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