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Class List

Here are the classes, structs, unions and interfaces with brief descriptions:
org::openscience::cdk::io::formats::ABINITFormat
org::openscience::cdk::qsar::AbstractAtomicDescriptor
org::openscience::cdk::qsar::AbstractBondDescriptor
org::openscience::cdk::tools::diff::tree::AbstractDifference
org::openscience::cdk::tools::diff::tree::AbstractDifferenceList
org::openscience::cdk::validate::AbstractValidator
org::openscience::cdk::io::formats::Aces2Format
org::openscience::cdk::formula::AdductFormula
org::openscience::cdk::reaction::mechanism::AdductionLPMechanism
org::openscience::cdk::reaction::mechanism::AdductionPBMechanism
org::openscience::cdk::reaction::type::AdductionProtonLPReaction
org::openscience::cdk::reaction::type::AdductionProtonPBReaction
org::openscience::cdk::reaction::type::AdductionSodiumLPReaction
org::openscience::cdk::io::formats::ADFFormat
org::openscience::cdk::graph::matrix::AdjacencyMatrix
org::openscience::cdk::qsar::descriptors::atomic::ProtonAffinityHOSEDescriptor::Affinitydb
org::openscience::cdk::io::formats::AlchemyFormat
org::openscience::cdk::isomorphism::matchers::smarts::AliphaticAtom
org::openscience::cdk::isomorphism::matchers::smarts::AliphaticSymbolAtom
org::openscience::cdk::ringsearch::AllRingsFinder
org::openscience::cdk::qsar::descriptors::molecular::ALOGPDescriptor
org::openscience::cdk::AminoAcid
org::openscience::cdk::qsar::descriptors::molecular::AminoAcidCountDescriptor
org::openscience::cdk::tools::manipulator::AminoAcidManipulator
org::openscience::cdk::templates::AminoAcids
org::openscience::cdk::modeling::forcefield::AngleBending
org::openscience::cdk::math::qm::AngularMomentum
org::openscience::cdk::isomorphism::matchers::smarts::AnyAtom
org::openscience::cdk::isomorphism::matchers::smarts::AnyOrderQueryBond
org::openscience::cdk::qsar::descriptors::molecular::APolDescriptor
org::openscience::cdk::isomorphism::matchers::smarts::AromaticAtom
org::openscience::cdk::qsar::descriptors::molecular::AromaticAtomsCountDescriptor
org::openscience::cdk::qsar::descriptors::molecular::AromaticBondsCountDescriptor
org::openscience::cdk::aromaticity::AromaticityCalculator
org::openscience::cdk::isomorphism::matchers::smarts::AromaticOrSingleQueryBond
org::openscience::cdk::isomorphism::matchers::smarts::AromaticQueryBond
org::openscience::cdk::isomorphism::matchers::smarts::AromaticSymbolAtom
org::openscience::cdk::Association
org::openscience::cdk::smiles::smarts::parser::ASTAliphatic
org::openscience::cdk::smiles::smarts::parser::ASTAnyAtom
org::openscience::cdk::smiles::smarts::parser::ASTAromatic
org::openscience::cdk::smiles::smarts::parser::ASTAtom
org::openscience::cdk::smiles::smarts::parser::ASTAtomicMass
org::openscience::cdk::smiles::smarts::parser::ASTAtomicNumber
org::openscience::cdk::smiles::smarts::parser::ASTCharge
org::openscience::cdk::smiles::smarts::parser::ASTChirality
org::openscience::cdk::smiles::smarts::parser::ASTElement
org::openscience::cdk::smiles::smarts::parser::ASTExplicitAtom
org::openscience::cdk::smiles::smarts::parser::ASTExplicitConnectivity
org::openscience::cdk::smiles::smarts::parser::ASTExplicitHighAndBond
org::openscience::cdk::smiles::smarts::parser::ASTExplicitHighAndExpression
org::openscience::cdk::smiles::smarts::parser::ASTGroup
org::openscience::cdk::smiles::smarts::parser::ASTHybrdizationNumber
org::openscience::cdk::smiles::smarts::parser::ASTImplicitHCount
org::openscience::cdk::smiles::smarts::parser::ASTImplicitHighAndBond
org::openscience::cdk::smiles::smarts::parser::ASTImplicitHighAndExpression
org::openscience::cdk::smiles::smarts::parser::ASTLowAndBond
org::openscience::cdk::smiles::smarts::parser::ASTLowAndExpression
org::openscience::cdk::smiles::smarts::parser::ASTNonCHHeavyAtom
org::openscience::cdk::smiles::smarts::parser::ASTNotBond
org::openscience::cdk::smiles::smarts::parser::ASTNotExpression
org::openscience::cdk::smiles::smarts::parser::ASTOrBond
org::openscience::cdk::smiles::smarts::parser::ASTOrExpression
org::openscience::cdk::smiles::smarts::parser::ASTPeriodicGroupNumber
org::openscience::cdk::smiles::smarts::parser::ASTPrimitiveAtomExpression
org::openscience::cdk::smiles::smarts::parser::ASTReaction
org::openscience::cdk::smiles::smarts::parser::ASTRecursiveSmartsExpression
org::openscience::cdk::smiles::smarts::parser::ASTRingConnectivity
org::openscience::cdk::smiles::smarts::parser::ASTRingIdentifier
org::openscience::cdk::smiles::smarts::parser::ASTRingMembership
org::openscience::cdk::smiles::smarts::parser::ASTSimpleBond
org::openscience::cdk::smiles::smarts::parser::ASTSmallestRingSize
org::openscience::cdk::smiles::smarts::parser::ASTSmarts
org::openscience::cdk::smiles::smarts::parser::ASTStart
org::openscience::cdk::smiles::smarts::parser::ASTTotalConnectivity
org::openscience::cdk::smiles::smarts::parser::ASTTotalHCount
org::openscience::cdk::smiles::smarts::parser::ASTValence
org::openscience::cdk::Atom
org::openscience::cdk::AtomContainer
org::openscience::cdk::graph::AtomContainerAtomPermutor
org::openscience::cdk::graph::AtomContainerBondPermutor
org::openscience::cdk::tools::manipulator::AtomContainerComparator
org::openscience::cdk::tools::diff::AtomContainerDiff
org::openscience::cdk::AtomContainerSet::AtomContainerIterator
org::openscience::cdk::tools::manipulator::AtomContainerManipulator
org::openscience::cdk::graph::AtomContainerPermutor
org::openscience::cdk::AtomContainerSet
org::openscience::cdk::tools::manipulator::AtomContainerSetManipulator
org::openscience::cdk::qsar::descriptors::molecular::AtomCountDescriptor
org::openscience::cdk::qsar::descriptors::atomic::AtomDegreeDescriptor
org::openscience::cdk::tools::diff::AtomDiff
org::openscience::cdk::qsar::descriptors::atomic::AtomHybridizationDescriptor
org::openscience::cdk::qsar::descriptors::atomic::AtomHybridizationVSEPRDescriptor
org::openscience::cdk::isomorphism::matchers::smarts::AtomicNumberAtom
org::openscience::cdk::qsar::descriptors::bond::AtomicNumberDifferenceDescriptor
org::openscience::cdk::tools::AtomicProperties
org::openscience::cdk::AtomContainer::AtomIterator
org::openscience::cdk::isomorphism::AtomMappingTools
org::openscience::cdk::AtomParity
org::openscience::cdk::layout::AtomPlacer
org::openscience::cdk::modeling::builder3d::AtomPlacer3D
org::openscience::cdk::Bond::AtomsIterator
org::openscience::cdk::modeling::builder3d::AtomTetrahedralLigandPlacer3D
org::openscience::cdk::geometry::AtomTools
org::openscience::cdk::AtomType
org::openscience::cdk::charges::AtomTypeCharges
org::openscience::cdk::tools::diff::AtomTypeDiff
org::openscience::cdk::config::AtomTypeFactory
org::openscience::cdk::config::atomtypes::AtomTypeHandler
org::openscience::cdk::tools::diff::tree::AtomTypeHybridizationDifference
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::descriptors::atomic::AtomValenceDescriptor
org::openscience::cdk::qsar::AtomValenceTool
org::openscience::cdk::iupac::parser::AttachedGroup
org::openscience::cdk::qsar::descriptors::molecular::AutocorrelationDescriptorCharge
org::openscience::cdk::qsar::descriptors::molecular::AutocorrelationDescriptorMass
org::openscience::cdk::qsar::descriptors::molecular::AutocorrelationDescriptorPolarizability
org::openscience::cdk::ringsearch::cyclebasis::SimpleCycleBasis::AuxiliaryGraph
org::openscience::cdk::ringsearch::cyclebasis::SimpleCycleBasis::AuxiliaryGraph2
org::openscience::cdk::graph::invariant::exception::BadMatrixFormatException
org::openscience::cdk::validate::BasicValidator
org::openscience::cdk::qsar::descriptors::molecular::BCUTDescriptor
org::openscience::cdk::graph::BFSShortestPath
org::openscience::cdk::io::formats::BGFFormat
net::sf::cdk::tools::bibtex::BibTeXMLEntry
net::sf::cdk::tools::bibtex::BibTeXMLFile
org::openscience::cdk::graph::BiconnectivityInspector
org::openscience::cdk::BioPolymer
org::openscience::cdk::Bond
org::openscience::cdk::qsar::descriptors::molecular::BondCountDescriptor
org::openscience::cdk::tools::diff::BondDiff
org::openscience::cdk::AtomContainer::BondIterator
org::openscience::cdk::tools::manipulator::BondManipulator
org::openscience::cdk::tools::diff::tree::BondOrderDifference
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
org::openscience::cdk::qsar::descriptors::atomic::BondsToAtomDescriptor
org::openscience::cdk::modeling::forcefield::BondStretching
org::openscience::cdk::geometry::BondTools
org::openscience::cdk::tools::diff::tree::BooleanArrayDifference
org::openscience::cdk::tools::diff::tree::BooleanDifference
org::openscience::cdk::io::setting::BooleanIOSetting
org::openscience::cdk::qsar::result::BooleanResult
org::openscience::cdk::qsar::result::BooleanResultType
org::openscience::cdk::qsar::descriptors::molecular::BPolDescriptor
org::openscience::cdk::tools::BremserOneSphereHOSECodePredictor
org::openscience::cdk::smiles::SmilesGenerator::BrokenBond
org::openscience::cdk::io::formats::BSFormat
org::openscience::cdk::graph::rebond::Bspt
org::openscience::cdk::qsar::descriptors::molecular::BCUTDescriptor::BurdenMatrix
org::openscience::cdk::io::formats::CacaoCartesianFormat
org::openscience::cdk::io::formats::CacaoInternalFormat
org::openscience::cdk::io::formats::CACheFormat
org::openscience::cdk::graph::invariant::CanonicalLabeler
org::openscience::cdk::qsar::descriptors::molecular::CarbonTypesDescriptor
org::openscience::cdk::reaction::type::CarbonylEliminationReaction
org::openscience::cdk::index::CASNumber
org::openscience::cdk::ConformerContainer::CCIterator
org::openscience::cdk::renderer::color::CDK2DAtomColors
org::openscience::cdk::renderer::color::CDKAtomColors
org::openscience::cdk::atomtype::CDKAtomTypeMatcher
org::openscience::cdk::config::CDKBasedAtomTypeConfigurator
net::sf::cdk::tools::doclets::CDKBugTaglet
net::sf::cdk::tools::doclets::CDKCiteTaglet
org::openscience::cdk::CDKConstants
org::openscience::cdk::io::cml::CDKConvention
org::openscience::cdk::dict::CDKDictionaryReferences
net::sf::cdk::tools::doclets::CDKDictRefTaglet
org::openscience::cdk::exception::CDKException
net::sf::cdk::tools::doclets::CDKGitTaglet
org::openscience::cdk::aromaticity::CDKHueckelAromaticityDetector
org::openscience::cdk::tools::CDKHydrogenAdder
net::sf::cdk::tools::doclets::CDKInChITaglet
net::sf::cdk::tools::doclets::CDKModuleTaglet
org::openscience::cdk::controller::CDKPopupMenu
org::openscience::cdk::io::formats::CDKSourceCodeFormat
org::openscience::cdk::io::CDKSourceCodeWriter
net::sf::cdk::tools::doclets::CDKThreadNonSafeTaglet
net::sf::cdk::tools::doclets::CDKThreadSafeTaglet
org::openscience::cdk::tools::CDKUtilities
org::openscience::cdk::tools::CDKValencyChecker
org::openscience::cdk::validate::CDKValidator
org::openscience::cdk::libio::md::ChargeGroup
org::openscience::cdk::formula::rules::ChargeRule
net::sf::cdk::tools::copyright::CheckCopyrightStatements
net::sf::cdk::tools::coverage::CheckModuleCoverage
org::openscience::cdk::io::formats::Chem3D_Cartesian_1Format
org::openscience::cdk::io::formats::Chem3D_Cartesian_2Format
org::openscience::cdk::io::formats::ChemDrawFormat
org::openscience::cdk::ChemFile
org::openscience::cdk::tools::manipulator::ChemFileManipulator
org::openscience::cdk::structgen::stochastic::operator::ChemGraph
org::openscience::cdk::ChemModel
org::openscience::cdk::ChemSequence::ChemModelIterator
org::openscience::cdk::tools::manipulator::ChemModelManipulator
org::openscience::cdk::ChemObject
org::openscience::cdk::event::ChemObjectChangeEvent
org::openscience::cdk::tools::diff::ChemObjectDiff
org::openscience::cdk::tools::diff::tree::ChemObjectDifference
org::openscience::cdk::Mapping::ChemObjectIterator
org::openscience::cdk::ChemSequence
org::openscience::cdk::ChemFile::ChemSequenceIterator
org::openscience::cdk::tools::manipulator::ChemSequenceManipulator
org::openscience::cdk::io::formats::ChemtoolFormat
org::openscience::cdk::qsar::descriptors::molecular::ChiChainDescriptor
org::openscience::cdk::qsar::descriptors::molecular::ChiClusterDescriptor
org::openscience::cdk::qsar::descriptors::molecular::ChiIndexUtils
org::openscience::cdk::qsar::descriptors::molecular::ChiPathClusterDescriptor
org::openscience::cdk::qsar::descriptors::molecular::ChiPathDescriptor
org::openscience::cdk::isomorphism::matchers::smarts::ChiralityAtom
org::openscience::cdk::io::formats::CIFFormat
org::openscience::cdk::io::CIFReader
org::openscience::cdk::math::qm::ClosedShellJob
org::openscience::cdk::io::cml::CMLCoreModule
org::openscience::cdk::io::cml::CMLErrorHandler
org::openscience::cdk::io::formats::CMLFormat
org::openscience::cdk::io::cml::CMLHandler
org::openscience::cdk::io::cml::CMLReactionModule
org::openscience::cdk::io::CMLReader
org::openscience::cdk::io::cml::CMLResolver
org::openscience::cdk::io::formats::CMLRSSFormat
org::openscience::cdk::io::cml::CMLStack
org::openscience::cdk::io::CMLWriter
org::openscience::cdk::qsar::model::R::CNNClassificationModel
org::openscience::cdk::qsar::model::R::CNNClassificationModelFit
org::openscience::cdk::qsar::model::R::CNNClassificationModelPredict
org::openscience::cdk::qsar::model::R::CNNRegressionModel
org::openscience::cdk::qsar::model::R2::CNNRegressionModel
org::openscience::cdk::qsar::model::R::CNNRegressionModelFit
org::openscience::cdk::qsar::model::R::CNNRegressionModelPredict
org::openscience::cdk::qsar::model::R::CNNRegressionModelSummary
org::openscience::cdk::formula::rules::RDBERule::Combinations
org::openscience::cdk::math::Complex
org::openscience::cdk::ConformerContainer
org::openscience::cdk::graph::invariant::ConjugatedPiSystemsDetector
org::openscience::cdk::modeling::forcefield::ConjugateGradientMethod
org::openscience::cdk::isomorphism::matchers::smarts::ConnectionCountAtom
org::openscience::cdk::graph::matrix::ConnectionMatrix
org::openscience::cdk::graph::ConnectivityChecker
org::openscience::cdk::libio::cml::Convertor
org::openscience::cdk::qsar::descriptors::atomic::CovalentRadiusDescriptor
org::openscience::cdk::renderer::color::CPKAtomColors
org::openscience::cdk::qsar::descriptors::molecular::CPSADescriptor
org::openscience::cdk::io::formats::CRK2DFormat
org::openscience::cdk::io::formats::CRK3DFormat
org::openscience::cdk::structgen::stochastic::operator::CrossoverMachine
org::openscience::cdk::Crystal
org::openscience::cdk::geometry::CrystalGeometryTools
org::openscience::cdk::io::formats::CrystClustFormat
org::openscience::cdk::io::CrystClustReader
org::openscience::cdk::io::CrystClustWriter
org::openscience::cdk::io::formats::CTXFormat
org::openscience::cdk::io::CTXReader
org::openscience::cdk::io::cml::CustomSerializer
org::openscience::cdk::ringsearch::cyclebasis::CycleBasis
org::openscience::cdk::io::formats::DaltonFormat
org::openscience::cdk::tools::DataFeatures
org::openscience::cdk::tools::DataFeaturesTool
org::openscience::cdk::tools::DeAromatizationTool
org::openscience::cdk::debug::DebugAdductFormula
org::openscience::cdk::debug::DebugAminoAcid
org::openscience::cdk::debug::DebugAtom
org::openscience::cdk::debug::DebugAtomContainer
org::openscience::cdk::debug::DebugAtomContainerSet
org::openscience::cdk::debug::DebugAtomParity
org::openscience::cdk::debug::DebugAtomType
org::openscience::cdk::debug::DebugBioPolymer
org::openscience::cdk::debug::DebugBond
org::openscience::cdk::debug::DebugChemFile
org::openscience::cdk::debug::DebugChemModel
org::openscience::cdk::debug::DebugChemObject
org::openscience::cdk::debug::DebugChemObjectBuilder
org::openscience::cdk::debug::DebugChemSequence
org::openscience::cdk::debug::DebugCrystal
org::openscience::cdk::debug::DebugElectronContainer
org::openscience::cdk::debug::DebugElement
org::openscience::cdk::debug::DebugFragmentAtom
org::openscience::cdk::debug::DebugIsotope
org::openscience::cdk::debug::DebugLonePair
org::openscience::cdk::debug::DebugMapping
org::openscience::cdk::debug::DebugMolecularFormula
org::openscience::cdk::debug::DebugMolecularFormulaSet
org::openscience::cdk::debug::DebugMolecule
org::openscience::cdk::debug::DebugMoleculeSet
org::openscience::cdk::debug::DebugMonomer
org::openscience::cdk::debug::DebugPDBAtom
org::openscience::cdk::debug::DebugPDBMonomer
org::openscience::cdk::debug::DebugPDBPolymer
org::openscience::cdk::debug::DebugPDBStructure
org::openscience::cdk::debug::DebugPolymer
org::openscience::cdk::debug::DebugPseudoAtom
org::openscience::cdk::debug::DebugReaction
org::openscience::cdk::debug::DebugReactionScheme
org::openscience::cdk::debug::DebugReactionSet
org::openscience::cdk::debug::DebugRing
org::openscience::cdk::debug::DebugRingSet
org::openscience::cdk::debug::DebugSingleElectron
org::openscience::cdk::debug::DebugStrand
org::openscience::cdk::smiles::DeduceBondSystemTool
org::openscience::cdk::DefaultChemObjectBuilder
org::openscience::cdk::io::DefaultChemObjectReader
org::openscience::cdk::io::DefaultChemObjectWriter
org::openscience::cdk::io::iterator::event::DefaultEventChemObjectReader
org::openscience::cdk::io::iterator::DefaultIteratingChemObjectReader
org::openscience::cdk::io::random::DefaultRandomAccessChemObjectReader
org::openscience::cdk::isomorphism::matchers::smarts::DegreeAtom
org::openscience::cdk::qsar::DescriptorEngine
org::openscience::cdk::qsar::DescriptorException
org::openscience::cdk::qsar::DescriptorSpecification
org::openscience::cdk::qsar::DescriptorValue
org::openscience::cdk::dict::Dictionary
org::openscience::cdk::dict::DictionaryDatabase
org::openscience::cdk::dict::DictionaryHandler
org::openscience::cdk::validate::DictionaryValidator
org::openscience::cdk::dict::DictRef
org::openscience::cdk::similarity::DistanceMoment
org::openscience::cdk::qsar::descriptors::atomic::DistanceToAtomDescriptor
org::openscience::cdk::io::formats::DMol3Format
org::openscience::cdk::io::formats::DOCK5Format
org::openscience::cdk::qsar::result::DoubleArrayResult
org::openscience::cdk::qsar::result::DoubleArrayResultType
org::openscience::cdk::tools::diff::tree::DoubleDifference
org::openscience::cdk::qsar::result::DoubleResult
org::openscience::cdk::qsar::result::DoubleResultType
org::openscience::cdk::qsar::descriptors::molecular::EccentricConnectivityIndexDescriptor
org::openscience::cdk::qsar::descriptors::atomic::EffectiveAtomPolarizabilityDescriptor
org::openscience::cdk::ElectronContainer
org::openscience::cdk::tools::diff::ElectronContainerDiff
org::openscience::cdk::AtomContainer::ElectronContainerIterator
org::openscience::cdk::charges::Electronegativity
org::openscience::cdk::reaction::type::ElectronImpactNBEReaction
org::openscience::cdk::reaction::type::ElectronImpactPDBReaction
org::openscience::cdk::reaction::type::ElectronImpactSDBReaction
org::openscience::cdk::modeling::forcefield::ElectrostaticInteractions
org::openscience::cdk::Element
org::openscience::cdk::graph::rebond::Bspt::Element
org::openscience::cdk::tools::ElementComparator
org::openscience::cdk::tools::diff::ElementDiff
org::openscience::cdk::config::ElementPTFactory
org::openscience::cdk::config::elements::ElementPTHandler
org::openscience::cdk::config::elements::ElementPTReader
org::openscience::cdk::formula::rules::ElementRule
org::openscience::cdk::config::Elements
org::openscience::cdk::dict::Entry
org::openscience::cdk::dict::EntryReact
org::openscience::cdk::graph::rebond::Bspt::EnumerateAll
org::openscience::cdk::graph::rebond::Bspt::EnumerateNear
org::openscience::cdk::graph::rebond::Bspt::EnumerateSphere
org::openscience::cdk::EnzymeResidueLocator
org::openscience::cdk::graph::invariant::EquivalentClassPartitioner
org::openscience::cdk::atomtype::EStateAtomTypeMatcher
org::openscience::cdk::fingerprint::EStateFingerprinter
org::openscience::cdk::config::fragments::EStateFragments
org::openscience::cdk::io::iterator::event::EventCMLHandler
org::openscience::cdk::io::iterator::event::EventCMLReader
org::openscience::cdk::isomorphism::matchers::smarts::ExplicitConnectionAtom
org::openscience::cdk::fingerprint::ExtendedFingerprinter
org::openscience::cdk::io::formats::FenskeHall_ZMatrixFormat
org::openscience::cdk::ringsearch::FiguerasSSSRFinder
org::openscience::cdk::fingerprint::Fingerprinter
org::openscience::cdk::fingerprint::FingerprinterTool
org::openscience::cdk::io::formats::FingerprintFormat
org::openscience::cdk::tools::FixedSizeStack
org::openscience::cdk::modeling::forcefield::ForceField
org::openscience::cdk::modeling::builder3d::ForceFieldConfigurator
org::openscience::cdk::modeling::forcefield::ForceFieldTools
org::openscience::cdk::isomorphism::matchers::smarts::FormalChargeAtom
org::openscience::cdk::tools::FormatStringBuffer::Format
org::openscience::cdk::io::FormatFactory
org::openscience::cdk::tools::FormatStringBuffer
org::openscience::cdk::math::FortranFormat
org::openscience::cdk::math::qm::FourierGridBasis
org::openscience::cdk::FragmentAtom
org::openscience::cdk::qsar::descriptors::molecular::FragmentComplexityDescriptor
org::openscience::cdk::io::formats::GamessFormat
org::openscience::cdk::io::GamessReader
org::openscience::cdk::charges::GasteigerMarsiliPartialCharges
org::openscience::cdk::charges::GasteigerPEPEPartialCharges
org::openscience::cdk::io::formats::Gaussian03Format
org::openscience::cdk::io::Gaussian03Reader
org::openscience::cdk::io::formats::Gaussian90Format
org::openscience::cdk::io::formats::Gaussian92Format
org::openscience::cdk::io::formats::Gaussian94Format
org::openscience::cdk::io::formats::Gaussian95Format
org::openscience::cdk::io::formats::Gaussian98Format
org::openscience::cdk::io::Gaussian98Reader
org::openscience::cdk::io::formats::GaussianInputFormat
org::openscience::cdk::io::program::GaussianInputWriter
org::openscience::cdk::math::qm::GaussiansBasis
org::openscience::cdk::tools::GenerateFragments
org::openscience::cdk::modeling::forcefield::GeometricMinimizer
org::openscience::cdk::validate::Geometry3DValidator
org::openscience::cdk::geometry::GeometryTools
org::openscience::cdk::io::formats::GhemicalMMFormat
org::openscience::cdk::io::GhemicalMMReader
org::openscience::cdk::io::formats::GhemicalSPMFormat
org::openscience::cdk::graph::invariant::GIMatrix
org::openscience::cdk::fingerprint::GraphOnlyFingerprinter
org::openscience::cdk::renderer::GraphRendererModel
org::openscience::cdk::qsar::descriptors::molecular::GravitationalIndexDescriptor
org::openscience::cdk::tools::GridGenerator
org::openscience::cdk::io::formats::GROMOS96Format
org::openscience::cdk::qsar::descriptors::molecular::HBondAcceptorCountDescriptor
org::openscience::cdk::qsar::descriptors::molecular::HBondDonorCountDescriptor
org::openscience::cdk::reaction::mechanism::HeterolyticCleavageMechanism
org::openscience::cdk::reaction::type::HeterolyticCleavagePBReaction
org::openscience::cdk::reaction::type::HeterolyticCleavageSBReaction
org::openscience::cdk::io::formats::HINFormat
org::openscience::cdk::io::HINReader
org::openscience::cdk::io::HINWriter
org::openscience::cdk::reaction::mechanism::HomolyticCleavageMechanism
org::openscience::cdk::reaction::type::HomolyticCleavageReaction
org::openscience::cdk::tools::HOSECodeAnalyser
org::openscience::cdk::tools::HOSECodeGenerator
org::openscience::cdk::tools::BremserOneSphereHOSECodePredictor::HOSECodeShiftRange
org::openscience::cdk::graph::invariant::HuLuIndexTool
org::openscience::cdk::isomorphism::matchers::smarts::HybridizationNumberAtom
org::openscience::cdk::isomorphism::matchers::smarts::HydrogenAtom
org::openscience::cdk::layout::HydrogenPlacer
org::openscience::cdk::reaction::type::HyperconjugationReaction
org::openscience::cdk::interfaces::IAdductFormula
org::openscience::cdk::interfaces::IAminoAcid
org::openscience::cdk::interfaces::IAtom
org::openscience::cdk::renderer::color::IAtomColorer
org::openscience::cdk::interfaces::IAtomContainer
org::openscience::cdk::interfaces::IAtomContainerSet
org::openscience::cdk::qsar::IAtomicDescriptor
org::openscience::cdk::qsar::IAtomPairDescriptor
org::openscience::cdk::interfaces::IAtomParity
org::openscience::cdk::interfaces::IAtomType
org::openscience::cdk::config::IAtomTypeConfigurator
org::openscience::cdk::atomtype::IAtomTypeGuesser
org::openscience::cdk::atomtype::IAtomTypeMatcher
org::openscience::cdk::math::qm::IBasis
org::openscience::cdk::interfaces::IBioPolymer
org::openscience::cdk::interfaces::IBond
org::openscience::cdk::qsar::IBondDescriptor
org::openscience::cdk::event::ICDKChangeListener
org::openscience::cdk::event::ICDKSelectionChangeListener
org::openscience::cdk::charges::IChargeCalculator
org::openscience::cdk::interfaces::IChemFile
org::openscience::cdk::io::formats::IChemFormat
org::openscience::cdk::io::formats::IChemFormatMatcher
org::openscience::cdk::interfaces::IChemModel
org::openscience::cdk::interfaces::IChemObject
org::openscience::cdk::interfaces::IChemObjectBuilder
org::openscience::cdk::interfaces::IChemObjectChangeEvent
org::openscience::cdk::io::IChemObjectIO
org::openscience::cdk::io::listener::IChemObjectIOListener
org::openscience::cdk::interfaces::IChemObjectListener
org::openscience::cdk::io::IChemObjectReader
org::openscience::cdk::io::IChemObjectWriter
org::openscience::cdk::interfaces::IChemSequence
org::openscience::cdk::io::cml::ICMLConvention
org::openscience::cdk::libio::cml::ICMLCustomizer
org::openscience::cdk::io::cml::ICMLModule
org::openscience::cdk::interfaces::ICrystal
org::openscience::cdk::tools::IDCreator
org::openscience::cdk::tools::IDeduceBondOrderTool
org::openscience::cdk::qsar::IDescriptor
org::openscience::cdk::qsar::result::IDescriptorResult
org::openscience::cdk::tools::diff::tree::IDifference
org::openscience::cdk::tools::diff::tree::IDifferenceList
org::openscience::cdk::interfaces::IElectronContainer
org::openscience::cdk::charges::IElectronicPropertyCalculator
org::openscience::cdk::interfaces::IElement
org::openscience::cdk::io::iterator::event::IEventChemObjectReader
org::openscience::cdk::fingerprint::IFingerprinter
org::openscience::cdk::interfaces::IFragmentAtom
org::openscience::cdk::math::IFunction
org::openscience::cdk::graph::matrix::IGraphMatrix
org::openscience::cdk::IImplementationSpecification
org::openscience::cdk::interfaces::IIsotope
org::openscience::cdk::io::iterator::IIteratingChemObjectReader
org::openscience::cdk::interfaces::ILonePair
org::openscience::cdk::interfaces::IMapping
org::openscience::cdk::math::IMatrix
org::openscience::cdk::qsar::model::IModel
org::openscience::cdk::qsar::IMolecularDescriptor
org::openscience::cdk::interfaces::IMolecularFormula
org::openscience::cdk::interfaces::IMolecularFormulaSet
org::openscience::cdk::interfaces::IMolecule
org::openscience::cdk::interfaces::IMoleculeSet
org::openscience::cdk::interfaces::IMonomer
org::openscience::cdk::controller::IMouseEventRelay
org::openscience::cdk::isomorphism::matchers::smarts::ImplicitHCountAtom
org::openscience::cdk::io::inchi::INChIContentProcessorTool
org::openscience::cdk::io::formats::INChIFormat
org::openscience::cdk::inchi::InChIGenerator
org::openscience::cdk::inchi::InChIGeneratorFactory
org::openscience::cdk::io::inchi::INChIHandler
org::openscience::cdk::io::formats::INChIPlainTextFormat
org::openscience::cdk::io::INChIPlainTextReader
org::openscience::cdk::io::INChIReader
org::openscience::cdk::inchi::InChIToStructure
org::openscience::cdk::exception::IncorrectUseOfCDKCoreClassError
org::openscience::cdk::graph::invariant::exception::IndexOutOfBoundsException
org::openscience::cdk::qsar::descriptors::atomic::InductiveAtomicHardnessDescriptor
org::openscience::cdk::qsar::descriptors::atomic::InductiveAtomicSoftnessDescriptor
org::openscience::cdk::charges::InductivePartialCharges
org::openscience::cdk::qsar::result::IntegerArrayResult
org::openscience::cdk::qsar::result::IntegerArrayResultType
org::openscience::cdk::tools::diff::tree::IntegerDifference
org::openscience::cdk::io::setting::IntegerIOSetting
org::openscience::cdk::qsar::result::IntegerResult
org::openscience::cdk::qsar::result::IntegerResultType
org::openscience::cdk::exception::InvalidSmilesException
org::openscience::cdk::isomorphism::matchers::InverseSymbolSetQueryAtom
org::openscience::cdk::smiles::InvPair
org::openscience::cdk::tools::IonizationPotentialTool
org::openscience::cdk::io::setting::IOSetting
org::openscience::cdk::reaction::type::parameters::IParameterReact
org::openscience::cdk::qsar::descriptors::atomic::IPAtomicHOSEDescriptor
org::openscience::cdk::qsar::descriptors::atomic::IPAtomicLearningDescriptor
org::openscience::cdk::qsar::descriptors::bond::IPBondLearningDescriptor
org::openscience::cdk::qsar::descriptors::atomic::IPAtomicHOSEDescriptor::IPdb
org::openscience::cdk::interfaces::IPDBAtom
org::openscience::cdk::interfaces::IPDBMonomer
org::openscience::cdk::interfaces::IPDBPolymer
org::openscience::cdk::interfaces::IPDBStructure
org::openscience::cdk::qsar::descriptors::molecular::IPMolecularLearningDescriptor
org::openscience::cdk::interfaces::IPolymer
org::openscience::cdk::modeling::forcefield::IPotentialFunction
org::openscience::cdk::interfaces::IPseudoAtom
org::openscience::cdk::isomorphism::matchers::IQueryAtom
org::openscience::cdk::isomorphism::matchers::IQueryAtomContainer
org::openscience::cdk::isomorphism::matchers::IQueryBond
org::openscience::cdk::io::random::IRandomAccessChemObjectReader< T >
org::openscience::cdk::geometry::IRDFWeightFunction
org::openscience::cdk::interfaces::IReaction
org::openscience::cdk::reaction::IReactionMechanism
org::openscience::cdk::reaction::IReactionProcess
org::openscience::cdk::interfaces::IReactionScheme
org::openscience::cdk::interfaces::IReactionSet
org::openscience::cdk::io::listener::IReaderListener
org::openscience::cdk::io::formats::IResourceFormat
org::openscience::cdk::interfaces::IRing
org::openscience::cdk::interfaces::IRingSet
org::openscience::cdk::formula::rules::IRule
org::openscience::cdk::io::ISimpleChemObjectReader
org::openscience::cdk::interfaces::ISingleElectron
org::openscience::cdk::templates::saturatedhydrocarbons::IsoAlkanes
org::openscience::cdk::isomorphism::IsomorphismTester
org::openscience::cdk::Isotope
org::openscience::cdk::formula::IsotopeContainer
org::openscience::cdk::tools::diff::IsotopeDiff
org::openscience::cdk::config::IsotopeFactory
org::openscience::cdk::config::isotopes::IsotopeHandler
org::openscience::cdk::formula::IsotopePattern
org::openscience::cdk::formula::IsotopePatternGenerator
org::openscience::cdk::formula::IsotopePatternManipulator
org::openscience::cdk::formula::rules::IsotopePatternRule
org::openscience::cdk::formula::IsotopePatternSimilarity
org::openscience::cdk::config::isotopes::IsotopeReader
org::openscience::cdk::qsar::descriptors::atomic::IsProtonInAromaticSystemDescriptor
org::openscience::cdk::qsar::descriptors::atomic::IsProtonInConjugatedPiSystemDescriptor
org::openscience::cdk::interfaces::IStrand
org::openscience::cdk::structgen::IStructureGenerationListener
org::openscience::cdk::io::iterator::IteratingMDLConformerReader
org::openscience::cdk::io::iterator::IteratingMDLReader
org::openscience::cdk::io::iterator::IteratingPCCompoundASNReader
org::openscience::cdk::io::iterator::IteratingPCCompoundXMLReader
org::openscience::cdk::io::iterator::IteratingPCSubstancesXMLReader
org::openscience::cdk::io::iterator::IteratingSMILESReader
org::openscience::cdk::tools::IValencyChecker
org::openscience::cdk::validate::IValidator
org::openscience::cdk::math::IVector
org::openscience::cdk::controller::IViewEventRelay
org::openscience::cdk::io::listener::IWriterListener
org::openscience::cdk::io::formats::JaguarFormat
net::sf::cdk::tools::coverage::CheckModuleCoverage::JavaFilesFilter
org::openscience::cdk::renderer::JCPAction2D
org::openscience::cdk::iupac::parser::NomParser::JJCalls
org::openscience::cdk::smiles::smarts::parser::SMARTSParser::JJCalls
org::openscience::cdk::smiles::smarts::parser::JJTSMARTSParserState
org::openscience::cdk::io::formats::JMEFormat
org::openscience::cdk::io::cml::JMOLANIMATIONConvention
org::openscience::cdk::geometry::alignment::KabschAlignment
org::openscience::cdk::qsar::descriptors::molecular::KappaShapeIndicesDescriptor
org::openscience::cdk::qsar::descriptors::molecular::KierHallSmartsDescriptor
org::openscience::cdk::qsar::descriptors::molecular::LargestChainDescriptor
org::openscience::cdk::qsar::descriptors::molecular::LargestPiSystemDescriptor
org::openscience::cdk::graph::rebond::Bspt::Leaf
org::openscience::cdk::qsar::descriptors::molecular::LengthOverBreadthDescriptor
org::openscience::cdk::qsar::model::R::LinearRegressionModel
org::openscience::cdk::qsar::model::R2::LinearRegressionModel
org::openscience::cdk::qsar::model::R::LinearRegressionModelFit
org::openscience::cdk::qsar::model::R::LinearRegressionModelPredict
org::openscience::cdk::qsar::model::R::LinearRegressionModelSummary
org::openscience::cdk::modeling::forcefield::LineSearch
org::openscience::cdk::modeling::forcefield::LineSearchForTheWolfeConditions
org::openscience::cdk::tools::LoggingTool
org::openscience::cdk::isomorphism::matchers::smarts::LogicalOperatorAtom
org::openscience::cdk::isomorphism::matchers::smarts::LogicalOperatorBond
org::openscience::cdk::LonePair
org::openscience::cdk::tools::diff::LonePairDiff
org::openscience::cdk::tools::LonePairElectronChecker
org::openscience::cdk::AtomContainer::LonePairIterator
org::openscience::cdk::qsar::descriptors::molecular::LongestAliphaticChainDescriptor
org::openscience::cdk::iupac::parser::NomParser::LookaheadSuccess
org::openscience::cdk::smiles::smarts::parser::SMARTSParser::LookaheadSuccess
org::openscience::cdk::fingerprint::MACCSFingerprinter
org::openscience::cdk::fingerprint::MACCSFingerprinter::MaccsKey
org::openscience::cdk::io::formats::MacroModelFormat
net::sf::cdk::tools::MakeJavafilesFiles
org::openscience::cdk::Mapping
org::openscience::cdk::Reaction::MappingIterator
org::openscience::cdk::isomorphism::matchers::smarts::MassAtom
org::openscience::cdk::formula::MassToFormulaTool
org::openscience::cdk::math::MathTools
org::openscience::cdk::math::Matrix
org::openscience::cdk::graph::invariant::exception::MatrixNotInvertibleException
org::openscience::cdk::qsar::descriptors::molecular::MDEDescriptor
org::openscience::cdk::io::formats::MDLFormat
org::openscience::cdk::io::cml::MDLMolConvention
org::openscience::cdk::io::MDLReader
org::openscience::cdk::io::formats::MDLRXNFormat
org::openscience::cdk::io::MDLRXNReader
org::openscience::cdk::io::MDLRXNV2000Reader
org::openscience::cdk::io::formats::MDLRXNV3000Format
org::openscience::cdk::io::MDLRXNV3000Reader
org::openscience::cdk::io::MDLRXNWriter
org::openscience::cdk::io::formats::MDLV2000Format
org::openscience::cdk::io::MDLV2000Reader
org::openscience::cdk::io::formats::MDLV3000Format
org::openscience::cdk::io::MDLV3000Reader
org::openscience::cdk::io::MDLWriter
org::openscience::cdk::libio::md::MDMolecule
org::openscience::cdk::io::cml::MDMoleculeConvention
org::openscience::cdk::libio::cml::MDMoleculeCustomizer
org::openscience::cdk::graph::MinimalPathIterator
org::openscience::cdk::atomtype::MM2AtomTypeMatcher
org::openscience::cdk::modeling::builder3d::MM2BasedAtomTypePattern
org::openscience::cdk::modeling::builder3d::MM2BasedParameterSetReader
org::openscience::cdk::formula::rules::MMElementRule
org::openscience::cdk::atomtype::MMFF94AtomTypeMatcher
org::openscience::cdk::modeling::builder3d::MMFF94BasedAtomTypePattern
org::openscience::cdk::modeling::builder3d::MMFF94BasedParameterSetReader
org::openscience::cdk::modeling::forcefield::MMFF94EnergyFunction
org::openscience::cdk::modeling::builder3d::MMFF94ParametersCall
org::openscience::cdk::charges::MMFF94PartialCharges
org::openscience::cdk::io::formats::MMODFormat
org::openscience::cdk::modeling::builder3d::ModelBuilder3D
org::openscience::cdk::io::formats::Mol2Format
org::openscience::cdk::io::Mol2Reader
org::openscience::cdk::io::Mol2Writer
org::openscience::cdk::formula::MolecularFormula
org::openscience::cdk::formula::MolecularFormulaChecker
org::openscience::cdk::tools::manipulator::MolecularFormulaManipulator
org::openscience::cdk::formula::MolecularFormulaRange
org::openscience::cdk::tools::manipulator::MolecularFormulaRangeManipulator
org::openscience::cdk::formula::MolecularFormulaSet
org::openscience::cdk::tools::manipulator::MolecularFormulaSetManipulator
org::openscience::cdk::Molecule
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::MoleculeSet
org::openscience::cdk::tools::manipulator::MoleculeSetManipulator
org::openscience::cdk::qsar::descriptors::molecular::MomentOfInertiaDescriptor
org::openscience::cdk::Monomer
org::openscience::cdk::io::formats::MOPAC2002Format
org::openscience::cdk::io::formats::MOPAC7Format
org::openscience::cdk::io::formats::MOPAC93Format
org::openscience::cdk::io::formats::MOPAC97Format
org::openscience::cdk::graph::invariant::MorganNumbersTools
org::openscience::cdk::io::formats::MPQCFormat
org::openscience::cdk::graph::BFSShortestPath::MyBreadthFirstIterator
org::openscience::cdk::graph::MinimalPathIterator::MyBreadthFirstIterator
org::openscience::cdk::geometry::surface::NeighborList
org::openscience::cdk::modeling::forcefield::NewtonRaphsonMethod
org::openscience::cdk::formula::rules::NitrogenRule
org::openscience::cdk::nonotify::NNAdductFormula
org::openscience::cdk::nonotify::NNAminoAcid
org::openscience::cdk::nonotify::NNAtom
org::openscience::cdk::nonotify::NNAtomContainer
org::openscience::cdk::nonotify::NNAtomContainerSet
org::openscience::cdk::nonotify::NNAtomParity
org::openscience::cdk::nonotify::NNAtomType
org::openscience::cdk::nonotify::NNBioPolymer
org::openscience::cdk::nonotify::NNBond
org::openscience::cdk::nonotify::NNChemFile
org::openscience::cdk::nonotify::NNChemModel
org::openscience::cdk::nonotify::NNChemObject
org::openscience::cdk::nonotify::NNChemSequence
org::openscience::cdk::nonotify::NNCrystal
org::openscience::cdk::nonotify::NNElectronContainer
org::openscience::cdk::nonotify::NNElement
org::openscience::cdk::nonotify::NNFragmentAtom
org::openscience::cdk::nonotify::NNIsotope
org::openscience::cdk::nonotify::NNLonePair
org::openscience::cdk::nonotify::NNMapping
org::openscience::cdk::nonotify::NNMolecularFormula
org::openscience::cdk::nonotify::NNMolecularFormulaSet
org::openscience::cdk::nonotify::NNMolecule
org::openscience::cdk::nonotify::NNMoleculeSet
org::openscience::cdk::nonotify::NNMonomer
org::openscience::cdk::nonotify::NNPDBAtom
org::openscience::cdk::nonotify::NNPDBMonomer
org::openscience::cdk::nonotify::NNPDBPolymer
org::openscience::cdk::nonotify::NNPDBStructure
org::openscience::cdk::nonotify::NNPolymer
org::openscience::cdk::nonotify::NNPseudoAtom
org::openscience::cdk::nonotify::NNReaction
org::openscience::cdk::nonotify::NNReactionScheme
org::openscience::cdk::nonotify::NNReactionSet
org::openscience::cdk::nonotify::NNRing
org::openscience::cdk::nonotify::NNRingSet
org::openscience::cdk::nonotify::NNSingleElectron
org::openscience::cdk::nonotify::NNStrand
org::openscience::cdk::smiles::smarts::parser::Node
org::openscience::cdk::graph::rebond::Bspt::Node
org::openscience::cdk::iupac::parser::NomParser
org::openscience::cdk::iupac::parser::NomParserConstants
org::openscience::cdk::iupac::parser::NomParserTokenManager
org::openscience::cdk::isomorphism::matchers::smarts::NonCHHeavyAtom
org::openscience::cdk::nonotify::NoNotificationChemObjectBuilder
org::openscience::cdk::tools::Normalizer
org::openscience::cdk::exception::NoSuchAtomException
org::openscience::cdk::exception::NoSuchAtomTypeException
org::openscience::cdk::geometry::surface::NumericalSurface
org::openscience::cdk::io::formats::NWChemFormat
org::openscience::cdk::math::qm::OneElectronJob
org::openscience::cdk::io::setting::OptionIOSetting
org::openscience::cdk::math::qm::Orbitals
org::openscience::cdk::isomorphism::matchers::smarts::OrderQueryBond
org::openscience::cdk::isomorphism::matchers::OrderQueryBond
org::openscience::cdk::isomorphism::matchers::OrderQueryBondOrderOnly
org::openscience::cdk::layout::OverlapResolver::OverlapPair
org::openscience::cdk::layout::OverlapResolver
org::openscience::cdk::config::atomtypes::OWLAtomTypeHandler
org::openscience::cdk::config::atomtypes::OWLAtomTypeMappingHandler
org::openscience::cdk::config::atomtypes::OWLAtomTypeMappingReader
org::openscience::cdk::config::atomtypes::OWLAtomTypeReader
org::openscience::cdk::config::OWLBasedAtomTypeConfigurator
org::openscience::cdk::dict::OWLFile
org::openscience::cdk::dict::OWLReact
org::openscience::cdk::qsar::descriptors::molecular::GravitationalIndexDescriptor::pair
org::openscience::cdk::reaction::type::parameters::ParameterReact
org::openscience::cdk::iupac::parser::ParseException
org::openscience::cdk::smiles::smarts::parser::ParseException
org::openscience::cdk::renderer::color::PartialAtomicChargeColors
org::openscience::cdk::structgen::stochastic::PartialFilledStructureMerger
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::ringsearch::Path
org::openscience::cdk::graph::PathTools
org::openscience::cdk::qsar::descriptors::molecular::WHIMDescriptor::PCA
org::openscience::cdk::io::PCCompoundASNReader
org::openscience::cdk::io::PCCompoundXMLReader
org::openscience::cdk::io::formats::PCModelFormat
org::openscience::cdk::io::PCSubstanceXMLReader
org::openscience::cdk::protein::data::PDBAtom
org::openscience::cdk::libio::cml::PDBAtomCustomizer
org::openscience::cdk::io::cml::PDBConvention
org::openscience::cdk::io::formats::PDBFormat
org::openscience::cdk::io::formats::PDBMLFormat
org::openscience::cdk::protein::data::PDBMonomer
org::openscience::cdk::protein::data::PDBPolymer
org::openscience::cdk::io::PDBReader
org::openscience::cdk::protein::data::PDBStrand
org::openscience::cdk::protein::data::PDBStructure
org::openscience::cdk::io::PDBWriter
org::openscience::cdk::isomorphism::matchers::smarts::PeriodicGroupNumberAtom
org::openscience::cdk::tools::PeriodicTable
org::openscience::cdk::PeriodicTableElement
org::openscience::cdk::qsar::descriptors::atomic::PeriodicTablePositionDescriptor
org::openscience::cdk::qsar::descriptors::molecular::PetitjeanNumberDescriptor
org::openscience::cdk::qsar::descriptors::molecular::PetitjeanShapeIndexDescriptor
org::openscience::cdk::pharmacophore::PharmacophoreAngleBond
org::openscience::cdk::pharmacophore::PharmacophoreAtom
org::openscience::cdk::pharmacophore::PharmacophoreBond
org::openscience::cdk::pharmacophore::PharmacophoreMatcher
org::openscience::cdk::pharmacophore::PharmacophoreQueryAngleBond
org::openscience::cdk::pharmacophore::PharmacophoreQueryAtom
org::openscience::cdk::pharmacophore::PharmacophoreQueryBond
org::openscience::cdk::pharmacophore::PharmacophoreUtils
org::openscience::cdk::PhysicalConstants
org::openscience::cdk::reaction::type::PiBondingMovementReaction
org::openscience::cdk::qsar::descriptors::atompair::PiContactDetectionDescriptor
org::openscience::cdk::charges::PiElectronegativity
org::openscience::cdk::qsar::descriptors::atomic::PiElectronegativityDescriptor
org::openscience::cdk::qsar::model::R::PLSRegressionModel
org::openscience::cdk::qsar::model::R::PLSRegressionModelFit
org::openscience::cdk::qsar::model::R::PLSRegressionModelPredict
org::openscience::cdk::qsar::model::R::PLSTraining
org::openscience::cdk::qsar::model::R::PLSValidation
org::openscience::cdk::io::cml::PMPConvention
org::openscience::cdk::io::formats::PMPFormat
org::openscience::cdk::io::PMPReader
org::openscience::cdk::graph::rebond::Point
org::openscience::cdk::tools::diff::tree::Point2dDifference
org::openscience::cdk::tools::diff::tree::Point3dDifference
org::openscience::cdk::charges::Polarizability
org::openscience::cdk::Polymer
org::openscience::cdk::io::formats::POVRayFormat
org::openscience::cdk::io::formats::PQSChemFormat
org::openscience::cdk::math::Primes
org::openscience::cdk::validate::ProblemMarker
org::openscience::cdk::geometry::Projector
org::openscience::cdk::io::listener::PropertiesListener
org::openscience::cdk::tools::ProteinBuilderTool
org::openscience::cdk::protein::ProteinPocketFinder
org::openscience::cdk::qsar::descriptors::atomic::ProtonAffinityHOSEDescriptor
org::openscience::cdk::qsar::descriptors::atomic::ProtonTotalPartialChargeDescriptor
org::openscience::cdk::PseudoAtom
org::openscience::cdk::io::formats::PubChemASNFormat
org::openscience::cdk::io::formats::PubChemCompoundsXMLFormat
org::openscience::cdk::io::formats::PubChemCompoundXMLFormat
org::openscience::cdk::io::formats::PubChemFormat
org::openscience::cdk::io::formats::PubChemSubstancesASNFormat
org::openscience::cdk::io::formats::PubChemSubstancesXMLFormat
org::openscience::cdk::io::formats::PubChemSubstanceXMLFormat
org::openscience::cdk::io::pubchemxml::PubChemXMLHelper
org::openscience::cdk::io::formats::QChemFormat
org::openscience::cdk::io::cml::QSARConvention
org::openscience::cdk::libio::cml::QSARCustomizer
org::openscience::cdk::qsar::model::QSARModelException
org::openscience::cdk::math::Quaternion
org::openscience::cdk::isomorphism::matchers::QueryAtomContainer
org::openscience::cdk::isomorphism::matchers::QueryAtomContainerCreator
org::openscience::cdk::ringsearch::Queue
org::openscience::cdk::reaction::type::RadicalChargeSiteInitiationHReaction
org::openscience::cdk::reaction::type::RadicalChargeSiteInitiationReaction
org::openscience::cdk::reaction::type::RadicalSiteHrAlphaReaction
org::openscience::cdk::reaction::type::RadicalSiteHrBetaReaction
org::openscience::cdk::reaction::type::RadicalSiteHrDeltaReaction
org::openscience::cdk::reaction::type::RadicalSiteHrGammaReaction
org::openscience::cdk::reaction::type::RadicalSiteInitiationHReaction
org::openscience::cdk::reaction::type::RadicalSiteInitiationReaction
org::openscience::cdk::reaction::mechanism::RadicalSiteIonizationMechanism
org::openscience::cdk::reaction::mechanism::RadicalSiteRearrangementMechanism
org::openscience::cdk::reaction::type::RadicalSiteRrAlphaReaction
org::openscience::cdk::reaction::type::RadicalSiteRrBetaReaction
org::openscience::cdk::reaction::type::RadicalSiteRrDeltaReaction
org::openscience::cdk::reaction::type::RadicalSiteRrGammaReaction
org::openscience::cdk::io::random::RandomAccessReader
org::openscience::cdk::io::random::RandomAccessSDFReader
org::openscience::cdk::structgen::RandomGenerator
org::openscience::cdk::math::RandomNumbersTool
org::openscience::cdk::io::formats::RawCopyFormat
org::openscience::cdk::formula::rules::RDBERule
org::openscience::cdk::geometry::RDFCalculator
org::openscience::cdk::qsar::descriptors::atomic::RDFProtonDescriptor_G3R
org::openscience::cdk::qsar::descriptors::atomic::RDFProtonDescriptor_GDR
org::openscience::cdk::qsar::descriptors::atomic::RDFProtonDescriptor_GHR
org::openscience::cdk::qsar::descriptors::atomic::RDFProtonDescriptor_GHR_topol
org::openscience::cdk::qsar::descriptors::atomic::RDFProtonDescriptor_GSR
org::openscience::cdk::Reaction
org::openscience::cdk::reaction::ReactionChain
org::openscience::cdk::reaction::ReactionEngine
org::openscience::cdk::ReactionSet::ReactionIterator
org::openscience::cdk::tools::manipulator::ReactionManipulator
org::openscience::cdk::ReactionScheme
org::openscience::cdk::tools::manipulator::ReactionSchemeManipulator
org::openscience::cdk::ReactionSet
org::openscience::cdk::tools::manipulator::ReactionSetManipulator
org::openscience::cdk::reaction::ReactionSpecification
org::openscience::cdk::io::ReaderEvent
org::openscience::cdk::io::ReaderFactory
org::openscience::cdk::reaction::type::RearrangementAnionReaction
org::openscience::cdk::reaction::type::RearrangementCationReaction
org::openscience::cdk::reaction::mechanism::RearrangementChargeMechanism
org::openscience::cdk::reaction::type::RearrangementLonePairReaction
org::openscience::cdk::reaction::type::RearrangementRadicalReaction
org::openscience::cdk::graph::rebond::RebondTool
org::openscience::cdk::io::random::RecordReaderEvent
org::openscience::cdk::isomorphism::matchers::smarts::RecursiveSmartsAtom
org::openscience::cdk::reaction::mechanism::RemovingSEofBMechanism
org::openscience::cdk::reaction::mechanism::RemovingSEofNBMechanism
org::openscience::cdk::libio::md::Residue
org::openscience::cdk::isomorphism::mcss::RGraph
org::openscience::cdk::Ring
org::openscience::cdk::isomorphism::matchers::smarts::RingAtom
org::openscience::cdk::isomorphism::matchers::smarts::RingBond
org::openscience::cdk::isomorphism::matchers::smarts::RingIdentifierAtom
org::openscience::cdk::tools::manipulator::RingManipulator
org::openscience::cdk::isomorphism::matchers::smarts::RingMembershipAtom
org::openscience::cdk::ringsearch::RingPartitioner
org::openscience::cdk::layout::RingPlacer
org::openscience::cdk::RingSet
org::openscience::cdk::tools::manipulator::RingSetManipulator
org::openscience::cdk::tools::manipulator::RingSizeComparator
org::openscience::cdk::isomorphism::mcss::RMap
org::openscience::cdk::qsar::model::R2::RModel
org::openscience::cdk::qsar::model::R::RModel
org::openscience::cdk::isomorphism::mcss::RNode
org::openscience::cdk::qsar::descriptors::molecular::RotatableBondsCountDescriptor
org::openscience::cdk::io::RssWriter
org::openscience::cdk::qsar::descriptors::molecular::RuleOfFiveDescriptor
org::openscience::cdk::tools::SaturationChecker
org::openscience::cdk::io::formats::SDFFormat
org::openscience::cdk::io::SDFWriter
org::openscience::cdk::reaction::type::parameters::SetReactionCenter
org::openscience::cdk::reaction::type::SharingAnionReaction
org::openscience::cdk::reaction::type::SharingChargeDBReaction
org::openscience::cdk::reaction::type::SharingChargeSBReaction
org::openscience::cdk::reaction::mechanism::SharingElectronMechanism
org::openscience::cdk::reaction::type::SharingLonePairReaction
org::openscience::cdk::io::formats::ShelXFormat
org::openscience::cdk::io::ShelXReader
org::openscience::cdk::io::ShelXWriter
org::openscience::cdk::qsar::descriptors::atomic::SigmaElectronegativityDescriptor
org::openscience::cdk::math::qm::SimpleBasisSet
org::openscience::cdk::iupac::parser::SimpleCharStream
org::openscience::cdk::smiles::smarts::parser::SimpleCharStream
org::openscience::cdk::ringsearch::cyclebasis::SimpleCycle
org::openscience::cdk::ringsearch::cyclebasis::SimpleCycleBasis
org::openscience::cdk::smiles::smarts::parser::SimpleNode
org::openscience::cdk::SingleElectron
org::openscience::cdk::tools::diff::SingleElectronDiff
org::openscience::cdk::AtomContainer::SingleElectronIterator
org::openscience::cdk::structgen::SingleStructureRandomGenerator
org::openscience::cdk::isomorphism::matchers::smarts::SmallestRingAtom
org::openscience::cdk::smiles::smarts::parser::visitor::Smarts2MQLVisitor
org::openscience::cdk::isomorphism::matchers::smarts::SMARTSAtom
org::openscience::cdk::isomorphism::matchers::smarts::SMARTSBond
org::openscience::cdk::smiles::smarts::parser::visitor::SmartsDumpVisitor
org::openscience::cdk::io::formats::SMARTSFormat
org::openscience::cdk::smiles::smarts::parser::SMARTSParser
org::openscience::cdk::smiles::smarts::parser::SMARTSParserConstants
org::openscience::cdk::smiles::smarts::parser::SMARTSParserTokenManager
org::openscience::cdk::smiles::smarts::parser::SMARTSParserTreeConstants
org::openscience::cdk::smiles::smarts::parser::SMARTSParserVisitor
org::openscience::cdk::smiles::smarts::SMARTSQueryTool
org::openscience::cdk::smiles::smarts::parser::visitor::SmartsQueryVisitor
org::openscience::cdk::io::formats::SMILESFIXFormat
org::openscience::cdk::io::formats::SMILESFormat
org::openscience::cdk::smiles::SmilesGenerator
org::openscience::cdk::smiles::SmilesParser
org::openscience::cdk::io::SMILESReader
org::openscience::cdk::tools::SmilesValencyChecker
org::openscience::cdk::io::SMILESWriter
org::openscience::cdk::modeling::forcefield::SmoothingFunctions
org::openscience::cdk::graph::SpanningTree
org::openscience::cdk::io::formats::SpartanFormat
org::openscience::cdk::ringsearch::SSSRFinder
org::openscience::cdk::charges::StabilizationCharges
org::openscience::cdk::qsar::descriptors::atomic::StabilizationPlusChargeDescriptor
org::openscience::cdk::fingerprint::StandardSubstructureSets
org::openscience::cdk::modeling::forcefield::SteepestDescentsMethod
org::openscience::cdk::isomorphism::matchers::smarts::StereoBond
org::openscience::cdk::Strand
org::openscience::cdk::modeling::forcefield::StretchBendInteractions
org::openscience::cdk::tools::diff::tree::StringDifference
org::openscience::cdk::io::setting::StringIOSetting
org::openscience::cdk::atomtype::StructGenAtomTypeGuesser
org::openscience::cdk::atomtype::StructGenMatcher
org::openscience::cdk::layout::StructureDiagramGenerator
org::openscience::cdk::tools::StructureResonanceGenerator
org::openscience::cdk::fingerprint::SubstructureFingerprinter
org::openscience::cdk::io::formats::SVGFormat
org::openscience::cdk::controller::SwingEventRelay
org::openscience::cdk::io::listener::SwingGUIListener
org::openscience::cdk::controller::SwingMouseEventRelay
org::openscience::cdk::tools::SwissArmyKnife
org::openscience::cdk::atomtype::SybylAtomTypeMatcher
org::openscience::cdk::io::formats::SybylDescriptorFormat
org::openscience::cdk::isomorphism::matchers::SymbolAndChargeQueryAtom
org::openscience::cdk::isomorphism::matchers::SymbolChargeIDQueryAtom
org::openscience::cdk::isomorphism::matchers::SymbolQueryAtom
org::openscience::cdk::config::Symbols
org::openscience::cdk::isomorphism::matchers::SymbolSetQueryAtom
org::openscience::cdk::qsar::descriptors::protein::TaeAminoAcidDescriptor
org::openscience::cdk::similarity::Tanimoto
org::openscience::cdk::reaction::mechanism::TautomerizationMechanism
org::openscience::cdk::reaction::type::TautomerizationReaction
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::annotations::TestClass
org::openscience::cdk::annotations::TestMethod
org::openscience::cdk::io::listener::TextGUIListener
org::openscience::cdk::io::formats::TinkerMM2Format
org::openscience::cdk::io::formats::TinkerXYZFormat
org::openscience::cdk::iupac::parser::Token
org::openscience::cdk::smiles::smarts::parser::Token
org::openscience::cdk::iupac::parser::TokenMgrError
org::openscience::cdk::smiles::smarts::parser::TokenMgrError
org::openscience::cdk::formula::rules::ToleranceRangeRule
org::openscience::cdk::graph::matrix::TopologicalMatrix
org::openscience::cdk::modeling::forcefield::Torsions
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::qsar::descriptors::molecular::TPSADescriptor
org::openscience::cdk::tools::HOSECodeGenerator::TreeNode
org::openscience::cdk::tools::HOSECodeGenerator::TreeNodeComparator
org::openscience::cdk::geometry::surface::Triangle
org::openscience::cdk::graph::rebond::Bspt::Tuple
org::openscience::cdk::graph::rebond::RebondTool::TupleAtom
org::openscience::cdk::io::formats::TurboMoleFormat
org::openscience::cdk::config::TXTBasedAtomTypeConfigurator
org::openscience::cdk::controller::UndoAdapter
org::openscience::cdk::io::formats::UniChemXYZFormat
org::openscience::cdk::isomorphism::UniversalIsomorphismTester
org::openscience::cdk::exception::UnsupportedChemObjectException
org::openscience::cdk::io::PCCompoundASNReader::URN
org::openscience::cdk::qsar::model::R::V2M
org::openscience::cdk::qsar::descriptors::molecular::VAdjMaDescriptor
org::openscience::cdk::validate::ValidationReport
org::openscience::cdk::validate::ValidationTest
org::openscience::cdk::validate::ValidatorEngine
org::openscience::cdk::modeling::forcefield::VanDerWaalsInteractions
org::openscience::cdk::io::formats::VASPFormat
org::openscience::cdk::io::VASPReader
org::openscience::cdk::qsar::descriptors::atomic::VdWRadiusDescriptor
org::openscience::cdk::math::Vector
org::openscience::cdk::Vibration
org::openscience::cdk::structgen::VicinitySampler
org::openscience::cdk::io::formats::ViewmolFormat
org::openscience::cdk::qsar::descriptors::molecular::WeightDescriptor
org::openscience::cdk::qsar::descriptors::molecular::WeightedPathDescriptor
org::openscience::cdk::qsar::descriptors::molecular::WHIMDescriptor
org::openscience::cdk::qsar::descriptors::molecular::WienerNumbersDescriptor
org::openscience::cdk::io::WriterFactory
org::openscience::cdk::io::formats::XEDFormat
org::openscience::cdk::qsar::descriptors::molecular::XLogPDescriptor
org::openscience::cdk::io::formats::XYZFormat
org::openscience::cdk::io::XYZReader
org::openscience::cdk::io::XYZWriter
org::openscience::cdk::io::formats::YasaraFormat
org::openscience::cdk::qsar::descriptors::molecular::ZagrebIndexDescriptor
org::openscience::cdk::io::formats::ZindoFormat
org::openscience::cdk::io::formats::ZMatrixFormat
org::openscience::cdk::io::ZMatrixReader
org::openscience::cdk::geometry::ZMatrixTools

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