Here is a list of all documented class members with links to the class documentation for each member:

- s -

• sample() : org::openscience::cdk::structgen::VicinitySampler
• saturate() : org::openscience::cdk::tools::SaturationChecker , org::openscience::cdk::tools::SmilesValencyChecker , org::openscience::cdk::tools::ValencyHybridChecker , org::openscience::cdk::tools::ValencyChecker , org::openscience::cdk::tools::SmilesValencyChecker , org::openscience::cdk::tools::ValencyChecker
• saturateByIncreasingBondOrder() : org::openscience::cdk::tools::SmilesValencyChecker , org::openscience::cdk::tools::ValencyChecker , org::openscience::cdk::tools::ValencyHybridChecker
• SaveAction() : org::openscience::cdk::applications::jchempaint::action::SaveAction
• SaveAsAction() : org::openscience::cdk::applications::jchempaint::action::SaveAsAction
• scaleAndCenterMolecule() : org::openscience::cdk::applications::jchempaint::JChemPaintPanel
• scaledAtomicMasses() : org::openscience::cdk::qsar::descriptors::molecular::AutocorrelationDescriptorMass
• scaleMolecule() : org::openscience::cdk::geometry::GeometryTools , org::openscience::cdk::geometry::GeometryToolsInternalCoordinates
• scalesCoordinatesUnits() : org::openscience::cdk::io::GamessReader
• SCI : org::openscience::cdk::tools::FormatStringBuffer
• sdf : org::openscience::cdk::applications::jchempaint::io::JCPFileFilter
• search() : org::openscience::cdk::isomorphism::UniversalIsomorphismTester
• searchAndPlaceBranches() : org::openscience::cdk::modeling::builder3d::ModelBuilder3D
• selectAtom() : org::openscience::cdk::ringsearch::AllRingsFinder
• selectButton : org::openscience::cdk::applications::jchempaint::JChemPaintPanel
• selectNearestChemObjectIfNoneSelected() : org::openscience::cdk::controller::AbstractController2D
• selectRectangularArea() : org::openscience::cdk::controller::AbstractController2D
• serialVersionUID : org::openscience::cdk::AminoAcid , org::openscience::cdk::debug::DebugMolecule , org::openscience::cdk::nonotify::NNAtom , org::openscience::cdk::nonotify::NNAtomContainer , org::openscience::cdk::debug::DebugMoleculeSet , org::openscience::cdk::nonotify::NNAtomContainerSet , org::openscience::cdk::nonotify::NNAtomParity , org::openscience::cdk::Association , org::openscience::cdk::debug::DebugMonomer , org::openscience::cdk::nonotify::NNAtomType , org::openscience::cdk::nonotify::NNBioPolymer , org::openscience::cdk::debug::DebugPDBAtom , org::openscience::cdk::nonotify::NNBond , org::openscience::cdk::nonotify::NNChemFile , org::openscience::cdk::Atom , org::openscience::cdk::debug::DebugPDBMonomer , org::openscience::cdk::nonotify::NNChemModel , org::openscience::cdk::nonotify::NNChemObject , org::openscience::cdk::debug::DebugPDBPolymer , org::openscience::cdk::nonotify::NNChemSequence , org::openscience::cdk::nonotify::NNCrystal , org::openscience::cdk::AtomContainer , org::openscience::cdk::debug::DebugPDBStructure , org::openscience::cdk::nonotify::NNElectronContainer , org::openscience::cdk::nonotify::NNElement , org::openscience::cdk::debug::DebugPolymer , org::openscience::cdk::nonotify::NNIsotope , org::openscience::cdk::nonotify::NNLonePair , org::openscience::cdk::AtomContainerSet , org::openscience::cdk::debug::DebugPseudoAtom , org::openscience::cdk::nonotify::NNMapping , org::openscience::cdk::nonotify::NNMolecule , org::openscience::cdk::debug::DebugReaction , org::openscience::cdk::nonotify::NNMoleculeSet , org::openscience::cdk::nonotify::NNMonomer , org::openscience::cdk::AtomParity , org::openscience::cdk::debug::DebugReactionSet , org::openscience::cdk::nonotify::NNPDBAtom , org::openscience::cdk::nonotify::NNPDBMonomer , org::openscience::cdk::debug::DebugRing , org::openscience::cdk::nonotify::NNPDBPolymer , org::openscience::cdk::nonotify::NNPDBStructure , org::openscience::cdk::AtomType , org::openscience::cdk::debug::DebugRingSet , org::openscience::cdk::nonotify::NNPolymer , org::openscience::cdk::nonotify::NNPseudoAtom , org::openscience::cdk::debug::DebugSingleElectron , org::openscience::cdk::nonotify::NNReaction , org::openscience::cdk::nonotify::NNReactionSet , org::openscience::cdk::BioPolymer , org::openscience::cdk::debug::DebugStrand , org::openscience::cdk::nonotify::NNRing , org::openscience::cdk::nonotify::NNRingSet , org::openscience::cdk::ElectronContainer , org::openscience::cdk::nonotify::NNSingleElectron , org::openscience::cdk::nonotify::NNStrand , org::openscience::cdk::Bond , org::openscience::cdk::Element , org::openscience::cdk::PeriodicTableElement , org::openscience::cdk::Polymer , org::openscience::cdk::EnzymeResidueLocator , org::openscience::cdk::protein::data::PDBAtom , org::openscience::cdk::protein::data::PDBMonomer , org::openscience::cdk::ChemFile , org::openscience::cdk::Fragment , org::openscience::cdk::protein::data::PDBPolymer , org::openscience::cdk::protein::data::PDBStrand , org::openscience::cdk::FragmentAtom , org::openscience::cdk::protein::data::PDBStructure , org::openscience::cdk::PseudoAtom , org::openscience::cdk::ChemModel , org::openscience::cdk::isomorphism::matchers::InverseSymbolSetQueryAtom , org::openscience::cdk::Reaction , org::openscience::cdk::ReactionSet , org::openscience::cdk::isomorphism::matchers::OrderQueryBond , org::openscience::cdk::Ring , org::openscience::cdk::RingSet , org::openscience::cdk::ChemObject , org::openscience::cdk::isomorphism::matchers::QueryAtomContainer , org::openscience::cdk::SingleElectron , org::openscience::cdk::Strand , org::openscience::cdk::isomorphism::matchers::smarts::AliphaticAtom , org::openscience::cdk::ChemSequence , org::openscience::cdk::isomorphism::matchers::smarts::AliphaticSymbolAtom , org::openscience::cdk::isomorphism::matchers::smarts::AnyAtom , org::openscience::cdk::Crystal , org::openscience::cdk::isomorphism::matchers::smarts::AnyOrderQueryBond , org::openscience::cdk::isomorphism::matchers::smarts::AromaticAtom , org::openscience::cdk::debug::DebugAminoAcid , org::openscience::cdk::isomorphism::matchers::smarts::AromaticQueryBond , org::openscience::cdk::isomorphism::matchers::smarts::AromaticSymbolAtom , org::openscience::cdk::debug::DebugAtom , org::openscience::cdk::isomorphism::matchers::smarts::AtomicNumberAtom , org::openscience::cdk::isomorphism::matchers::smarts::ConnectionCountAtom , org::openscience::cdk::debug::DebugAtomContainer , org::openscience::cdk::isomorphism::matchers::smarts::DegreeAtom , org::openscience::cdk::isomorphism::matchers::smarts::ExplicitConnectionAtom , org::openscience::cdk::debug::DebugAtomContainerSet , org::openscience::cdk::isomorphism::matchers::smarts::FormalChargeAtom , org::openscience::cdk::isomorphism::matchers::smarts::ImplicitHCountAtom , org::openscience::cdk::debug::DebugAtomParity , org::openscience::cdk::isomorphism::matchers::smarts::LogicalOperatorAtom , org::openscience::cdk::isomorphism::matchers::smarts::LogicalOperatorBond , org::openscience::cdk::debug::DebugAtomType , org::openscience::cdk::isomorphism::matchers::smarts::OrderQueryBond , org::openscience::cdk::isomorphism::matchers::smarts::RecursiveSmartsAtom , org::openscience::cdk::debug::DebugBioPolymer , org::openscience::cdk::isomorphism::matchers::smarts::RingAtom , org::openscience::cdk::isomorphism::matchers::smarts::RingBond , org::openscience::cdk::debug::DebugBond , org::openscience::cdk::isomorphism::matchers::smarts::RingIdentifierAtom , org::openscience::cdk::isomorphism::matchers::smarts::RingMembershipAtom , org::openscience::cdk::debug::DebugChemFile , org::openscience::cdk::isomorphism::matchers::smarts::SmallestRingAtom , org::openscience::cdk::isomorphism::matchers::smarts::SMARTSBond , org::openscience::cdk::debug::DebugChemModel , org::openscience::cdk::isomorphism::matchers::smarts::StereoBond , org::openscience::cdk::isomorphism::matchers::smarts::TotalConnectionAtom , org::openscience::cdk::debug::DebugChemObject , org::openscience::cdk::isomorphism::matchers::smarts::TotalHCountAtom , org::openscience::cdk::isomorphism::matchers::smarts::TotalValencyAtom , org::openscience::cdk::debug::DebugChemSequence , org::openscience::cdk::isomorphism::matchers::SymbolAndChargeQueryAtom , org::openscience::cdk::isomorphism::matchers::SymbolChargeIDQueryAtom , org::openscience::cdk::debug::DebugCrystal , org::openscience::cdk::isomorphism::matchers::SymbolQueryAtom , org::openscience::cdk::isomorphism::matchers::SymbolSetQueryAtom , org::openscience::cdk::debug::DebugElectronContainer , org::openscience::cdk::Isotope , org::openscience::cdk::libio::md::ChargeGroup , org::openscience::cdk::debug::DebugElement , org::openscience::cdk::libio::md::MDMolecule , org::openscience::cdk::libio::md::Residue , org::openscience::cdk::debug::DebugIsotope , org::openscience::cdk::LonePair , org::openscience::cdk::Mapping , org::openscience::cdk::debug::DebugLonePair , org::openscience::cdk::Molecule , org::openscience::cdk::MoleculeSet , org::openscience::cdk::debug::DebugMapping , org::openscience::cdk::Monomer , org::openscience::cdk::nonotify::NNAminoAcid
• set2ndOrderErrorApproximateGradientMMFF94SumEA() : org::openscience::cdk::modeling::forcefield::AngleBending
• set2ndOrderErrorApproximateGradientMMFF94SumEBA() : org::openscience::cdk::modeling::forcefield::StretchBendInteractions
• set2ndOrderErrorApproximateGradientMMFF94SumET() : org::openscience::cdk::modeling::forcefield::Torsions
• set2ndOrderErrorApproximateGradientMMFF94SumEvdW() : org::openscience::cdk::modeling::forcefield::VanDerWaalsInteractions
• set2ndOrderErrorApproximateHessianMMFF94SumEA() : org::openscience::cdk::modeling::forcefield::AngleBending
• set2ndOrderErrorApproximateHessianMMFF94SumEB() : org::openscience::cdk::modeling::forcefield::BondStretching
• set2ndOrderErrorApproximateHessianMMFF94SumET() : org::openscience::cdk::modeling::forcefield::Torsions
• set5thOrderApproximateGradientMMFF94SumET() : org::openscience::cdk::modeling::forcefield::Torsions
• set5thOrderErrorApproximateGradientMMFF94SumEA() : org::openscience::cdk::modeling::forcefield::AngleBending
• set5thOrderErrorApproximateGradientMMFF94SumEBA() : org::openscience::cdk::modeling::forcefield::StretchBendInteractions
• set5thOrderErrorApproximateGradientMMFF94SumEvdW() : org::openscience::cdk::modeling::forcefield::VanDerWaalsInteractions
• setA() : org::openscience::cdk::Crystal , org::openscience::cdk::debug::DebugCrystal , org::openscience::cdk::interfaces::ICrystal
• setAbout() : org::openscience::cdk::io::RssWriter
• setActiveCenters() : org::openscience::cdk::reaction::type::BreakingBondReaction , org::openscience::cdk::reaction::type::CarbonylEliminationReaction , org::openscience::cdk::reaction::type::CleavageBondMultiReaction , org::openscience::cdk::reaction::type::CleavageBondReaction , org::openscience::cdk::reaction::type::DisplacementChargeFromAcceptorReaction , org::openscience::cdk::reaction::type::DisplacementChargeFromDonorReaction , org::openscience::cdk::reaction::type::ElectronImpactNBEReaction , org::openscience::cdk::reaction::type::ElectronImpactPDBReaction , org::openscience::cdk::reaction::type::HydrogenRearrangementDeltaReaction , org::openscience::cdk::reaction::type::HydrogenRearrangementGammaReaction , org::openscience::cdk::reaction::type::HyperconjugationReaction , org::openscience::cdk::reaction::type::RadicalSiteInitiationHReaction , org::openscience::cdk::reaction::type::RadicalSiteInitiationReaction , org::openscience::cdk::reaction::type::RearrangementAnion1Reaction , org::openscience::cdk::reaction::type::RearrangementAnion2Reaction , org::openscience::cdk::reaction::type::RearrangementAnion3Reaction , org::openscience::cdk::reaction::type::RearrangementCation1Reaction , org::openscience::cdk::reaction::type::RearrangementCation2Reaction , org::openscience::cdk::reaction::type::RearrangementCation3Reaction , org::openscience::cdk::reaction::type::RearrangementRadical1Reaction , org::openscience::cdk::reaction::type::RearrangementRadical2Reaction , org::openscience::cdk::reaction::type::RearrangementRadical3Reaction
• setAllMap() : org::openscience::cdk::isomorphism::mcss::RGraph
• setAllStructure() : org::openscience::cdk::isomorphism::mcss::RGraph
• setAltLoc() : org::openscience::cdk::debug::DebugPDBAtom , org::openscience::cdk::interfaces::IPDBAtom , org::openscience::cdk::protein::data::PDBAtom
• setAngle() : org::openscience::cdk::modeling::builder3d::MM2BasedParameterSetReader , org::openscience::cdk::modeling::builder3d::MMFF94BasedParameterSetReader
• setAngle3() : org::openscience::cdk::modeling::builder3d::MM2BasedParameterSetReader
• setAngle4() : org::openscience::cdk::modeling::builder3d::MM2BasedParameterSetReader
• setAngleBending2ndOrderErrorApproximateGradient() : org::openscience::cdk::modeling::forcefield::AngleBending
• setAngleBending2ndOrderErrorApproximateHessian() : org::openscience::cdk::modeling::forcefield::AngleBending
• setAngleBendingFirstDerivative() : org::openscience::cdk::modeling::forcefield::AngleBending
• setAngleBendingSecondDerivative() : org::openscience::cdk::modeling::forcefield::AngleBending
• setArrayValue() : org::openscience::cdk::graph::invariant::GIMatrix
• setAtom() : org::openscience::cdk::AtomContainer , org::openscience::cdk::Bond , org::openscience::cdk::debug::DebugAminoAcid , org::openscience::cdk::debug::DebugAtomContainer , org::openscience::cdk::debug::DebugBioPolymer , org::openscience::cdk::debug::DebugBond , org::openscience::cdk::debug::DebugCrystal , org::openscience::cdk::debug::DebugLonePair , org::openscience::cdk::debug::DebugMolecule , org::openscience::cdk::debug::DebugMonomer , org::openscience::cdk::debug::DebugPolymer , org::openscience::cdk::debug::DebugRing , org::openscience::cdk::debug::DebugSingleElectron , org::openscience::cdk::debug::DebugStrand , org::openscience::cdk::interfaces::IAtomContainer , org::openscience::cdk::interfaces::IBond , org::openscience::cdk::interfaces::ILonePair , org::openscience::cdk::interfaces::ISingleElectron , org::openscience::cdk::LonePair , org::openscience::cdk::modeling::builder3d::ForceFieldConfigurator , org::openscience::cdk::SingleElectron
• setAtomAt() : org::openscience::cdk::Association
• setAtomAtomMappingLineColor() : org::openscience::cdk::renderer::Renderer2DModel
• setAtomCheckRadius() : org::openscience::cdk::protein::ProteinPocketFinder
• setAtomColorer() : org::openscience::cdk::renderer::Renderer2DModel
• setAtomContainer() : org::openscience::cdk::applications::swing::MoleculeViewer2D , org::openscience::cdk::applications::swing::MoleculeViewer2DPanel , org::openscience::cdk::structgen::SingleStructureRandomGenerator , org::openscience::cdk::structgen::stochastic::PartialFilledStructureMerger
• setAtomDistance() : org::openscience::cdk::modeling::forcefield::VanDerWaalsInteractions
• setAtomicNumber() : org::openscience::cdk::debug::DebugAtomType , org::openscience::cdk::debug::DebugElement , org::openscience::cdk::debug::DebugIsotope , org::openscience::cdk::debug::DebugPseudoAtom , org::openscience::cdk::Element , org::openscience::cdk::interfaces::IElement , org::openscience::cdk::debug::DebugAtom
• setAtomProperties() : org::openscience::cdk::tools::manipulator::AtomContainerManipulator , org::openscience::cdk::tools::manipulator::ChemModelManipulator
• setAtomRadius() : org::openscience::cdk::renderer::Renderer2DModel
• setAtoms() : org::openscience::cdk::Association , org::openscience::cdk::AtomContainer , org::openscience::cdk::Bond , org::openscience::cdk::debug::DebugAminoAcid , org::openscience::cdk::debug::DebugAtomContainer , org::openscience::cdk::debug::DebugBioPolymer , org::openscience::cdk::debug::DebugBond , org::openscience::cdk::debug::DebugCrystal , org::openscience::cdk::debug::DebugMolecule , org::openscience::cdk::debug::DebugMonomer , org::openscience::cdk::debug::DebugPolymer , org::openscience::cdk::debug::DebugRing , org::openscience::cdk::debug::DebugStrand , org::openscience::cdk::interfaces::IAtomContainer , org::openscience::cdk::interfaces::IBond , org::openscience::cdk::isomorphism::matchers::OrderQueryBond , org::openscience::cdk::isomorphism::matchers::smarts::LogicalOperatorBond
• setAtomsDistancesFirstOrderDerivative() : org::openscience::cdk::modeling::forcefield::VanDerWaalsInteractions
• setAtomsToPlace() : org::openscience::cdk::modeling::builder3d::ModelBuilder3D
• setAtomsToUnPlaced() : org::openscience::cdk::modeling::builder3d::ModelBuilder3D
• setAtomsToUnVisited() : org::openscience::cdk::modeling::builder3d::ModelBuilder3D
• setAtomTypeData() : org::openscience::cdk::modeling::builder3d::MMFF94BasedParameterSetReader
• setAtomTypeName() : org::openscience::cdk::AtomType , org::openscience::cdk::debug::DebugAtom , org::openscience::cdk::debug::DebugAtomType , org::openscience::cdk::debug::DebugPseudoAtom , org::openscience::cdk::interfaces::IAtomType
• setAtomTypes() : org::openscience::cdk::modeling::builder3d::ForceFieldConfigurator , org::openscience::cdk::modeling::builder3d::MM2BasedParameterSetReader , org::openscience::cdk::modeling::builder3d::MMFF94BasedParameterSetReader
• setAuthor() : org::openscience::cdk::applications::jchempaint::JChemPaintModel
• setAutoUpdateImplicitHydrogens() : org::openscience::cdk::controller::Controller2DModel
• setB() : org::openscience::cdk::Crystal , org::openscience::cdk::debug::DebugCrystal , org::openscience::cdk::interfaces::ICrystal
• setBackColor() : org::openscience::cdk::renderer::Renderer2DModel
• setBackgroundDimension() : org::openscience::cdk::renderer::Renderer2DModel
• setBaseTable() : org::openscience::cdk::isomorphism::IsomorphismTester
• setBasis() : org::openscience::cdk::math::qm::GaussiansBasis
• setBond() : org::openscience::cdk::modeling::builder3d::MM2BasedParameterSetReader , org::openscience::cdk::modeling::builder3d::MMFF94BasedParameterSetReader
• setBond3() : org::openscience::cdk::modeling::builder3d::MM2BasedParameterSetReader
• setBond4() : org::openscience::cdk::modeling::builder3d::MM2BasedParameterSetReader
• setBondDistance() : org::openscience::cdk::renderer::Renderer2DModel
• setBondLength() : org::openscience::cdk::layout::StructureDiagramGenerator , org::openscience::cdk::layout::TemplateHandler , org::openscience::cdk::renderer::Renderer2DModel
• setBondLengthsFirstDerivative() : org::openscience::cdk::modeling::forcefield::BondStretching
• setBondLengthsSecondDerivative() : org::openscience::cdk::modeling::forcefield::BondStretching , org::openscience::cdk::modeling::forcefield::VanDerWaalsInteractions
• setBondOrderSum() : org::openscience::cdk::AtomType , org::openscience::cdk::debug::DebugAtom , org::openscience::cdk::debug::DebugAtomType , org::openscience::cdk::debug::DebugPseudoAtom , org::openscience::cdk::interfaces::IAtomType
• setBondPointerLength() : org::openscience::cdk::controller::Controller2DModel
• setBonds() : org::openscience::cdk::AtomContainer , org::openscience::cdk::interfaces::IAtomContainer
• setBondWidth() : org::openscience::cdk::renderer::Renderer2DModel
• setBranchAtom() : org::openscience::cdk::modeling::builder3d::ModelBuilder3D
• setC() : org::openscience::cdk::Crystal , org::openscience::cdk::debug::DebugCrystal , org::openscience::cdk::interfaces::ICrystal
• setC2dm() : org::openscience::cdk::applications::undoredo::JCPUndoRedoHandler
• setCASid() : org::openscience::cdk::PeriodicTableElement
• setChainID() : org::openscience::cdk::debug::DebugPDBAtom , org::openscience::cdk::debug::DebugPDBMonomer , org::openscience::cdk::interfaces::IPDBAtom , org::openscience::cdk::interfaces::IPDBMonomer , org::openscience::cdk::protein::data::PDBAtom , org::openscience::cdk::protein::data::PDBMonomer
• setChangeListeners() : org::openscience::cdk::applications::jchempaint::JChemPaintModel
• setCharge() : org::openscience::cdk::Atom , org::openscience::cdk::debug::DebugAtom , org::openscience::cdk::debug::DebugPseudoAtom , org::openscience::cdk::interfaces::IAtom , org::openscience::cdk::modeling::builder3d::MM2BasedParameterSetReader , org::openscience::cdk::PseudoAtom
• setCharges() : org::openscience::cdk::charges::AtomTypeCharges
• setChemicalSerie() : org::openscience::cdk::PeriodicTableElement
• setChemModel() : org::openscience::cdk::controller::Controller2D
• setChemObject() : org::openscience::cdk::applications::jchempaint::dialogs::EditDictRefs , org::openscience::cdk::applications::swing::DictRefEditorTableModel
• setChiCatHydrogen() : org::openscience::cdk::charges::GasteigerMarsiliPartialCharges
• setClassName() : org::openscience::cdk::dict::Entry
• setClipboardContent() : org::openscience::cdk::renderer::Renderer2DModel
• setCoefficients() : org::openscience::cdk::math::qm::Orbitals , org::openscience::cdk::qsar::model::R::LinearRegressionModelFit
• setColorHash() : org::openscience::cdk::renderer::Renderer2DModel
• setColumn() : org::openscience::cdk::graph::invariant::GIMatrix
• setCompareTable() : org::openscience::cdk::isomorphism::IsomorphismTester
• setConjugateGradientDirection() : org::openscience::cdk::modeling::forcefield::ConjugateGradientMethod
• setController2DModel() : org::openscience::cdk::controller::AbstractController2D
• setControllerModel() : org::openscience::cdk::applications::jchempaint::JChemPaintModel
• setControlViewer() : org::openscience::cdk::applications::swing::PeriodicTablePanel
• setConvergenceParametersForCGM() : org::openscience::cdk::modeling::forcefield::GeometricMinimizer
• setConvergenceParametersForNRM() : org::openscience::cdk::modeling::forcefield::GeometricMinimizer
• setConvergenceParametersForSDM() : org::openscience::cdk::modeling::forcefield::GeometricMinimizer
• setCountElectrons() : org::openscience::cdk::math::qm::Orbitals
• setCovalentRadius() : org::openscience::cdk::AtomType , org::openscience::cdk::debug::DebugAtom , org::openscience::cdk::debug::DebugAtomType , org::openscience::cdk::debug::DebugPseudoAtom , org::openscience::cdk::interfaces::IAtomType
• setCreator() : org::openscience::cdk::io::RssWriter
• setCreatormap() : org::openscience::cdk::io::RssWriter
• setCrystal() : org::openscience::cdk::ChemModel , org::openscience::cdk::debug::DebugChemModel , org::openscience::cdk::interfaces::IChemModel
• setCTerminus() : org::openscience::cdk::AminoAcid
• setCurrentOpenFileFilter() : org::openscience::cdk::applications::jchempaint::JChemPaintPanel
• setCurrentSaveFileFilter() : org::openscience::cdk::applications::jchempaint::JChemPaintPanel
• setCurrentWorkDirectory() : org::openscience::cdk::applications::jchempaint::JChemPaintPanel
• setDatemap() : org::openscience::cdk::io::RssWriter
• setDefaultElementSymbol() : org::openscience::cdk::controller::Controller2DModel
• setDefaultStrBnd() : org::openscience::cdk::modeling::builder3d::MMFF94BasedParameterSetReader
• setDeltarijAndDeltarkj() : org::openscience::cdk::modeling::forcefield::StretchBendInteractions
• setDeltav() : org::openscience::cdk::modeling::forcefield::AngleBending
• setDescription() : org::openscience::cdk::io::RssWriter
• setDescriptorInstances() : org::openscience::cdk::qsar::DescriptorEngine
• setDescriptorSpecifications() : org::openscience::cdk::qsar::DescriptorEngine
• setDF() : org::openscience::cdk::qsar::model::R::LinearRegressionModelPredict
• setdfResidual() : org::openscience::cdk::qsar::model::R::LinearRegressionModelFit
• setDim() : org::openscience::cdk::tools::GridGenerator
• setDimension() : org::openscience::cdk::tools::GridGenerator
• setDipole() : org::openscience::cdk::modeling::builder3d::MM2BasedParameterSetReader
• setDipole3() : org::openscience::cdk::modeling::builder3d::MM2BasedParameterSetReader
• setDirection() : org::openscience::cdk::debug::DebugReaction , org::openscience::cdk::interfaces::IReaction , org::openscience::cdk::modeling::forcefield::ConjugateGradientMethod , org::openscience::cdk::Reaction
• setDisplayMode() : org::openscience::cdk::renderer::GraphRendererModel
• setDocumentProperty() : org::openscience::cdk::io::iterator::event::EventCMLHandler
• setDrawMode() : org::openscience::cdk::controller::Controller2DModel
• setDrawNumbers() : org::openscience::cdk::renderer::Renderer2DModel
• setEditBus() : org::openscience::cdk::applications::plugin::ICDKPlugin
• setElectronCount() : org::openscience::cdk::debug::DebugBond , org::openscience::cdk::debug::DebugElectronContainer , org::openscience::cdk::debug::DebugLonePair , org::openscience::cdk::debug::DebugSingleElectron , org::openscience::cdk::ElectronContainer , org::openscience::cdk::interfaces::IElectronContainer
• setEmbedded() : org::openscience::cdk::applications::jchempaint::JChemPaintPanel
• setEndChainID() : org::openscience::cdk::debug::DebugPDBStructure , org::openscience::cdk::interfaces::IPDBStructure , org::openscience::cdk::protein::data::PDBStructure
• setEndInsertionCode() : org::openscience::cdk::debug::DebugPDBStructure , org::openscience::cdk::interfaces::IPDBStructure , org::openscience::cdk::protein::data::PDBStructure
• setEndSequenceNumber() : org::openscience::cdk::debug::DebugPDBStructure , org::openscience::cdk::interfaces::IPDBStructure , org::openscience::cdk::protein::data::PDBStructure
• setEnergyGradient() : org::openscience::cdk::modeling::forcefield::IPotentialFunction , org::openscience::cdk::modeling::forcefield::MMFF94EnergyFunction
• setEnergyHessian() : org::openscience::cdk::modeling::forcefield::IPotentialFunction , org::openscience::cdk::modeling::forcefield::MMFF94EnergyFunction
• setExactMass() : org::openscience::cdk::debug::DebugAtom , org::openscience::cdk::debug::DebugAtomType , org::openscience::cdk::debug::DebugIsotope , org::openscience::cdk::debug::DebugPseudoAtom , org::openscience::cdk::interfaces::IIsotope , org::openscience::cdk::Isotope , org::openscience::cdk::PseudoAtom
• setExtendGrid() : org::openscience::cdk::tools::GridGenerator
• setExtension() : org::openscience::cdk::isomorphism::mcss::RNode
• setExternalHighlightColor() : org::openscience::cdk::renderer::Renderer2DModel
• setExternalSelectedPart() : org::openscience::cdk::renderer::Renderer2DModel
• setFirstGraphSize() : org::openscience::cdk::isomorphism::mcss::RGraph
• setFitted() : org::openscience::cdk::qsar::model::R::CNNClassificationModelFit , org::openscience::cdk::qsar::model::R::CNNRegressionModelFit , org::openscience::cdk::qsar::model::R::LinearRegressionModelFit
• setFlag() : org::openscience::cdk::ChemObject , 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::DebugChemSequence , org::openscience::cdk::debug::DebugCrystal , org::openscience::cdk::debug::DebugElectronContainer , org::openscience::cdk::debug::DebugElement , org::openscience::cdk::debug::DebugIsotope , org::openscience::cdk::debug::DebugLonePair , org::openscience::cdk::debug::DebugMapping , org::openscience::cdk::debug::DebugMolecule , org::openscience::cdk::debug::DebugMoleculeSet , org::openscience::cdk::debug::DebugMonomer , org::openscience::cdk::debug::DebugPolymer , org::openscience::cdk::debug::DebugPseudoAtom , org::openscience::cdk::debug::DebugReaction , org::openscience::cdk::debug::DebugReactionSet , org::openscience::cdk::debug::DebugRing , org::openscience::cdk::debug::DebugSingleElectron , org::openscience::cdk::debug::DebugStrand , org::openscience::cdk::interfaces::IChemObject
• setFlags() : org::openscience::cdk::ChemObject , 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::DebugChemSequence , org::openscience::cdk::debug::DebugCrystal , org::openscience::cdk::debug::DebugElectronContainer , org::openscience::cdk::debug::DebugElement , org::openscience::cdk::debug::DebugIsotope , org::openscience::cdk::debug::DebugLonePair , org::openscience::cdk::debug::DebugMapping , org::openscience::cdk::debug::DebugMolecule , org::openscience::cdk::debug::DebugMoleculeSet , org::openscience::cdk::debug::DebugMonomer , org::openscience::cdk::debug::DebugPolymer , org::openscience::cdk::debug::DebugPseudoAtom , org::openscience::cdk::debug::DebugReaction , org::openscience::cdk::debug::DebugReactionSet , org::openscience::cdk::debug::DebugRing , org::openscience::cdk::debug::DebugSingleElectron , org::openscience::cdk::debug::DebugStrand , org::openscience::cdk::interfaces::IChemObject
• setFletcherReeves_uk() : org::openscience::cdk::modeling::forcefield::ConjugateGradientMethod
• setForbidden() : org::openscience::cdk::isomorphism::mcss::RNode
• setForceField() : org::openscience::cdk::modeling::builder3d::ModelBuilder3D
• setForceFieldConfigurator() : org::openscience::cdk::modeling::builder3d::ForceFieldConfigurator
• setForceFieldDefinitions() : org::openscience::cdk::modeling::builder3d::MM2BasedParameterSetReader
• setForeColor() : org::openscience::cdk::renderer::Renderer2DModel
• setFormalCharge() : org::openscience::cdk::AtomType , org::openscience::cdk::debug::DebugAtom , org::openscience::cdk::debug::DebugAtomType , org::openscience::cdk::debug::DebugPseudoAtom , org::openscience::cdk::interfaces::IAtomType , org::openscience::cdk::PseudoAtom
• setFormalNeighbourCount() : org::openscience::cdk::debug::DebugAtomType , org::openscience::cdk::debug::DebugPseudoAtom , org::openscience::cdk::interfaces::IAtomType , org::openscience::cdk::AtomType , org::openscience::cdk::debug::DebugAtom
• setFractionalPoint3d() : org::openscience::cdk::Atom , org::openscience::cdk::debug::DebugAtom , org::openscience::cdk::debug::DebugPseudoAtom , org::openscience::cdk::interfaces::IAtom
• setFrame() : org::openscience::cdk::applications::swing::MoleculeViewer2D
• setFreeValences() : org::openscience::cdk::Fragment
• setFunctionMMFF94SumEBA() : org::openscience::cdk::modeling::forcefield::StretchBendInteractions
• setFunctionMMFF94SumEvdW() : org::openscience::cdk::modeling::forcefield::VanDerWaalsInteractions
• setGendate() : org::openscience::cdk::applications::jchempaint::JChemPaintModel
• setGradientMMFF94SumEA() : org::openscience::cdk::modeling::forcefield::AngleBending
• setGradientMMFF94SumEB() : org::openscience::cdk::modeling::forcefield::BondStretching
• setGradientMMFF94SumEBA() : org::openscience::cdk::modeling::forcefield::StretchBendInteractions
• setGradientMMFF94SumEQ() : org::openscience::cdk::modeling::forcefield::ElectrostaticInteractions
• setGradientMMFF94SumET() : org::openscience::cdk::modeling::forcefield::Torsions
• setGradientMMFF94SumEvdW() : org::openscience::cdk::modeling::forcefield::VanDerWaalsInteractions
• setGrid() : org::openscience::cdk::protein::ProteinPocketFinder , org::openscience::cdk::tools::GridGenerator
• setGroup() : org::openscience::cdk::PeriodicTableElement
• setHessian() : org::openscience::cdk::qsar::model::R::CNNClassificationModelFit , org::openscience::cdk::qsar::model::R::CNNRegressionModelFit
• setHessianMMFF94SumEA() : org::openscience::cdk::modeling::forcefield::AngleBending
• setHessianMMFF94SumEB() : org::openscience::cdk::modeling::forcefield::BondStretching
• setHessianMMFF94SumEBA() : org::openscience::cdk::modeling::forcefield::StretchBendInteractions
• setHessianMMFF94SumEQ() : org::openscience::cdk::modeling::forcefield::ElectrostaticInteractions
• setHessianMMFF94SumET() : org::openscience::cdk::modeling::forcefield::Torsions
• setHessianMMFF94SumEvdW() : org::openscience::cdk::modeling::forcefield::VanDerWaalsInteractions
• setHighlightedAtom() : org::openscience::cdk::renderer::Renderer2DModel
• setHighlightedBond() : org::openscience::cdk::renderer::Renderer2DModel
• setHighlightRadius() : org::openscience::cdk::renderer::Renderer2DModel
• setHoverOverColor() : org::openscience::cdk::renderer::Renderer2DModel
• setHybridization() : org::openscience::cdk::AtomType , org::openscience::cdk::debug::DebugAtom , org::openscience::cdk::debug::DebugAtomType , org::openscience::cdk::debug::DebugPseudoAtom , org::openscience::cdk::interfaces::IAtomType
• setHydrogenCount() : org::openscience::cdk::Atom , org::openscience::cdk::debug::DebugAtom , org::openscience::cdk::debug::DebugPseudoAtom , org::openscience::cdk::interfaces::IAtom , org::openscience::cdk::PseudoAtom
• setICode() : org::openscience::cdk::debug::DebugPDBAtom , org::openscience::cdk::debug::DebugPDBMonomer , org::openscience::cdk::interfaces::IPDBAtom , org::openscience::cdk::interfaces::IPDBMonomer , org::openscience::cdk::protein::data::PDBAtom , org::openscience::cdk::protein::data::PDBMonomer
• setID() : org::openscience::cdk::ChemObject , 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::DebugChemSequence , org::openscience::cdk::debug::DebugCrystal , org::openscience::cdk::debug::DebugElectronContainer , org::openscience::cdk::debug::DebugElement , org::openscience::cdk::debug::DebugIsotope , org::openscience::cdk::debug::DebugLonePair , org::openscience::cdk::debug::DebugMapping , org::openscience::cdk::debug::DebugMolecule , org::openscience::cdk::debug::DebugMoleculeSet , org::openscience::cdk::debug::DebugMonomer , org::openscience::cdk::debug::DebugPolymer , org::openscience::cdk::debug::DebugPseudoAtom , org::openscience::cdk::debug::DebugReaction , org::openscience::cdk::debug::DebugReactionSet , org::openscience::cdk::debug::DebugRing , org::openscience::cdk::debug::DebugSingleElectron , org::openscience::cdk::debug::DebugStrand , org::openscience::cdk::interfaces::IChemObject , org::openscience::cdk::tools::IDCreator , org::openscience::cdk::tools::StructureResonanceGenerator
• setId1() : org::openscience::cdk::isomorphism::mcss::RMap
• setId2() : org::openscience::cdk::isomorphism::mcss::RMap
• setImagelink() : org::openscience::cdk::io::RssWriter
• setImaginaryPart() : org::openscience::cdk::math::Complex
• setInchimap() : org::openscience::cdk::io::RssWriter
• setInitialCharges() : org::openscience::cdk::charges::AtomTypeCharges
• setInputFileToConvert() : org::openscience::cdk::libio::openbabel::OpenBabelConvert
• setInputReader() : org::openscience::cdk::io::listener::TextGUIListener
• setInputStream() : org::openscience::cdk::config::CDKBasedAtomTypeConfigurator , org::openscience::cdk::config::IAtomTypeConfigurator , org::openscience::cdk::config::TXTBasedAtomTypeConfigurator , org::openscience::cdk::modeling::builder3d::ForceFieldConfigurator , org::openscience::cdk::modeling::builder3d::MM2BasedParameterSetReader , org::openscience::cdk::modeling::builder3d::MMFF94BasedParameterSetReader
• setInternuclearSeparation() : org::openscience::cdk::modeling::forcefield::ElectrostaticInteractions
• setInternuclearSeparationFirstOrderDerivative() : org::openscience::cdk::modeling::forcefield::ElectrostaticInteractions
• setInternuclearSeparationSecondDerivative() : org::openscience::cdk::modeling::forcefield::ElectrostaticInteractions
• setIsAlreadyAFile() : org::openscience::cdk::applications::jchempaint::JChemPaintPanel
• setIsOpenedByViewer() : org::openscience::cdk::applications::jchempaint::JChemPaintPanel
• setIsPopupAction() : org::openscience::cdk::applications::jchempaint::action::JCPAction
• setJChemPaintModel() : org::openscience::cdk::applications::jchempaint::applet::AppletCanvas , org::openscience::cdk::applications::jchempaint::JChemPaintPanel
• setJChemPaintPanel() : org::openscience::cdk::applications::jchempaint::action::JCPAction
• setLabel() : org::openscience::cdk::debug::DebugPseudoAtom , org::openscience::cdk::interfaces::IPseudoAtom , org::openscience::cdk::PseudoAtom
• setLastAction() : org::openscience::cdk::applications::jchempaint::JChemPaintModel
• setLastEventReason() : org::openscience::cdk::applications::jchempaint::JChemPaintEditorPanel
• setLastOpenedFile() : org::openscience::cdk::applications::jchempaint::JChemPaintPanel
• setLastSavedFile() : org::openscience::cdk::applications::jchempaint::JChemPaintPanel
• setLatticeConstant() : org::openscience::cdk::protein::ProteinPocketFinder , org::openscience::cdk::tools::GridGenerator
• setLength() : org::openscience::cdk::iupac::parser::AttachedGroup
• setLine() : org::openscience::cdk::graph::invariant::GIMatrix
• setLineStep() : org::openscience::cdk::modeling::forcefield::LineSearch
• setLink() : org::openscience::cdk::io::RssWriter
• setLinkageRadius() : org::openscience::cdk::protein::ProteinPocketFinder
• setLinkmap() : org::openscience::cdk::io::RssWriter
• setLocations() : org::openscience::cdk::iupac::parser::AttachedGroup
• setLower() : org::openscience::cdk::qsar::model::R::LinearRegressionModelPredict
• SetMainCyclic() : org::openscience::cdk::iupac::parser::NomParser
• setMassNumber() : org::openscience::cdk::debug::DebugAtom , org::openscience::cdk::debug::DebugAtomType , org::openscience::cdk::debug::DebugIsotope , org::openscience::cdk::debug::DebugPseudoAtom , org::openscience::cdk::interfaces::IIsotope , org::openscience::cdk::Isotope
• setMaxBondOrder() : org::openscience::cdk::AtomType , org::openscience::cdk::debug::DebugAtom , org::openscience::cdk::debug::DebugAtomType , org::openscience::cdk::debug::DebugPseudoAtom , org::openscience::cdk::interfaces::IAtomType
• setMaxGasteigerDamp() : org::openscience::cdk::charges::GasteigerMarsiliPartialCharges
• setMaxGasteigerIters() : org::openscience::cdk::charges::GasteigerMarsiliPartialCharges , org::openscience::cdk::charges::GasteigerPEPEPartialCharges
• setMaxIteration() : org::openscience::cdk::isomorphism::mcss::RGraph
• setMaxResoStruc() : org::openscience::cdk::charges::GasteigerPEPEPartialCharges
• setMinPSCluster() : org::openscience::cdk::protein::ProteinPocketFinder
• setMinPSPocket() : org::openscience::cdk::protein::ProteinPocketFinder
• setMM2Parameters() : org::openscience::cdk::modeling::builder3d::ForceFieldConfigurator
• setMMFF94AngleBendingParameters() : org::openscience::cdk::modeling::forcefield::AngleBending
• setMMFF94BondStretchingParameters() : org::openscience::cdk::modeling::forcefield::BondStretching
• setMMFF94ElectrostaticParameters() : org::openscience::cdk::modeling::forcefield::ElectrostaticInteractions
• setMMFF94StretchBendParameters() : org::openscience::cdk::modeling::forcefield::StretchBendInteractions
• setMMFF94Tables() : org::openscience::cdk::modeling::forcefield::GeometricMinimizer
• setMMFF94TorsionsParameters() : org::openscience::cdk::modeling::forcefield::Torsions
• setMMFF94VanDerWaalsParameters() : org::openscience::cdk::modeling::forcefield::VanDerWaalsInteractions
• setMolecule() : org::openscience::cdk::layout::AtomPlacer , org::openscience::cdk::layout::StructureDiagramGenerator , org::openscience::cdk::structgen::RandomGenerator
• setMolecules() : org::openscience::cdk::debug::DebugMoleculeSet , org::openscience::cdk::interfaces::IMoleculeSet
• setMoleculeSet() : org::openscience::cdk::ChemModel , org::openscience::cdk::debug::DebugChemModel , org::openscience::cdk::interfaces::IChemModel
• setMolFileWithReplace() : org::openscience::cdk::applications::jchempaint::applet::JChemPaintAbstractApplet
• setMolViewDim() : org::openscience::cdk::applications::swing::MoleculeListPanel , org::openscience::cdk::applications::swing::MoleculeListViewer
• setMonomerName() : org::openscience::cdk::debug::DebugAminoAcid , org::openscience::cdk::debug::DebugMonomer , org::openscience::cdk::interfaces::IMonomer , org::openscience::cdk::Monomer
• setMonomerType() : org::openscience::cdk::debug::DebugAminoAcid , org::openscience::cdk::debug::DebugMonomer , org::openscience::cdk::interfaces::IMonomer , org::openscience::cdk::Monomer
• setMovingAllowed() : org::openscience::cdk::controller::Controller2DModel
• setMultiMap() : org::openscience::cdk::io::RssWriter
• setMultiplier() : org::openscience::cdk::AtomContainerSet , org::openscience::cdk::debug::DebugAtomContainerSet , org::openscience::cdk::debug::DebugMoleculeSet , org::openscience::cdk::interfaces::IAtomContainerSet
• setMultipliers() : org::openscience::cdk::AtomContainerSet , org::openscience::cdk::debug::DebugAtomContainerSet , org::openscience::cdk::debug::DebugMoleculeSet , org::openscience::cdk::interfaces::IAtomContainerSet
• setName() : org::openscience::cdk::interfaces::IPDBAtom , org::openscience::cdk::debug::DebugPDBAtom , org::openscience::cdk::iupac::parser::AttachedGroup , org::openscience::cdk::PeriodicTableElement , org::openscience::cdk::protein::data::PDBAtom
• setNaturalAbundance() : org::openscience::cdk::interfaces::IIsotope , org::openscience::cdk::debug::DebugAtom , org::openscience::cdk::debug::DebugAtomType , org::openscience::cdk::debug::DebugIsotope , org::openscience::cdk::debug::DebugPseudoAtom , org::openscience::cdk::Isotope
• setNotEmbedded() : org::openscience::cdk::applications::jchempaint::JChemPaintPanel
• setNotification() : org::openscience::cdk::ChemObject , org::openscience::cdk::debug::DebugChemObject , org::openscience::cdk::interfaces::IChemObject
• setNTerminus() : org::openscience::cdk::AminoAcid
• setNumOfConnection() : org::openscience::cdk::isomorphism::matchers::smarts::ExplicitConnectionAtom
• setObjectProperty() : org::openscience::cdk::io::iterator::event::EventCMLHandler
• setOccupancy() : org::openscience::cdk::debug::DebugPDBAtom , org::openscience::cdk::interfaces::IPDBAtom , org::openscience::cdk::protein::data::PDBAtom
• setOfMolecules : org::openscience::cdk::ChemModel
• setOfReactions : org::openscience::cdk::ChemModel
• setOpBend() : org::openscience::cdk::modeling::builder3d::MM2BasedParameterSetReader , org::openscience::cdk::modeling::builder3d::MMFF94BasedParameterSetReader
• setOptions() : org::openscience::cdk::qsar::model::weka::IWekaModel
• setOrder() : org::openscience::cdk::Bond , org::openscience::cdk::debug::DebugBond , org::openscience::cdk::interfaces::IBond
• setOrder2ndErrorApproximateEnergyGradient() : org::openscience::cdk::modeling::forcefield::MMFF94EnergyFunction
• setOrder5thErrorApproximateEnergyGradient() : org::openscience::cdk::modeling::forcefield::MMFF94EnergyFunction
• setOutputWriter() : org::openscience::cdk::io::listener::PropertiesListener , org::openscience::cdk::io::listener::TextGUIListener
• setParameters() : org::openscience::cdk::reaction::type::RearrangementRadical3Reaction , org::openscience::cdk::reaction::type::RearrangementAnion1Reaction , org::openscience::cdk::reaction::type::DisplacementChargeFromDonorReaction , org::openscience::cdk::reaction::type::HydrogenRearrangementGammaReaction , org::openscience::cdk::qsar::model::R2::LinearRegressionModel , org::openscience::cdk::qsar::descriptors::molecular::XLogPDescriptor , org::openscience::cdk::qsar::model::R::CNNRegressionModel , org::openscience::cdk::qsar::descriptors::molecular::TPSADescriptor , org::openscience::cdk::qsar::descriptors::molecular::LongestAliphaticChainDescriptor , org::openscience::cdk::qsar::descriptors::molecular::PetitjeanShapeIndexDescriptor , org::openscience::cdk::qsar::descriptors::molecular::GravitationalIndexDescriptor , org::openscience::cdk::qsar::descriptors::molecular::ChiPathDescriptor , org::openscience::cdk::qsar::descriptors::molecular::AtomCountDescriptor , org::openscience::cdk::qsar::descriptors::bond::BondSigmaElectronegativityDescriptor , org::openscience::cdk::qsar::descriptors::molecular::AminoAcidCountDescriptor , org::openscience::cdk::qsar::descriptors::atomic::RDFProtonDescriptor_GHR_topol , org::openscience::cdk::qsar::descriptors::atomic::PartialTChargeMMFF94Descriptor , org::openscience::cdk::qsar::descriptors::atomic::ProtonTotalPartialChargeDescriptor , org::openscience::cdk::qsar::descriptors::atomic::EffectiveAtomPolarizabilityDescriptor , org::openscience::cdk::modeling::builder3d::ForceFieldConfigurator , org::openscience::cdk::qsar::descriptors::atomic::AtomValenceDescriptor , org::openscience::cdk::qsar::descriptors::atomic::AtomDegreeDescriptor , org::openscience::cdk::qsar::descriptors::atomic::AtomHybridizationDescriptor , org::openscience::cdk::qsar::descriptors::atomic::AtomHybridizationVSEPRDescriptor , org::openscience::cdk::qsar::descriptors::atomic::BondsToAtomDescriptor , org::openscience::cdk::qsar::descriptors::atomic::CovalentRadiusDescriptor , org::openscience::cdk::qsar::descriptors::atomic::DistanceToAtomDescriptor , org::openscience::cdk::qsar::descriptors::atomic::InductiveAtomicHardnessDescriptor , org::openscience::cdk::qsar::descriptors::atomic::InductiveAtomicSoftnessDescriptor , org::openscience::cdk::qsar::descriptors::atomic::IPAtomicDescriptor , org::openscience::cdk::qsar::descriptors::atomic::IsProtonInAromaticSystemDescriptor , org::openscience::cdk::qsar::descriptors::atomic::IsProtonInConjugatedPiSystemDescriptor , org::openscience::cdk::qsar::descriptors::atomic::PartialPiChargeDescriptor , org::openscience::cdk::qsar::descriptors::atomic::PartialSigmaChargeDescriptor , org::openscience::cdk::qsar::descriptors::atomic::PartialTChargePEOEDescriptor , org::openscience::cdk::qsar::descriptors::atomic::PeriodicTablePositionDescriptor , org::openscience::cdk::qsar::descriptors::atomic::PiElectronegativityDescriptor , 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_GSR , org::openscience::cdk::qsar::descriptors::atomic::SigmaElectronegativityDescriptor , org::openscience::cdk::qsar::descriptors::atomic::VdWRadiusDescriptor , org::openscience::cdk::qsar::descriptors::atompair::PiContactDetectionDescriptor , 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::IPBondDescriptor , org::openscience::cdk::qsar::descriptors::bond::ResonancePositiveChargeDescriptor , org::openscience::cdk::qsar::descriptors::molecular::ALOGP , org::openscience::cdk::qsar::descriptors::molecular::APolDescriptor , org::openscience::cdk::qsar::descriptors::molecular::AromaticAtomsCountDescriptor , org::openscience::cdk::qsar::descriptors::molecular::AromaticBondsCountDescriptor , org::openscience::cdk::qsar::descriptors::molecular::AutocorrelationDescriptorCharge , org::openscience::cdk::qsar::descriptors::molecular::AutocorrelationDescriptorMass , org::openscience::cdk::qsar::descriptors::molecular::AutocorrelationDescriptorPolarizability , org::openscience::cdk::qsar::descriptors::molecular::BCUTDescriptor , org::openscience::cdk::qsar::descriptors::molecular::BondCountDescriptor , org::openscience::cdk::qsar::descriptors::molecular::BPolDescriptor , org::openscience::cdk::qsar::descriptors::molecular::CarbonConnectivityOrderOneDescriptor , org::openscience::cdk::qsar::descriptors::molecular::CarbonConnectivityOrderZeroDescriptor , org::openscience::cdk::qsar::descriptors::molecular::ChiChainDescriptor , org::openscience::cdk::qsar::descriptors::molecular::ChiClusterDescriptor , org::openscience::cdk::qsar::descriptors::molecular::ChiPathClusterDescriptor , org::openscience::cdk::qsar::descriptors::molecular::CPSADescriptor , org::openscience::cdk::qsar::descriptors::molecular::EccentricConnectivityIndexDescriptor , org::openscience::cdk::qsar::descriptors::molecular::FragmentComplexityDescriptor , org::openscience::cdk::qsar::descriptors::molecular::HBondAcceptorCountDescriptor , org::openscience::cdk::qsar::descriptors::molecular::HBondDonorCountDescriptor , org::openscience::cdk::qsar::descriptors::molecular::IPMolecularDescriptor , org::openscience::cdk::qsar::descriptors::molecular::KappaShapeIndicesDescriptor , org::openscience::cdk::qsar::descriptors::molecular::LargestChainDescriptor , org::openscience::cdk::qsar::descriptors::molecular::LargestPiSystemDescriptor , org::openscience::cdk::qsar::descriptors::molecular::LengthOverBreadthDescriptor , org::openscience::cdk::qsar::descriptors::molecular::MDEDescriptor , org::openscience::cdk::qsar::descriptors::molecular::MomentOfInertiaDescriptor , org::openscience::cdk::qsar::descriptors::molecular::PetitjeanNumberDescriptor , org::openscience::cdk::qsar::descriptors::molecular::RotatableBondsCountDescriptor , org::openscience::cdk::qsar::descriptors::molecular::RuleOfFiveDescriptor , org::openscience::cdk::qsar::descriptors::molecular::TaeAminoAcidDescriptor , org::openscience::cdk::qsar::descriptors::molecular::VAdjMaDescriptor , org::openscience::cdk::qsar::descriptors::molecular::ValenceCarbonConnectivityOrderOneDescriptor , org::openscience::cdk::qsar::descriptors::molecular::ValenceCarbonConnectivityOrderZeroDescriptor , 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::qsar::descriptors::molecular::ZagrebIndexDescriptor , org::openscience::cdk::qsar::IDescriptor , org::openscience::cdk::qsar::model::R::CNNClassificationModel , org::openscience::cdk::qsar::model::R::LinearRegressionModel , org::openscience::cdk::qsar::model::R::PLSRegressionModel , org::openscience::cdk::qsar::model::R2::CNNRegressionModel , org::openscience::cdk::qsar::model::weka::IWekaModel , org::openscience::cdk::reaction::IReactionProcess , org::openscience::cdk::reaction::type::BreakingBondReaction , org::openscience::cdk::reaction::type::CarbonylEliminationReaction , org::openscience::cdk::reaction::type::CleavageBondMultiReaction , org::openscience::cdk::reaction::type::CleavageBondReaction , org::openscience::cdk::reaction::type::DisplacementChargeFromAcceptorReaction , org::openscience::cdk::reaction::type::ElectronImpactNBEReaction , org::openscience::cdk::reaction::type::ElectronImpactPDBReaction , org::openscience::cdk::reaction::type::HydrogenRearrangementDeltaReaction , org::openscience::cdk::reaction::type::HyperconjugationReaction , org::openscience::cdk::reaction::type::RadicalSiteInitiationHReaction , org::openscience::cdk::reaction::type::RadicalSiteInitiationReaction , org::openscience::cdk::reaction::type::RearrangementAnion2Reaction , org::openscience::cdk::reaction::type::RearrangementAnion3Reaction , org::openscience::cdk::reaction::type::RearrangementCation1Reaction , org::openscience::cdk::reaction::type::RearrangementCation2Reaction , org::openscience::cdk::reaction::type::RearrangementCation3Reaction , org::openscience::cdk::reaction::type::RearrangementRadical1Reaction , org::openscience::cdk::reaction::type::RearrangementRadical2Reaction
• setParametersCDK() : org::openscience::cdk::qsar::model::weka::IWekaModel
• setParameterSet() : org::openscience::cdk::modeling::builder3d::AtomTetrahedralLigandPlacer3D
• setPATH() : org::openscience::cdk::libio::openbabel::OpenBabelConvert
• setPeriod() : org::openscience::cdk::PeriodicTableElement
• setPhase() : org::openscience::cdk::PeriodicTableElement
• setPhi() : org::openscience::cdk::modeling::forcefield::Torsions
• setPiAtom() : org::openscience::cdk::modeling::builder3d::MM2BasedParameterSetReader
• setPiBond() : org::openscience::cdk::modeling::builder3d::MM2BasedParameterSetReader
• setPocketSize() : org::openscience::cdk::protein::ProteinPocketFinder
• setPoint2d() : org::openscience::cdk::Atom , org::openscience::cdk::debug::DebugAtom , org::openscience::cdk::debug::DebugPseudoAtom , org::openscience::cdk::interfaces::IAtom
• setPoint3d() : org::openscience::cdk::debug::DebugPseudoAtom , org::openscience::cdk::Atom , org::openscience::cdk::debug::DebugAtom , org::openscience::cdk::interfaces::IAtom
• setPointerVectorEnd() : org::openscience::cdk::renderer::Renderer2DModel
• setPointerVectorStart() : org::openscience::cdk::renderer::Renderer2DModel
• setPolankRibierePlus_uk() : org::openscience::cdk::modeling::forcefield::ConjugateGradientMethod
• setPopupMenu() : org::openscience::cdk::controller::PopupController2D
• setPredicted() : org::openscience::cdk::qsar::model::R::CNNRegressionModelPredict , org::openscience::cdk::qsar::model::R::LinearRegressionModelPredict
• setPredictedRaw() : org::openscience::cdk::qsar::model::R::CNNClassificationModelPredict
• setProductCoefficient() : org::openscience::cdk::debug::DebugReaction , org::openscience::cdk::interfaces::IReaction , org::openscience::cdk::Reaction
• setProductCoefficients() : org::openscience::cdk::debug::DebugReaction , org::openscience::cdk::interfaces::IReaction , org::openscience::cdk::Reaction
• setProducts() : org::openscience::cdk::debug::DebugReaction , org::openscience::cdk::Reaction , org::openscience::cdk::interfaces::IReaction
• setProperties() : org::openscience::cdk::ChemObject , org::openscience::cdk::debug::DebugAminoAcid , org::openscience::cdk::debug::DebugAtomContainer , org::openscience::cdk::debug::DebugAtomContainerSet , org::openscience::cdk::debug::DebugAtomParity , 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::DebugChemSequence , org::openscience::cdk::debug::DebugCrystal , org::openscience::cdk::debug::DebugElement , org::openscience::cdk::debug::DebugIsotope , org::openscience::cdk::debug::DebugLonePair , org::openscience::cdk::debug::DebugMolecule , org::openscience::cdk::debug::DebugMoleculeSet , org::openscience::cdk::debug::DebugMonomer , org::openscience::cdk::debug::DebugPseudoAtom , org::openscience::cdk::debug::DebugReaction , org::openscience::cdk::debug::DebugReactionSet , org::openscience::cdk::debug::DebugRing , org::openscience::cdk::debug::DebugSingleElectron , org::openscience::cdk::debug::DebugStrand , org::openscience::cdk::interfaces::IChemObject , org::openscience::cdk::debug::DebugPolymer , org::openscience::cdk::debug::DebugMapping , org::openscience::cdk::debug::DebugElectronContainer , org::openscience::cdk::debug::DebugAtomType , org::openscience::cdk::debug::DebugAtom
• setProperty() : org::openscience::cdk::debug::DebugStrand , org::openscience::cdk::debug::DebugPseudoAtom , org::openscience::cdk::debug::DebugReaction , org::openscience::cdk::debug::DebugAminoAcid , org::openscience::cdk::debug::DebugAtom , org::openscience::cdk::debug::DebugAtomContainer , org::openscience::cdk::debug::DebugAtomParity , org::openscience::cdk::debug::DebugAtomType , org::openscience::cdk::debug::DebugBioPolymer , org::openscience::cdk::debug::DebugElement , org::openscience::cdk::debug::DebugMoleculeSet , org::openscience::cdk::debug::DebugChemFile , org::openscience::cdk::debug::DebugChemModel , org::openscience::cdk::debug::DebugMolecule , org::openscience::cdk::debug::DebugChemObject , org::openscience::cdk::debug::DebugCrystal , org::openscience::cdk::debug::DebugElectronContainer , org::openscience::cdk::debug::DebugPolymer , org::openscience::cdk::debug::DebugIsotope , org::openscience::cdk::debug::DebugLonePair , org::openscience::cdk::debug::DebugMapping , org::openscience::cdk::debug::DebugMonomer , org::openscience::cdk::debug::DebugChemSequence , org::openscience::cdk::debug::DebugReactionSet , org::openscience::cdk::debug::DebugRing , org::openscience::cdk::debug::DebugSingleElectron , org::openscience::cdk::interfaces::IChemObject , org::openscience::cdk::debug::DebugBond , org::openscience::cdk::debug::DebugAtomContainerSet , org::openscience::cdk::ChemObject
• setPropertyDirectory() : org::openscience::cdk::applications::plugin::ICDKPlugin
• setProtein() : org::openscience::cdk::protein::ProteinPocketFinder
• setProteinInterior() : org::openscience::cdk::protein::ProteinPocketFinder
• setPublisher() : org::openscience::cdk::io::RssWriter
• setQuery() : org::openscience::cdk::internet::WWMMatrixReader , org::openscience::cdk::internet::DADMLReader
• setRandom() : org::openscience::cdk::math::RandomNumbersTool
• setRandomSeed() : org::openscience::cdk::math::RandomNumbersTool
• setRank() : org::openscience::cdk::qsar::model::R::LinearRegressionModelFit
• setRAtom() : org::openscience::cdk::protein::ProteinPocketFinder
• setRawContent() : org::openscience::cdk::dict::Entry
• setReactantCoefficient() : org::openscience::cdk::Reaction , org::openscience::cdk::interfaces::IReaction , org::openscience::cdk::debug::DebugReaction
• setReactantCoefficients() : org::openscience::cdk::Reaction , org::openscience::cdk::interfaces::IReaction , org::openscience::cdk::debug::DebugReaction
• setReactants() : org::openscience::cdk::Reaction , org::openscience::cdk::debug::DebugReaction , org::openscience::cdk::interfaces::IReaction
• setReactionSet() : org::openscience::cdk::debug::DebugChemModel , org::openscience::cdk::interfaces::IChemModel , org::openscience::cdk::ChemModel
• setReader() : org::openscience::cdk::io::CIFReader , org::openscience::cdk::io::HINReader , org::openscience::cdk::io::SMILESReader , org::openscience::cdk::io::Gaussian98Reader , org::openscience::cdk::io::MDLRXNV3000Reader , org::openscience::cdk::io::MDLRXNReader , org::openscience::cdk::io::MACiEReader , org::openscience::cdk::io::SMILESReader , org::openscience::cdk::io::PMPReader , org::openscience::cdk::io::Mol2Reader , org::openscience::cdk::io::ZMatrixReader , org::openscience::cdk::io::PCCompoundASNReader , org::openscience::cdk::io::VASPReader , org::openscience::cdk::io::ShelXReader , org::openscience::cdk::io::PDBReader , org::openscience::cdk::io::INChIPlainTextReader , org::openscience::cdk::io::MACiEReader , org::openscience::cdk::io::MDLRXNV3000Reader , org::openscience::cdk::io::MDLV2000Reader , org::openscience::cdk::io::MDLRXNV2000Reader , org::openscience::cdk::io::MDLReader , org::openscience::cdk::io::INChIReader , org::openscience::cdk::io::HINReader , org::openscience::cdk::io::IChemObjectReader , org::openscience::cdk::io::GhemicalMMReader , org::openscience::cdk::io::Gaussian03Reader , org::openscience::cdk::io::CTXReader , org::openscience::cdk::io::CIFReader , org::openscience::cdk::io::CMLReader , org::openscience::cdk::io::XYZReader , org::openscience::cdk::io::INChIPlainTextReader , org::openscience::cdk::io::PCCompoundASNReader , org::openscience::cdk::io::GamessReader , org::openscience::cdk::io::CMLReader , org::openscience::cdk::io::CrystClustReader , org::openscience::cdk::io::CTXReader , org::openscience::cdk::io::Gaussian03Reader , org::openscience::cdk::io::Gaussian98Reader , org::openscience::cdk::io::GhemicalMMReader , org::openscience::cdk::io::CrystClustReader , org::openscience::cdk::io::IChemObjectReader , org::openscience::cdk::io::INChIReader , org::openscience::cdk::io::MDLReader , org::openscience::cdk::io::MDLRXNReader , org::openscience::cdk::io::MDLRXNV2000Reader , org::openscience::cdk::io::MDLV2000Reader , org::openscience::cdk::io::MDLV3000Reader , org::openscience::cdk::io::Mol2Reader , org::openscience::cdk::io::PDBReader , org::openscience::cdk::io::PMPReader , org::openscience::cdk::io::ShelXReader , org::openscience::cdk::io::VASPReader , org::openscience::cdk::io::XYZReader , org::openscience::cdk::io::ZMatrixReader
• setRealPart() : org::openscience::cdk::math::Complex
• setRecord() : org::openscience::cdk::debug::DebugPDBAtom , org::openscience::cdk::interfaces::IPDBAtom , org::openscience::cdk::protein::data::PDBAtom
• setRenderer() : org::openscience::cdk::applications::jchempaint::applet::AppletCanvas
• setRenderer2DModel() : org::openscience::cdk::renderer::ISimpleRenderer2D , org::openscience::cdk::applications::swing::MoleculeViewer2DPanel , org::openscience::cdk::applications::swing::MoleculeViewer2D , org::openscience::cdk::renderer::AbstractRenderer2D
• setRendererModel() : org::openscience::cdk::applications::jchempaint::JChemPaintModel
• setResiduals() : org::openscience::cdk::qsar::model::R::CNNRegressionModelFit , org::openscience::cdk::qsar::model::R::LinearRegressionModelFit , org::openscience::cdk::qsar::model::R::CNNClassificationModelFit
• setResidualScale() : org::openscience::cdk::qsar::model::R::LinearRegressionModelPredict
• setResName() : org::openscience::cdk::protein::data::PDBAtom , org::openscience::cdk::interfaces::IPDBAtom , org::openscience::cdk::debug::DebugPDBAtom
• setResSeq() : org::openscience::cdk::interfaces::IPDBMonomer , org::openscience::cdk::protein::data::PDBAtom , org::openscience::cdk::interfaces::IPDBAtom , org::openscience::cdk::protein::data::PDBMonomer , org::openscience::cdk::debug::DebugPDBAtom
• setRingFinder() : org::openscience::cdk::smiles::SmilesGenerator
• setRingFlags() : org::openscience::cdk::aromaticity::HueckelAromaticityDetector
• setRingPointerLength() : org::openscience::cdk::controller::Controller2DModel
• setRings() : org::openscience::cdk::smiles::SmilesGenerator
• setRingSet() : org::openscience::cdk::debug::DebugChemModel , org::openscience::cdk::interfaces::IChemModel , org::openscience::cdk::ChemModel
• setRingSize() : org::openscience::cdk::controller::Controller2DModel
• setRMap() : org::openscience::cdk::isomorphism::mcss::RNode
• setRSolvent() : org::openscience::cdk::protein::ProteinPocketFinder
• setScaleFactor() : org::openscience::cdk::renderer::Renderer2DModel
• setSdFields() : org::openscience::cdk::io::MDLWriter
• setSecondGraphSize() : org::openscience::cdk::isomorphism::mcss::RGraph
• setSEFit() : org::openscience::cdk::qsar::model::R::LinearRegressionModelPredict
• setSegID() : org::openscience::cdk::interfaces::IPDBAtom , org::openscience::cdk::protein::data::PDBAtom , org::openscience::cdk::debug::DebugPDBAtom
• setSelectedElement() : org::openscience::cdk::applications::swing::PeriodicTablePanel
• setSelectedPart() : org::openscience::cdk::renderer::Renderer2DModel
• setSelectedPartColor() : org::openscience::cdk::renderer::Renderer2DModel
• setSelectRect() : org::openscience::cdk::renderer::Renderer2DModel
• setSerial() : org::openscience::cdk::debug::DebugPDBAtom , org::openscience::cdk::interfaces::IPDBAtom , org::openscience::cdk::protein::data::PDBAtom
• setSetting() : org::openscience::cdk::io::setting::IntegerIOSetting , org::openscience::cdk::io::setting::StringIOSetting , org::openscience::cdk::io::setting::IOSetting , org::openscience::cdk::io::setting::OptionIOSetting , org::openscience::cdk::io::setting::BooleanIOSetting , org::openscience::cdk::io::setting::OptionIOSetting
• setShowAtomAtomMapping() : org::openscience::cdk::renderer::Renderer2DModel
• setShowInsertTextField() : org::openscience::cdk::applications::jchempaint::JChemPaintEditorPanel
• setShowMenuBar() : org::openscience::cdk::applications::jchempaint::JChemPaintEditorPanel
• setShowStatusBar() : org::openscience::cdk::applications::jchempaint::JChemPaintEditorPanel
• setShowToolBar() : org::openscience::cdk::applications::jchempaint::JChemPaintEditorPanel
• setShowTooltip() : org::openscience::cdk::renderer::Renderer2DModel
• setSk() : org::openscience::cdk::modeling::forcefield::SteepestDescentsMethod
• setSmoothingFunction() : org::openscience::cdk::modeling::forcefield::SmoothingFunctions
• setSnapAngle() : org::openscience::cdk::controller::Controller2DModel
• setSnapCartesian() : org::openscience::cdk::controller::Controller2DModel
• setSnapToGridAngle() : org::openscience::cdk::controller::Controller2DModel
• setSnapToGridCartesian() : org::openscience::cdk::controller::Controller2DModel
• setSoftware() : org::openscience::cdk::applications::jchempaint::JChemPaintModel
• setSolvantValue() : org::openscience::cdk::protein::ProteinPocketFinder
• setSpaceGroup() : org::openscience::cdk::Crystal , org::openscience::cdk::interfaces::ICrystal , org::openscience::cdk::debug::DebugCrystal
• setStackLength() : org::openscience::cdk::tools::LoggingTool
• setStartChainID() : org::openscience::cdk::debug::DebugPDBStructure , org::openscience::cdk::protein::data::PDBStructure , org::openscience::cdk::interfaces::IPDBStructure
• setStartInsertionCode() : org::openscience::cdk::interfaces::IPDBStructure , org::openscience::cdk::protein::data::PDBStructure , org::openscience::cdk::debug::DebugPDBStructure
• setStartSequenceNumber() : org::openscience::cdk::debug::DebugPDBStructure , org::openscience::cdk::protein::data::PDBStructure , org::openscience::cdk::interfaces::IPDBStructure
• setStatus() : org::openscience::cdk::applications::jchempaint::StatusBar , org::openscience::cdk::applications::jchempaint::JChemPaintModel
• setStereo() : org::openscience::cdk::debug::DebugBond , org::openscience::cdk::Bond , org::openscience::cdk::interfaces::IBond
• setStereoParity() : org::openscience::cdk::Atom , org::openscience::cdk::debug::DebugPseudoAtom , org::openscience::cdk::debug::DebugAtom , org::openscience::cdk::PseudoAtom , org::openscience::cdk::interfaces::IAtom
• setStrandName() : org::openscience::cdk::debug::DebugStrand , org::openscience::cdk::interfaces::IStrand , org::openscience::cdk::Strand
• setStrandType() : org::openscience::cdk::Strand , org::openscience::cdk::interfaces::IStrand , org::openscience::cdk::debug::DebugStrand
• setStrBnd() : org::openscience::cdk::modeling::builder3d::MMFF94BasedParameterSetReader , org::openscience::cdk::modeling::builder3d::MM2BasedParameterSetReader
• setStructureType() : org::openscience::cdk::interfaces::IPDBStructure , org::openscience::cdk::protein::data::PDBStructure , org::openscience::cdk::debug::DebugPDBStructure
• setSymbol() : org::openscience::cdk::interfaces::IElement , org::openscience::cdk::debug::DebugElement , org::openscience::cdk::debug::DebugAtom , org::openscience::cdk::debug::DebugPseudoAtom , org::openscience::cdk::debug::DebugIsotope , org::openscience::cdk::debug::DebugAtomType , org::openscience::cdk::isomorphism::matchers::smarts::TotalConnectionAtom , org::openscience::cdk::Element , org::openscience::cdk::isomorphism::matchers::smarts::TotalHCountAtom
• setTempFactor() : org::openscience::cdk::interfaces::IPDBAtom , org::openscience::cdk::protein::data::PDBAtom , org::openscience::cdk::debug::DebugPDBAtom
• setTemplateHandler() : org::openscience::cdk::layout::StructureDiagramGenerator , org::openscience::cdk::modeling::builder3d::ModelBuilder3D
• setTheJcpp() : org::openscience::cdk::applications::jchempaint::applet::JChemPaintAbstractApplet
• setTimeout() : org::openscience::cdk::ringsearch::AllRingsFinder , org::openscience::cdk::aromaticity::HueckelAromaticityDetector
• setTimezone() : org::openscience::cdk::io::RssWriter
• setTitle() : org::openscience::cdk::io::RssWriter , org::openscience::cdk::renderer::GraphRendererModel , org::openscience::cdk::applications::jchempaint::JChemPaintModel , org::openscience::cdk::Fragment
• setTitlemap() : org::openscience::cdk::io::RssWriter
• setToolTipTextMap() : org::openscience::cdk::renderer::Renderer2DModel
• setTorsion() : org::openscience::cdk::modeling::builder3d::MMFF94BasedParameterSetReader , org::openscience::cdk::modeling::builder3d::MM2BasedParameterSetReader
• setTorsion4() : org::openscience::cdk::modeling::builder3d::MM2BasedParameterSetReader
• setType() : org::openscience::cdk::applications::jchempaint::io::JCPExportFileFilter , org::openscience::cdk::applications::jchempaint::io::JCPCompChemInputSaveFileFilter , org::openscience::cdk::applications::jchempaint::io::JCPFileFilter , org::openscience::cdk::applications::jchempaint::io::IJCPFileFilter , org::openscience::cdk::applications::jchempaint::action::JCPAction
• setUndoableChange() : org::openscience::cdk::controller::AbstractController2D
• setUndoManager() : org::openscience::cdk::applications::jchempaint::JChemPaintPanel
• setUndoSupport() : org::openscience::cdk::applications::jchempaint::JChemPaintPanel
• setUpper() : org::openscience::cdk::qsar::model::R::LinearRegressionModelPredict
• setUseAromaticityFlag() : org::openscience::cdk::smiles::SmilesGenerator
• setUseTemplates() : org::openscience::cdk::layout::StructureDiagramGenerator
• setValency() : org::openscience::cdk::interfaces::IAtomType , org::openscience::cdk::debug::DebugPseudoAtom , org::openscience::cdk::AtomType , org::openscience::cdk::debug::DebugAtomType , org::openscience::cdk::debug::DebugAtom
• setValue() : org::openscience::cdk::qsar::model::R::CNNClassificationModelFit , org::openscience::cdk::qsar::model::R::CNNRegressionModelFit
• setValueAt() : org::openscience::cdk::applications::swing::SortedTableModel , org::openscience::cdk::graph::invariant::GIMatrix , org::openscience::cdk::applications::swing::ListeningTableModel
• setVanDerWaalsFile() : org::openscience::cdk::protein::ProteinPocketFinder
• setVanderwaalsRadius() : org::openscience::cdk::debug::DebugAtom , org::openscience::cdk::debug::DebugAtomType , org::openscience::cdk::interfaces::IAtomType , org::openscience::cdk::debug::DebugPseudoAtom , org::openscience::cdk::AtomType
• setvdWaalpr() : org::openscience::cdk::modeling::builder3d::MM2BasedParameterSetReader
• setvdWaals() : org::openscience::cdk::modeling::builder3d::MM2BasedParameterSetReader
• setViewerDimension() : org::openscience::cdk::applications::jchempaint::JChemPaintPanel
• setViewerOnly() : org::openscience::cdk::applications::jchempaint::JChemPaintPanel
• setWeights() : org::openscience::cdk::qsar::model::R::CNNClassificationModelFit , org::openscience::cdk::qsar::model::R::CNNRegressionModelFit
• setWriter() : org::openscience::cdk::io::HINWriter , org::openscience::cdk::io::RssWriter , org::openscience::cdk::io::Mol2Writer , org::openscience::cdk::io::CMLWriter , org::openscience::cdk::io::MDLRXNWriter , org::openscience::cdk::io::SVGWriter , org::openscience::cdk::io::CrystClustWriter , org::openscience::cdk::io::MDLWriter , org::openscience::cdk::io::MDLRXNWriter , org::openscience::cdk::io::RssWriter , org::openscience::cdk::io::ShelXWriter , org::openscience::cdk::io::PDBWriter , org::openscience::cdk::io::SMILESWriter , org::openscience::cdk::io::ShelXWriter , org::openscience::cdk::io::XYZWriter , org::openscience::cdk::io::Mol2Writer , org::openscience::cdk::io::SVGWriter , org::openscience::cdk::io::XYZWriter , org::openscience::cdk::io::SMILESWriter , org::openscience::cdk::io::program::GaussianInputWriter , org::openscience::cdk::io::PDBWriter , org::openscience::cdk::io::program::GaussianInputWriter , org::openscience::cdk::io::MDLWriter , org::openscience::cdk::io::IChemObjectWriter , org::openscience::cdk::io::CrystClustWriter , org::openscience::cdk::io::HINWriter , org::openscience::cdk::io::CMLWriter , org::openscience::cdk::io::CDKSourceCodeWriter , org::openscience::cdk::io::IChemObjectWriter
• setX() : org::openscience::cdk::renderer::GraphRendererModel
• setXTitle() : org::openscience::cdk::renderer::GraphRendererModel
• setY() : org::openscience::cdk::renderer::GraphRendererModel
• setYTitle() : org::openscience::cdk::renderer::GraphRendererModel
• setZ() : org::openscience::cdk::interfaces::ICrystal , org::openscience::cdk::Crystal , org::openscience::cdk::debug::DebugCrystal
• setZeroAxes() : org::openscience::cdk::Crystal
• setZoomFactor() : org::openscience::cdk::renderer::Renderer2DModel
• shallowCopy() : org::openscience::cdk::ChemObject
• ShelXReader() : org::openscience::cdk::io::ShelXReader
• ShelXWriter() : org::openscience::cdk::io::ShelXWriter
• shortenBond() : org::openscience::cdk::renderer::AbstractRenderer2D
• show() : org::openscience::cdk::applications::swing::JExternalFrame
• showAromaticity : org::openscience::cdk::renderer::Renderer2DModel
• showChemFile() : org::openscience::cdk::applications::plugin::ICDKEditBus , org::openscience::cdk::applications::jchempaint::JChemPaintPanel
• showChemModel() : org::openscience::cdk::applications::plugin::ICDKEditBus
• showEndCarbons : org::openscience::cdk::renderer::Renderer2DModel
• showExplicitHydrogens : org::openscience::cdk::renderer::Renderer2DModel
• showImplicitHydrogens : org::openscience::cdk::renderer::Renderer2DModel
• SigmaElectronegativityDescriptor() : org::openscience::cdk::qsar::descriptors::atomic::SigmaElectronegativityDescriptor
• similar() : org::openscience::cdk::math::IMatrix , org::openscience::cdk::math::Matrix , org::openscience::cdk::math::IMatrix
• SimpleBasisSet() : org::openscience::cdk::math::qm::SimpleBasisSet
• SimpleCycle() : org::openscience::cdk::ringsearch::cyclebasis::SimpleCycle
• SimpleRenderer2D() : org::openscience::cdk::renderer::SimpleRenderer2D
• SingleElectron() : org::openscience::cdk::SingleElectron
• singleElectronCount : org::openscience::cdk::AtomContainer
• singleElectrons() : org::openscience::cdk::debug::DebugPolymer , org::openscience::cdk::AtomContainer , org::openscience::cdk::debug::DebugAminoAcid , org::openscience::cdk::debug::DebugMolecule , org::openscience::cdk::debug::DebugStrand , org::openscience::cdk::debug::DebugCrystal , org::openscience::cdk::debug::DebugBioPolymer , org::openscience::cdk::interfaces::IAtomContainer , org::openscience::cdk::debug::DebugMonomer , org::openscience::cdk::debug::DebugRing , org::openscience::cdk::AtomContainer , org::openscience::cdk::debug::DebugAtomContainer
• SingleStructureRandomGenerator() : org::openscience::cdk::structgen::SingleStructureRandomGenerator
• sitefinder() : org::openscience::cdk::protein::ProteinPocketFinder
• size : org::openscience::cdk::math::Vector
• skipDigits() : org::openscience::cdk::tools::FormatStringBuffer
• SMALL_FIRST : org::openscience::cdk::RingSet , org::openscience::cdk::tools::manipulator::RingSizeComparator
• SMALLEST_RINGS : org::openscience::cdk::CDKConstants
• smallestRingSize : org::openscience::cdk::isomorphism::matchers::smarts::SmallestRingAtom
• SMARTSOperatorAtom() : org::openscience::cdk::isomorphism::matchers::smarts::SMARTSOperatorAtom
• smi : org::openscience::cdk::applications::jchempaint::io::JCPFileFilter
• SMILES : org::openscience::cdk::CDKConstants
• SmilesGenerator() : org::openscience::cdk::smiles::SmilesGenerator
• SmilesParser() : org::openscience::cdk::smiles::SmilesParser
• SMILESWriter() : org::openscience::cdk::io::SMILESWriter
• SmoothingFunctions() : org::openscience::cdk::modeling::forcefield::SmoothingFunctions
• snapAngle() : org::openscience::cdk::controller::AbstractController2D
• solution() : org::openscience::cdk::isomorphism::mcss::RGraph
• sort() : org::openscience::cdk::math::qm::OneElectronJob , org::openscience::cdk::math::qm::ClosedShellJob , org::openscience::cdk::tools::manipulator::RingSetManipulator , org::openscience::cdk::tools::manipulator::AtomContainerSetManipulator
• sortArrayList() : org::openscience::cdk::graph::invariant::CanonicalLabeler
• sortBy2DDistance() : org::openscience::cdk::geometry::GeometryToolsInternalCoordinates , org::openscience::cdk::geometry::GeometryTools
• sortNodesByScore() : org::openscience::cdk::tools::HOSECodeGenerator
• sortPockets() : org::openscience::cdk::protein::ProteinPocketFinder
• SPACE : org::openscience::cdk::tools::FormatStringBuffer
• spaceGroup : org::openscience::cdk::Crystal
• SPECIAL : org::openscience::cdk::tools::FormatStringBuffer
• specialCase() : org::openscience::cdk::iupac::parser::NomParser
• specialConstructor : org::openscience::cdk::iupac::parser::ParseException
• specialToken : org::openscience::cdk::iupac::parser::Token
• sphere : org::openscience::cdk::tools::HOSECodeGenerator
• sphereDelimiters : org::openscience::cdk::tools::HOSECodeGenerator
• sphereNodes : org::openscience::cdk::tools::HOSECodeGenerator
• spheres : org::openscience::cdk::tools::HOSECodeGenerator
• SPHERICAL_MATCHER : org::openscience::cdk::CDKConstants
• SPLIT_MODE_BREADTH_FIRST : org::openscience::cdk::structgen::stochastic::operator::CrossoverMachine
• SPLIT_MODE_DEPTH_FIRST : org::openscience::cdk::structgen::stochastic::operator::CrossoverMachine
• SPLIT_MODE_RADNDOM : org::openscience::cdk::structgen::stochastic::operator::CrossoverMachine
• splitMode : org::openscience::cdk::structgen::stochastic::operator::CrossoverMachine
• SSSRFinder() : org::openscience::cdk::ringsearch::SSSRFinder
• start() : org::openscience::cdk::applications::plugin::ICDKPlugin
• startDocument() : org::openscience::cdk::io::iterator::event::EventCMLHandler
• startElement() : org::openscience::cdk::io::cml::MDMoleculeConvention , org::openscience::cdk::io::inchi::INChIHandler
• startObject() : org::openscience::cdk::io::iterator::event::EventCMLHandler
• stateChanged() : org::openscience::cdk::ChemSequence , org::openscience::cdk::debug::DebugMonomer , org::openscience::cdk::applications::swing::AtomicTable , org::openscience::cdk::debug::DebugCrystal , org::openscience::cdk::applications::plugin::CDKPluginManager , org::openscience::cdk::applications::swing::MoleculeViewer2D , org::openscience::cdk::applications::swing::MoleculeViewer2DPanel , org::openscience::cdk::ChemFile , org::openscience::cdk::applications::plugin::ICDKPlugin , org::openscience::cdk::applications::jchempaint::JChemPaintEditorPanel , org::openscience::cdk::event::ICDKSelectionChangeListener , org::openscience::cdk::debug::DebugRing , org::openscience::cdk::AtomContainer , org::openscience::cdk::interfaces::IChemObjectListener , org::openscience::cdk::AtomContainerSet , org::openscience::cdk::debug::DebugPolymer , org::openscience::cdk::event::ICDKChangeListener , org::openscience::cdk::ReactionSet , org::openscience::cdk::applications::swing::MoleculesTable , org::openscience::cdk::debug::DebugStrand , org::openscience::cdk::applications::jchempaint::JChemPaintPanel , org::openscience::cdk::applications::jchempaint::JChemPaintModel , org::openscience::cdk::debug::DebugAminoAcid , org::openscience::cdk::ChemModel , org::openscience::cdk::debug::DebugBioPolymer , org::openscience::cdk::applications::jchempaint::JChemPaintEditorPanel , org::openscience::cdk::MoleculeSet
• StatusBar() : org::openscience::cdk::applications::jchempaint::StatusBar
• statusBar : org::openscience::cdk::applications::jchempaint::JChemPaintPanel
• SteepestDescentsMethod() : org::openscience::cdk::modeling::forcefield::SteepestDescentsMethod
• steepestDescentsMinimization() : org::openscience::cdk::modeling::forcefield::GeometricMinimizer
• step2() : org::openscience::cdk::graph::invariant::CanonicalLabeler
• step3() : org::openscience::cdk::graph::invariant::CanonicalLabeler
• stereo : org::openscience::cdk::Bond
• STEREO_ATOM_PARITY_MINUS : org::openscience::cdk::CDKConstants
• STEREO_ATOM_PARITY_PLUS : org::openscience::cdk::CDKConstants
• STEREO_ATOM_PARITY_UNDEFINED : org::openscience::cdk::CDKConstants
• STEREO_BOND_DOWN : org::openscience::cdk::CDKConstants
• STEREO_BOND_DOWN_INV : org::openscience::cdk::CDKConstants
• STEREO_BOND_NONE : org::openscience::cdk::CDKConstants
• STEREO_BOND_UNDEFINED : org::openscience::cdk::CDKConstants
• STEREO_BOND_UP : org::openscience::cdk::CDKConstants
• STEREO_BOND_UP_INV : org::openscience::cdk::CDKConstants
• stereoParity : org::openscience::cdk::Atom
• stereosAreOpposite() : org::openscience::cdk::geometry::BondTools
• stop() : org::openscience::cdk::applications::plugin::ICDKPlugin
• storeRingSystem() : org::openscience::cdk::smiles::DeduceBondSystemTool
• Strand() : org::openscience::cdk::Strand
• strandName : org::openscience::cdk::Strand
• strandType : org::openscience::cdk::Strand
• StretchBendInteractions() : org::openscience::cdk::modeling::forcefield::StretchBendInteractions
• STRING : org::openscience::cdk::tools::FormatStringBuffer
• StrucContainer() : org::openscience::cdk::applications::swing::MoleculeListPanel::StrucContainer
• StructGenAtomTypeGuesser() : org::openscience::cdk::atomtype::StructGenAtomTypeGuesser
• StructGenMatcher() : org::openscience::cdk::atomtype::StructGenMatcher
• StructureDiagramGenerator() : org::openscience::cdk::layout::StructureDiagramGenerator
• StructureResonanceGenerator() : org::openscience::cdk::tools::StructureResonanceGenerator
• sub() : org::openscience::cdk::math::IMatrix , org::openscience::cdk::math::Matrix , org::openscience::cdk::math::Complex , org::openscience::cdk::math::Vector , org::openscience::cdk::math::IMatrix
• subChain() : org::openscience::cdk::iupac::parser::NomParser
• summary() : org::openscience::cdk::qsar::model::R::LinearRegressionModel , org::openscience::cdk::qsar::model::R::CNNRegressionModel , org::openscience::cdk::qsar::model::R2::LinearRegressionModel , org::openscience::cdk::qsar::model::R2::CNNRegressionModel
• SVGWriter() : org::openscience::cdk::io::SVGWriter
• SwingGUIListener() : org::openscience::cdk::io::listener::SwingGUIListener
• symbol : org::openscience::cdk::Element
• symbolRankings : org::openscience::cdk::tools::HOSECodeGenerator
• SymbolSetQueryAtom() : org::openscience::cdk::isomorphism::matchers::SymbolSetQueryAtom