscience::cdk::qsar::descriptors::bond)   
AromaticityCalculator (org::openscience::cdk::aromaticity)   DADMLReader (org::openscience::cdk::internet)   IBondDescriptor (org::openscience::cdk::qsar)   MMFF94BasedParameterSetReader (org::openscience::cdk::modeling::builder3d)   RGraph (org::openscience::cdk::isomorphism::mcss)   
AromaticQueryBond (org::openscience::cdk::isomorphism::matchers::smarts)   DADMLResult (org::openscience::cdk::internet)   ICDKChangeListener (org::openscience::cdk::event)   MMFF94EnergyFunction (org::openscience::cdk::modeling::forcefield)   Ring (org::openscience::cdk)   
AromaticSymbolAtom (org::openscience::cdk::isomorphism::matchers::smarts)   DaltonFormat (org::openscience::cdk::io::formats)   ICDKEditBus (org::openscience::cdk::applications::plugin)   MMFF94ParametersCall (org::openscience::cdk::modeling::builder3d)   RingAtom (org::openscience::cdk::isomorphism::matchers::smarts)   
Arrow (org::openscience::cdk::renderer)   DataFeatures (org::openscience::cdk::tools)   ICDKPlugin (org::openscience::cdk::applications::plugin)   MMFF94PartialCharges (org::openscience::cdk::charges)   RingBond (org::openscience::cdk::isomorphism::matchers::smarts)   
ArrowRenderer2D (org::openscience::cdk::renderer)   DataFeaturesTool (org::openscience::cdk::tools)   ICDKSelectionChangeListener (org::openscience::cdk::event)   MMODFormat (org::openscience::cdk::io::formats)   RingIdentifierAtom (org::openscience::cdk::isomorphism::matchers::smarts)   
Association (org::openscience::cdk)   DeAromatizationTool (org::openscience::cdk::tools)   IChemFile (org::openscience::cdk::interfaces)   ModelBuilder3D (org::openscience::cdk::modeling::builder3d)   RingMembershipAtom (org::openscience::cdk::isomorphism::matchers::smarts)   
Atom (org::openscience::cdk)   DebugAminoAcid (org::openscience::cdk::debug)   IChemFormat (org::openscience::cdk::io::formats)   ModelPropsAction (org::openscience::cdk::applications::jchempaint::action)   RingPartitioner (org::openscience::cdk::ringsearch)   
AtomContainer (org::openscience::cdk)   DebugAtom (org::openscience::cdk::debug)   IChemFormatMatcher (org::openscience::cdk::io::formats)   ModifyDisplaySettingsAction (org::openscience::cdk::applications::jchempaint::action)   RingPlacer (org::openscience::cdk::layout)   
AtomContainer::AtomIterator (org::openscience::cdk)   DebugAtomContainer (org::openscience::cdk::debug)   IChemModel (org::openscience::cdk::interfaces)   ModifyGeneralSettingsAction (org::openscience::cdk::applications::jchempaint::action)   RingSet (org::openscience::cdk)   
AtomContainer::BondIterator (org::openscience::cdk)   DebugAtomContainerSet (org::openscience::cdk::debug)   IChemObject (org::openscience::cdk::interfaces)   ModifyGeneralSettingsDialog (org::openscience::cdk::applications::jchempaint::dialogs)   RingSetManipulator (org::openscience::cdk::tools::manipulator)   
AtomContainer::ElectronContainerIterator (org::openscience::cdk)   DebugAtomParity (org::openscience::cdk::debug)   IChemObjectBuilder (org::openscience::cdk::interfaces)   ModifyRenderOptionsDialog (org::openscience::cdk::applications::jchempaint::dialogs)   RingSizeComparator (org::openscience::cdk::tools::manipulator)   
AtomContainer::LonePairIterator (org::openscience::cdk)   DebugAtomType (org::openscience::cdk::debug)   IChemObjectChangeEvent (org::openscience::cdk::interfaces)   Mol2Format (org::openscience::cdk::io::formats)   RMap (org::openscience::cdk::isomorphism::mcss)   
AtomContainer::SingleElectronIterator (org::openscience::cdk)   DebugBioPolymer (org::openscience::cdk::debug)   IChemObjectIO (org::openscience::cdk::io)   Mol2Reader (org::openscience::cdk::io)   RModel (org::openscience::cdk::qsar::model::R2)   
AtomContainerAtomPermutor (org::openscience::cdk::graph)   DebugBond (org::openscience::cdk::debug)   IChemObjectIOListener (org::openscience::cdk::io::listener)   Mol2Writer (org::openscience::cdk::io)   RModel (org::openscience::cdk::qsar::model::R)   
AtomContainerBondPermutor (org::openscience::cdk::graph)   DebugChemFile (org::openscience::cdk::debug)   IChemObjectListener (org::openscience::cdk::interfaces)   Molecule (org::openscience::cdk)   RNode (org::openscience::cdk::isomorphism::mcss)   
AtomContainerComparator (org::openscience::cdk::tools::manipulator)   DebugChemModel (org::openscience::cdk::debug)   IChemObjectReader (org::openscience::cdk::io)   MoleculeBuilder (org::openscience::cdk::iupac::parser)   RotatableBondsCountDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   
AtomContainerEditor (org::openscience::cdk::applications::swing::editor)   DebugChemObject (org::openscience::cdk::debug)   IChemObjectWriter (org::openscience::cdk::io)   MoleculeFactory (org::openscience::cdk::templates)   RssWriter (org::openscience::cdk::io)   
AtomContainerManipulator (org::openscience::cdk::tools::manipulator)   DebugChemObjectBuilder (org::openscience::cdk::debug)   IChemSequence (org::openscience::cdk::interfaces)   MoleculeFeaturesTool (org::openscience::cdk::tools::features)   RuleOfFiveDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   
AtomContainerPermutor (org::openscience::cdk::graph)   DebugChemSequence (org::openscience::cdk::debug)   ICMLConvention (org::openscience::cdk::io::cml)   MoleculeGraphs (org::openscience::cdk::graph)   
  S  
AtomContainerSet (org::openscience::cdk)   DebugCrystal (org::openscience::cdk::debug)   ICMLCustomizer (org::openscience::cdk::libio::cml)   MoleculeListPanel (org::openscience::cdk::applications::swing)   SaturationChecker (org::openscience::cdk::tools)   
AtomContainerSet::AtomContainerIterator (org::openscience::cdk)   DebugElectronContainer (org::openscience::cdk::debug)   ICMLModule (org::openscience::cdk::io::cml)   MoleculeListPanel::StrucContainer (org::openscience::cdk::applications::swing)   SaveAction (org::openscience::cdk::applications::jchempaint::action)   
AtomContainerSetManipulator (org::openscience::cdk::tools::manipulator)   DebugElement (org::openscience::cdk::debug)   ICrystal (org::openscience::cdk::interfaces)   MoleculeListViewer (org::openscience::cdk::applications::swing)   SaveAsAction (org::openscience::cdk::applications::jchempaint::action)   
AtomCountDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   DebugIsotope (org::openscience::cdk::debug)   IDCreator (org::openscience::cdk::tools)   MoleculeSet (org::openscience::cdk)   SDFFormat (org::openscience::cdk::io::formats)   
AtomDegreeDescriptor (org::openscience::cdk::qsar::descriptors::atomic)   DebugLonePair (org::openscience::cdk::debug)   IDeduceBondOrderTool (org::openscience::cdk::tools)   MoleculeSetManipulator (org::openscience::cdk::tools::manipulator)   SDFSubstructureFinder (org::openscience::cdk::applications)   
AtomEditor (org::openscience::cdk::applications::swing::editor)   DebugMapping (org::openscience::cdk::debug)   IDescriptor (org::openscience::cdk::qsar)   MoleculesTable (org::openscience::cdk::applications::swing)   SetColorSchemeAction (org::openscience::cdk::applications::jchempaint::action)   
AtomHybridizationDescriptor (org::openscience::cdk::qsar::descriptors::atomic)   DebugMolecule (org::openscience::cdk::debug)   IDescriptorResult (org::openscience::cdk::qsar::result)   MoleculeViewer2D (org::openscience::cdk::applications::swing)   ShelXFormat (org::openscience::cdk::io::formats)   
AtomHybridizationVSEPRDescriptor (org::openscience::cdk::qsar::descriptors::atomic)   DebugMoleculeSet (org::openscience::cdk::debug)   IElectronContainer (org::openscience::cdk::interfaces)   MoleculeViewer2DPanel (org::openscience::cdk::applications::swing)   ShelXReader (org::openscience::cdk::io)   
AtomicNumberAtom (org::openscience::cdk::isomorphism::matchers::smarts)   DebugMonomer (org::openscience::cdk::debug)   IElement (org::openscience::cdk::interfaces)   MomentOfInertiaDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   ShelXWriter (org::openscience::cdk::io)   
AtomicTable (org::openscience::cdk::applications::swing)   DebugPDBAtom (org::openscience::cdk::debug)   IEventChemObjectReader (org::openscience::cdk::io::iterator::event)   Monomer (org::openscience::cdk)   ShowChemObjectDumpAction (org::openscience::cdk::applications::jchempaint::action)   
AtomParity (org::openscience::cdk)   DebugPDBMonomer (org::openscience::cdk::debug)   IFingerprinter (org::openscience::cdk::fingerprint)   MOPAC2002Format (org::openscience::cdk::io::formats)   ShowChemObjectProperty (org::openscience::cdk::applications::jchempaint::action)   
AtomPlacer (org::openscience::cdk::layout)   DebugPDBPolymer (org::openscience::cdk::debug)   IFunction (org::openscience::cdk::math)   MOPAC7Format (org::openscience::cdk::io::formats)   ShowDictionariesAction (org::openscience::cdk::applications::jchempaint::action)   
AtomPlacer3D (org::openscience::cdk::modeling::builder3d)   DebugPDBStructure (org::openscience::cdk::debug)   IGraphMatrix (org::openscience::cdk::graph::matrix)   MOPAC93Format (org::openscience::cdk::io::formats)   SigmaElectronegativityDescriptor (org::openscience::cdk::qsar::descriptors::atomic)   
AtomTetrahedralLigandPlacer3D (org::openscience::cdk::modeling::builder3d)   DebugPolymer (org::openscience::cdk::debug)   IImplementationSpecification (org::openscience::cdk)   MOPAC97Format (org::openscience::cdk::io::formats)   SimpleBasisSet (org::openscience::cdk::math::qm)   
AtomTools (org::openscience::cdk::geometry)   DebugPseudoAtom (org::openscience::cdk::debug)   IIsotope (org::openscience::cdk::interfaces)   MorganNumbersTools (org::openscience::cdk::graph::invariant)   SimpleCharStream (org::openscience::cdk::iupac::parser)   
AtomType (org::openscience::cdk)   DebugReaction (org::openscience::cdk::debug)   IIteratingChemObjectReader (org::openscience::cdk::io::iterator)   MoveAtomEdit (org::openscience::cdk::applications::undoredo)   SimpleController2D (org::openscience::cdk::controller)   
AtomTypeCharges (org::openscience::cdk::charges)   DebugReactionSet (org::openscience::cdk::debug)   IJCPFileFilter (org::openscience::cdk::applications::jchempaint::io)   MPQCFormat (org::openscience::cdk::io::formats)   SimpleCycle (org::openscience::cdk::ringsearch::cyclebasis)   
AtomTypeFactory (org::openscience::cdk::config)   DebugRing (org::openscience::cdk::debug)   ILonePair (org::openscience::cdk::interfaces)   
  N  
SimpleCycleBasis (org::openscience::cdk::ringsearch::cyclebasis)   
AtomTypeHandler (org::openscience::cdk::config::atomtypes)   DebugRingSet (org::openscience::cdk::debug)   IMapping (org::openscience::cdk::interfaces)   NeighborList (org::openscience::cdk::geometry::surface)   SimpleRenderer2D (org::openscience::cdk::renderer)   
AtomTypeManipulator (org::openscience::cdk::tools::manipulator)   DebugSingleElectron (org::openscience::cdk::debug)   IMatrix (org::openscience::cdk::math)   NewAction (org::openscience::cdk::applications::jchempaint::action)   SingleElectron (org::openscience::cdk)   
AtomTypeReader (org::openscience::cdk::config::atomtypes)   DebugStrand (org::openscience::cdk::debug)   IModel (org::openscience::cdk::qsar::model)   NewtonRaphsonMethod (org::openscience::cdk::modeling::forcefield)   SingleStructureRandomGenerator (org::openscience::cdk::structgen)   
AtomTypeTools (org::openscience::cdk::tools)   DeduceBondSystemTool (org::openscience::cdk::smiles)   IMolecularDescriptor (org::openscience::cdk::qsar)   NNAminoAcid (org::openscience::cdk::nonotify)   SmallestRingAtom (org::openscience::cdk::isomorphism::matchers::smarts)   
AtomValenceDescriptor (org::openscience::cdk::qsar::descriptors::atomic)   DefaultChemObjectBuilder (org::openscience::cdk)   IMolecule (org::openscience::cdk::interfaces)   NNAtom (org::openscience::cdk::nonotify)   SMARTSAtom (org::openscience::cdk::isomorphism::matchers::smarts)   
AttachedGroup (org::openscience::cdk::iupac::parser)   DefaultChemObjectReader (org::openscience::cdk::io)   IMoleculeSet (org::openscience::cdk::interfaces)   NNAtomContainer (org::openscience::cdk::nonotify)   SMARTSBond (org::openscience::cdk::isomorphism::matchers::smarts)   
AutocorrelationDescriptorCharge (org::openscience::cdk::qsar::descriptors::molecular)   DefaultChemObjectWriter (org::openscience::cdk::io)   IMonomer (org::openscience::cdk::interfaces)   NNAtomContainerSet (org::openscience::cdk::nonotify)   SMARTSFormat (org::openscience::cdk::io::formats)   
AutocorrelationDescriptorMass (org::openscience::cdk::qsar::descriptors::molecular)   DefaultEventChemObjectReader (org::openscience::cdk::io::iterator::event)   ImplicitHCountAtom (org::openscience::cdk::isomorphism::matchers::smarts)   NNAtomParity (org::openscience::cdk::nonotify)   SMARTSOperatorAtom (org::openscience::cdk::isomorphism::matchers::smarts)   
AutocorrelationDescriptorPolarizability (org::openscience::cdk::qsar::descriptors::molecular)   DefaultIteratingChemObjectReader (org::openscience::cdk::io::iterator)   INChIContentProcessorTool (org::openscience::cdk::io::inchi)   NNAtomType (org::openscience::cdk::nonotify)   SMILESFIXFormat (org::openscience::cdk::io::formats)   
  B  
DegreeAtom (org::openscience::cdk::isomorphism::matchers::smarts)   INChIFormat (org::openscience::cdk::io::formats)   NNBioPolymer (org::openscience::cdk::nonotify)   SMILESFormat (org::openscience::cdk::io::formats)   
BasicValidator (org::openscience::cdk::validate)   DescriptorCalculator (org::openscience::cdk::applications)   InChIGenerator (org::openscience::cdk::inchi)   NNBond (org::openscience::cdk::nonotify)   SmilesGenerator (org::openscience::cdk::smiles)   
BCUTDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   DescriptorEngine (org::openscience::cdk::qsar)   InChIGeneratorFactory (org::openscience::cdk::inchi)   NNChemFile (org::openscience::cdk::nonotify)   SmilesParser (org::openscience::cdk::smiles)   
BFSShortestPath (org::openscience::cdk::graph)   DescriptorException (org::openscience::cdk::qsar)   INChIHandler (org::openscience::cdk::io::inchi)   NNChemModel (org::openscience::cdk::nonotify)   SMILESReader (org::openscience::cdk::io)   
BGFFormat (org::openscience::cdk::io::formats)   DescriptorSpecification (org::openscience::cdk::qsar)   INChIPlainTextFormat (org::openscience::cdk::io::formats)   NNChemObject (org::openscience::cdk::nonotify)   SmilesValencyChecker (org::openscience::cdk::tools)   
BibTeXMLEntry (net::sf::cdk::tools::bibtex)   DescriptorValue (org::openscience::cdk::qsar)   INChIPlainTextReader (org::openscience::cdk::io)   NNChemSequence (org::openscience::cdk::nonotify)   SmilesViewerforDeterministicGenerator (org::openscience::cdk::applications::demo)   
BibTeXMLFile (net::sf::cdk::tools::bibtex)   DevelStatusBar (org::openscience::cdk::applications::jchempaint)   INChIReader (org::openscience::cdk::io)   NNCrystal (org::openscience::cdk::nonotify)   SMILESWriter (org::openscience::cdk::io)   
BiconnectivityInspector (org::openscience::cdk::graph)   Dictionary (org::openscience::cdk::dict)   InChIToStructure (org::openscience::cdk::inchi)   NNElectronContainer (org::openscience::cdk::nonotify)   SmoothingFunctions (org::openscience::cdk::modeling::forcefield)   
BioPolymer (org::openscience::cdk)   DictionaryAction (org::openscience::cdk::applications::jchempaint::action)   IncorrectUseOfCDKCoreClassError (org::openscience::cdk::exception)   NNElement (org::openscience::cdk::nonotify)   SortedTableModel (org::openscience::cdk::applications::swing)   
Bond (org::openscience::cdk)   DictionaryDatabase (org::openscience::cdk::dict)   InductiveAtomicHardnessDescriptor (org::openscience::cdk::qsar::descriptors::atomic)   NNIsotope (org::openscience::cdk::nonotify)   SpanningTree (org::openscience::cdk::graph)   
Bond::AtomsIterator (org::openscience::cdk)   DictionaryDialog (org::openscience::cdk::applications::jchempaint::dialogs)   InductiveAtomicSoftnessDescriptor (org::openscience::cdk::qsar::descriptors::atomic)   NNLonePair (org::openscience::cdk::nonotify)   SpartanFormat (org::openscience::cdk::io::formats)   
BondChangeEdit (org::openscience::cdk::applications::undoredo)   DictionaryHandler (org::openscience::cdk::dict)   InductivePartialCharges (org::openscience::cdk::charges)   NNMapping (org::openscience::cdk::nonotify)   SSSRFinder (org::openscience::cdk::ringsearch)   
BondCountDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   DictionaryValidator (org::openscience::cdk::validate)   InfoDialog (org::openscience::cdk::applications::jchempaint::dialogs)   NNMolecule (org::openscience::cdk::nonotify)   StandardSubstructureSets (org::openscience::cdk::fingerprint)   
BondEditor (org::openscience::cdk::applications::swing::editor)   DictRef (org::openscience::cdk::dict)   InsertSmilesAction (org::openscience::cdk::applications::jchempaint::action)   NNMoleculeSet (org::openscience::cdk::nonotify)   StatusBar (org::openscience::cdk::applications::jchempaint)   
BondManipulator (org::openscience::cdk::tools::manipulator)   DictRefEditorTableModel (org::openscience::cdk::applications::swing)   InsertStructureAction (org::openscience::cdk::applications::jchempaint::action)   NNMonomer (org::openscience::cdk::nonotify)   StatusBarAction (org::openscience::cdk::applications::jchempaint::action)   
BondPartialPiChargeDescriptor (org::openscience::cdk::qsar::descriptors::bond)   DisplacementChargeFromAcceptorReaction (org::openscience::cdk::reaction::type)   InsertTextPanel (org::openscience::cdk::applications::jchempaint)   NNPDBAtom (org::openscience::cdk::nonotify)   SteepestDescentsMethod (org::openscience::cdk::modeling::forcefield)   
BondPartialSigmaChargeDescriptor (org::openscience::cdk::qsar::descriptors::bond)   DisplacementChargeFromDonorReaction (org::openscience::cdk::reaction::type)   IntegerArrayResult (org::openscience::cdk::qsar::result)   NNPDBMonomer (org::openscience::cdk::nonotify)   StereoBond (org::openscience::cdk::isomorphism::matchers::smarts)   
BondPartialTChargeDescriptor (org::openscience::cdk::qsar::descriptors::bond)   DistanceMoment (org::openscience::cdk::similarity)   IntegerIOSetting (org::openscience::cdk::io::setting)   NNPDBPolymer (org::openscience::cdk::nonotify)   Strand (org::openscience::cdk)   
BondSigmaElectronegativityDescriptor (org::openscience::cdk::qsar::descriptors::bond)   DistanceToAtomDescriptor (org::openscience::cdk::qsar::descriptors::atomic)   IntegerResult (org::openscience::cdk::qsar::result)   NNPDBStructure (org::openscience::cdk::nonotify)   StretchBendInteractions (org::openscience::cdk::modeling::forcefield)   
BondsToAtomDescriptor (org::openscience::cdk::qsar::descriptors::atomic)   DistLargeInfo (org::openscience::cdk::applications)   InterruptableSmilesParser (org::openscience::cdk::smiles)   NNPolymer (org::openscience::cdk::nonotify)   StringHelper (org::openscience::cdk::applications::jchempaint)   
BondStretching (org::openscience::cdk::modeling::forcefield)   DMol3Format (org::openscience::cdk::io::formats)   InvalidSmilesException (org::openscience::cdk::exception)   NNPseudoAtom (org::openscience::cdk::nonotify)   StringIOSetting (org::openscience::cdk::io::setting)   
BondTools (org::openscience::cdk::geometry)   DOCK5Format (org::openscience::cdk::io::formats)   InverseSymbolSetQueryAtom (org::openscience::cdk::isomorphism::matchers)   NNReaction (org::openscience::cdk::nonotify)   StructGenAtomTypeGuesser (org::openscience::cdk::atomtype)   
BooleanIOSetting (org::openscience::cdk::io::setting)   DoubleArrayResult (org::openscience::cdk::qsar::result)   InvPair (org::openscience::cdk::smiles)   NNReactionSet (org::openscience::cdk::nonotify)   StructGenMatcher (org::openscience::cdk::atomtype)   
BooleanResult (org::openscience::cdk::qsar::result)   DoubleResult (org::openscience::cdk::qsar::result)   IOSetting (org::openscience::cdk::io::setting)   NNRing (org::openscience::cdk::nonotify)   StructureDiagramGenerator (org::openscience::cdk::layout)   
BPolDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   DrawingPanel (org::openscience::cdk::applications::jchempaint)   IPAtomicDescriptor (org::openscience::cdk::qsar::descriptors::atomic)   NNRingSet (org::openscience::cdk::nonotify)   StructureResonanceGenerator (org::openscience::cdk::tools)   
BracketAtom (org::openscience::cdk::isomorphism::matchers::smarts)   
  E  
IPBondDescriptor (org::openscience::cdk::qsar::descriptors::bond)   NNSingleElectron (org::openscience::cdk::nonotify)   SubstructureFingerprinter (org::openscience::cdk::fingerprint)   
BreakingBondReaction (org::openscience::cdk::reaction::type)   EccentricConnectivityIndexDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   IPDBAtom (org::openscience::cdk::interfaces)   NNStrand (org::openscience::cdk::nonotify)   SVGFormat (org::openscience::cdk::io::formats)   
BremserOneSphereHOSECodePredictor (org::openscience::cdk::tools)   EditAction (org::openscience::cdk::applications::jchempaint::action)   IPDBMonomer (org::openscience::cdk::interfaces)   NomParser (org::openscience::cdk::iupac::parser)   SVGWriter (org::openscience::cdk::io)   
BSFormat (org::openscience::cdk::io::formats)   EditAtomContainerPropsAction (org::openscience::cdk::applications::jchempaint::action)   IPDBPolymer (org::openscience::cdk::interfaces)   NoNotificationChemObjectBuilder (org::openscience::cdk::nonotify)   SwingGUIListener (org::openscience::cdk::io::listener)   
Bspt (org::openscience::cdk::graph::rebond)   EditChemObjectPropsAction (org::openscience::cdk::applications::jchempaint::action)   IPDBStructure (org::openscience::cdk::interfaces)   Normalizer (org::openscience::cdk::tools)   SwissArmyKnife (org::openscience::cdk::tools)   
  C  
EditDictRefs (org::openscience::cdk::applications::jchempaint::dialogs)   IPMolecularDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   NoSuchAtomException (org::openscience::cdk::exception)   SybylDescriptorFormat (org::openscience::cdk::io::formats)   
CacaoCartesianFormat (org::openscience::cdk::io::formats)   EditDictRefsAction (org::openscience::cdk::applications::jchempaint::action)   IPolymer (org::openscience::cdk::interfaces)   NoSuchAtomTypeException (org::openscience::cdk::exception)   SymbolAndChargeQueryAtom (org::openscience::cdk::isomorphism::matchers)   
CacaoInternalFormat (org::openscience::cdk::io::formats)   EffectiveAtomPolarizabilityDescriptor (org::openscience::cdk::qsar::descriptors::atomic)   IPotentialFunction (org::openscience::cdk::modeling::forcefield)   NumericalSurface (org::openscience::cdk::geometry::surface)   SymbolChargeIDQueryAtom (org::openscience::cdk::isomorphism::matchers)   
CACheFormat (org::openscience::cdk::io::formats)   ElectronContainer (org::openscience::cdk)   IPseudoAtom (org::openscience::cdk::interfaces)   NWChemFormat (org::openscience::cdk::io::formats)   SymbolQueryAtom (org::openscience::cdk::isomorphism::matchers)   
CanonicalLabeler (org::openscience::cdk::graph::invariant)   ElectronImpactNBEReaction (org::openscience::cdk::reaction::type)   IQueryAtom (org::openscience::cdk::isomorphism::matchers)   
  O  
Symbols (org::openscience::cdk::config)   
CarbonConnectivityOrderOneDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   ElectronImpactPDBReaction (org::openscience::cdk::reaction::type)   IQueryAtomContainer (org::openscience::cdk::isomorphism::matchers)   OneElectronJob (org::openscience::cdk::math::qm)   SymbolSetQueryAtom (org::openscience::cdk::isomorphism::matchers)   
CarbonConnectivityOrderZeroDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   ElectrostaticInteractions (org::openscience::cdk::modeling::forcefield)   IQueryBond (org::openscience::cdk::isomorphism::matchers)   OpenAction (org::openscience::cdk::applications::jchempaint::action)   
  T  
CarbonylEliminationReaction (org::openscience::cdk::reaction::type)   Element (org::openscience::cdk)   IRDFWeightFunction (org::openscience::cdk::geometry)   OpenBabelConvert (org::openscience::cdk::libio::openbabel)   TaeAminoAcidDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   
CASNumber (org::openscience::cdk::index)   ElementAction (org::openscience::cdk::applications::jchempaint::action)   IReaction (org::openscience::cdk::interfaces)   OperatorContainer (org::openscience::cdk::isomorphism::matchers::smarts)   Tanimoto (org::openscience::cdk::similarity)   
CDK2DAtomColors (org::openscience::cdk::renderer::color)   ElementComparator (org::openscience::cdk::tools)   IReactionProcess (org::openscience::cdk::reaction)   OptionIOSetting (org::openscience::cdk::io::setting)   TanimotoCoefficient (org::openscience::cdk::applications)   
CDKAtomColors (org::openscience::cdk::renderer::color)   ElementPTFactory (org::openscience::cdk::config)   IReactionSet (org::openscience::cdk::interfaces)   Orbitals (org::openscience::cdk::math::qm)   TemplateExtractor (org::openscience::cdk::modeling::builder3d)   
CDKBasedAtomTypeConfigurator (org::openscience::cdk::config)   ElementPTHandler (org::openscience::cdk::config::elements)   IReaderListener (org::openscience::cdk::io::listener)   OrderQueryBond (org::openscience::cdk::isomorphism::matchers::smarts)   TemplateHandler (org::openscience::cdk::layout)   
CDKBugTaglet (net::sf::cdk::tools::doclets)   ElementPTReader (org::openscience::cdk::config::elements)   IRenderer2D (org::openscience::cdk::renderer)   OrderQueryBond (org::openscience::cdk::isomorphism::matchers)   TemplateHandler3D (org::openscience::cdk::modeling::builder3d)   
CDKCiteTaglet (net::sf::cdk::tools::doclets)   Elements (org::openscience::cdk::config)   IResourceFormat (org::openscience::cdk::io::formats)   OverlapResolver (org::openscience::cdk::layout)   Tessellate (org::openscience::cdk::geometry::surface)   
CDKConstants (org::openscience::cdk)   Entry (org::openscience::cdk::dict)   IRing (org::openscience::cdk::interfaces)   OverlapResolver::OverlapPair (org::openscience::cdk::layout)   TextGUIListener (org::openscience::cdk::io::listener)   
CDKConvention (org::openscience::cdk::io::cml)   EnzymeResidueLocator (org::openscience::cdk)   IRingSet (org::openscience::cdk::interfaces)   OWLFile (org::openscience::cdk::dict)   TextViewDialog (org::openscience::cdk::applications::jchempaint::dialogs)   
CDKDictionaryReferences (org::openscience::cdk::dict)   EquivalentClassesDeterministicGenerator (org::openscience::cdk::structgen::deterministic)   ISimpleRenderer2D (org::openscience::cdk::renderer)   
  P  
TinkerMM2Format (org::openscience::cdk::io::formats)   
CDKDictRefTaglet (net::sf::cdk::tools::doclets)   EquivalentClassPartitioner (org::openscience::cdk::graph::invariant)   ISingleElectron (org::openscience::cdk::interfaces)   ParseException (org::openscience::cdk::iupac::parser)   TinkerXYZFormat (org::openscience::cdk::io::formats)   
CDKException (org::openscience::cdk::exception)   EStateAtomTypeMatcher (org::openscience::cdk::atomtype)   IsoAlkanes (org::openscience::cdk::templates::saturatedhydrocarbons)   PartialAtomicChargeColors (org::openscience::cdk::renderer::color)   Token (org::openscience::cdk::iupac::parser)   
CDKModuleTaglet (net::sf::cdk::tools::doclets)   EventCMLDemo (org::openscience::cdk::applications::demo)   IsomorphismTester (org::openscience::cdk::isomorphism)   PartialFilledStructureMerger (org::openscience::cdk::structgen::stochastic)   ToolBarAction (org::openscience::cdk::applications::jchempaint::action)   
CDKPluginManager (org::openscience::cdk::applications::plugin)   EventCMLHandler (org::openscience::cdk::io::iterator::event)   Isotope (org::openscience::cdk)   PartialPiChargeDescriptor (org::openscience::cdk::qsar::descriptors::atomic)   ToolBarMaker (org::openscience::cdk::applications::jchempaint)   
CDKPluginManager::PluginDialogAction (org::openscience::cdk::applications::plugin)   EventCMLReader (org::openscience::cdk::io::iterator::event)   IsotopeFactory (org::openscience::cdk::config)   PartialSigmaChargeDescriptor (org::openscience::cdk::qsar::descriptors::atomic)   TopologicalMatrix (org::openscience::cdk::graph::matrix)   
CDKPopupMenu (org::openscience::cdk::controller)   ExitAction (org::openscience::cdk::applications::jchempaint::action)   IsotopeGenerator (org::openscience::cdk::tools)   PartialTChargeMMFF94Descriptor (org::openscience::cdk::qsar::descriptors::atomic)   Torsions (org::openscience::cdk::modeling::forcefield)   
CDKSourceCodeFormat (org::openscience::cdk::io::formats)   ExplicitConnectionAtom (org::openscience::cdk::isomorphism::matchers::smarts)   IsotopeHandler (org::openscience::cdk::config::isotopes)   PartialTChargePEOEDescriptor (org::openscience::cdk::qsar::descriptors::atomic)   TotalConnectionAtom (org::openscience::cdk::isomorphism::matchers::smarts)   
CDKSourceCodeWriter (org::openscience::cdk::io)   ExportAction (org::openscience::cdk::applications::jchempaint::action)   IsotopeReader (org::openscience::cdk::config::isotopes)   Path (org::openscience::cdk::ringsearch)   TotalHCountAtom (org::openscience::cdk::isomorphism::matchers::smarts)   
CDKUtilities (org::openscience::cdk::tools)   ExportCompChemAction (org::openscience::cdk::applications::jchempaint::action)   IsProtonInAromaticSystemDescriptor (org::openscience::cdk::qsar::descriptors::atomic)   PathTools (org::openscience::cdk::graph)   TotalRingConnectionAtom (org::openscience::cdk::isomorphism::matchers::smarts)   
CDKValidator (org::openscience::cdk::validate)   ExtendedFingerprinter (org::openscience::cdk::fingerprint)   IsProtonInConjugatedPiSystemDescriptor (org::openscience::cdk::qsar::descriptors::atomic)   PCCompoundASNReader (org::openscience::cdk::io)   TotalValencyAtom (org::openscience::cdk::isomorphism::matchers::smarts)   
ChangeAtomSymbolAction (org::openscience::cdk::applications::jchempaint::action)   
  F  
IStrand (org::openscience::cdk::interfaces)   PCModelFormat (org::openscience::cdk::io::formats)   TPSADescriptor (org::openscience::cdk::qsar::descriptors::molecular)   
ChangeAtomSymbolEdit (org::openscience::cdk::applications::undoredo)   FenskeHall_ZMatrixFormat (org::openscience::cdk::io::formats)   IStructureGenerationListener (org::openscience::cdk::structgen)   PDBAtom (org::openscience::cdk::protein::data)   Triangle (org::openscience::cdk::geometry::surface)   
ChangeChargeEdit (org::openscience::cdk::applications::undoredo)   FieldTablePanel (org::openscience::cdk::applications::swing)   IteratingMDLReader (org::openscience::cdk::io::iterator)   PDBAtomCustomizer (org::openscience::cdk::libio::cml)   TurboMoleFormat (org::openscience::cdk::io::formats)   
ChangeCoordsEdit (org::openscience::cdk::applications::undoredo)   FiguerasSSSRFinder (org::openscience::cdk::ringsearch)   IteratingSMILESReader (org::openscience::cdk::io::iterator)   PDBConvention (org::openscience::cdk::io::cml)   TXTBasedAtomTypeConfigurator (org::openscience::cdk::config)   
ChangeIsotopeAction (org::openscience::cdk::applications::jchempaint::action)   File2Text (org::openscience::cdk::applications)   IUndoRedoHandler (org::openscience::cdk::applications::undoredo)   PDBFormat (org::openscience::cdk::io::formats)   
  U  
ChangeIsotopeEdit (org::openscience::cdk::applications::undoredo)   FileConvertor (org::openscience::cdk::applications)   IValencyChecker (org::openscience::cdk::tools)   PDBMLFormat (org::openscience::cdk::io::formats)   UndoAction (org::openscience::cdk::applications::jchempaint::action)   
ChargeGroup (org::openscience::cdk::libio::md)   FileFormatGuesser (org::openscience::cdk::applications)   IValidator (org::openscience::cdk::validate)   PDBMonomer (org::openscience::cdk::protein::data)   UndoAdapter (org::openscience::cdk::applications::undoredo)   
Chem3D_Cartesian_1Format (org::openscience::cdk::io::formats)   FingerPrinter (org::openscience::cdk::applications)   IWekaModel (org::openscience::cdk::qsar::model::weka)   PDBPolymer (org::openscience::cdk::protein::data)   UndoStack (org::openscience::cdk::applications::jchempaint)   
Chem3D_Cartesian_2Format (org::openscience::cdk::io::formats)   Fingerprinter (org::openscience::cdk::fingerprint)   IWriterListener (org::openscience::cdk::io::listener)   PDBReader (org::openscience::cdk::io)   UniChemXYZFormat (org::openscience::cdk::io::formats)   
ChemAction (org::openscience::cdk::applications::jchempaint::action)   FingerprinterTool (org::openscience::cdk::fingerprint)   
  J  
PDBStrand (org::openscience::cdk::protein::data)   UniversalIsomorphismTester (org::openscience::cdk::isomorphism)   
ChemDrawFormat (org::openscience::cdk::io::formats)   FingerprintFormat (org::openscience::cdk::io::formats)   JaguarFormat (org::openscience::cdk::io::formats)   PDBStructure (org::openscience::cdk::protein::data)   UnsupportedChemObjectException (org::openscience::cdk::exception)   
ChemFile (org::openscience::cdk)   FixedSizeStack (org::openscience::cdk::tools)   JChemPaint (org::openscience::cdk::applications::jchempaint::application)   PDBValidator (org::openscience::cdk::validate)   
  V  
ChemFile::ChemSequenceIterator (org::openscience::cdk)   FlipAction (org::openscience::cdk::applications::jchempaint::action)   JChemPaintAbstractApplet (org::openscience::cdk::applications::jchempaint::applet)   PDBWriter (org::openscience::cdk::io)   V2M (org::openscience::cdk::qsar::model::R)   
ChemFileManipulator (org::openscience::cdk::tools::manipulator)   FlipEdit (org::openscience::cdk::applications::undoredo)   JChemPaintEditorApplet (org::openscience::cdk::applications::jchempaint::applet)   PerceiveAtomTypesAction (org::openscience::cdk::applications::jchempaint::action)   VAdjMaDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   
ChemGraph (org::openscience::cdk::structgen::stochastic::operator)   ForceField (org::openscience::cdk::modeling::forcefield)   JChemPaintEditorPanel (org::openscience::cdk::applications::jchempaint)   PeriodicTableElement (org::openscience::cdk)   ValenceCarbonConnectivityOrderOneDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   
ChemModel (org::openscience::cdk)   ForceFieldConfigurator (org::openscience::cdk::modeling::builder3d)   JChemPaintMenuBar (org::openscience::cdk::applications::jchempaint)   PeriodicTablePanel (org::openscience::cdk::applications::swing)   ValenceCarbonConnectivityOrderZeroDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   
ChemModelManipulator (org::openscience::cdk::tools::manipulator)   ForceFieldTools (org::openscience::cdk::modeling::forcefield)   JChemPaintModel (org::openscience::cdk::applications::jchempaint)   PeriodicTablePanel::BackAction (org::openscience::cdk::applications::swing)   ValencyChecker (org::openscience::cdk::tools)   
ChemObject (org::openscience::cdk)   FormalChargeAtom (org::openscience::cdk::isomorphism::matchers::smarts)   JChemPaintModelPropsEditor (org::openscience::cdk::applications::jchempaint::dialogs)   PeriodicTablePanel::ElementButtonAction (org::openscience::cdk::applications::swing)   ValencyHybridChecker (org::openscience::cdk::tools)   
ChemObjectChangeEvent (org::openscience::cdk::event)   FormatStringBuffer (org::openscience::cdk::tools)   JChemPaintPanel (org::openscience::cdk::applications::jchempaint)   PeriodicTablePositionDescriptor (org::openscience::cdk::qsar::descriptors::atomic)   ValencyMatcher (org::openscience::cdk::atomtype)   
ChemObjectEditor (org::openscience::cdk::applications::swing::editor)   FormatStringBuffer::Format (org::openscience::cdk::tools)   JChemPaintPanel::AppCloser (org::openscience::cdk::applications::jchempaint)   PetitjeanNumberDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   ValencyValidator (org::openscience::cdk::validate)   
ChemObjectPropertyDialog (org::openscience::cdk::applications::jchempaint::dialogs)   FortranFormat (org::openscience::cdk::math)   JChemPaintPanel::PopupListener (org::openscience::cdk::applications::jchempaint)   PetitjeanShapeIndexDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   ValidateAction (org::openscience::cdk::applications::jchempaint::action)   
ChemObjectPropertyEditorTableModel (org::openscience::cdk::applications::swing)   FourierGridBasis (org::openscience::cdk::math::qm)   JChemPaintPopupMenu (org::openscience::cdk::applications::jchempaint)   PhysicalConstants (org::openscience::cdk)   ValidateFrame (org::openscience::cdk::applications::jchempaint::dialogs)   
ChemObjectTree (org::openscience::cdk::applications::swing)   Fragment (org::openscience::cdk)   JChemPaintViewerOnlyApplet (org::openscience::cdk::applications::jchempaint::applet)   PiContactDetectionDescriptor (org::openscience::cdk::qsar::descriptors::atompair)   ValidationReport (org::openscience::cdk::validate)   
ChemObjectTreeNode (org::openscience::cdk::applications::swing)   FragmentAtom (org::openscience::cdk)   JChemPaintViewerOnlyPanel (org::openscience::cdk::applications::jchempaint)   PiElectronegativityDescriptor (org::openscience::cdk::qsar::descriptors::atomic)   ValidationTest (org::openscience::cdk::validate)   
ChemSequence (org::openscience::cdk)   FragmentComplexityDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   JCPAction (org::openscience::cdk::applications::jchempaint::action)   PLSRegressionModel (org::openscience::cdk::qsar::model::R)   Validator (org::openscience::cdk::applications)   
ChemSequence::ChemModelIterator (org::openscience::cdk)   
  G  
JCPCompChemInputSaveFileFilter (org::openscience::cdk::applications::jchempaint::io)   PLSRegressionModelPredict (org::openscience::cdk::qsar::model::R)   ValidatorEngine (org::openscience::cdk::validate)   
ChemSequenceManipulator (org::openscience::cdk::tools::manipulator)   GamessFormat (org::openscience::cdk::io::formats)   JCPConstants (org::openscience::cdk::applications::jchempaint)   PluginClassLoader (org::openscience::cdk::applications::plugin)   VanDerWaalsInteractions (org::openscience::cdk::modeling::forcefield)   
ChemtoolFormat (org::openscience::cdk::io::formats)   GamessReader (org::openscience::cdk::io)   JCPExportFileFilter (org::openscience::cdk::applications::jchempaint::io)   PMPFormat (org::openscience::cdk::io::formats)   VASPFormat (org::openscience::cdk::io::formats)   
ChiChainDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   GasteigerMarsiliPartialCharges (org::openscience::cdk::charges)   JCPFileFilter (org::openscience::cdk::applications::jchempaint::io)   PMPReader (org::openscience::cdk::io)   VASPReader (org::openscience::cdk::io)   
ChiClusterDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   GasteigerPEPEPartialCharges (org::openscience::cdk::charges)   JCPFileView (org::openscience::cdk::applications::jchempaint::io)   Point (org::openscience::cdk::graph::rebond)   VdWRadiusDescriptor (org::openscience::cdk::qsar::descriptors::atomic)   
ChiIndexUtils (org::openscience::cdk::qsar)   Gaussian03Format (org::openscience::cdk::io::formats)   JCPLocalizationHandler (org::openscience::cdk::applications::jchempaint)   Polarizability (org::openscience::cdk::charges)   Vector (org::openscience::cdk::math)   
ChiPathClusterDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   Gaussian03Reader (org::openscience::cdk::io)   JCPPropertyHandler (org::openscience::cdk::applications::jchempaint)   Polymer (org::openscience::cdk)   Vibration (org::openscience::cdk)   
ChiPathDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   Gaussian90Format (org::openscience::cdk::io::formats)   JCPSaveFileFilter (org::openscience::cdk::applications::jchempaint::io)   PopupController2D (org::openscience::cdk::controller)   VicinitySampler (org::openscience::cdk::structgen)   
ChiralityAtom (org::openscience::cdk::isomorphism::matchers::smarts)   Gaussian92Format (org::openscience::cdk::io::formats)   JCPTransferHandler (org::openscience::cdk::applications::jchempaint::dnd)   POVRayFormat (org::openscience::cdk::io::formats)   ViewmolFormat (org::openscience::cdk::io::formats)   
CIFFormat (org::openscience::cdk::io::formats)   Gaussian94Format (org::openscience::cdk::io::formats)   JCPUndoRedoHandler (org::openscience::cdk::applications::undoredo)   PQSChemFormat (org::openscience::cdk::io::formats)   
  W  
CIFReader (org::openscience::cdk::io)   Gaussian95Format (org::openscience::cdk::io::formats)   JExternalFrame (org::openscience::cdk::applications::swing)   PreferencesAction (org::openscience::cdk::applications::jchempaint::action)   WebDialog (org::openscience::cdk::applications::jchempaint::dialogs)   
CleanupAction (org::openscience::cdk::applications::jchempaint::action)   Gaussian98Format (org::openscience::cdk::io::formats)   JMEFormat (org::openscience::cdk::io::formats)   Primes (org::openscience::cdk::math)   WebDialog::PageLoader (org::openscience::cdk::applications::jchempaint::dialogs)   
CleanUpEdit (org::openscience::cdk::applications::undoredo)   Gaussian98Reader (org::openscience::cdk::io)   JMOLANIMATIONConvention (org::openscience::cdk::io::cml)   PrintAction (org::openscience::cdk::applications::jchempaint::action)   WebLinkAction (org::openscience::cdk::applications::jchempaint::action)   
ClearAllEdit (org::openscience::cdk::applications::undoredo)   GaussianInputFormat (org::openscience::cdk::io::formats)   
  K  
ProblemMarker (org::openscience::cdk::validate)   WeightDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   
CleavageBondMultiReaction (org::openscience::cdk::reaction::type)   GaussianInputWriter (org::openscience::cdk::io::program)   KabschAlignment (org::openscience::cdk::geometry::alignment)   Projector (org::openscience::cdk::geometry)   WeightedPathDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   
CleavageBondReaction (org::openscience::cdk::reaction::type)   GaussiansBasis (org::openscience::cdk::math::qm)   KappaShapeIndicesDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   PropertiesListener (org::openscience::cdk::io::listener)   WHIMDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   
CloseAction (org::openscience::cdk::applications::jchempaint::action)   GeneralFieldEditor (org::openscience::cdk::applications::jchempaint::dialogs)   
  L  
ProteinBuilderTool (org::openscience::cdk::tools)   WienerNumbersDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   
ClosedShellJob (org::openscience::cdk::math::qm)   GeneralSettingsEditor (org::openscience::cdk::applications::jchempaint::dialogs)   LargestChainDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   ProteinPocketFinder (org::openscience::cdk::protein)   WriterFactory (org::openscience::cdk::io)   
CMLCoreModule (org::openscience::cdk::io::cml)   GenerateFragments (org::openscience::cdk::tools)   LargestPiSystemDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   ProtonTotalPartialChargeDescriptor (org::openscience::cdk::qsar::descriptors::atomic)   WWMMatrixReader (org::openscience::cdk::internet)   
CMLErrorHandler (org::openscience::cdk::io::cml)   GENMDeterministicGenerator (org::openscience::cdk::structgen::deterministic)   LengthOverBreadthDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   PseudoAtom (org::openscience::cdk)   
  X  
CMLFormat (org::openscience::cdk::io::formats)   GENMDeterministicGenerator::BasicFragment (org::openscience::cdk::structgen::deterministic)   LicenseAction (org::openscience::cdk::applications::jchempaint::action)   PseudoAtomEditor (org::openscience::cdk::applications::swing::editor)   XEDFormat (org::openscience::cdk::io::formats)   
CMLHandler (org::openscience::cdk::io::cml)   GeometricMinimizer (org::openscience::cdk::modeling::forcefield)   LicenseDialog (org::openscience::cdk::applications::jchempaint::dialogs)   PTDialog (org::openscience::cdk::applications::jchempaint::dialogs)   XindiceReader (org::openscience::cdk::database)   
CMLReactionModule (org::openscience::cdk::io::cml)   Geometry3DValidator (org::openscience::cdk::validate)   LinearRegressionModel (org::openscience::cdk::qsar::model::R2)   PubChemASNFormat (org::openscience::cdk::io::formats)   XLogPDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   
CMLReader (org::openscience::cdk::io)   GeometryTools (org::openscience::cdk::geometry)   LinearRegressionModel (org::openscience::cdk::qsar::model::R)   PubChemFormat (org::openscience::cdk::io::formats)   XYZFormat (org::openscience::cdk::io::formats)   
CMLResolver (org::openscience::cdk::io::cml)   GeometryToolsInternalCoordinates (org::openscience::cdk::geometry)   LinearRegressionModelFit (org::openscience::cdk::qsar::model::R)   
  Q  
XYZReader (org::openscience::cdk::io)   
CMLRSSFormat (org::openscience::cdk::io::formats)   GhemicalMMFormat (org::openscience::cdk::io::formats)   LinearRegressionModelPredict (org::openscience::cdk::qsar::model::R)   QChemFormat (org::openscience::cdk::io::formats)   XYZWriter (org::openscience::cdk::io)   
CMLStack (org::openscience::cdk::io::cml)   GhemicalMMReader (org::openscience::cdk::io)   LinearRegressionModelSummary (org::openscience::cdk::qsar::model::R)   QSARConvention (org::openscience::cdk::io::cml)   
  Y  
CMLWriter (org::openscience::cdk::io)   GhemicalSPMFormat (org::openscience::cdk::io::formats)   LineSearch (org::openscience::cdk::modeling::forcefield)   QSARCustomizer (org::openscience::cdk::libio::cml)   YasaraFormat (org::openscience::cdk::io::formats)   
CNNClassificationModel (org::openscience::cdk::qsar::model::R)   GIMatrix (org::openscience::cdk::graph::invariant)   LineSearchForTheWolfeConditions (org::openscience::cdk::modeling::forcefield)   QSARModelException (org::openscience::cdk::qsar::model)   
  Z  
CNNClassificationModelFit (org::openscience::cdk::qsar::model::R)   Graph (org::openscience::cdk::structgen::deterministic)   ListeningTableModel (org::openscience::cdk::applications::swing)   Quaternion (org::openscience::cdk::math)   ZagrebIndexDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   
CNNClassificationModelPredict (org::openscience::cdk::qsar::model::R)   GraphOnlyFingerprinter (org::openscience::cdk::fingerprint)   LoggingTool (org::openscience::cdk::tools)   QueryAtomContainer (org::openscience::cdk::isomorphism::matchers)   ZindoFormat (org::openscience::cdk::io::formats)   
CNNRegressionModel (org::openscience::cdk::qsar::model::R2)   GraphRenderer (org::openscience::cdk::applications::swing)   LogicalOperatorAtom (org::openscience::cdk::isomorphism::matchers::smarts)   QueryAtomContainerCreator (org::openscience::cdk::isomorphism::matchers)   ZMatrixFormat (org::openscience::cdk::io::formats)   
CNNRegressionModel (org::openscience::cdk::qsar::model::R)   GraphRendererModel (org::openscience::cdk::renderer)   LogicalOperatorBond (org::openscience::cdk::isomorphism::matchers::smarts)   Queue (org::openscience::cdk::ringsearch)   ZMatrixReader (org::openscience::cdk::io)   
CNNRegressionModelFit (org::openscience::cdk::qsar::model::R)   GravitationalIndexDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   LonePair (org::openscience::cdk)   
  R  
ZMatrixTools (org::openscience::cdk::geometry)   
CNNRegressionModelPredict (org::openscience::cdk::qsar::model::R)   GridGenerator (org::openscience::cdk::tools)   LonePairElectronChecker (org::openscience::cdk::tools)   RadicalSiteInitiationHReaction (org::openscience::cdk::reaction::type)   ZoomAction (org::openscience::cdk::applications::jchempaint::action)   
CNNRegressionModelSummary (org::openscience::cdk::qsar::model::R)   GROMOS96Format (org::openscience::cdk::io::formats)   LongestAliphaticChainDescriptor (org::openscience::cdk::qsar::descriptors::molecular)   RadicalSiteInitiationReaction (org::openscience::cdk::reaction::type)   

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